Skip to main content

Program Publications

Publications Search by Program

Search Results

The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.

Title Authors Journal PubMedID Publication Date
Ethical, legal, and social considerations in conducting the Human Microbiome Project. McGuire, Amy L; Colgrove, James; Whitney, Simon N; Diaz, Christina M; Bustillos, Daniel; Versalovic, James Genome research 18971311 2008 Dec
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Langmead, Ben; Trapnell, Cole; Pop, Mihai; Salzberg, Steven L Genome biology 19261174 2009
Metagenomic pyrosequencing and microbial identification. Petrosino, Joseph F; Highlander, Sarah; Luna, Ruth Ann; Gibbs, Richard A; Versalovic, James Clinical chemistry 19264858 2009 May
Helping patients make informed choices about probiotics: a need for research. Sharp, Richard R; Achkar, Jean-Paul; Brinich, Margaret A; Farrell, Ruth M The American journal of gastroenterology 19343022 2009 Apr
Statistical methods for detecting differentially abundant features in clinical metagenomic samples. White, James Robert; Nagarajan, Niranjan; Pop, Mihai PLoS computational biology 19360128 2009 Apr
16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. Wang, Yunwei; Hoenig, Jeanette D; Malin, Kathryn J; Qamar, Sanaa; Petrof, Elaine O; Sun, Jun; Antonopoulos, Dionysios A; Chang, Eugene B; Claud, Erika C The ISME journal 19369970 2009 Aug
Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome. Yang, Liying; Lu, Xiaohua; Nossa, Carlos W; Francois, Fritz; Peek, Richard M; Pei, Zhiheng Gastroenterology 19394334 2009 Aug
Diversity of 23S rRNA genes within individual prokaryotic genomes. Pei, Anna; Nossa, Carlos W; Chokshi, Pooja; Blaser, Martin J; Yang, Liying; Rosmarin, David M; Pei, Zhiheng PloS one 19415112 2009
Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Preidis, Geoffrey A; Versalovic, James Gastroenterology 19462507 2009 May
Genome assembly reborn: recent computational challenges. Pop, Mihai Briefings in bioinformatics 19482960 2009 Jul
An ORFome assembly approach to metagenomics sequences analysis. Ye, Yuzhen; Tang, Haixu Journal of bioinformatics and computational biology 19507285 2009 Jun
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Brady, Arthur; Salzberg, Steven L Nature methods 19648916 2009 Sep
Microfluidic cell sorter with integrated piezoelectric actuator. Chen, Chun H; Cho, Sung Hwan; Tsai, Frank; Erten, Ahmet; Lo, Yu-Hwa Biomedical microdevices 19649710 2009 Dec
A method for isolating and analyzing human mRNA from newborn stool. Bennett Jr, William E; Gonzalez-Rivera, Rosbel; Shaikh, Nurmohammad; Magrini, Vincent; Boykin, Michelle; Warner, Barbara B; Hamvas, Aaron; Tarr, Phillip I Journal of immunological methods 19660464 2009 Sep 30
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. Ye, Yuzhen; Doak, Thomas G PLoS computational biology 19680427 2009 Aug
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Hildebrandt, Marie A; Hoffmann, Christian; Sherrill-Mix, Scott A; Keilbaugh, Sue A; Hamady, Micah; Chen, Ying-Yu; Knight, Rob; Ahima, Rexford S; Bushman, Frederic; Wu, Gary D Gastroenterology 19706296 2009 Nov
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. Hamady, Micah; Lozupone, Catherine; Knight, Rob The ISME journal 19710709 2010 Jan
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. Lazarevic, Vladimir; Whiteson, Katrine; Huse, Susan; Hernandez, David; Farinelli, Laurent; Osteras, Magne; Schrenzel, Jacques; Francois, Patrice Journal of microbiological methods 19796657 2009 Dec
Genomics. Genome project standards in a new era of sequencing. Chain, P S G; Grafham, D V; Fulton, R S; Fitzgerald, M G; Hostetler, J; Muzny, D; Ali, J; Birren, B; Bruce, D C; Buhay, C; Cole, J R; Ding, Y; Dugan, S; Field, D; Garrity, G M; Gibbs, R; Graves, T; Han, C S; Harrison, S H; Highlander, S; Hugenholtz, P; Kh Science (New York, N.Y.) 19815760 2009 Oct 9
Bacterial communities of disease vectors sampled across time, space, and species. Jones, Ryan T; Knight, Rob; Martin, Andrew P The ISME journal 19865184 2010 Feb
BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. Frank, Daniel N BMC bioinformatics 19874596 2009
What are the consequences of the disappearing human microbiota? Blaser, Martin J; Falkow, Stanley Nature reviews. Microbiology 19898491 2009 Dec
PyNAST: a flexible tool for aligning sequences to a template alignment. Caporaso, J Gregory; Bittinger, Kyle; Bushman, Frederic D; DeSantis, Todd Z; Andersen, Gary L; Knight, Rob Bioinformatics (Oxford, England) 19914921 2010 Jan 15
Searching for SNPs with cloud computing. Langmead, Ben; Schatz, Michael C; Lin, Jimmy; Pop, Mihai; Salzberg, Steven L Genome biology 19930550 2009
Micro-fabricated fluorescence-activated cell sorter. Cho, Sung Hwan; Chen, Chun H; Tsai, Frank S; Lo, Yu-Hwa Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 19965141 2009
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. Selengut, Jeremy D; Rusch, Douglas B; Haft, Daniel H BMC bioinformatics 20102603 2010
Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives. Zaneveld, Jesse R; Lozupone, Catherine; Gordon, Jeffrey I; Knight, Rob Nucleic acids research 20197316 2010 Jul
Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Huse, Susan M; Welch, David Mark; Morrison, Hilary G; Sogin, Mitchell L Environmental microbiology 20236171 2010 Jul
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. White, James R; Navlakha, Saket; Nagarajan, Niranjan; Ghodsi, Mohammad-Reza; Kingsford, Carl; Pop, Mihai BMC bioinformatics 20334679 2010
Harnessing the power of the human microbiome. Blaser, Martin J Proceedings of the National Academy of Sciences of the United States of America 20360554 2010 Apr 6
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. Wang, Gary P; Sherrill-Mix, Scott A; Chang, Kyong-Mi; Quince, Chris; Bushman, Frederic D Journal of virology 20375170 2010 Jun
Role of the gut microbiota in defining human health. Fujimura, Kei E; Slusher, Nicole A; Cabana, Michael D; Lynch, Susan V Expert review of anti-infective therapy 20377338 2010 Apr
Human mammalian cell sorting using a highly integrated micro-fabricated fluorescence-activated cell sorter (microFACS). Cho, Sung Hwan; Chen, Chun H; Tsai, Frank S; Godin, Jessica M; Lo, Yu-Hwa Lab on a chip 20379604 2010 Jun 21
Personal genome research : what should the participant be told? McGuire, Amy L; Lupski, James R Trends in genetics : TIG 20381895 2010 May
QIIME allows analysis of high-throughput community sequencing data. Caporaso, J Gregory; Kuczynski, Justin; Stombaugh, Jesse; Bittinger, Kyle; Bushman, Frederic D; Costello, Elizabeth K; Fierer, Noah; Pena, Antonio Gonzalez; Goodrich, Julia K; Gordon, Jeffrey I; Huttley, Gavin A; Kelley, Scott T; Knights, Dan; Koenig, Jer Nature methods 20383131 2010 May
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. Lauber, Christian L; Zhou, Nicholas; Gordon, Jeffrey I; Knight, Rob; Fierer, Noah FEMS microbiology letters 20412303 2010 Jun
Diversity of 16S rRNA genes within individual prokaryotic genomes. Pei, Anna Y; Oberdorf, William E; Nossa, Carlos W; Agarwal, Ankush; Chokshi, Pooja; Gerz, Erika A; Jin, Zhida; Lee, Peng; Yang, Liying; Poles, Michael; Brown, Stuart M; Sotero, Steven; Desantis, Todd; Brodie, Eoin; Nelson, Karen; Pei, Zhiheng Applied and environmental microbiology 20418441 2010 Jun
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Pati, Amrita; Ivanova, Natalia N; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D; Lykidis, Athanasios; Kyrpides, Nikos C Nature methods 20436475 2010 Jun
Informed consent in genomics and genetic research. McGuire, Amy L; Beskow, Laura M Annual review of genomics and human genetics 20477535 2010 Sep 22
A catalog of reference genomes from the human microbiome. Human Microbiome Jumpstart Reference Strains Consortium; Nelson, Karen E; Weinstock, George M; Highlander, Sarah K; Worley, Kim C; Creasy, Heather Huot; Wortman, Jennifer Russo; Rusch, Douglas B; Mitreva, Makedonka; Sodergren, Erica; Chinwalla, Asif T; Fe Science (New York, N.Y.) 20489017 2010 May 21
Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. Haft, Daniel H; Basu, Malay Kumar; Mitchell, Douglas A BMC biology 20500830 2010
Postprandial remodeling of the gut microbiota in Burmese pythons. Costello, Elizabeth K; Gordon, Jeffrey I; Secor, Stephen M; Knight, Rob The ISME journal 20520652 2010 Nov
Vaginal microbiome of reproductive-age women. Ravel, Jacques; Gajer, Pawel; Abdo, Zaid; Schneider, G Maria; Koenig, Sara S K; McCulle, Stacey L; Karlebach, Shara; Gorle, Reshma; Russell, Jennifer; Tacket, Carol O; Brotman, Rebecca M; Davis, Catherine C; Ault, Kevin; Peralta, Ligia; Forney, Larry J Proceedings of the National Academy of Sciences of the United States of America 20534435 2011 Mar 15
Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies. Harwich Jr, Michael D; Alves, Joao M; Buck, Gregory A; Strauss 3rd, Jerome F; Patterson, Jennifer L; Oki, Aminat T; Girerd, Philippe H; Jefferson, Kimberly K BMC genomics 20540756 2010
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Redford, Amanda J; Bowers, Robert M; Knight, Rob; Linhart, Yan; Fierer, Noah Environmental microbiology 20545741 2010 Nov
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Dominguez-Bello, Maria G; Costello, Elizabeth K; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Fierer, Noah; Knight, Rob Proceedings of the National Academy of Sciences of the United States of America 20566857 2010 Jun 29
The right to ignore genetic status of late onset genetic disease in the genomic era; Prenatal testing for Huntington disease as a paradigm. Erez, A; Plunkett, K; Sutton, V R; McGuire, A L American journal of medical genetics. Part A 20583190 2010 Jul
Metagenomics: Facts and Artifacts, and Computational Challenges* Wooley, John C; Ye, Yuzhen Journal of computer science and technology 20648230 2009 Jan
Rapid fluctuation of the vaginal microbiota measured by Gram stain analysis. Brotman, Rebecca M; Ravel, Jacques; Cone, Richard A; Zenilman, Jonathan M Sexually transmitted infections 20660593 2010 Aug
Probiotics-host communication: Modulation of signaling pathways in the intestine. Thomas, Carissa M; Versalovic, James Gut microbes 20672012 2010 May-Jun
Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. Selengut, Jeremy D; Haft, Daniel H Journal of bacteriology 20675471 2010 Nov
Genome sequencing reveals widespread virulence gene exchange among human Neisseria species. Marri, Pradeep Reddy; Paniscus, Mary; Weyand, Nathan J; Rendon, Maria A; Calton, Christine M; Hernandez, Diana R; Higashi, Dustin L; Sodergren, Erica; Weinstock, George M; Rounsley, Steven D; So, Magdalene PloS one 20676376 2010
Quantitation of major human cutaneous bacterial and fungal populations. Gao, Zhan; Perez-Perez, Guillermo I; Chen, Yu; Blaser, Martin J Journal of clinical microbiology 20702672 2010 Oct
Optofluidic Waveguides in Teflon AF-Coated PDMS Microfluidic Channels. Cho, Sung Hwan; Godin, Jessica; Lo, Yu-Hwa IEEE photonics technology letters : a publication of the IEEE Laser and Electro-optics Society. 20729984 2009 Aug 1;
METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics. Goll, Johannes; Rusch, Douglas B; Tanenbaum, David M; Thiagarajan, Mathangi; Li, Kelvin; Methe, Barbara A; Yooseph, Shibu Bioinformatics (Oxford, England) 20798169 2010 Oct 15
FragGeneScan: predicting genes in short and error-prone reads. Rho, Mina; Tang, Haixu; Ye, Yuzhen Nucleic acids research 20805240 2010 Nov
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Reeder, Jens; Knight, Rob Nature methods 20805793 2010 Sep
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. Nossa, Carlos W; Oberdorf, William E; Yang, Liying; Aas, Jorn A; Paster, Bruce J; Desantis, Todd Z; Brodie, Eoin L; Malamud, Daniel; Poles, Michael A; Pei, Zhiheng World journal of gastroenterology : WJG 20806429 2010 Sep 7
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Kuczynski, Justin; Liu, Zongzhi; Lozupone, Catherine; McDonald, Daniel; Fierer, Noah; Knight, Rob Nature methods 20818378 2010 Oct
Molecular microbiological methods in the diagnosis of neonatal sepsis. Venkatesh, Mohan; Flores, Angela; Luna, Ruth Ann; Versalovic, James Expert review of anti-infective therapy 20818947 2010 Sep
Creation and initial evaluation of a Stool Form Scale for children. Chumpitazi, Bruno P; Lane, Mariella M; Czyzewski, Danita I; Weidler, Erica M; Swank, Paul R; Shulman, Robert J The Journal of pediatrics 20826285 2010 Oct
An algorithm for automated closure during assembly. Koren, Sergey; Miller, Jason R; Walenz, Brian P; Sutton, Granger BMC bioinformatics 20831800 2010
Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Frank, Daniel N; Robertson, Charles E; Hamm, Christina M; Kpadeh, Zegbeh; Zhang, Tianyi; Chen, Hongyan; Zhu, Wei; Sartor, R Balfour; Boedeker, Edgar C; Harpaz, Noam; Pace, Norman R; Li, Ellen Inflammatory bowel diseases 20839241 2011 Jan
Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heat shock proteins. Hu, Shien; Wang, Yunwei; Lichtenstein, Lev; Tao, Yun; Musch, Mark W; Jabri, Bana; Antonopoulos, Dionysios; Claud, Erika C; Chang, Eugene B American journal of physiology. Gastrointestinal and liver physiology 20864653 2010 Dec
Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. Yeoman, Carl J; Yildirim, Suleyman; Thomas, Susan M; Durkin, A Scott; Torralba, Manolito; Sutton, Granger; Buhay, Christian J; Ding, Yan; Dugan-Rocha, Shannon P; Muzny, Donna M; Qin, Xiang; Gibbs, Richard A; Leigh, Steven R; Stumpf, Rebecca; White, Bryan PloS one 20865041 2010
Lab-on-a-chip flow cytometer employing color-space-time coding. Cho, Sung Hwan; Qiao, Wen; Tsai, Frank S; Yamashita, Kenichi; Lo, Yu-Hwa Applied physics letters. 20877655 2010 Aug 30;
Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Wang, Yunwei; Antonopoulos, Dionysios A; Zhu, Xiaorong; Harrell, Laura; Hanan, Ira; Alverdy, John C; Meyer, Folker; Musch, Mark W; Young, Vincent B; Chang, Eugene B Applied microbiology and biotechnology 20931185 2010 Dec
Growth and Development Symposium: promoting healthier humans through healthier livestock: animal agriculture enters the metagenomics era. Frank, D N Journal of animal science 20935136 2011 Mar
Human oral, gut, and plaque microbiota in patients with atherosclerosis. Koren, Omry; Spor, Ayme; Felin, Jenny; Fak, Frida; Stombaugh, Jesse; Tremaroli, Valentina; Behre, Carl Johan; Knight, Rob; Fagerberg, Bjorn; Ley, Ruth E; Backhed, Fredrik Proceedings of the National Academy of Sciences of the United States of America 20937873 2011 Mar 15
A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions. Krentz, Benjamin D; Mulheron, Heidi J; Semrau, Jeremy D; Dispirito, Alan A; Bandow, Nathan L; Haft, Daniel H; Vuilleumier, Stephane; Murrell, J Colin; McEllistrem, Marcus T; Hartsel, Scott C; Gallagher, Warren H Biochemistry 20961038 2010 Nov 30
SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Harrington, Eoghan D; Arumugam, Manimozhiyan; Raes, Jeroen; Bork, Peer; Relman, David A Bioinformatics (Oxford, England) 20966005 2010 Dec 1
Regional mucosa-associated microbiota determine physiological expression of TLR2 and TLR4 in murine colon. Wang, Yunwei; Devkota, Suzanne; Musch, Mark W; Jabri, Bana; Nagler, Cathryn; Antonopoulos, Dionysios A; Chervonsky, Alexander; Chang, Eugene B PloS one 21042588 2010
Digital MDA for enumeration of total nucleic acid contamination. Blainey, Paul C; Quake, Stephen R Nucleic acids research 21071419 2011 Mar
Probiotics, enteric and diarrheal diseases, and global health. Preidis, Geoffrey A; Hill, Colin; Guerrant, Richard L; Ramakrishna, B S; Tannock, Gerald W; Versalovic, James Gastroenterology 21075108 2011 Jan
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Shah, Neethu; Tang, Haixu; Doak, Thomas G; Ye, Yuzhen Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 21121044 2011
Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. Nelson, David E; Van Der Pol, Barbara; Dong, Qunfeng; Revanna, Kashi V; Fan, Baochang; Easwaran, Shraddha; Sodergren, Erica; Weinstock, George M; Diao, Lixia; Fortenberry, J Dennis PloS one 21124791 2010
Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth. Zhou, Xia; Brotman, Rebecca M; Gajer, Pawel; Abdo, Zaid; Schuette, Ursel; Ma, Sam; Ravel, Jacques; Forney, Larry J Infectious diseases in obstetrics and gynecology 21197076 2010
Microbial diversity in saliva of oral squamous cell carcinoma. Pushalkar, Smruti; Mane, Shrinivasrao P; Ji, Xiaojie; Li, Yihong; Evans, Clive; Crasta, Oswald R; Morse, Douglas; Meagher, Robert; Singh, Anup; Saxena, Deepak FEMS immunology and medical microbiology 21205002 2011 Apr
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Haas, Brian J; Gevers, Dirk; Earl, Ashlee M; Feldgarden, Mike; Ward, Doyle V; Giannoukos, Georgia; Ciulla, Dawn; Tabbaa, Diana; Highlander, Sarah K; Sodergren, Erica; Methe, Barbara; DeSantis, Todd Z; Human Microbiome Consortium; Petrosino, Joseph F; Knig Genome research 21212162 2011 Mar
A primer on a hepatocellular carcinoma bioresource bank using the cancer genome atlas guidelines: practical issues and pitfalls. Nguyen, N Thao T; Cotton, Ron T; Harring, Theresa R; Guiteau, Jacfranz J; Gingras, Marie-Claude; Wheeler, David A; O'Mahony, Christine A; Gibbs, Richard A; Brunicardi, F Charles; Goss, John A World journal of surgery 21221581 2011 Aug
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. Haft, Daniel H BMC genomics 21223593 2011
Dielectrophoresis of Caenorhabditis elegans. Chuang, Han-Sheng; Raizen, David M; Lamb, Annesia; Dabbish, Nooreen; Bau, Haim H Lab on a chip 21225036 2011 Feb 21
Building a comprehensive genomic program for hepatocellular carcinoma. Harring, Theresa R; Guiteau, Jacfranz J; Nguyen, N Thao T; Cotton, Ron T; Gingras, Marie-Claude; Wheeler, David A; O'Mahony, Christine A; Gibbs, Richard A; Brunicardi, F Charles; Goss, John A World journal of surgery 21225260 2011 Aug
Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice. Kellermayer, Richard; Dowd, Scot E; Harris, R Alan; Balasa, Alfred; Schaible, Tiffany D; Wolcott, Randy D; Tatevian, Nina; Szigeti, Reka; Li, Zhijie; Versalovic, James; Smith, C Wayne FASEB journal : official publication of the Federation of American Societies for Experimental Biology 21228220 2011 May
Review Article: Recent advancements in optofluidic flow cytometer. Cho, Sung Hwan; Godin, Jessica M; Chen, Chun-Hao; Qiao, Wen; Lee, Hosuk; Lo, Yu-Hwa Biomicrofluidics. 21267434 2010 Dec 30;
The age of necrotizing enterocolitis onset: an application of Sartwell's incubation period model. Gonzalez-Rivera, R; Culverhouse, R C; Hamvas, A; Tarr, P I; Warner, B B Journal of perinatology : official journal of the California Perinatal Association 21273988 2011 Aug
Inexact Local Alignment Search over Suffix Arrays. Ghodsi, Mohammadreza; Pop, Mihai Proceedings. IEEE International Conference on Bioinformatics and Biomedicine 21278916 2009 Nov 1
The microbe-derived short chain fatty acid butyrate targets miRNA-dependent p21 gene expression in human colon cancer. Hu, Shien; Dong, Tien Sy; Dalal, Sushila R; Wu, Feng; Bissonnette, Marc; Kwon, John H; Chang, Eugene B PloS one 21283757 2011
The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data. Tanenbaum, David M; Goll, Johannes; Murphy, Sean; Kumar, Prateek; Zafar, Nikhat; Thiagarajan, Mathangi; Madupu, Ramana; Davidsen, Tanja; Kagan, Leonid; Kravitz, Saul; Rusch, Douglas B; Yooseph, Shibu Standards in genomic sciences. 21304707 2010 Mar 30;
Current concepts of the intestinal microbiota and the pathogenesis of infection. Wardwell, Leslie H; Huttenhower, Curtis; Garrett, Wendy S Current infectious disease reports 21308452 2011 Feb
Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts. Ballal, Sonia A; Gallini, Carey Ann; Segata, Nicola; Huttenhower, Curtis; Garrett, Wendy S Cellular microbiology 21314883 2011 Apr
A randomised trial of sheathed versus standard forceps for obtaining uncontaminated biopsy specimens of microbiota from the terminal ileum. Dave, Maneesh; Johnson, Laura A; Walk, Seth T; Young, Vincent B; Stidham, Ryan W; Chaudhary, Meghana N; Funnell, Jessica; Higgins, Peter D R Gut 21317176 2011 Aug
Microdroplet-enabled highly parallel co-cultivation of microbial communities. Park, Jihyang; Kerner, Alissa; Burns, Mark A; Lin, Xiaoxia Nina PloS one 21364881 2011
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. Blainey, Paul C; Mosier, Annika C; Potanina, Anastasia; Francis, Christopher A; Quake, Stephen R PloS one 21364937 2011
Host-associated and free-living phage communities differ profoundly in phylogenetic composition. Caporaso, J Gregory; Knight, Rob; Kelley, Scott T PloS one 21383980 2011
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. Wu, Yu-Wei; Ye, Yuzhen Journal of computational biology : a journal of computational molecular cell biology 21385052 2011 Mar
Beyond natural antibodies: the power of in vitro display technologies. Bradbury, Andrew R M; Sidhu, Sachdev; Dubel, Stefan; McCafferty, John Nature biotechnology 21390033 2011 Mar
Next generation sequence assembly with AMOS. Treangen, Todd J; Sommer, Dan D; Angly, Florent E; Koren, Sergey; Pop, Mihai Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 21400694 2011 Mar
Unravelling the effects of the environment and host genotype on the gut microbiome. Spor, Ayme; Koren, Omry; Ley, Ruth Nature reviews. Microbiology 21407244 2011 Apr
Overview of the development of personalized genomic medicine and surgery. Brunicardi, F Charles; Gibbs, Richard A; Wheeler, David A; Nemunaitis, John; Fisher, William; Goss, John; Chen, Changyi World journal of surgery 21424870 2011 Aug
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. Haft, Daniel H; Basu, Malay Kumar Journal of bacteriology 21478363 2011 Jun
The mind-body-microbial continuum. Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J; Gordon, Jeffrey I; Knight, Rob Dialogues in clinical neuroscience 21485746 2011
Reliability and validity of a modified Bristol Stool Form Scale for children. Lane, Mariella M; Czyzewski, Danita I; Chumpitazi, Bruno P; Shulman, Robert J The Journal of pediatrics 21489557 2011 Sep
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. Niu, Beifang; Zhu, Zhengwei; Fu, Limin; Wu, Sitao; Li, Weizhong Bioinformatics (Oxford, England) 21505035 2011 Jun 15
Simrank: Rapid and sensitive general-purpose k-mer search tool. DeSantis, Todd Z; Keller, Keith; Karaoz, Ulas; Alekseyenko, Alexander V; Singh, Navjeet N S; Brodie, Eoin L; Pei, Zhiheng; Andersen, Gary L; Larsen, Niels BMC ecology 21524302 2011
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Sun, Yijun; Cai, Yunpeng; Huse, Susan M; Knight, Rob; Farmerie, William G; Wang, Xiaoyu; Mai, Volker Briefings in bioinformatics 21525143 2012 Jan
Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Dominguez-Bello, Maria Gloria; Blaser, Martin J; Ley, Ruth E; Knight, Rob Gastroenterology 21530737 2011 May
Brief communication: DNA from early Holocene American dog. Tito, Raul Y; Belknap 3rd, Samuel L; Sobolik, Kristin D; Ingraham, Robert C; Cleeland, Lauren M; Lewis Jr, Cecil M American journal of physical anthropology 21541929 2011 Aug
Boulder ALignment Editor (ALE): a web-based RNA alignment tool. Stombaugh, Jesse; Widmann, Jeremy; McDonald, Daniel; Knight, Rob Bioinformatics (Oxford, England) 21546392 2011 Jun 15
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R; Amaral-Zettler, Linda; Gilbert, Jack A; Karsch-Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy; Vaughan, Robert; Hunter, Christopher; Park, Joonhong; Morrison, Norman; Rocca-Serr Nature biotechnology 21552244 2011 May
Evolution and classification of the CRISPR-Cas systems. Makarova, Kira S; Haft, Daniel H; Barrangou, Rodolphe; Brouns, Stan J J; Charpentier, Emmanuelle; Horvath, Philippe; Moineau, Sylvain; Mojica, Francisco J M; Wolf, Yuri I; Yakunin, Alexander F; van der Oost, John; Koonin, Eugene V Nature reviews. Microbiology 21552286 2011 Jun
RAPSearch: a fast protein similarity search tool for short reads. Ye, Yuzhen; Choi, Jeong-Hyeon; Tang, Haixu BMC bioinformatics 21575167 2011
Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Ravussin, Yann; Koren, Omry; Spor, Ayme; LeDuc, Charles; Gutman, Roee; Stombaugh, Jesse; Knight, Rob; Ley, Ruth E; Leibel, Rudolph L Obesity (Silver Spring, Md.) 21593810 2012 Apr
The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. Dong, Qunfeng; Nelson, David E; Toh, Evelyn; Diao, Lixia; Gao, Xiang; Fortenberry, J Dennis; Van der Pol, Barbara PloS one 21603636 2011
Mammalian Cell Sorting using ýýFACS. Cho, Sung Hwan; Chen, Chun Hao; Tsai, Frank S; Godin, Jessica; Lo, Yu-Hwa Conference on Lasers and Electro-optics : (CLEO). Conference on Lasers and Electro-optics 21614147 2010 May 16
Moving pictures of the human microbiome. Caporaso, J Gregory; Lauber, Christian L; Costello, Elizabeth K; Berg-Lyons, Donna; Gonzalez, Antonio; Stombaugh, Jesse; Knights, Dan; Gajer, Pawel; Ravel, Jacques; Fierer, Noah; Gordon, Jeffrey I; Knight, Rob Genome biology 21624126 2011
Interleukin-1ýý (IL-1ýý) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis. Carvalho, Frederic A; Nalbantoglu, Ilke; Ortega-Fernandez, Sophie; Aitken, Jesse D; Su, Yueju; Koren, Omry; Walters, William A; Knight, Rob; Ley, Ruth E; Vijay-Kumar, Matam; Gewirtz, Andrew T Gut 21646247 2012 Mar
Bacterial DNA content in the intestinal wall from infants with necrotizing enterocolitis. Bucher, Brian T; McDuffie, Lucas A; Shaikh, Nurmohammad; Tarr, Phillip I; Warner, Barbara B; Hamvas, Aaron; White, Frances V; Erwin, Christopher R; Warner, Brad W Journal of pediatric surgery 21683193 2011 Jun
UCHIME improves sensitivity and speed of chimera detection. Edgar, Robert C; Haas, Brian J; Clemente, Jose C; Quince, Christopher; Knight, Rob Bioinformatics (Oxford, England) 21700674 2011 Aug 15
Metagenomic biomarker discovery and explanation. Segata, Nicola; Izard, Jacques; Waldron, Levi; Gevers, Dirk; Miropolsky, Larisa; Garrett, Wendy S; Huttenhower, Curtis Genome biology 21702898 2011
How patients view probiotics: findings from a multicenter study of patients with inflammatory bowel disease and irritable bowel syndrome. Mercer, MaryBeth; Brinich, Margaret A; Geller, Gail; Harrison, Krista; Highland, Janelle; James, Katherine; Marshall, Patricia; McCormick, Jennifer B; Tilburt, Jon; Achkar, Jean-Paul; Farrell, Ruth M; Sharp, Richard R Journal of clinical gastroenterology 21716123 2012 Feb
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E The ISME journal 21716311 2012 Jan
DNACLUST: accurate and efficient clustering of phylogenetic marker genes. Ghodsi, Mohammadreza; Liu, Bo; Pop, Mihai BMC bioinformatics 21718538 2011
Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown. Lladser, Manuel E; Gouet, Raul; Reeder, Jens PloS one 21738613 2011
Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Saulnier, Delphine M; Riehle, Kevin; Mistretta, Toni-Ann; Diaz, Maria-Alejandra; Mandal, Debasmita; Raza, Sabeen; Weidler, Erica M; Qin, Xiang; Coarfa, Cristian; Milosavljevic, Aleksandar; Petrosino, Joseph F; Highlander, Sarah; Gibbs, Richard; Lynch, Sus Gastroenterology 21741921 2011 Nov
Microfluidic fluorescence in situ hybridization and flow cytometry (ýýFlowFISH). Liu, Peng; Meagher, Robert J; Light, Yooli K; Yilmaz, Suzan; Chakraborty, Romy; Arkin, Adam P; Hazen, Terry C; Singh, Anup K Lab on a chip 21755095 2011 Aug 21
Bayesian community-wide culture-independent microbial source tracking. Knights, Dan; Kuczynski, Justin; Charlson, Emily S; Zaneveld, Jesse; Mozer, Michael C; Collman, Ronald G; Bushman, Frederic D; Knight, Rob; Kelley, Scott T Nature methods 21765408 2011 Sep
Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward. Young, Vincent B; Kahn, Stacy A; Schmidt, Thomas M; Chang, Eugene B Frontiers in microbiology 21772835 2011
Investigating the biological and clinical significance of human dysbioses. Frank, Daniel N; Zhu, Wei; Sartor, R Balfour; Li, Ellen Trends in microbiology 21775143 2011 Sep
The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong The ISME journal 21796217 2012 Feb
The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection. Reeves, Angela E; Theriot, Casey M; Bergin, Ingrid L; Huffnagle, Gary B; Schloss, Patrick D; Young, Vincent B Gut microbes 21804357 2011 May-Jun
Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization. Chen, Chun H; Cho, Sung H; Chiang, Hsin-I; Tsai, Frank; Zhang, Kun; Lo, Yu-Hwa Analytical chemistry 21809842 2011 Oct 1
Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. Ahn, Jiyoung; Yang, Liying; Paster, Bruce J; Ganly, Ian; Morris, Luc; Pei, Zhiheng; Hayes, Richard B PloS one 21829515 2011
Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. Zaneveld, Jesse R R; Parfrey, Laura Wegener; Van Treuren, Will; Lozupone, Catherine; Clemente, Jose C; Knights, Dan; Stombaugh, Jesse; Kuczynski, Justin; Knight, Rob Trends in microbiology 21872475 2011 Oct
Antibiotic effects on bacterial profile in osteonecrosis of the jaw. Ji, X; Pushalkar, S; Li, Y; Glickman, R; Fleisher, K; Saxena, D Oral diseases 21883710 2012 Jan
Linking long-term dietary patterns with gut microbial enterotypes. Wu, Gary D; Chen, Jun; Hoffmann, Christian; Bittinger, Kyle; Chen, Ying-Yu; Keilbaugh, Sue A; Bewtra, Meenakshi; Knights, Dan; Walters, William A; Knight, Rob; Sinha, Rohini; Gilroy, Erin; Gupta, Kernika; Baldassano, Robert; Nessel, Lisa; Li, Hongzhe; Bus Science (New York, N.Y.) 21885731 2011 Oct 7
Genetic basis for in vivo daptomycin resistance in enterococci. Arias, Cesar A; Panesso, Diana; McGrath, Danielle M; Qin, Xiang; Mojica, Maria F; Miller, Corwin; Diaz, Lorena; Tran, Truc T; Rincon, Sandra; Barbu, E Magda; Reyes, Jinnethe; Roh, Jung H; Lobos, Elizabeth; Sodergren, Erica; Pasqualini, Renata; Arap, Wadih The New England journal of medicine 21899450 2011 Sep 8
WebMGA: a customizable web server for fast metagenomic sequence analysis. Wu, Sitao; Zhu, Zhengwei; Fu, Liming; Niu, Beifang; Li, Weizhong BMC genomics 21899761 2011
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. Pirrung, Meg; Kennedy, Ryan; Caporaso, J Gregory; Stombaugh, Jesse; Wendel, Doug; Knight, Rob Bioinformatics (Oxford, England) 21903626 2011 Nov 1
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Youssef, Noha H; Blainey, Paul C; Quake, Stephen R; Elshahed, Mostafa S Applied and environmental microbiology 21908640 2011 Nov
Applying an optical space-time coding method to enhance light scattering signals in microfluidic devices. Mei, Zhe; Wu, Tsung-Feng; Pion-Tonachini, Luca; Qiao, Wen; Zhao, Chao; Liu, Zhiwen; Lo, Yu-Hwa Biomicrofluidics. 21915241 2011 Sep;
The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Sczesnak, Andrew; Segata, Nicola; Qin, Xiang; Gevers, Dirk; Petrosino, Joseph F; Huttenhower, Curtis; Littman, Dan R; Ivanov, Ivaylo I Cell host & microbe 21925113 2011 Sep 15
Bambus 2: scaffolding metagenomes. Koren, Sergey; Treangen, Todd J; Pop, Mihai Bioinformatics (Oxford, England) 21926123 2011 Nov 1
Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. Segata, Nicola; Huttenhower, Curtis PloS one 21931822 2011
Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. Liu, Zhenqiu; Hsiao, William; Cantarel, Brandi L; Drabek, Elliott Franco; Fraser-Liggett, Claire Bioinformatics (Oxford, England) 21984758 2011 Dec 1
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. Liu, Bo; Gibbons, Theodore; Ghodsi, Mohammad; Treangen, Todd; Pop, Mihai BMC genomics 21989143 2011
Fluorescent labeling of antibody fragments using split GFP. Ferrara, Fortunato; Listwan, Pawel; Waldo, Geoffrey S; Bradbury, Andrew R M PloS one 21998685 2011
Human-associated microbial signatures: examining their predictive value. Knights, Dan; Parfrey, Laura Wegener; Zaneveld, Jesse; Lozupone, Catherine; Knight, Rob Cell host & microbe. 22018228 2011 Oct 20;
Microbiome and malignancy. Plottel, Claudia S; Blaser, Martin J Cell host & microbe 22018233 2011 Oct 20
Graph accordance of next-generation sequence assemblies. Yao, Guohui; Ye, Liang; Gao, Hongyu; Minx, Patrick; Warren, Wesley C; Weinstock, George M Bioinformatics (Oxford, England) 22025481 2012 Jan 1
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Zhao, Yongan; Tang, Haixu; Ye, Yuzhen Bioinformatics (Oxford, England) 22039206 2012 Jan 1
De minimis risk: a proposal for a new category of research risk. Rhodes, Rosamond; Azzouni, Jody; Baumrin, Stefan Bernard; Benkov, Keith; Blaser, Martin J; Brenner, Barbara; Dauben, Joseph W; Earle, William J; Frank, Lily; Gligorov, Nada; Goldfarb, Joseph; Hirschhorn, Kurt; Hirschhorn, Rochelle; Holzman, Ian; Indyk, De The American journal of bioethics : AJOB 22047112 2011 Nov
Saying privacy, meaning confidentiality. Schwab, Abraham P; Frank, Lily; Gligorov, Nada The American journal of bioethics : AJOB 22047127 2011 Nov
2,2'-Bis(meth-oxy-meth-oxy)-3-methyl-1,1'-binaphth-yl. Carrilho, Rui M B; Abreu, Artur R; Pereira, Mariette M; Rodrigues, V H Acta crystallographica. Section E, Structure reports online. 22058976 2011 Sep 01;
Tetra-?-acetato-?O:O'-bis-[(3,5-di-methyl-1H-pyrazole-?N)-copper(II)]. van Wyk, Juanita; Omondi, Bernard; Darkwa, James Acta crystallographica. Section E, Structure reports online. 22065823 2011 Sep 01;
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. Basu, Malay K; Selengut, Jeremy D; Haft, Daniel H BMC bioinformatics 22070167 2011
Epigenetic priors for identifying active transcription factor binding sites. Cuellar-Partida, Gabriel; Buske, Fabian A; McLeay, Robert C; Whitington, Tom; Noble, William Stafford; Bailey, Timothy L Bioinformatics (Oxford, England) 22072382 2012 Jan 1
The intestinal microbiota in health and disease. Young, Vincent B Current opinion in gastroenterology 22080827 2012 Jan
IMG/M: the integrated metagenome data management and comparative analysis system. Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Pati, Amrita; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natali Nucleic acids research 22086953 2012 Jan
Astrovirus MLB2 viremia in febrile child. Holtz, Lori R; Wylie, Kristine M; Sodergren, Erica; Jiang, Yanfang; Franz, Carl J; Weinstock, George M; Storch, Gregory A; Wang, David Emerging infectious diseases 22099095 2011 Nov
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment. Ye, Yuzhen Proceedings. IEEE International Conference on Bioinformatics and Biomedicine 22102981 2011 Feb 4
The Human Microbiome Project: lessons from human genomics. Lewis Jr, Cecil M; Obregon-Tito, Alexandra; Tito, Raul Y; Foster, Morris W; Spicer, Paul G Trends in microbiology 22112388 2012 Jan
An optical-coding method to measure particle distribution in microfluidic devices. Wu, Tsung-Feng; Mei, Zhe; Pion-Tonachini, Luca; Zhao, Chao; Qiao, Wen; Arianpour, Ashkan; Lo, Yu-Hwa AIP advances. 22125760 2011 Jun;
Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. Cantarel, Brandi L; Erickson, Alison R; VerBerkmoes, Nathan C; Erickson, Brian K; Carey, Patricia A; Pan, Chongle; Shah, Manesh; Mongodin, Emmanuel F; Jansson, Janet K; Fraser-Liggett, Claire M; Hettich, Robert L PloS one 22132090 2011
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip The ISME journal 22134646 2012 Mar
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M; Kyrpides, Nikos C Nucleic acids research 22135293 2012 Jan
CharProtDB: a database of experimentally characterized protein annotations. Madupu, Ramana; Richter, Alexander; Dodson, Robert J; Brinkac, Lauren; Harkins, Derek; Durkin, Scott; Shrivastava, Susmita; Sutton, Granger; Haft, Daniel Nucleic acids research 22140108 2012 Jan
GAGE: A critical evaluation of genome assemblies and assembly algorithms. Salzberg, Steven L; Phillippy, Adam M; Zimin, Aleksey; Puiu, Daniela; Magoc, Tanja; Koren, Sergey; Treangen, Todd J; Schatz, Michael C; Delcher, Arthur L; Roberts, Michael; Marcais, Guillaume; Pop, Mihai; Yorke, James A Genome research 22147368 2012 Mar
Characterizing microbial communities through space and time. Gonzalez, Antonio; King, Andrew; Robeson 2nd, Michael S; Song, Sejin; Shade, Ashley; Metcalf, Jessica L; Knight, Rob Current opinion in biotechnology 22154467 2012 Jun
Single cell genome sequencing. Yilmaz, Suzan; Singh, Anup K Current opinion in biotechnology 22154471 2012 Jun
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; Gonzalez, Antonio; Caporaso, J Gregory; Knight, Rob Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 22161565 2011 Dec
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences. Wang, Xiaoyu; Cai, Yunpeng; Sun, Yijun; Knight, Rob; Mai, Volker The ISME journal 22170430 2012 Jul
SitePainter: a tool for exploring biogeographical patterns. Gonzalez, Antonio; Stombaugh, Jesse; Lauber, Christian L; Fierer, Noah; Knight, Rob Bioinformatics (Oxford, England) 22171330 2012 Feb 1
Advancing analytical algorithms and pipelines for billions of microbial sequences. Gonzalez, Antonio; Knight, Rob Current opinion in biotechnology 22172529 2012 Feb
Artificial functional difference between microbial communities caused by length difference of sequencing reads. Zhang, Quan; Doak, Thomas G; Ye, Yuzhen Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 22174281 2012
Experimental and analytical tools for studying the human microbiome. Kuczynski, Justin; Lauber, Christian L; Walters, William A; Parfrey, Laura Wegener; Clemente, Jose C; Gevers, Dirk; Knight, Rob Nature reviews. Genetics 22179717 2012 Jan
Single-cell protein analysis. Wu, Meiye; Singh, Anup K Current opinion in biotechnology 22189001 2012 Feb
Human microbiome and HIV/AIDS. Saxena, Deepak; Li, Yihong; Yang, Liying; Pei, Zhiheng; Poles, Michael; Abrams, William R; Malamud, Daniel Current HIV/AIDS reports 22193889 2012 Mar
IMG: the Integrated Microbial Genomes database and comparative analysis system. Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos Nucleic acids research 22194640 2012 Jan
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. Schloss, Patrick D; Gevers, Dirk; Westcott, Sarah L PloS one 22194782 2011
GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. Haft, Daniel H; Varghese, Neha PloS one 22194940 2011
Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. Smajs, David; Norris, Steven J; Weinstock, George M Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 22198325 2012 Mar
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Schatz, Michael C; Phillippy, Adam M; Sommer, Daniel D; Delcher, Arthur L; Puiu, Daniela; Narzisi, Giuseppe; Salzberg, Steven L; Pop, Mihai Briefings in bioinformatics 22199379 2013 Mar
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. Soergel, David A W; Dey, Neelendu; Knight, Rob; Brenner, Steven E The ISME journal 22237546 2012 Jul
Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments. Ozok, A R; Persoon, I F; Huse, S M; Keijser, B J F; Wesselink, P R; Crielaard, W; Zaura, E International endodontic journal 22251411 2012 Jun
Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis. Feazel, Leah M; Robertson, Charles E; Ramakrishnan, Vijay R; Frank, Daniel N The Laryngoscope 22253013 2012 Feb
Perturbation dynamics of the rumen microbiota in response to exogenous butyrate. Li, Robert W; Wu, Sitao; Baldwin 6th, Ransom L; Li, Weizhong; Li, Congjun PloS one 22253719 2012
Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine. Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Finegold, Milton J; Petrosino, Joseph F; Conner, Margaret E; Versalovic, James FASEB journal : official publication of the Federation of American Societies for Experimental Biology 22267340 2012 May
The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Bergmann, Gaddy T; Bates, Scott T; Eilers, Kathryn G; Lauber, Christian L; Caporaso, J Gregory; Walters, William A; Knight, Rob; Fierer, Noah Soil biology & biochemistry 22267877 2011 Jul
Significance of the microbiome in obstructive lung disease. Han, Meilan K; Huang, Yvonne J; Lipuma, John J; Boushey, Homer A; Boucher, Richard C; Cookson, William O; Curtis, Jeffrey L; Erb-Downward, John; Lynch, Susan V; Sethi, Sanjay; Toews, Galen B; Young, Vincent B; Wolfgang, Matthew C; Huffnagle, Gary B; Marti Thorax 22318161 2012 May
Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. Mei, Junjie; Liu, Yuhong; Dai, Ning; Hoffmann, Christian; Hudock, Kristin M; Zhang, Peggy; Guttentag, Susan H; Kolls, Jay K; Oliver, Paula M; Bushman, Frederic D; Worthen, G Scott The Journal of clinical investigation 22326959 2012 Mar 1
Altered vaginal microbiota are associated with perinatal mother-to-child transmission of HIV in African women from Burkina Faso. Frank, Daniel N; Manigart, Olivier; Leroy, Valeriane; Meda, Nicolas; Valea, Diane; Zhang, Weiming; Dabis, Francois; Pace, Norman R; Van de Perre, Philippe; Janoff, Edward N Journal of acquired immune deficiency syndromes (1999) 22343176 2012 Jul 1
Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice. Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Barrish, James P; Finegold, Milton J; Petrosino, Joseph F; Guerrant, Richard L; Conner, Margaret E; Versalovic, James Journal of pediatric gastroenterology and nutrition 22343914 2012 Sep
Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus. Yang, Liying; Francois, Fritz; Pei, Zhiheng Clinical cancer research : an official journal of the American Association for Cancer Research 22344232 2012 Apr 15
Hypervariable loci in the human gut virome. Minot, Samuel; Grunberg, Stephanie; Wu, Gary D; Lewis, James D; Bushman, Frederic D Proceedings of the National Academy of Sciences of the United States of America 22355105 2012 Mar 6
Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment. Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre PloS one 22355378 2012
Of microbes and meals: the health consequences of dietary endotoxemia. Kelly, Caleb J; Colgan, Sean P; Frank, Daniel N Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition. 22378797 2012 Apr;
A format for phylogenetic placements. Matsen, Frederick A; Hoffman, Noah G; Gallagher, Aaron; Stamatakis, Alexandros PloS one 22383988 2012
Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon. Harrell, Laura; Wang, Yunwei; Antonopoulos, Dionysios; Young, Vincent; Lichtenstein, Lev; Huang, Yong; Hanauer, Stephen; Chang, Eugene PloS one 22389708 2012
Experiences of patients with chronic gastrointestinal conditions: in their own words. McCormick, Jennifer B; Hammer, Rachel R; Farrell, Ruth M; Geller, Gail; James, Katherine M; Loftus Jr, Edward V; Mercer, Mary Beth; Tilburt, Jon C; Sharp, Richard R Health and quality of life outcomes 22401607 2012
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. Caporaso, J Gregory; Lauber, Christian L; Walters, William A; Berg-Lyons, Donna; Huntley, James; Fierer, Noah; Owens, Sarah M; Betley, Jason; Fraser, Louise; Bauer, Markus; Gormley, Niall; Gilbert, Jack A; Smith, Geoff; Knight, Rob The ISME journal. 22402401 2012 Aug;
The human microbiome: at the interface of health and disease. Cho, Ilseung; Blaser, Martin J Nature reviews. Genetics 22411464 2012 Apr
Dichlorido{1-[N-(5-chloro-2-oxidophen-yl)carboximido-yl]naphthalen-2-olato-?O,N,O'}(methanol-?O)tin(IV). Shahverdizadeh, Gholam Hossein; Ng, Seik Weng; Tiekink, Edward R T; Mirtamizdoust, Babak Acta crystallographica. Section E, Structure reports online. 22412406 2012 Mar 01;
4,5-Diphen-oxy-benzene-1,2-dicarbo-nitrile. Foo, Chuan Ching; Tan, Ai Ling; Wimmer, Franz L; Mirza, Aminul Huq; Young, David J; Ng, Seik Weng; Tiekink, Edward R T Acta crystallographica. Section E, Structure reports online. 22412514 2012 Mar 01;
The impact of the gut microbiota on human health: an integrative view. Clemente, Jose C; Ursell, Luke K; Parfrey, Laura Wegener; Knight, Rob Cell. 22424233 2012 Mar 16;
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Pamp, Sunje J; Harrington, Eoghan D; Quake, Stephen R; Relman, David A; Blainey, Paul C Genome research 22434425 2012 Jun
AntiFam: a tool to help identify spurious ORFs in protein annotation. Eberhardt, Ruth Y; Haft, Daniel H; Punta, Marco; Martin, Maria; O'Donovan, Claire; Bateman, Alex Database : the journal of biological databases and curation 22434837 2012
Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. Hill, David A; Siracusa, Mark C; Abt, Michael C; Kim, Brian S; Kobuley, Dmytro; Kubo, Masato; Kambayashi, Taku; Larosa, David F; Renner, Ellen D; Orange, Jordan S; Bushman, Frederic D; Artis, David Nature medicine 22447074 2012 Apr
Decade-long bacterial community dynamics in cystic fibrosis airways. Zhao, Jiangchao; Schloss, Patrick D; Kalikin, Linda M; Carmody, Lisa A; Foster, Bridget K; Petrosino, Joseph F; Cavalcoli, James D; VanDevanter, Donald R; Murray, Susan; Li, Jun Z; Young, Vincent B; LiPuma, John J Proceedings of the National Academy of Sciences of the United States of America 22451929 2012 Apr 10
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Giannoukos, Georgia; Ciulla, Dawn M; Huang, Katherine; Haas, Brian J; Izard, Jacques; Levin, Joshua Z; Livny, Jonathan; Earl, Ashlee M; Gevers, Dirk; Ward, Doyle V; Nusbaum, Chad; Birren, Bruce W; Gnirke, Andreas Genome biology 22455878 2012
Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis. Li, Robert W; Wu, Sitao; Li, Weizhong; Navarro, Karl; Couch, Robin D; Hill, Dolores; Urban Jr, Joseph F Infection and immunity 22493085 2012 Jun
Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism. Pathak, Darshankumar T; Wei, Xueming; Bucuvalas, Alex; Haft, Daniel H; Gerloff, Dietlind L; Wall, Daniel PLoS genetics 22511878 2012
Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection. Wu, Sitao; Li, Robert W; Li, Weizhong; Beshah, Ethiopia; Dawson, Harry D; Urban Jr, Joseph F PloS one 22532855 2012
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. Ursell, Luke K; Clemente, Jose C; Rideout, Jai Ram; Gevers, Dirk; Caporaso, J Gregory; Knight, Rob The Journal of allergy and clinical immunology 22541361 2012 May
We are what we eat: how the diet of infants affects their gut microbiome. Pop, Mihai Genome biology 22546514 2012
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. Matsen, Frederick A; Gallagher, Aaron Algorithms for molecular biology : AMB. 22549005 2012 May 02;
Temporal dynamics of the human vaginal microbiota. Gajer, Pawel; Brotman, Rebecca M; Bai, Guoyun; Sakamoto, Joyce; Schutte, Ursel M E; Zhong, Xue; Koenig, Sara S K; Fu, Li; Ma, Zhanshan Sam; Zhou, Xia; Abdo, Zaid; Forney, Larry J; Ravel, Jacques Science translational medicine 22553250 2012 May 2
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. Xiong, Xuejian; Frank, Daniel N; Robertson, Charles E; Hung, Stacy S; Markle, Janet; Canty, Angelo J; McCoy, Kathy D; Macpherson, Andrew J; Poussier, Philippe; Danska, Jayne S; Parkinson, John PloS one 22558305 2012
Food and the gut microbiota in inflammatory bowel diseases: a critical connection. Albenberg, Lindsey G; Lewis, James D; Wu, Gary D Current opinion in gastroenterology 22573192 2012 Jul
A new era of the vaginal microbiome: advances using next-generation sequencing. Fettweis, Jennifer M; Serrano, Myrna G; Girerd, Philippe H; Jefferson, Kimberly K; Buck, Gregory A Chemistry & biodiversity 22589096 2012 May
Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance. Britton, Robert A; Young, Vincent B Trends in microbiology 22595318 2012 Jul
Bacterial communities of the coronal sulcus and distal urethra of adolescent males. Nelson, David E; Dong, Qunfeng; Van der Pol, Barbara; Toh, Evelyn; Fan, Baochang; Katz, Barry P; Mi, Deming; Rong, Ruichen; Weinstock, George M; Sodergren, Erica; Fortenberry, J Dennis PloS one 22606251 2012
An ileal Crohn's disease gene signature based on whole human genome expression profiles of disease unaffected ileal mucosal biopsies. Zhang, Tianyi; Song, Bowen; Zhu, Wei; Xu, Xiao; Gong, Qing Qing; Morando, Christopher; Dassopoulos, Themistocles; Newberry, Rodney D; Hunt, Steven R; Li, Ellen PloS one 22606341 2012
Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells. Wu, Sitao; Li, Robert W; Li, Weizhong; Li, Cong-Jun PloS one 22615851 2012
'Omics' of the mammalian gut--new insights into function. Lamendella, Regina; VerBerkmoes, Nathan; Jansson, Janet K Current opinion in biotechnology 22626866 2012 Jun
RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. Widmann, Jeremy; Stombaugh, Jesse; McDonald, Daniel; Chocholousova, Jana; Gardner, Paul; Iyer, Matthew K; Liu, Zongzhi; Lozupone, Catherine A; Quinn, John; Smit, Sandra; Wikman, Shandy; Zaneveld, Jesse R R; Knight, Rob RNA (New York, N.Y.) 22645380 2012 Jul
Spatial and temporal variability of the human microbiota. Parfrey, L W; Knight, R Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 22647040 2012 Jul
Quantification of Transcriptome Responses of the Rumen Epithelium to Butyrate Infusion using RNA-seq Technology. Baldwin 6th, Ransom L; Wu, Sitao; Li, Weizhong; Li, Congjun; Bequette, Brian J; Li, Robert W Gene regulation and systems biology 22654504 2012
Comparison of storage conditions for human vaginal microbiome studies. Bai, Guoyun; Gajer, Pawel; Nandy, Melissa; Ma, Bing; Yang, Hongqiu; Sakamoto, Joyce; Blanchard, May H; Ravel, Jacques; Brotman, Rebecca M PloS one 22655031 2012
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Lozupone, Catherine; Faust, Karoline; Raes, Jeroen; Faith, Jeremiah J; Frank, Daniel N; Zaneveld, Jesse; Gordon, Jeffrey I; Knight, Rob Genome research 22665442 2012 Oct
Deep sequencing of the oral microbiome reveals signatures of periodontal disease. Liu, Bo; Faller, Lina L; Klitgord, Niels; Mazumdar, Varun; Ghodsi, Mohammad; Sommer, Daniel D; Gibbons, Theodore R; Treangen, Todd J; Chang, Yi-Chien; Li, Shan; Stine, O Colin; Hasturk, Hatice; Kasif, Simon; Segre, Daniel; Pop, Mihai; Amar, Salomon PloS one 22675498 2012
High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)). Earl, Ashlee M; Desjardins, Christopher A; Fitzgerald, Michael G; Arachchi, Harindra M; Zeng, Qiandong; Mehta, Teena; Griggs, Allison; Birren, Bruce W; Toney, Nadege C; Carr, Janice; Posey, James; Butler, W Ray Standards in genomic sciences. 22675588 2011 Dec 31;
Unlocking the potential of metagenomics through replicated experimental design. Knight, Rob; Jansson, Janet; Field, Dawn; Fierer, Noah; Desai, Narayan; Fuhrman, Jed A; Hugenholtz, Phil; van der Lelie, Daniel; Meyer, Folker; Stevens, Rick; Bailey, Mark J; Gordon, Jeffrey I; Kowalchuk, George A; Gilbert, Jack A Nature biotechnology. 22678395 2012 Jun;
The microbiome of the lung. Beck, James M; Young, Vincent B; Huffnagle, Gary B Translational research : the journal of laboratory and clinical medicine 22683412 2012 Oct
Understanding vaginal microbiome complexity from an ecological perspective. Hickey, Roxana J; Zhou, Xia; Pierson, Jacob D; Ravel, Jacques; Forney, Larry J Translational research : the journal of laboratory and clinical medicine 22683415 2012 Oct
Emerging view of the human virome. Wylie, Kristine M; Weinstock, George M; Storch, Gregory A Translational research : the journal of laboratory and clinical medicine 22683423 2012 Oct
Metagenomic microbial community profiling using unique clade-specific marker genes. Segata, Nicola; Waldron, Levi; Ballarini, Annalisa; Narasimhan, Vagheesh; Jousson, Olivier; Huttenhower, Curtis Nature methods 22688413 2012 Aug
Stabilization of the murine gut microbiome following weaning. Schloss, Patrick D; Schubert, Alyxandria M; Zackular, Joseph P; Iverson, Kathryn D; Young, Vincent B; Petrosino, Joseph F Gut microbes 22688727 2012 Jul-Aug
mcaGUI: microbial community analysis R-Graphical User Interface (GUI). Copeland, Wade K; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schutte, Ursel M E; Zhou, Xia; Williams, Christopher J; Forney, Larry J; Abdo, Zaid Bioinformatics (Oxford, England) 22692220 2012 Aug 15
Host genetic and environmental effects on mouse intestinal microbiota. Campbell, James H; Foster, Carmen M; Vishnivetskaya, Tatiana; Campbell, Alisha G; Yang, Zamin K; Wymore, Ann; Palumbo, Anthony V; Chesler, Elissa J; Podar, Mircea The ISME journal 22695862 2012 Nov
A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community. Wang, Mingjie; Ye, Yuzhen; Tang, Haixu Journal of computational biology : a journal of computational molecular cell biology 22697249 2012 Jun
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Segata, Nicola; Haake, Susan Kinder; Mannon, Peter; Lemon, Katherine P; Waldron, Levi; Gevers, Dirk; Huttenhower, Curtis; Izard, Jacques Genome biology 22698087 2012
Structure, function and diversity of the healthy human microbiome. Human Microbiome Project Consortium Nature 22699609 2012 Jun 14
A framework for human microbiome research. Human Microbiome Project Consortium Nature 22699610 2012 Jun 14
Associating microbiome composition with environmental covariates using generalized UniFrac distances. Chen, Jun; Bittinger, Kyle; Charlson, Emily S; Hoffmann, Christian; Lewis, James; Wu, Gary D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe Bioinformatics (Oxford, England) 22711789 2012 Aug 15
Metabolic reconstruction for metagenomic data and its application to the human microbiome. Abubucker, Sahar; Segata, Nicola; Goll, Johannes; Schubert, Alyxandria M; Izard, Jacques; Cantarel, Brandi L; Rodriguez-Mueller, Beltran; Zucker, Jeremy; Thiagarajan, Mathangi; Henrissat, Bernard; White, Owen; Kelley, Scott T; Methe, Barbara; Schloss, Pat PLoS computational biology 22719234 2012
Diverse CRISPRs evolving in human microbiomes. Rho, Mina; Wu, Yu-Wei; Tang, Haixu; Doak, Thomas G; Ye, Yuzhen PLoS genetics 22719260 2012
Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. Li, Ellen; Hamm, Christina M; Gulati, Ajay S; Sartor, R Balfour; Chen, Hongyan; Wu, Xiao; Zhang, Tianyi; Rohlf, F James; Zhu, Wei; Gu, Chi; Robertson, Charles E; Pace, Norman R; Boedeker, Edgar C; Harpaz, Noam; Yuan, Jeffrey; Weinstock, George M; Sodergre PloS one 22719818 2012
Sequence analysis of the human virome in febrile and afebrile children. Wylie, Kristine M; Mihindukulasuriya, Kathie A; Sodergren, Erica; Weinstock, George M; Storch, Gregory A PloS one 22719819 2012
Complex carbohydrate utilization by the healthy human microbiome. Cantarel, Brandi L; Lombard, Vincent; Henrissat, Bernard PloS one 22719820 2012
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). Goll, Johannes; Thiagarajan, Mathangi; Abubucker, Sahar; Huttenhower, Curtis; Yooseph, Shibu; Methe, Barbara A PloS one 22719821 2012
Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition. Zhang, Tianyi; DeSimone, Robert A; Jiao, Xiangmin; Rohlf, F James; Zhu, Wei; Gong, Qing Qing; Hunt, Steven R; Dassopoulos, Themistocles; Newberry, Rodney D; Sodergren, Erica; Weinstock, George; Robertson, Charles E; Frank, Daniel N; Li, Ellen PloS one 22719822 2012
Analyses of the microbial diversity across the human microbiome. Li, Kelvin; Bihan, Monika; Yooseph, Shibu; Methe, Barbara A PloS one 22719823 2012
A core human microbiome as viewed through 16S rRNA sequence clusters. Huse, Susan M; Ye, Yuzhen; Zhou, Yanjiao; Fodor, Anthony A PloS one 22719824 2012
Novel bacterial taxa in the human microbiome. Wylie, Kristine M; Truty, Rebecca M; Sharpton, Thomas J; Mihindukulasuriya, Kathie A; Zhou, Yanjiao; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Pollard, Katherine S PloS one 22719826 2012
Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. Martin, John; Sykes, Sean; Young, Sarah; Kota, Karthik; Sanka, Ravi; Sheth, Nihar; Orvis, Joshua; Sodergren, Erica; Wang, Zhengyuan; Weinstock, George M; Mitreva, Makedonka PloS one 22719831 2012
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. Aagaard, Kjersti; Riehle, Kevin; Ma, Jun; Segata, Nicola; Mistretta, Toni-Ann; Coarfa, Cristian; Raza, Sabeen; Rosenbaum, Sean; Van den Veyver, Ignatia; Milosavljevic, Aleksandar; Gevers, Dirk; Huttenhower, Curtis; Petrosino, Joseph; Versalovic, James PloS one 22719832 2012
Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria. Srinivasan, Sujatha; Hoffman, Noah G; Morgan, Martin T; Matsen, Frederick A; Fiedler, Tina L; Hall, Robert W; Ross, Frederick J; McCoy, Connor O; Bumgarner, Roger; Marrazzo, Jeanne M; Fredricks, David N PloS one 22719852 2012
Alternative splicing regulated by butyrate in bovine epithelial cells. Wu, Sitao; Li, Congjun; Huang, Wen; Li, Weizhong; Li, Robert W PloS one 22720068 2012
Evaluation of 16S rDNA-based community profiling for human microbiome research. Jumpstart Consortium Human Microbiome Project Data Generation Working Group PloS one 22720093 2012
Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Devkota, Suzanne; Wang, Yunwei; Musch, Mark W; Leone, Vanessa; Fehlner-Peach, Hannah; Nadimpalli, Anuradha; Antonopoulos, Dionysios A; Jabri, Bana; Chang, Eugene B Nature 22722865 2012 Jul 5
The world within: living with our microbial guests and guides. Janoff, Edward N; Gustafson, Claire; Frank, Daniel N Translational research : the journal of laboratory and clinical medicine 22732305 2012 Oct
Vaginal microbiome: rethinking health and disease. Ma, Bing; Forney, Larry J; Ravel, Jacques Annual review of microbiology 22746335 2012
Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. Filkins, L M; Hampton, T H; Gifford, A H; Gross, M J; Hogan, D A; Sogin, M L; Morrison, H G; Paster, B J; O'Toole, G A Journal of bacteriology 22753064 2012 Sep
Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine. Ma, Zhanshan Sam; Abdo, Zaid; Forney, Larry J Personalized medicine 22754581 2011 Nov
A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Dollive, Serena; Peterfreund, Gregory L; Sherrill-Mix, Scott; Bittinger, Kyle; Sinha, Rohini; Hoffmann, Christian; Nabel, Christopher S; Hill, David A; Artis, David; Bachman, Michael A; Custers-Allen, Rebecca; Grunberg, Stephanie; Wu, Gary D; Lewis, James D; Bushman, Frederic D Genome biology. 22759449 2012;
Diversity of 5S rRNA genes within individual prokaryotic genomes. Pei, Anna; Li, Hongru; Oberdorf, William E; Alekseyenko, Alexander V; Parsons, Tamasha; Yang, Liying; Gerz, Erika A; Lee, Peng; Xiang, Charlie; Nossa, Carlos W; Pei, Zhiheng FEMS microbiology letters 22765222 2012 Oct
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. Qin, Xiang; Galloway-Pena, Jessica R; Sillanpaa, Jouko; Roh, Jung Hyeob; Nallapareddy, Sreedhar R; Chowdhury, Shahreen; Bourgogne, Agathe; Choudhury, Tina; Muzny, Donna M; Buhay, Christian J; Ding, Yan; Dugan-Rocha, Shannon; Liu, Wen; Kovar, Christie; Sod BMC microbiology 22769602 2012
Ultrafast clustering algorithms for metagenomic sequence analysis. Li, Weizhong; Fu, Limin; Niu, Beifang; Wu, Sitao; Wooley, John Briefings in bioinformatics 22772836 2012 Nov
Ethical Discourse about the Modification of Food for Therapeutic Purposes: How Patients with Gastrointestinal Diseases View the Good, the Bad, and the Healthy. Harrison, Krista L; Geller, Gail; Marshall, Patricia; Tilburt, Jon; Mercer, Marybeth; Brinich, Margaret A; Highland, Janelle; Farrell, Ruth M; Sharp, Richard R AJOB primary research 22773953 2012 Jul 1
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Jacob, Biju; Ratner, Anna; Liolios, Konstantinos; Pagani, Ioanna; Huntemann, Marcel; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos C PloS one 22792232 2012
Microbial co-occurrence relationships in the human microbiome. Faust, Karoline; Sathirapongsasuti, J Fah; Izard, Jacques; Segata, Nicola; Gevers, Dirk; Raes, Jeroen; Huttenhower, Curtis PLoS computational biology 22807668 2012
Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. Pushalkar, Smruti; Ji, Xiaojie; Li, Yihong; Estilo, Cherry; Yegnanarayana, Ramanathan; Singh, Bhuvanesh; Li, Xin; Saxena, Deepak BMC microbiology 22817758 2012
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. Trimble, William L; Keegan, Kevin P; D'Souza, Mark; Wilke, Andreas; Wilkening, Jared; Gilbert, Jack; Meyer, Folker BMC bioinformatics 22839106 2012
The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples. Evans, Steven N; Matsen, Frederick A Journal of the Royal Statistical Society. Series B, Statistical methodology 22844205 2012 Jun 1
The "most wanted" taxa from the human microbiome for whole genome sequencing. Fodor, Anthony A; DeSantis, Todd Z; Wylie, Kristine M; Badger, Jonathan H; Ye, Yuzhen; Hepburn, Theresa; Hu, Ping; Sodergren, Erica; Liolios, Konstantinos; Huot-Creasy, Heather; Birren, Bruce W; Earl, Ashlee M PloS one 22848458 2012
Perspectives on human microbiome research ethics. McGuire, Amy L; Achenbaum, Laura S; Whitney, Simon N; Slashinski, Melody J; Versalovic, James; Keitel, Wendy A; McCurdy, Sheryl A Journal of empirical research on human research ethics : JERHRE 22850139 2012 Jul
Defining the human microbiome. Ursell, Luke K; Metcalf, Jessica L; Parfrey, Laura Wegener; Knight, Rob Nutrition reviews 22861806 2012 Aug
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. Blaser, Martin J; Dominguez-Bello, Maria G; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Estrada, Isidoro; Gao, Zhan; Clemente, Jose C; Costello, Elizabeth K; Knight, Rob The ISME journal 22895161 2013 Jan
Conservation of gene cassettes among diverse viruses of the human gut. Minot, Samuel; Wu, Gary D; Lewis, James D; Bushman, Frederic D PloS one 22900013 2012
The Human Microbiome Project: a community resource for the healthy human microbiome. Gevers, Dirk; Knight, Rob; Petrosino, Joseph F; Huang, Katherine; McGuire, Amy L; Birren, Bruce W; Nelson, Karen E; White, Owen; Methe, Barbara A; Huttenhower, Curtis PLoS biology 22904687 2012
Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome. Zupancic, Margaret L; Cantarel, Brandi L; Liu, Zhenqiu; Drabek, Elliott F; Ryan, Kathleen A; Cirimotich, Shana; Jones, Cheron; Knight, Rob; Walters, William A; Knights, Daniel; Mongodin, Emmanuel F; Horenstein, Richard B; Mitchell, Braxton D; Steinle, Nan PloS one 22905200 2012
Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures. Madan, J C; Koestler, D C; Stanton, B A; Davidson, L; Moulton, L A; Housman, M L; Moore, J H; Guill, M F; Morrison, H G; Sogin, M L; Hampton, T H; Karagas, M R; Palumbo, P E; Foster, J A; Hibberd, P L; O'Toole, G A mBio 22911969 2012
Current technology in the diagnosis of developmentally related lung disorders. Hamvas, Aaron Neonatology 22940625 2012
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Wu, Yu-Wei; Rho, Mina; Doak, Thomas G; Ye, Yuzhen Bioinformatics (Oxford, England) 22962453 2012 Sep 15
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. Wendl, Michael C; Kota, Karthik; Weinstock, George M; Mitreva, Makedonka Journal of mathematical biology 22965653 2013 Nov
Genomic approaches to studying the human microbiota. Weinstock, George M Nature 22972298 2012 Sep 13
Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Semova, Ivana; Carten, Juliana D; Stombaugh, Jesse; Mackey, Lantz C; Knight, Rob; Farber, Steven A; Rawls, John F Cell host & microbe 22980325 2012 Sep 13
Prevention of virus-induced type 1 diabetes with antibiotic therapy. Hara, Naoko; Alkanani, Aimon K; Ir, Diana; Robertson, Charles E; Wagner, Brandie D; Frank, Daniel N; Zipris, Danny Journal of immunology (Baltimore, Md. : 1950) 22988033 2012 Oct 15
Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women. Brotman, Rebecca M; Bradford, L Latey; Conrad, Melissa; Gajer, Pawel; Ault, Kevin; Peralta, Ligia; Forney, Larry J; Carlton, Jane M; Abdo, Zaid; Ravel, Jacques Sexually transmitted diseases 23007708 2012 Oct
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Morgan, Xochitl C; Tickle, Timothy L; Sokol, Harry; Gevers, Dirk; Devaney, Kathryn L; Ward, Doyle V; Reyes, Joshua A; Shah, Samir A; LeLeiko, Neal; Snapper, Scott B; Bousvaros, Athos; Korzenik, Joshua; Sands, Bruce E; Xavier, Ramnik J; Huttenhower, Curtis Genome biology 23013615 2012
Secondary structure improves OTU assignments of 16S rRNA gene sequences. Schloss, Patrick D The ISME journal 23018771 2013 Mar
Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. Blainey, Paul C; Milla, Carlos E; Cornfield, David N; Quake, Stephen R Science translational medicine 23019655 2012 Sep 26
The L1-norm best-fit hyperplane problem. Brooks, J P; Dula, J H Applied mathematics letters 23024460 2012 Jan 1
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. Zhu, Zhengwei; Niu, Beifang; Chen, Jing; Wu, Sitao; Sun, Shulei; Li, Weizhong Bioinformatics (Oxford, England) 23044549 2013 Jan 1
CD-HIT: accelerated for clustering the next-generation sequencing data. Fu, Limin; Niu, Beifang; Zhu, Zhengwei; Wu, Sitao; Li, Weizhong Bioinformatics (Oxford, England) 23060610 2012 Dec 1
Succession in the gut microbiome following antibiotic and antibody therapies for Clostridium difficile. Peterfreund, Gregory L; Vandivier, Lee E; Sinha, Rohini; Marozsan, Andre J; Olson, William C; Zhu, Jun; Bushman, Frederic D PloS one 23071679 2012
Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis. Chen, Jun; Bushman, Frederic D; Lewis, James D; Wu, Gary D; Li, Hongzhe Biostatistics (Oxford, England) 23074263 2013 Apr
Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa. Williams, Tiffany M; Loman, Nicholas J; Ebruke, Chinelo; Musher, Daniel M; Adegbola, Richard A; Pallen, Mark J; Weinstock, George M; Antonio, Martin PloS one 23082106 2012
Dietary issues in recurrent abdominal pain. Shulman, Robert J Journal of pediatric gastroenterology and nutrition 23103654 2012 Nov
Snake-oil, "quack medicine," and "industrially cultured organisms:" biovalue and the commercialization of human microbiome research. Slashinski, Melody J; McCurdy, Sheryl A; Achenbaum, Laura S; Whitney, Simon N; McGuire, Amy L BMC medical ethics 23110633 2012
Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy. Tran, Truc T; Panesso, Diana; Gao, Hongyu; Roh, Jung H; Munita, Jose M; Reyes, Jinnethe; Diaz, Lorena; Lobos, Elizabeth A; Shamoo, Yousif; Mishra, Nagendra N; Bayer, Arnold S; Murray, Barbara E; Weinstock, George M; Arias, Cesar A Antimicrobial agents and chemotherapy 23114757 2013 Jan
Detection of viruses in young children with fever without an apparent source. Colvin, Joshua M; Muenzer, Jared T; Jaffe, David M; Smason, Avraham; Deych, Elena; Shannon, William D; Arens, Max Q; Buller, Richard S; Lee, Wai-Ming; Weinstock, Erica J Sodergren; Weinstock, George M; Storch, Gregory A Pediatrics 23129086 2012 Dec
Estimation of distribution overlap of urn models. Hampton, Jerrad; Lladser, Manuel E PloS one 23139734 2012
Biodiversity and functional genomics in the human microbiome. Morgan, Xochitl C; Segata, Nicola; Huttenhower, Curtis Trends in genetics : TIG 23140990 2013 Jan
Statistical object data analysis of taxonomic trees from human microbiome data. La Rosa, Patricio S; Shands, Berkley; Deych, Elena; Zhou, Yanjiao; Sodergren, Erica; Weinstock, George; Shannon, William D PloS one 23152838 2012
The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. Aagaard, Kjersti; Petrosino, Joseph; Keitel, Wendy; Watson, Mark; Katancik, James; Garcia, Nathalia; Patel, Shital; Cutting, Mary; Madden, Tessa; Hamilton, Holli; Harris, Emily; Gevers, Dirk; Simone, Gina; McInnes, Pamela; Versalovic, James FASEB journal : official publication of the Federation of American Societies for Experimental Biology 23165986 2013 Mar
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; Gonzalez, Antonio; Caporaso, J Gregory; Knight, Rob Current protocols in microbiology 23184592 2012 Nov
TIGRFAMs and Genome Properties in 2013. Haft, Daniel H; Selengut, Jeremy D; Richter, Roland A; Harkins, Derek; Basu, Malay K; Beck, Erin Nucleic acids research 23197656 2013 Jan
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Bokulich, Nicholas A; Subramanian, Sathish; Faith, Jeremiah J; Gevers, Dirk; Gordon, Jeffrey I; Knight, Rob; Mills, David A; Caporaso, J Gregory Nature methods 23202435 2013 Jan
Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome. Kontur, Wayne S; Schackwitz, Wendy S; Ivanova, Natalia; Martin, Joel; Labutti, Kurt; Deshpande, Shweta; Tice, Hope N; Pennacchio, Christa; Sodergren, Erica; Weinstock, George M; Noguera, Daniel R; Donohue, Timothy J Journal of bacteriology 23209255 2012 Dec
Bioinformatics for the Human Microbiome Project. Gevers, Dirk; Pop, Mihai; Schloss, Patrick D; Huttenhower, Curtis PLoS computational biology 23209389 2012
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. Erickson, Alison R; Cantarel, Brandi L; Lamendella, Regina; Darzi, Youssef; Mongodin, Emmanuel F; Pan, Chongle; Shah, Manesh; Halfvarson, Jonas; Tysk, Curt; Henrissat, Bernard; Raes, Jeroen; Verberkmoes, Nathan C; Fraser, Claire M; Hettich, Robert L; Jans PloS one 23209564 2012
Nestly--a framework for running software with nested parameter choices and aggregating results. McCoy, Connor O; Gallagher, Aaron; Hoffman, Noah G; Matsen, Frederick A Bioinformatics (Oxford, England) 23220574 2013 Feb 1
Genomic variation landscape of the human gut microbiome. Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi; Mitreva, Makedonka; Tap, Julien; Zhu, Ana; Waller, Alison; Mende, Daniel R; Kultima, Jens Roat; Martin, John; Kota, Karthik; Sunyaev, Shamil R; Weinstock, George M; Bork, Peer Nature 23222524 2013 Jan 3
Increased prevalence of anellovirus in pediatric patients with fever. McElvania TeKippe, Erin; Wylie, Kristine M; Deych, Elena; Sodergren, Erica; Weinstock, George; Storch, Gregory A PloS one 23226428 2012
Insights from characterizing extinct human gut microbiomes. Tito, Raul Y; Knights, Dan; Metcalf, Jessica; Obregon-Tito, Alexandra J; Cleeland, Lauren; Najar, Fares; Roe, Bruce; Reinhard, Karl; Sobolik, Kristin; Belknap, Samuel; Foster, Morris; Spicer, Paul; Knight, Rob; Lewis Jr, Cecil M PloS one 23251439 2012
'Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics. Harrison, Krista L; Farrell, Ruth M; Brinich, Margaret A; Highland, Janelle; Mercer, Marybeth; McCormick, Jennifer B; Tilburt, Jon; Geller, Gail; Marshall, Patricia; Sharp, Richard R Health expectations : an international journal of public participation in health care and health policy 23279082 2012 Dec 28
Genomic sequence analysis and characterization of Sneathia amnii sp. nov. Harwich Jr, Michael D; Serrano, Myrna G; Fettweis, Jennifer M; Alves, Joao M P; Reimers, Mark A; Vaginal Microbiome Consortium (additional members); Buck, Gregory A; Jefferson, Kimberly K BMC genomics 23281612 2012
Species-level classification of the vaginal microbiome. Fettweis, Jennifer M; Serrano, Myrna G; Sheth, Nihar U; Mayer, Carly M; Glascock, Abigail L; Brooks, J Paul; Jefferson, Kimberly K; Vaginal Microbiome Consortium (additional members); Buck, Gregory A BMC genomics 23282177 2012
Hypothesis testing and power calculations for taxonomic-based human microbiome data. La Rosa, Patricio S; Brooks, J Paul; Deych, Elena; Boone, Edward L; Edwards, David J; Wang, Qin; Sodergren, Erica; Weinstock, George; Shannon, William D PloS one 23284876 2012
The future is now: single-cell genomics of bacteria and archaea. Blainey, Paul C FEMS microbiology reviews 23298390 2013 May
Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men. Redel, Henry; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Zhou, Yanjiao; Perez-Perez, Guillermo I; Weinstock, George; Sodergren, Erica; Blaser, Martin J The Journal of infectious diseases 23300163 2013 Apr
Chapter 12: Human microbiome analysis. Morgan, Xochitl C; Huttenhower, Curtis PLoS computational biology 23300406 2012
The Jeremiah Metzger lecture: Global warming redux: the disappearing microbiota and epidemic obesity. Blaser, Martin J Transactions of the American Clinical and Climatological Association 23303990 2012
An analysis of online messages about probiotics. Brinich, Margaret A; Mercer, Mary Beth; Sharp, Richard R BMC gastroenterology 23311418 2013
Biogeography of the ecosystems of the healthy human body. Zhou, Yanjiao; Gao, Hongyu; Mihindukulasuriya, Kathie A; La Rosa, Patricio S; Wylie, Kristine M; Vishnivetskaya, Tatiana; Podar, Mircea; Warner, Barb; Tarr, Phillip I; Nelson, David E; Fortenberry, J Dennis; Holland, Martin J; Burr, Sarah E; Shannon, Will Genome biology 23316946 2013 Jan 14
Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Hemarajata, Peera; Versalovic, James Therapeutic advances in gastroenterology. 23320049 2013 Jan;
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. Riehle, Kevin; Coarfa, Cristian; Jackson, Andrew; Ma, Jun; Tandon, Arpit; Paithankar, Sameer; Raghuraman, Sriram; Mistretta, Toni-Ann; Saulnier, Delphine; Raza, Sabeen; Diaz, Maria Alejandra; Shulman, Robert; Aagaard, Kjersti; Versalovic, James; Milosavlj BMC bioinformatics 23320832 2012
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Treangen, Todd J; Koren, Sergey; Sommer, Daniel D; Liu, Bo; Astrovskaya, Irina; Ondov, Brian; Darling, Aaron E; Phillippy, Adam M; Pop, Mihai Genome biology. 23320958 2013;
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. Koren, Omry; Knights, Dan; Gonzalez, Antonio; Waldron, Levi; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E PLoS computational biology 23326225 2013 Jan
Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Markle, Janet G M; Frank, Daniel N; Mortin-Toth, Steven; Robertson, Charles E; Feazel, Leah M; Rolle-Kampczyk, Ulrike; von Bergen, Martin; McCoy, Kathy D; Macpherson, Andrew J; Danska, Jayne S Science (New York, N.Y.) 23328391 2013 Mar 1
Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne. Fitz-Gibbon, Sorel; Tomida, Shuta; Chiu, Bor-Han; Nguyen, Lin; Du, Christine; Liu, Minghsun; Elashoff, David; Erfe, Marie C; Loncaric, Anya; Kim, Jenny; Modlin, Robert L; Miller, Jeff F; Sodergren, Erica; Craft, Noah; Weinstock, George M; Li, Huiying The Journal of investigative dermatology 23337890 2013 Jan 21
Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. Ansong, Charles; Ortega, Corrie; Payne, Samuel H; Haft, Daniel H; Chauvigne-Hines, Lacie M; Lewis, Michael P; Ollodart, Anja R; Purvine, Samuel O; Shukla, Anil K; Fortuin, Suereta; Smith, Richard D; Adkins, Joshua N; Grundner, Christoph; Wright, Aaron T Chemistry & biology 23352146 2013 Jan 24
Single cell microRNA analysis using microfluidic flow cytometry. Wu, Meiye; Piccini, Matthew; Koh, Chung-Yan; Lam, Kit S; Singh, Anup K PloS one 23383050 2013
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Shakya, Migun; Quince, Christopher; Campbell, James H; Yang, Zamin K; Schadt, Christopher W; Podar, Mircea Environmental microbiology 23387867 2013 Jun
The human gut microbiome and body metabolism: implications for obesity and diabetes. Devaraj, Sridevi; Hemarajata, Peera; Versalovic, James Clinical chemistry 23401286 2013 Apr
Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. Ballarini, Annalisa; Segata, Nicola; Huttenhower, Curtis; Jousson, Olivier PloS one 23409037 2013
The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. Liolios, Konstantinos; Schriml, Lynn; Hirschman, Lynette; Pagani, Ioanna; Nosrat, Bahador; Sterk, Peter; White, Owen; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Taylor, Chris; Kyrpides, Nikos C; Field, Dawn Standards in genomic sciences. 23409217 2012 Jul 30;
Shallow breathing: bacterial life at low O(2). Morris, Rachel L; Schmidt, Thomas M Nature reviews. Microbiology 23411864 2013 Mar
Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk. Munch, Erika M; Harris, R Alan; Mohammad, Mahmoud; Benham, Ashley L; Pejerrey, Sasha M; Showalter, Lori; Hu, Min; Shope, Cynthia D; Maningat, Patricia D; Gunaratne, Preethi H; Haymond, Morey; Aagaard, Kjersti PloS one 23418415 2013
SPA: a short peptide assembler for metagenomic data. Yang, Youngik; Yooseph, Shibu Nucleic acids research 23435317 2013 Apr
Challenges in IBD research: update on progress and prioritization of the CCFA's research agenda. Denson, Lee A; Long, Millie D; McGovern, Dermot P B; Kugathasan, Subra; Wu, Gary D; Young, Vincent B; Pizarro, Theresa T; de Zoeten, Edwin F; Stappenbeck, Thaddeus S; Plevy, Scott E; Abraham, Clara; Nusrat, Asma; Jobin, Christian; McCole, Declan F; Siegel Inflammatory bowel diseases 23448796 2013 Mar-Apr
Effects of different complementary feeding regimens on iron status and enteric microbiota in breastfed infants. Krebs, Nancy F; Sherlock, Laurie G; Westcott, Jamie; Culbertson, Diana; Hambidge, K Michael; Feazel, Leah M; Robertson, Charles E; Frank, Daniel N The Journal of pediatrics 23452586 2013 Aug
Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces. O Cuív, Páraic; Klaassens, Eline S; Smith, Wendy J; Mondot, Stanislas; Durkin, A Scott; Harkins, Derek M; Foster, Les; McCorrison, Jamison; Torralba, Manolito; Nelson, Karen E; Morrison, Mark Genome announcements. 23469340 2013 Jan;
Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Hettich, Robert L; Pan, Chongle; Chourey, Karuna; Giannone, Richard J Analytical chemistry 23469896 2013 May 7
Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players. Ursell, Luke K; Knight, Rob Cell metabolism 23473028 2013 Mar 5
Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases. Leone, Vanessa; Chang, Eugene B; Devkota, Suzanne Journal of gastroenterology 23475322 2013 Mar
Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Morris, Alison; Beck, James M; Schloss, Patrick D; Campbell, Thomas B; Crothers, Kristina; Curtis, Jeffrey L; Flores, Sonia C; Fontenot, Andrew P; Ghedin, Elodie; Huang, Laurence; Jablonski, Kathleen; Kleerup, Eric; Lynch, Susan V; Sodergren, Erica; Twigg American journal of respiratory and critical care medicine 23491408 2013 May 15
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Fitzsimons, Michael S; Novotny, Mark; Lo, Chien-Chi; Dichosa, Armand E K; Yee-Greenbaum, Joyclyn L; Snook, Jeremy P; Gu, Wei; Chertkov, Olga; Davenport, Karen W; McMurry, Kim; Reitenga, Krista G; Daughton, Ashlynn R; He, Jian; Johnson, Shannon L; Gleasner Genome research 23493677 2013 May
Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling. Wu, Xiao; Berkow, Kathryn; Frank, Daniel N; Li, Ellen; Gulati, Ajay S; Zhu, Wei BMC bioinformatics 23497007 2013
Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. Matsen 4th, Frederick A; Evans, Steven N PloS one 23505415 2013
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Campbell, James H; O'Donoghue, Patrick; Campbell, Alisha G; Schwientek, Patrick; Sczyrba, Alexander; Woyke, Tanja; Soll, Dieter; Podar, Mircea Proceedings of the National Academy of Sciences of the United States of America 23509275 2013 Apr 2
Culture-independent analysis of aerosol microbiology in a metropolitan subway system. Robertson, Charles E; Baumgartner, Laura K; Harris, J Kirk; Peterson, Kristen L; Stevens, Mark J; Frank, Daniel N; Pace, Norman R Applied and environmental microbiology 23542619 2013 Jun
Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. Jiao, Dazhi; Ye, Yuzhen; Tang, Haixu PLoS computational biology 23555216 2013 Mar
Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity. Campbell, Alisha G; Campbell, James H; Schwientek, Patrick; Woyke, Tanja; Sczyrba, Alexander; Allman, Steve; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, Mircea PloS one 23555659 2013
Gastrointestinal viruses were not found as an aetiology of culture-negative illness in NICU patients. Melamed, Rimma; Storch, Gregory A; Warner, Barbara B; Tarr, Phillip I Archives of disease in childhood. Fetal and neonatal edition 23563694 2013 Jul
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Koeth, Robert A; Wang, Zeneng; Levison, Bruce S; Buffa, Jennifer A; Org, Elin; Sheehy, Brendan T; Britt, Earl B; Fu, Xiaoming; Wu, Yuping; Li, Lin; Smith, Jonathan D; DiDonato, Joseph A; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Warrier, Manya; Nature medicine 23563705 2013 May
Cohabiting family members share microbiota with one another and with their dogs. Song, Se Jin; Lauber, Christian; Costello, Elizabeth K; Lozupone, Catherine A; Humphrey, Gregory; Berg-Lyons, Donna; Caporaso, J Gregory; Knights, Dan; Clemente, Jose C; Nakielny, Sara; Gordon, Jeffrey I; Fierer, Noah; Knight, Rob eLife. 23599893 2013 Apr 16;
Investigators' perspectives on translating human microbiome research into clinical practice. Slashinski, M J; Whitney, S N; Achenbaum, L S; Keitel, W A; McCurdy, S A; McGuire, A L Public health genomics 23615375 2013
Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. Tomida, Shuta; Nguyen, Lin; Chiu, Bor-Han; Liu, Jared; Sodergren, Erica; Weinstock, George M; Li, Huiying mBio 23631911 2013
Composition of dietary fat source shapes gut microbiota architecture and alters host inflammatory mediators in mouse adipose tissue. Huang, Edmond Y; Leone, Vanessa A; Devkota, Suzanne; Wang, Yunwei; Brady, Matthew J; Chang, Eugene B JPEN. Journal of parenteral and enteral nutrition 23639897 2013 Nov
Analysis of the human gut microbiome and association with disease. Wu, Gary D; Lewis, James D Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association 23643636 2013 Jul
Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular Approach. Cleeland, Lauren M; Reichard, Mason V; Tito, Raul Y; Reinhard, Karl J; Lewis Jr, Cecil M Journal of archaeological science 23645967 2013 Jul 01
Butyrate Induced IGF2 Activation Correlated with Distinct Chromatin Signatures Due to Histone Modification. Shin, Joo Heon; Li, Robert W; Gao, Yuan; Bickhart, Derek M; Liu, George E; Li, Weizhong; Wu, Sitao; Li, Cong-Jun Gene regulation and systems biology. 23645985 2013;
Computational meta'omics for microbial community studies. Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, Curtis Molecular systems biology 23670539 2013
Analyses of the stability and core taxonomic memberships of the human microbiome. Li, Kelvin; Bihan, Monika; Methe, Barbara A PloS one 23671663 2013
Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period. Shkoporov, A N; Efimov, B A; Khokhlova, E V; Chaplin, A V; Kafarskaya, L I; Durkin, A S; McCorrison, J; Torralba, M; Gillis, M; Sutton, G; Weibel, D B; Nelson, K E; Smeianov, V V Genome announcements. 23682142 2013;
DRISEE overestimates errors in metagenomic sequencing data. Eren, A Murat; Morrison, Hilary G; Huse, Susan M; Sogin, Mitchell L Briefings in bioinformatics. 23698723 2014 Sep;
Colitis-induced Bone Loss is Gender Dependent and Associated with Increased Inflammation. Irwin, Regina; Lee, Taehyung; Young, Vincent B; Parameswaran, Narayanan; McCabe, Laura R Inflammatory bowel diseases 23702805 2013 Jul
Virome genomics: a tool for defining the human virome. Wylie, Kristine M; Weinstock, George M; Storch, Gregory A Current opinion in microbiology 23706900 2013 May 23
Sequencing viral genomes from a single isolated plaque. Depew, Jessica; Zhou, Bin; McCorrison, Jamison M; Wentworth, David E; Purushe, Janaki; Koroleva, Galina; Fouts, Derrick E Virology journal 23742765 2013
Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain. Kasimatis, Gabriela; Fitz-Gibbon, Sorel; Tomida, Shuta; Wong, Marthew; Li, Huiying BioMed research international 23762865 2013
Carrageenan-induced colonic inflammation is reduced in Bcl10 null mice and increased in IL-10-deficient mice. Bhattacharyya, Sumit; Xue, Liquan; Devkota, Suzanne; Chang, Eugene; Morris, Stephan; Tobacman, Joanne K Mediators of inflammation 23766559 2013
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Kozich, James J; Westcott, Sarah L; Baxter, Nielson T; Highlander, Sarah K; Schloss, Patrick D Applied and environmental microbiology 23793624 2013 Sep
Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses. Smeekens, Sanne P; Huttenhower, Curtis; Riza, Anca; van de Veerdonk, Frank L; Zeeuwen, Patrick L J M; Schalkwijk, Joost; van der Meer, Jos W M; Xavier, Ramnik J; Netea, Mihai G; Gevers, Dirk Journal of innate immunity. 23796786 2014;
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. Hoffmann, Christian; Dollive, Serena; Grunberg, Stephanie; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Bushman, Frederic D PloS one 23799070 2013
A filtering method to generate high quality short reads using illumina paired-end technology. Eren, A Murat; Vineis, Joseph H; Morrison, Hilary G; Sogin, Mitchell L PloS one 23799126 2013
Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Carmody, Lisa A; Zhao, Jiangchao; Schloss, Patrick D; Petrosino, Joseph F; Murray, Susan; Young, Vincent B; Li, Jun Z; LipPuma, John J Annals of the American Thoracic Society 23802813 2013 Jun
Are changes to the common rule necessary to address evolving areas of research? A case study focusing on the human microbiome project. Hoffmann, Diane E; Fortenberry, J Dennis; Ravel, Jacques The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics. 23802897 2013;
Microfluidic platforms for single-cell protein analysis. Liu, Yanli; Singh, Anup K Journal of laboratory automation 23821679 2013 Dec
The mean and variance of phylogenetic diversity under rarefaction. Nipperess, David A; Matsen 4th, Frederick A Methods in ecology and evolution / British Ecological Society 23833701 2013 Jun 1
Rapid evolution of the human gut virome. Minot, Samuel; Bryson, Alexandra; Chehoud, Christel; Wu, Gary D; Lewis, James D; Bushman, Frederic D Proceedings of the National Academy of Sciences of the United States of America 23836644 2013 Jul 23
Gene expression profiles in febrile children with defined viral and bacterial infection. Hu, Xinran; Yu, Jinsheng; Crosby, Seth D; Storch, Gregory A Proceedings of the National Academy of Sciences of the United States of America 23858444 2013 Jul 30
Urethral adenocarcinoma associated with intestinal-type metaplasia, case report and literature review. Hale, Christopher S; Huang, Hongying; Melamed, Jonathan; Xu, Ruliang; Roberts, Larry; Wieczorek, Rosemary; Pei, Zhiheng; Lee, Peng International journal of clinical and experimental pathology 23923086 2013
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Segata, Nicola; Bornigen, Daniela; Morgan, Xochitl C; Huttenhower, Curtis Nature communications 23942190 2013 Aug 14
Two-stage microbial community experimental design. Tickle, Timothy L; Segata, Nicola; Waldron, Levi; Weingart, Uri; Huttenhower, Curtis The ISME journal 23949665 2013 Aug 15
Association of gut microbiota with post-operative clinical course in Crohn's disease. Dey, Neelendu; Soergel, David A W; Repo, Susanna; Brenner, Steven E BMC gastroenterology 23964800 2013
De novo likelihood-based measures for comparing genome assemblies. Ghodsi, Mohammadreza; Hill, Christopher M; Astrovskaya, Irina; Lin, Henry; Sommer, Dan D; Koren, Sergey; Pop, Mihai BMC research notes 23965294 2013
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory; McDonald, Daniel; Knights, Dan; Reyes, Joshua A; Clemente, Jose C; Burkepile, Deron E; Vega Thurber, Rebecca L; Knight, Rob; Beiko, Robert G; Huttenhower, Curtis Nature biotechnology 23975157 2013 Sep
A Pure L1-norm Principal Component Analysis. Brooks, Jp; Dula, Jh; Boone, El Computational statistics & data analysis 23976807 2013 May 1
Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. Dollive, Serena; Chen, Ying-Yu; Grunberg, Stephanie; Bittinger, Kyle; Hoffmann, Christian; Vandivier, Lee; Cuff, Christopher; Lewis, James D; Wu, Gary D; Bushman, Frederic D PloS one 23977147 2013
Microbiomic signatures of psoriasis: feasibility and methodology comparison. Statnikov, Alexander; Alekseyenko, Alexander V; Li, Zhiguo; Henaff, Mikael; Perez-Perez, Guillermo I; Blaser, Martin J; Aliferis, Constantin F Scientific reports 24018484 2013
Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. Robertson, Charles E; Harris, J Kirk; Wagner, Brandie D; Granger, David; Browne, Kathy; Tatem, Beth; Feazel, Leah M; Park, Kristin; Pace, Norman R; Frank, Daniel N Bioinformatics (Oxford, England) 24021386 2013 Dec 1
Antibacterial property expressed by a novel calcium phosphate glass. Liu, Lela; Pushalkar, Smruti; Saxena, Deepak; LeGeros, Racquel Z; Zhang, Yu Journal of biomedical materials research. Part B, Applied biomaterials. 24039127 2014 Apr;
Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. Wang, Qiong; Quensen 3rd, John F; Fish, Jordan A; Lee, Tae Kwon; Sun, Yanni; Tiedje, James M; Cole, James R mBio 24045641 2013
Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis. Turabelidze, George; Lawrence, Steven J; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Abubucker, Sahar; Wylie, Todd; Mitreva, Makedonka; Shaikh, Nurmohammad; Gautom, Romesh; Tarr, Phillip I Journal of clinical microbiology 24048526 2013 Dec
Optofluidic cell selection from complex microbial communities for single-genome analysis. Landry, Zachary C; Giovanonni, Stephen J; Quake, Stephen R; Blainey, Paul C Methods in enzymology 24060116 2013
A metagenomics portal for a democratized sequencing world. Wilke, Andreas; Glass, Elizabeth M; Bartels, Daniela; Bischof, Jared; Braithwaite, Daniel; D'Souza, Mark; Gerlach, Wolfgang; Harrison, Travis; Keegan, Kevin; Matthews, Hunter; Kottmann, Renzo; Paczian, Tobias; Tang, Wei; Trimble, William L; Yilmaz, Pelin; Methods in enzymology 24060134 2013
Differential abundance analysis for microbial marker-gene surveys. Paulson, Joseph N; Stine, O Colin; Bravo, Hector Corrada; Pop, Mihai Nature methods 24076764 2013 Dec
Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy. Brotman, Rebecca M; Shardell, Michelle D; Gajer, Pawel; Fadrosh, Doug; Chang, Kathryn; Silver, Michelle I; Viscidi, Raphael P; Burke, Anne E; Ravel, Jacques; Gravitt, Patti E Menopause (New York, N.Y.) 24080849 2013 Oct 21
FunGene: the functional gene pipeline and repository. Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R Frontiers in microbiology. 24101916 2013;
Diet, gut enterotypes and health: is there a link? Bushman, Frederic D; Lewis, James D; Wu, Gary D Nestle Nutrition Institute workshop series 24107497 2013
A single-molecule long-read survey of the human transcriptome. Sharon, Donald; Tilgner, Hagen; Grubert, Fabian; Snyder, Michael Nature biotechnology. 24108091 2013 Nov;
Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. Lee, Sunghee; Cantarel, Brandi; Henrissat, Bernard; Gevers, Dirk; Birren, Bruce W; Huttenhower, Curtis; Ko, Gwangpyo The ISME journal 24108330 2013 Oct 10
Lactobacillus reuteri-specific immunoregulatory gene rsiR modulates histamine production and immunomodulation by Lactobacillus reuteri. Hemarajata, P; Gao, C; Pflughoeft, K J; Thomas, C M; Saulnier, D M; Spinler, J K; Versalovic, J Journal of bacteriology 24123819 2013 Dec
Interprovider variation of celiac disease testing in childhood chronic abdominal pain. Chumpitazi, Bruno Pedro; Mysore, Krupa; Tsai, Cynthia Man-Wai; Shulman, Robert Jay BMC gastroenterology 24124697 2013
Science and regulation. Probiotics: finding the right regulatory balance. Hoffmann, D E; Fraser, C M; Palumbo, F B; Ravel, J; Rothenberg, K; Rowthorn, V; Schwartz, J Science (New York, N.Y.) 24136953 2013 Oct 18
IMG/M 4 version of the integrated metagenome comparative analysis system. Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Pagani, Ioanna; Tringe, Susannah; Huntemann, Marcel; Billis, Konstantinos; Varghese, Neha; Tennessen, Kristin; Mavromatis, Kons Nucleic acids research 24136997 2014 Jan
Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective. Allen-Vercoe, Emma Current opinion in microbiology 24148301 2013 Oct
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Scher, Jose U; Sczesnak, Andrew; Longman, Randy S; Segata, Nicola; Ubeda, Carles; Bielski, Craig; Rostron, Tim; Cerundolo, Vincenzo; Pamer, Eric G; Abramson, Steven B; Huttenhower, Curtis; Littman, Dan R eLife 24192039 2013 Nov 05
The gut microbiome modulates colon tumorigenesis. Zackular, Joseph P; Baxter, Nielson T; Iverson, Kathryn D; Sadler, William D; Petrosino, Joseph F; Chen, Grace Y; Schloss, Patrick D mBio 24194538 2013
Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generator. Lian, Meng; Collier, C Patrick; Doktycz, Mitchel J; Retterer, Scott T Biomicrofluidics. 24198865 2012;
MetaRef: a pan-genomic database for comparative and community microbial genomics. Huang, Katherine; Brady, Arthur; Mahurkar, Anup; White, Owen; Gevers, Dirk; Huttenhower, Curtis; Segata, Nicola Nucleic acids research 24203705 2014 Jan
Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Gole, Jeff; Gore, Athurva; Richards, Andrew; Chiu, Yu-Jui; Fung, Ho-Lim; Bushman, Diane; Chiang, Hsin-I; Chun, Jerold; Lo, Yu-Hwa; Zhang, Kun Nature biotechnology 24213699 2013 Dec
Diversified microbiota of meconium is affected by maternal diabetes status. Hu, Jianzhong; Nomura, Yoko; Bashir, Ali; Fernandez-Hernandez, Heriberto; Itzkowitz, Steven; Pei, Zhiheng; Stone, Joanne; Loudon, Holly; Peter, Inga PloS one 24223144 2013
A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. Tong, Maomeng; Li, Xiaoxiao; Wegener Parfrey, Laura; Roth, Bennett; Ippoliti, Andrew; Wei, Bo; Borneman, James; McGovern, Dermot P B; Frank, Daniel N; Li, Ellen; Horvath, Steve; Knight, Rob; Braun, Jonathan PloS one 24260458 2013
Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. Close, Devin W; Ferrara, Fortunato; Dichosa, Armand E K; Kumar, Sandeep; Daughton, Ashlynn R; Daligault, Hajnalka E; Reitenga, Krista G; Velappan, Nileena; Sanchez, Timothy C; Iyer, Srinivas; Kiss, Csaba; Han, Cliff S; Bradbury, Andrew R M BMC microbiology 24279426 2013
Ribosomal Database Project: data and tools for high throughput rRNA analysis. Cole, James R; Wang, Qiong; Fish, Jordan A; Chai, Benli; McGarrell, Donna M; Sun, Yanni; Brown, C Titus; Porras-Alfaro, Andrea; Kuske, Cheryl R; Tiedje, James M Nucleic acids research 24288368 2014 Jan
More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis. Srinivasan, Sujatha; Morgan, Martin T; Liu, Congzhou; Matsen, Frederick A; Hoffman, Noah G; Fiedler, Tina L; Agnew, Kathy J; Marrazzo, Jeanne M; Fredricks, David N PloS one 24302980 2013
Inferring developmental stage composition from gene expression in human malaria. Joice, Regina; Narasimhan, Vagheesh; Montgomery, Jacqui; Sidhu, Amar Bir; Oh, Keunyoung; Meyer, Evan; Pierre-Louis, Willythssa; Seydel, Karl; Milner, Danny; Williamson, Kim; Wiegand, Roger; Ndiaye, Daouda; Daily, Johanna; Wirth, Dyann; Taylor, Terrie; Hut PLoS computational biology 24348235 2013 Dec
Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. Eren, A Murat; Maignien, Lois; Sul, Woo Jun; Murphy, Leslie G; Grim, Sharon L; Morrison, Hilary G; Sogin, Mitchell L Methods in ecology and evolution / British Ecological Society 24358444 2013 Dec 1
Mathematical modeling of primary succession of murine intestinal microbiota. Marino, Simeone; Baxter, Nielson T; Huffnagle, Gary B; Petrosino, Joseph F; Schloss, Patrick D Proceedings of the National Academy of Sciences of the United States of America 24367073 2014 Jan 7
The microbiome of the middle meatus in healthy adults. Ramakrishnan, Vijay R; Feazel, Leah M; Gitomer, Sarah A; Ir, Diana; Robertson, Charles E; Frank, Daniel N PloS one 24386477 2013
A brave new world: the lung microbiota in an era of change. Segal, Leopoldo N; Blaser, Martin J Annals of the American Thoracic Society 24437400 2014 Jan
Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. Price, Katherine E; Hampton, Thomas H; Gifford, Alex H; Dolben, Emily L; Hogan, Deborah A; Morrison, Hilary G; Sogin, Mitchell L; O'Toole, George A Microbiome 24451123 2013
Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. Ravel, Jacques; Brotman, Rebecca M; Gajer, Pawel; Ma, Bing; Nandy, Melissa; Fadrosh, Douglas W; Sakamoto, Joyce; Koenig, Sara Sk; Fu, Li; Zhou, Xia; Hickey, Roxana J; Schwebke, Jane R; Forney, Larry J Microbiome 24451163 2013
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. Mason, Olivia U; Scott, Nicole M; Gonzalez, Antonio; Robbins-Pianka, Adam; Baelum, Jacob; Kimbrel, Jeffrey; Bouskill, Nicholas J; Prestat, Emmanuel; Borglin, Sharon; Joyner, Dominique C; Fortney, Julian L; Jurelevicius, Diogo; Stringfellow, William T; Alv The ISME journal 24451203 2014 Jan 23
A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Vital, Marius; Penton, Christopher R; Wang, Qiong; Young, Vincent B; Antonopoulos, Dion A; Sogin, Mitchell L; Morrison, Hilary G; Raffals, Laura; Chang, Eugene B; Huffnagle, Gary B; Schmidt, Thomas M; Cole, James R; Tiedje, James M Microbiome 24451334 2013
Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Young, Vincent B; Raffals, Laura H; Huse, Susan M; Vital, Marius; Dai, Dongjuan; Schloss, Patrick D; Brulc, Jennifer M; Antonopoulos, Dionysios A; Arrieta, Rose L; Kwon, John H; Reddy, K Gautham; Hubert, Nathaniel A; Grim, Sharon L; Vineis, Joseph H; Dala Microbiome 24451366 2013
Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Hollister, Emily B; Gao, Chunxu; Versalovic, James Gastroenterology 24486050 2014 May
Meta'omic analytic techniques for studying the intestinal microbiome. Morgan, Xochitl C; Huttenhower, Curtis Gastroenterology 24486053 2014 May
Identification of a proton-chloride antiporter (EriC) by Himar1 transposon mutagenesis in Lactobacillus reuteri and its role in histamine production. Hemarajata, P; Spinler, J K; Balderas, M A; Versalovic, J Antonie van Leeuwenhoek 24488273 2014 Mar
Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen. Chen, Zehua; Martinez, Diego A; Gujja, Sharvari; Sykes, Sean M; Zeng, Qiandong; Szaniszlo, Paul J; Wang, Zheng; Cuomo, Christina A G3 (Bethesda, Md.) 24496724 2014 Apr
Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. Rooks, Michelle G; Veiga, Patrick; Wardwell-Scott, Leslie H; Tickle, Timothy; Segata, Nicola; Michaud, Monia; Gallini, Carey Ann; Beal, Chloe; van Hylckama-Vlieg, Johan E T; Ballal, Sonia A; Morgan, Xochitl C; Glickman, Jonathan N; Gevers, Dirk; Huttenhow The ISME journal 24500617 2014 Jul
Diet and the intestinal microbiome: associations, functions, and implications for health and disease. Albenberg, Lindsey G; Wu, Gary D Gastroenterology 24503132 2014 May
Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets. Ma, Yingfei; Madupu, Ramana; Karaoz, Ulas; Nossa, Carlos W; Yang, Liying; Yooseph, Shibu; Yachimski, Patrick S; Brodie, Eoin L; Nelson, Karen E; Pei, Zhiheng Journal of virology 24522917 2014 May
Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects. Huse, Susan M; Young, Vincent B; Morrison, Hilary G; Antonopoulos, Dionysios A; Kwon, John; Dalal, Sushila; Arrieta, Rose; Hubert, Nathaniel A; Shen, Lici; Vineis, Joseph H; Koval, Jason C; Sogin, Mitchell L; Chang, Eugene B; Raffals, Laura E Microbiome 24529162 2014
Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter. Greenwood, Corryn; Morrow, Ardythe L; Lagomarcino, Anne J; Altaye, Mekibib; Taft, Diana H; Yu, Zhuoteng; Newburg, David S; Ward, Doyle V; Schibler, Kurt R The Journal of pediatrics 24529620 2014 Feb 13
Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia. Beall, Clifford J; Campbell, Alisha G; Dayeh, Daniel M; Griffen, Ann L; Podar, Mircea; Leys, Eugene J PloS one 24551246 2014
An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Fadrosh, Douglas W; Ma, Bing; Gajer, Pawel; Sengamalay, Naomi; Ott, Sandra; Brotman, Rebecca M; Ravel, Jacques Microbiome. 24558975 2014;
The microbiome in inflammatory bowel disease: current status and the future ahead. Kostic, Aleksandar D; Xavier, Ramnik J; Gevers, Dirk Gastroenterology 24560869 2014 May
Whole-genome haplotyping using long reads and statistical methods. Kuleshov, Volodymyr; Xie, Dan; Chen, Rui; Pushkarev, Dmitry; Ma, Zhihai; Blauwkamp, Tim; Kertesz, Michael; Snyder, Michael Nature biotechnology 24561555 2014 Mar
Pathogens and host immunity in the ancient human oral cavity. Warinner, Christina; Rodrigues, Joao F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar- Nature genetics 24562188 2014 Apr
History and impact of RDP: a legacy from Carl Woese to microbiology. Cole, James R; Tiedje, James M RNA biology 24607969 2014 Mar
Immune and genetic gardening of the intestinal microbiome. Jacobs, Jonathan P; Braun, Jonathan FEBS letters 24613921 2014 Mar 5
Functional and phylogenetic assembly of microbial communities in the human microbiome. Shafquat, Afrah; Joice, Regina; Simmons, Sheri L; Huttenhower, Curtis Trends in microbiology 24618403 2014 Mar 4
The treatment-naive microbiome in new-onset Crohn's disease. Gevers, Dirk; Kugathasan, Subra; Denson, Lee A; Vazquez-Baeza, Yoshiki; Van Treuren, Will; Ren, Boyu; Schwager, Emma; Knights, Dan; Song, Se Jin; Yassour, Moran; Morgan, Xochitl C; Kostic, Aleksandar D; Luo, Chengwei; Gonzalez, Antonio; McDonald, Daniel; Cell host & microbe 24629344 2014 Mar 12
Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome. Chumpitazi, Bruno P; Hollister, Emily B; Oezguen, Numan; Tsai, Cynthia M; McMeans, Ann R; Luna, Ruth A; Savidge, Tor C; Versalovic, James; Shulman, Robert J Gut microbes 24637601 2014 Mar-Apr
Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Carl, Mike A; Ndao, I Malick; Springman, A Cody; Manning, Shannon D; Johnson, James R; Johnston, Brian D; Burnham, Carey-Ann D; Weinstock, Erica Sodergren; Weinstock, George M; Wylie, Todd N; Mitreva, Makedonka; Abubucker, Sahar; Zhou, Yanjiao; Stevens, H Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 24647013 2014 May
Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. Hyde, Embriette R; Andrade, Fernando; Vaksman, Zalman; Parthasarathy, Kavitha; Jiang, Hong; Parthasarathy, Deepa K; Torregrossa, Ashley C; Tribble, Gena; Kaplan, Heidi B; Petrosino, Joseph F; Bryan, Nathan S PloS one 24670812 2014
Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. Campbell, Alisha G; Schwientek, Patrick; Vishnivetskaya, Tatiana; Woyke, Tanja; Levy, Shawn; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, Mircea Environmental microbiology 24738594 2014 Apr 17
Transferable vancomycin resistance in a community-associated MRSA lineage. Rossi, Flavia; Diaz, Lorena; Wollam, Aye; Panesso, Diana; Zhou, Yanjiao; Rincon, Sandra; Narechania, Apurva; Xing, Galen; Di Gioia, Thais S R; Doi, Andre; Tran, Truc T; Reyes, Jinnethe; Munita, Jose M; Carvajal, Lina P; Hernandez-Roldan, Alejandra; Branda The New England journal of medicine 24738669 2014 Apr 17
Dynamics and associations of microbial community types across the human body. Ding, Tao; Schloss, Patrick D Nature 24739969 2014 May 15
Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. Swan, Brandon K; Chaffin, Mark D; Martinez-Garcia, Manuel; Morrison, Hilary G; Field, Erin K; Poulton, Nicole J; Masland, E Dashiell P; Harris, Christopher C; Sczyrba, Alexander; Chain, Patrick S G; Koren, Sergey; Woyke, Tanja; Stepanauskas, Ramunas PloS one 24743558 2014
Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. Vital, Marius; Howe, Adina Chuang; Tiedje, James M mBio 24757212 2014
Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. Tong, Maomeng; McHardy, Ian; Ruegger, Paul; Goudarzi, Maryam; Kashyap, Purna C; Haritunians, Talin; Li, Xiaoxiao; Graeber, Thomas G; Schwager, Emma; Huttenhower, Curtis; Fornace Jr, Albert J; Sonnenburg, Justin L; McGovern, Dermot Pb; Borneman, James; Bra The ISME journal 24781901 2014 Apr 29
Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. Schubert, Alyxandria M; Rogers, Mary A M; Ring, Cathrin; Mogle, Jill; Petrosino, Joseph P; Young, Vincent B; Aronoff, David M; Schloss, Patrick D mBio 24803517 2014
Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium. Sizova, Maria V; Muller, Paul A; Stancyk, David; Panikov, Nicolai S; Mandalakis, Manolis; Hazen, Amanda; Hohmann, Tine; Doerfert, Sebastian N; Fowle, William; Earl, Ashlee M; Nelson, Karen E; Epstein, Slava S International journal of systematic and evolutionary microbiology. 24824639 2014 Aug;
The prevalence of species and strains in the human microbiome: a resource for experimental efforts. Kraal, Laurens; Abubucker, Sahar; Kota, Karthik; Fischbach, Michael A; Mitreva, Makedonka PloS one 24827833 2014
Relating the metatranscriptome and metagenome of the human gut. Franzosa, Eric A; Morgan, Xochitl C; Segata, Nicola; Waldron, Levi; Reyes, Joshua; Earl, Ashlee M; Giannoukos, Georgia; Boylan, Matthew R; Ciulla, Dawn; Gevers, Dirk; Izard, Jacques; Garrett, Wendy S; Chan, Andrew T; Huttenhower, Curtis Proceedings of the National Academy of Sciences of the United States of America 24843156 2014 Jun 3
The placenta harbors a unique microbiome. Aagaard, Kjersti; Ma, Jun; Antony, Kathleen M; Ganu, Radhika; Petrosino, Joseph; Versalovic, James Science translational medicine 24848255 2014 May 21
Microbiome in reflux disorders and esophageal adenocarcinoma. Yang, Liying; Chaudhary, Noami; Baghdadi, Jonathan; Pei, Zhiheng Cancer journal (Sudbury, Mass.) 24855009 2014 May-Jun
Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251). Cuomo, Christina A; Rodriguez-Del Valle, Nuri; Perez-Sanchez, Lizaida; Abouelleil, Amr; Goldberg, Jonathan; Young, Sarah; Zeng, Qiandong; Birren, Bruce W Genome announcements. 24855299 2014;
BOTUX: bayesian-like operational taxonomic unit examiner. Koparde, Vishal N; Adkins, Ricky S; Fettweis, Jennifer M; Serrano, Myrna G; Buck, Gregory A A; Reimers, Mark A; Sheth, Nihar U International journal of computational biology and drug design. 24878725 2014;
Exploration of bacterial community classes in major human habitats. Zhou, Yanjiao; Mihindukulasuriya, Kathie A; Gao, Hongyu; La Rosa, Patricio S; Wylie, Kristine M; Martin, John C; Kota, Karthik; Shannon, William D; Mitreva, Makedonka; Sodergren, Erica; Weinstock, George M Genome biology 24887286 2014
CcpA is important for growth and virulence of Enterococcus faecium. Somarajan, Sudha R; Roh, Jung H; Singh, Kavindra V; Weinstock, George M; Murray, Barbara E Infection and immunity. 24914215 2014 Sep;
Evidence of extensive DNA transfer between bacteroidales species within the human gut. Coyne, Michael J; Zitomersky, Naamah Levy; McGuire, Abigail Manson; Earl, Ashlee M; Comstock, Laurie E mBio 24939888 2014
Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection. Brotman, Rebecca M; Shardell, Michelle D; Gajer, Pawel; Tracy, J Kathleen; Zenilman, Jonathan M; Ravel, Jacques; Gravitt, Patti E The Journal of infectious diseases. 24943724 2014 Dec 1;
Finding the missing links among metabolites, microbes, and the host. Dorrestein, Pieter C; Mazmanian, Sarkis K; Knight, Rob Immunity. 24950202 2014 Jun 19;
Inflammatory bowel disease as a model for translating the microbiome. Huttenhower, Curtis; Kostic, Aleksandar D; Xavier, Ramnik J Immunity 24950204 2014 Jun 19
From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. Spinler, Jennifer K; Sontakke, Amrita; Hollister, Emily B; Venable, Susan F; Oh, Phaik Lyn; Balderas, Miriam A; Saulnier, Delphine M A; Mistretta, Toni-Ann; Devaraj, Sridevi; Walter, Jens; Versalovic, James; Highlander, Sarah K Genome biology and evolution 24951561 2014 Jul
Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips. Ma, Liang; Datta, Sujit S; Karymov, Mikhail A; Pan, Qichao; Begolo, Stefano; Ismagilov, Rustem F Integrative biology : quantitative biosciences from nano to macro 24953827 2014 Jun 23
Defining a personal, allele-specific, and single-molecule long-read transcriptome. Tilgner, Hagen; Grubert, Fabian; Sharon, Donald; Snyder, Michael P Proceedings of the National Academy of Sciences of the United States of America. 24961374 2014 Jul 8;
Oligotyping analysis of the human oral microbiome. Eren, A Murat; Borisy, Gary G; Huse, Susan M; Mark Welch, Jessica L Proceedings of the National Academy of Sciences of the United States of America 24965363 2014 Jul 15
Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. Ma, Liang; Kim, Jungwoo; Hatzenpichler, Roland; Karymov, Mikhail A; Hubert, Nathaniel; Hanan, Ira M; Chang, Eugene B; Ismagilov, Rustem F Proceedings of the National Academy of Sciences of the United States of America 24965364 2014 Jul 8
Lactobacillus rhamnosus L34 and Lactobacillus casei L39 suppress Clostridium difficile-induced IL-8 production by colonic epithelial cells. Boonma, Prapaporn; Spinler, Jennifer K; Venable, Susan F; Versalovic, James; Tumwasorn, Somying BMC microbiology 24989059 2014
Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Parfrey, Laura Wegener; Walters, William A; Lauber, Christian L; Clemente, Jose C; Berg-Lyons, Donna; Teiling, Clotilde; Kodira, Chinnappa; Mohiuddin, Mohammed; Brunelle, Julie; Driscoll, Mark; Fierer, Noah; Gilbert, Jack A; Knight, Rob Frontiers in microbiology. 24995004 2014;
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Pop, Mihai; Walker, Alan W; Paulson, Joseph; Lindsay, Brianna; Antonio, Martin; Hossain, M Anowar; Oundo, Joseph; Tamboura, Boubou; Mai, Volker; Astrovskaya, Irina; Corrada Bravo, Hector; Rance, Richard; Stares, Mark; Levine, Myron M; Panchalingam, Sandra Genome biology 24995464 2014
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. Haberman, Yael; Tickle, Timothy L; Dexheimer, Phillip J; Kim, Mi-Ok; Tang, Dora; Karns, Rebekah; Baldassano, Robert N; Noe, Joshua D; Rosh, Joel; Markowitz, James; Heyman, Melvin B; Griffiths, Anne M; Crandall, Wallace V; Mack, David R; Baker, Susan S; Huttenhower, Curtis; Keljo, David J; Hyams, Jeffrey S; Kugathasan, Subra; Walters, Thomas D; Aronow, Bruce; Xavier, Ramnik J; Gevers, Dirk; Denson, Lee A The Journal of clinical investigation. 25003194 2014 Aug;
Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt. Lee, Soo Chan; Billmyre, R Blake; Li, Alicia; Carson, Sandra; Sykes, Sean M; Huh, Eun Young; Mieczkowski, Piotr; Ko, Dennis C; Cuomo, Christina A; Heitman, Joseph mBio 25006230 2014
Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays. VanDussen, Kelli L; Marinshaw, Jeffrey M; Shaikh, Nurmohammad; Miyoshi, Hiroyuki; Moon, Clara; Tarr, Phillip I; Ciorba, Matthew A; Stappenbeck, Thaddeus S Gut. 25007816 2015 Jun;
Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution. Wu, Meiye; Singh, Anup K Journal of laboratory automation. 25027027 2014 Dec;
Serum profiling using protein microarrays to identify disease related antigens. Sharon, Donald; Snyder, Michael Methods in molecular biology (Clifton, N.J.). 25030927 2014;
Conducting a microbiome study. Goodrich, Julia K; Di Rienzi, Sara C; Poole, Angela C; Koren, Omry; Walters, William A; Caporaso, J Gregory; Knight, Rob; Ley, Ruth E Cell. 25036628 2014 Jul 17;
Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Albenberg, Lindsey; Esipova, Tatiana V; Judge, Colleen P; Bittinger, Kyle; Chen, Jun; Laughlin, Alice; Grunberg, Stephanie; Baldassano, Robert N; Lewis, James D; Li, Hongzhe; Thom, Stephen R; Bushman, Frederic D; Vinogradov, Sergei A; Wu, Gary D Gastroenterology. 25046162 2014 Nov;
The dynamics of a family's gut microbiota reveal variations on a theme. Schloss, Patrick D; Iverson, Kathryn D; Petrosino, Joseph F; Schloss, Sarah J Microbiome. 25061514 2014;
The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention. Hampton, Thomas H; Green, Deanna M; Cutting, Garry R; Morrison, Hilary G; Sogin, Mitchell L; Gifford, Alex H; Stanton, Bruce A; O'Toole, George A Microbiome 25071935 2014
Differences in vaginal microbiome in African American women versus women of European ancestry. Fettweis, Jennifer M; Brooks, J Paul; Serrano, Myrna G; Sheth, Nihar U; Girerd, Philippe H; Edwards, David J; Strauss, Jerome F; Reimers, Mark A; Rivera, Maria C; Puma, Federico A; Huang, Bernice; Shyu, Conrad; Koparde, Vishal N; Lee, Vladimir; Jefferson, Microbiology (Reading, England) 25073854 2014 Jul 29
Phase variation of poly-N-acetylglucosamine expression in Staphylococcus aureus. Brooks, Jamie L; Jefferson, Kimberly K PLoS pathogens. 25077798 2014 Jul;
Phylogenetics and the human microbiome. Matsen 4th, Frederick A Systematic biology. 25102857 2015 Jan;
The Human Gut Microbiome as a Screening Tool for Colorectal Cancer. Zackular, Joseph P; Rogers, Mary A M; Ruffin 4th, Mack T; Schloss, Patrick D Cancer prevention research (Philadelphia, Pa.) 25104642 2014 Aug 7
Oral microbiota and host innate immune response in bisphosphonate-related osteonecrosis of the jaw. Pushalkar, Smruti; Li, Xin; Kurago, Zoya; Ramanathapuram, Lalitha V; Matsumura, Satoko; Fleisher, Kenneth E; Glickman, Robert; Yan, Wenbo; Li, Yihong; Saxena, Deepak International journal of oral science. 25105817 2014 Dec;
Patterned progression of bacterial populations in the premature infant gut. La Rosa, Patricio S; Warner, Barbara B; Zhou, Yanjiao; Weinstock, George M; Sodergren, Erica; Hall-Moore, Carla M; Stevens, Harold J; Bennett Jr, William E; Shaikh, Nurmohammad; Linneman, Laura A; Hoffmann, Julie A; Hamvas, Aaron; Deych, Elena; Shands, Berkley A; Shannon, William D; Tarr, Phillip I Proceedings of the National Academy of Sciences of the United States of America. 25114261 2014 Aug 26;
Mini-review: perspective of the microbiome in the pathogenesis of urothelial carcinoma. Xu, Weisheng; Yang, Liying; Lee, Peng; Huang, William C; Nossa, Carlos; Ma, Yingfei; Deng, Fang-Ming; Zhou, Ming; Melamed, Jonathan; Pei, Zhiheng American journal of clinical and experimental urology 25126590 2014 Apr 15
Probiotics: achieving a better regulatory fit. Hoffmann, Diane E; Fraser, Claire M; Palumbo, Francis; Ravel, Jacques; Rowthorn, Virginia; Schwartz, Jack Food and drug law journal 25163211 2014
Longitudinal analysis of microbial interaction between humans and the indoor environment. Lax, Simon; Smith, Daniel P; Hampton-Marcell, Jarrad; Owens, Sarah M; Handley, Kim M; Scott, Nicole M; Gibbons, Sean M; Larsen, Peter; Shogan, Benjamin D; Weiss, Sophie; Metcalf, Jessica L; Ursell, Luke K; Vázquez-Baeza, Yoshiki; Van Treuren, Will; Hasan, Nur A; Gibson, Molly K; Colwell, Rita; Dantas, Gautam; Knight, Rob; Gilbert, Jack A Science (New York, N.Y.). 25170151 2014 Aug 29;
From deep sequencing to actual clones. D'Angelo, Sara; Kumar, Sandeep; Naranjo, Leslie; Ferrara, Fortunato; Kiss, Csaba; Bradbury, Andrew R M Protein engineering, design & selection : PEDS. 25183780 2014 Oct;
Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35. Boonma, Prapaporn; Spinler, Jennifer K; Qin, Xiang; Jittaprasatsin, Chutima; Muzny, Donna M; Doddapaneni, Harsha; Gibbs, Richard; Petrosino, Joe; Tumwasorn, Somying; Versalovic, James Standards in genomic sciences. 25197459 2014 Jun 15;
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Zuo, Zheng; Stormo, Gary D Genetics. 25209146 2014 Nov;
The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Integrative HMP (iHMP) Research Network Consortium Cell host & microbe. 25211071 2014 Sep 10;
Metagenomic analysis of double-stranded DNA viruses in healthy adults. Wylie, Kristine M; Mihindukulasuriya, Kathie A; Zhou, Yanjiao; Sodergren, Erica; Storch, Gregory A; Weinstock, George M BMC biology. 25212266 2014;
MiRNA detection at single-cell resolution using microfluidic LNA flow-FISH. Wu, Meiye; Piccini, Matthew E; Singh, Anup K Methods in molecular biology (Clifton, N.J.). 25218391 2014;
An effective intervention to reduce intravaginal practices among HIV-1 uninfected Kenyan women. Sivapalasingam, Sumathi; McClelland, R Scott; Ravel, Jacques; Ahmed, Aabid; Cleland, Charles M; Gajer, Pawel; Mwamzaka, Musa; Marshed, Fatma; Shafi, Juma; Masese, Linnet; Fajans, Mark; Anderson, Molly E; Jaoko, Walter; Kurth, Ann E AIDS research and human retroviruses. 25265254 2014 Nov;
Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems. Rhee, Minsoung; Light, Yooli K; Yilmaz, Suzan; Adams, Paul D; Saxena, Deepak; Meagher, Robert J; Singh, Anup K Lab on a chip. 25270338 2014 Dec 7;
The microbiome revolution. Blaser, Martin J The Journal of clinical investigation. 25271724 2014 Oct;
Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study. Zhou, Yanjiao; Burnham, Carey-Ann D; Hink, Tiffany; Chen, Lei; Shaikh, Nurmohammad; Wollam, Aye; Sodergren, Erica; Weinstock, George M; Tarr, Phillip I; Dubberke, Erik R Journal of clinical microbiology. 25275005 2014 Dec;
Sinus culture poorly predicts resident microbiota. Hauser, Leah J; Feazel, Leah M; Ir, Diana; Fang, Rui; Wagner, Brandie D; Robertson, Charles E; Frank, Daniel N; Ramakrishnan, Vijay R International forum of allergy & rhinology. 25278448 2015 Jan;
Microbiology: An integrated view of the skin microbiome. Schloss, Patrick D Nature 25279916 2014 Oct 02
Advancing the microbiome research community. Huttenhower, Curtis; Knight, Rob; Brown, C Titus; Caporaso, J Gregory; Clemente, Jose C; Gevers, Dirk; Franzosa, Eric A; Kelley, Scott T; Knights, Dan; Ley, Ruth E; Mahurkar, Anup; Ravel, Jacques; Scientists for Advancement of Microbiome Research; White, Owen Cell. 25303518 2014 Oct 9;
Meta-analyses of human gut microbes associated with obesity and IBD. Walters, William A; Xu, Zech; Knight, Rob FEBS letters. 25307765 2014 Nov 17;
Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. Eren, A Murat; Morrison, Hilary G; Lescault, Pamela J; Reveillaud, Julie; Vineis, Joseph H; Sogin, Mitchell L The ISME journal. 25325381 2015 Mar 17;
An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease. Fettweis, Jennifer M; Serrano, Myrna G; Huang, Bernice; Brooks, J Paul; Glascock, Abigail L; Sheth, Nihar U; Vaginal Microbiome Consortium; Strauss 3rd, Jerome F; Jefferson, Kimberly K; Buck, Gregory A PloS one. 25337710 2014;
Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. Vital, Marius; Chai, Benli; Ostman, Bjorn; Cole, James; Konstantinidis, Konstantinos T; Tiedje, James M The ISME journal. 25343512 2015 May;
Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia. Vital, Marius; Gao, Jiarong; Rizzo, Mike; Harrison, Tara; Tiedje, James M The ISME journal. 25343515 2015 Apr;
High-resolution genetic mapping in the diversity outbred mouse population identifies Apobec1 as a candidate gene for atherosclerosis. Smallwood, Tangi L; Gatti, Daniel M; Quizon, Pamela; Weinstock, George M; Jung, Kuo-Chen; Zhao, Liyang; Hua, Kunjie; Pomp, Daniel; Bennett, Brian J G3 (Bethesda, Md.). 25344410 2014 Dec;
Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric peromyscus populations. Baxter, Nielson T; Wan, Judy J; Schubert, Alyxandria M; Jenior, Matthew L; Myers, Philip; Schloss, Patrick D Applied and environmental microbiology. 25362056 2015 Jan;
Spec-seq: determining protein-DNA-binding specificity by sequencing. Stormo, Gary D; Zuo, Zheng; Chang, Yiming Kenny Briefings in functional genomics. 25362070 2015 Jan;
Evolution of invasion in a diverse set of Fusobacterium species. Manson McGuire, Abigail; Cochrane, Kyla; Griggs, Allison D; Haas, Brian J; Abeel, Thomas; Zeng, Qiandong; Nice, Justin B; MacDonald, Hanlon; Birren, Bruce W; Berger, Bryan W; Allen-Vercoe, Emma; Earl, Ashlee M mBio. 25370491 2014;
Versatile on-demand droplet generation for controlled encapsulation. Rhee, Minsoung; Liu, Peng; Meagher, Robert J; Light, Yooli K; Singh, Anup K Biomicrofluidics. 25379072 2014 May;
The gut microbiome in health and in disease. Shreiner, Andrew B; Kao, John Y; Young, Vincent B Current opinion in gastroenterology. 25394236 2015 Jan;
Fetal exposures and perinatal influences on the stool microbiota of premature infants. Chernikova, Diana A; Koestler, Devin C; Hoen, Anne Gatewood; Housman, Molly L; Hibberd, Patricia L; Moore, Jason H; Morrison, Hilary G; Sogin, Mitchell L; Zain-Ul-Abideen, Muhammad; Madan, Juliette C The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians. 25394613 2016;
NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly. McCorrison, Jamison M; Venepally, Pratap; Singh, Indresh; Fouts, Derrick E; Lasken, Roger S; Methé, Barbara A BMC bioinformatics. 25407910 2014;
Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Wu, Gary D; Compher, Charlene; Chen, Eric Z; Smith, Sarah A; Shah, Rachana D; Bittinger, Kyle; Chehoud, Christel; Albenberg, Lindsey G; Nessel, Lisa; Gilroy, Erin; Star, Julie; Weljie, Aalim M; Flint, Harry J; Metz, David C; Bennett, Michael J; Li, Hongzhe; Bushman, Frederic D; Lewis, James D Gut. 25431456 2014 Nov 26;
The interrelationships of the gut microbiome and inflammation in colorectal carcinogenesis. Cho, Margaret; Carter, Janell; Harari, Saul; Pei, Zhiheng Clinics in laboratory medicine. 25439270 2014 Dec;
Microbiome, innate immunity, and esophageal adenocarcinoma. Baghdadi, Jonathan; Chaudhary, Noami; Pei, Zhiheng; Yang, Liying Clinics in laboratory medicine. 25439272 2014 Dec;
The changing landscape of the vaginal microbiome. Huang, Bernice; Fettweis, Jennifer M; Brooks, J Paul; Jefferson, Kimberly K; Buck, Gregory A Clinics in laboratory medicine. 25439274 2014 Dec;
Beyond infectious disease: welcome to the era of population microbiology. Pincus, Matthew R; Pei, Zhiheng Clinics in laboratory medicine. 25439278 2014 Dec;
Determining microbial products and identifying molecular targets in the human microbiome. Joice, Regina; Yasuda, Koji; Shafquat, Afrah; Morgan, Xochitl C; Huttenhower, Curtis Cell metabolism. 25440055 2014 Nov 4;
The conjunctival microbiome in health and trachomatous disease: a case control study. Zhou, Yanjiao; Holland, Martin J; Makalo, Pateh; Joof, Hassan; Roberts, Chrissy H; Mabey, David Cw; Bailey, Robin L; Burton, Matthew J; Weinstock, George M; Burr, Sarah E Genome medicine 25484919 2014
Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease. Esplin, Edward D; Oei, Ling; Snyder, Michael P Pharmacogenomics. 25493570 2014 Nov;
The EHEC-host interactome reveals novel targets for the translocated intimin receptor. Blasche, Sonja; Arens, Stefan; Ceol, Arnaud; Siszler, Gabriella; Schmidt, M Alexander; Hauser, Roman; Schwarz, Frank; Wuchty, Stefan; Aloy, Patrick; Uetz, Peter; Stradal, Theresia; Koegl, Manfred Scientific reports. 25519916 2014;
The preterm placental microbiome varies in association with excess maternal gestational weight gain. Antony, Kathleen M; Ma, Jun; Mitchell, Kristen B; Racusin, Diana A; Versalovic, James; Aagaard, Kjersti American journal of obstetrics and gynecology. 25557210 2015 May;
High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis. Goyette, Philippe; Boucher, Gabrielle; Mallon, Dermot; Ellinghaus, Eva; Jostins, Luke; Huang, Hailiang; Ripke, Stephan; Gusareva, Elena S; Annese, Vito; Hauser, Stephen L; Oksenberg, Jorge R; Thomsen, Ingo; Leslie, Stephen; International Inflammatory Bowel Disease Genetics Consortium; Australia and New Zealand IBDGC; Belgium IBD Genetics Consortium; Italian Group for IBD Genetic Consortium; NIDDK Inflammatory Bowel Disease Genetics Consortium; United Kingdom IBDGC; Wellcome Trust Case Control Consortium; Quebec IBD Genetics Consortium; Daly, Mark J; Van Steen, Kristel; Duerr, Richard H; Barrett, Jeffrey C; McGovern, Dermot P B; Schumm, L Philip; Traherne, James A; Carrington, Mary N; Kosmoliaptsis, Vasilis; Karlsen, Tom H; Franke, Andre; Rioux, John D Nature genetics. 25559196 2015 Feb;
A RESTful API for accessing microbial community data for MG-RAST. Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M; Desai, Narayan; Meyer, Folker PLoS computational biology. 25569221 2015 Jan;
The cutaneous microbiome in outpatients presenting with acute skin abscesses. Horton, James M; Gao, Zhan; Sullivan, D Matthew; Shopsin, Bo; Perez-Perez, Guillermo I; Blaser, Martin J The Journal of infectious diseases. 25583170 2015 Jun 15;
Complex host genetics influence the microbiome in inflammatory bowel disease. Knights, Dan; Silverberg, Mark S; Weersma, Rinse K; Gevers, Dirk; Dijkstra, Gerard; Huang, Hailiang; Tyler, Andrea D; van Sommeren, Suzanne; Imhann, Floris; Stempak, Joanne M; Huang, Hu; Vangay, Pajau; Al-Ghalith, Gabriel A; Russell, Caitlin; Sauk, Jenny; Knight, Jo; Daly, Mark J; Huttenhower, Curtis; Xavier, Ramnik J Genome medicine. 25587358 2014;
Asynchronous Magnetic Bead Rotation (AMBR) Microviscometer for Label-Free DNA Analysis. Li, Yunzi; Burke, David T; Kopelman, Raoul; Burns, Mark A Biosensors 25587411 2014 Mar
Diet in the pathogenesis and treatment of inflammatory bowel diseases. Lee, Dale; Albenberg, Lindsey; Compher, Charlene; Baldassano, Robert; Piccoli, David; Lewis, James D; Wu, Gary D Gastroenterology. 25597840 2015 May;
De novo large cell neuroendocrine carcinoma of the prostate, case report and literature review. Acosta-Gonzalez, Gabriel; Qin, Jia; Wieczorek, Rosemary; Melamed, Jonathan; Deng, Fang-Ming; Zhou, Ming; Makarov, Danil; Ye, Fei; Pei, Zhiheng; Pincus, Matthew R; Lee, Peng American journal of clinical and experimental urology. 25606580 2014;
Disease-specific alterations in the enteric virome in inflammatory bowel disease. Norman, Jason M; Handley, Scott A; Baldridge, Megan T; Droit, Lindsay; Liu, Catherine Y; Keller, Brian C; Kambal, Amal; Monaco, Cynthia L; Zhao, Guoyan; Fleshner, Phillip; Stappenbeck, Thaddeus S; McGovern, Dermot P B; Keshavarzian, Ali; Mutlu, Ece A; Sauk, Jenny; Gevers, Dirk; Xavier, Ramnik J; Wang, David; Parkes, Miles; Virgin, Herbert W Cell. 25619688 2015 Jan 29;
Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intraamniotic infection. Allen-Daniels, Matthew Josiah; Serrano, Myrna G; Pflugner, Lindsey P; Fettweis, Jennifer M; Prestosa, Melissa A; Koparde, Vishal N; Brooks, J Paul; Strauss 3rd, Jerome F; Romero, Roberto; Chaiworapongsa, Tinnakorn; Eschenbach, David A; Buck, Gregory A; Jefferson, Kimberly K American journal of obstetrics and gynecology. 25637842 2015 Jun;
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Kostic, Aleksandar D; Gevers, Dirk; Siljander, Heli; Vatanen, Tommi; Hyötyläinen, Tuulia; Hämäläinen, Anu-Maaria; Peet, Aleksandr; Tillmann, Vallo; Pöhö, Päivi; Mattila, Ismo; Lähdesmäki, Harri; Franzosa, Eric A; Vaarala, Outi; de Goffau, Marcus; Harmsen, Hermie; Ilonen, Jorma; Virtanen, Suvi M; Clish, Clary B; Ore?i?, Matej; Huttenhower, Curtis; Knip, Mikael; DIABIMMUNE Study Group; Xavier, Ramnik J Cell host & microbe. 25662751 2015 Feb 11;
Impact of allele-specific peptides in proteome quantification. Wu, Linfeng; Snyder, Michael Proteomics. Clinical applications. 25676416 2015 Apr;
A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. Didion, John P; Morgan, Andrew P; Clayshulte, Amelia M-F; Mcmullan, Rachel C; Yadgary, Liran; Petkov, Petko M; Bell, Timothy A; Gatti, Daniel M; Crowley, James J; Hua, Kunjie; Aylor, David L; Bai, Ling; Calaway, Mark; Chesler, Elissa J; French, John E; Geiger, Thomas R; Gooch, Terry J; Garland Jr, Theodore; Harrill, Alison H; Hunter, Kent; McMillan, Leonard; Holt, Matt; Miller, Darla R; O'Brien, Deborah A; Paigen, Kenneth; Pan, Wenqi; Rowe, Lucy B; Shaw, Ginger D; Simecek, Petr; Sullivan, Patrick F; Svenson, Karen L; Weinstock, George M; Threadgill, David W; Pomp, Daniel; Churchill, Gary A; Pardo-Manuel de Villena, Fernando PLoS genetics. 25679959 2015 Feb;
Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates. Ma, Jun; Purcell, Heidi; Showalter, Lori; Aagaard, Kjersti M American journal of obstetrics and gynecology. 25687567 2015 Apr;
A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification. Bigdeli, Saharnaz; Dettloff, Roger O; Frank, Curtis W; Davis, Ronald W; Crosby, Laurel D PloS one. 25689864 2015 Feb 17;
Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Yasuda, Koji; Oh, Keunyoung; Ren, Boyu; Tickle, Timothy L; Franzosa, Eric A; Wachtman, Lynn M; Miller, Andrew D; Westmoreland, Susan V; Mansfield, Keith G; Vallender, Eric J; Miller, Gregory M; Rowlett, James K; Gevers, Dirk; Huttenhower, Curtis; Morgan, Xochitl C Cell host & microbe. 25732063 2015 Mar 11;
Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases. Huang, Edmond Y; Inoue, Takuya; Leone, Vanessa A; Dalal, Sushila; Touw, Ketrija; Wang, Yunwei; Musch, Mark W; Theriault, Betty; Higuchi, Kazuhide; Donovan, Sharon; Gilbert, Jack; Chang, Eugene B Inflammatory bowel diseases. 25738379 2015 May;
Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study. Zhou, Yanjiao; Shan, Gururaj; Sodergren, Erica; Weinstock, George; Walker, W Allan; Gregory, Katherine E PloS one. 25741698 2015 Mar 5;
Optimized Analytical Procedures for the Untargeted Metabolomic Profiling of Human Urine and Plasma by Combining Hydrophilic Interaction (HILIC) and Reverse-Phase Liquid Chromatography (RPLC)-Mass Spectrometry. Contrepois, Kévin; Jiang, Lihua; Snyder, Michael Molecular & cellular proteomics : MCP. 25787789 2015 Jun;
Personal genomes, quantitative dynamic omics and personalized medicine. Mias, George I; Snyder, Michael Quantitative biology. 25798291 2013 Mar;
Subsistence strategies in traditional societies distinguish gut microbiomes. Obregon-Tito, Alexandra J; Tito, Raul Y; Metcalf, Jessica; Sankaranarayanan, Krithivasan; Clemente, Jose C; Ursell, Luke K; Zech Xu, Zhenjiang; Van Treuren, Will; Knight, Rob; Gaffney, Patrick M; Spicer, Paul; Lawson, Paul; Marin-Reyes, Luis; Trujillo-Villarroel, Omar; Foster, Morris; Guija-Poma, Emilio; Troncoso-Corzo, Luzmila; Warinner, Christina; Ozga, Andrew T; Lewis, Cecil M Nature communications. 25807110 2015 Mar 25;
Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis. Hoen, Anne G; Li, Jing; Moulton, Lisa A; O'Toole, George A; Housman, Molly L; Koestler, Devin C; Guill, Margaret F; Moore, Jason H; Hibberd, Patricia L; Morrison, Hilary G; Sogin, Mitchell L; Karagas, Margaret R; Madan, Juliette C The Journal of pediatrics. 25818499 2015 Jul;
Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome. Ramakrishnan, Vijay R; Hauser, Leah J; Feazel, Leah M; Ir, Diana; Robertson, Charles E; Frank, Daniel N The Journal of allergy and clinical immunology. 25819063 2015 Aug;
Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe Bioinformatics (Oxford, England). 25819674 2015 Aug 01;
The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin. Liu, Jared; Yan, Riceley; Zhong, Qiao; Ngo, Sam; Bangayan, Nathanael J; Nguyen, Lin; Lui, Timothy; Liu, Minghsun; Erfe, Marie C; Craft, Noah; Tomida, Shuta; Li, Huiying The ISME journal. 25848871 2015 Sep;
Serial fecal microbiota transplantation alters mucosal gene expression in pediatric ulcerative colitis. Kellermayer, Richard; Nagy-Szakal, Dorottya; Harris, R Alan; Luna, Ruth Ann; Pitashny, Milena; Schady, Deborah; Mir, Sabina A V; Lopez, Monica E; Gilger, Mark A; Belmont, John; Hollister, Emily B; Versalovic, James The American journal of gastroenterology. 25853207 2015 Apr;
New signaling pathways govern the host response to C. albicans infection in various niches. Liu, Yaoping; Shetty, Amol C; Schwartz, Jennifer A; Bradford, L Latey; Xu, Wenjie; Phan, Qyunh T; Kumari, Priti; Mahurkar, Anup; Mitchell, Aaron P; Ravel, Jacques; Fraser, Claire M; Filler, Scott G; Bruno, Vincent M Genome research. 25858952 2015 May;
Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Yano, Jessica M; Yu, Kristie; Donaldson, Gregory P; Shastri, Gauri G; Ann, Phoebe; Ma, Liang; Nagler, Cathryn R; Ismagilov, Rustem F; Mazmanian, Sarkis K; Hsiao, Elaine Y Cell. 25860609 2015 Apr 9;
Metabolic signatures of bacterial vaginosis. Srinivasan, Sujatha; Morgan, Martin T; Fiedler, Tina L; Djukovic, Danijel; Hoffman, Noah G; Raftery, Daniel; Marrazzo, Jeanne M; Fredricks, David N mBio. 25873373 2015 Apr 14;
Sex, body mass index, and dietary fiber intake influence the human gut microbiome. Dominianni, Christine; Sinha, Rashmi; Goedert, James J; Pei, Zhiheng; Yang, Liying; Hayes, Richard B; Ahn, Jiyoung PloS one. 25874569 2015 Apr 15;
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. Brooks, J Paul; Edwards, David J; Harwich Jr, Michael D; Rivera, Maria C; Fettweis, Jennifer M; Serrano, Myrna G; Reris, Robert A; Sheth, Nihar U; Huang, Bernice; Girerd, Philippe; Vaginal Microbiome Consortium; Strauss 3rd, Jerome F; Jefferson, Kimberly K; Buck, Gregory A BMC microbiology. 25880246 2015 Mar 21;
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Morgan, Xochitl C; Kabakchiev, Boyko; Waldron, Levi; Tyler, Andrea D; Tickle, Timothy L; Milgrom, Raquel; Stempak, Joanne M; Gevers, Dirk; Xavier, Ramnik J; Silverberg, Mark S; Huttenhower, Curtis Genome biology. 25887922 2015 Apr 8;
Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Leone, Vanessa; Gibbons, Sean M; Martinez, Kristina; Hutchison, Alan L; Huang, Edmond Y; Cham, Candace M; Pierre, Joseph F; Heneghan, Aaron F; Nadimpalli, Anuradha; Hubert, Nathaniel; Zale, Elizabeth; Wang, Yunwei; Huang, Yong; Theriault, Betty; Dinner, Aaron R; Musch, Mark W; Kudsk, Kenneth A; Prendergast, Brian J; Gilbert, Jack A; Chang, Eugene B Cell host & microbe. 25891358 2015 May 13;
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Franzosa, Eric A; Hsu, Tiffany; Sirota-Madi, Alexandra; Shafquat, Afrah; Abu-Ali, Galeb; Morgan, Xochitl C; Huttenhower, Curtis Nature reviews. Microbiology. 25915636 2015 Jun;
Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis. Segal, Leopoldo N; Blaser, Martin J The Journal of pediatrics. 25934071 2015 Jul;
Identifying personal microbiomes using metagenomic codes. Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, Curtis Proceedings of the National Academy of Sciences of the United States of America. 25964341 2015 Jun 2;
Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease. Lee, Dale; Baldassano, Robert N; Otley, Anthony R; Albenberg, Lindsey; Griffiths, Anne M; Compher, Charlene; Chen, Eric Z; Li, Hongzhe; Gilroy, Erin; Nessel, Lisa; Grant, Amy; Chehoud, Christel; Bushman, Frederic D; Wu, Gary D; Lewis, James D Inflammatory bowel diseases. 25970545 2015 Aug;
An integrative view of microbiome-host interactions in inflammatory bowel diseases. Wlodarska, Marta; Kostic, Aleksandar D; Xavier, Ramnik J Cell host & microbe. 25974300 2015 May 13;
The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins. Mehla, Jitender; Dedrick, Rebekah M; Caufield, J Harry; Siefring, Rachel; Mair, Megan; Johnson, Allison; Hatfull, Graham F; Uetz, Peter Journal of bacteriology. 25986902 2015 Aug 1;
High-throughput sequencing technologies. Reuter, Jason A; Spacek, Damek V; Snyder, Michael P Molecular cell. 26000844 2015 May 21;
Skin-to-Skin Care and the Development of the Preterm Infant Oral Microbiome. Hendricks-Muñoz, Karen D; Xu, Jie; Parikh, Hardik I; Xu, Ping; Fettweis, Jennifer M; Kim, Yang; Louie, Moi; Buck, Gregory A; Thacker, Leroy R; Sheth, Nihar U American journal of perinatology. 26007311 2015 Nov;
Carcass mass has little influence on the structure of gravesoil microbial communities. Weiss, Sophie; Carter, David O; Metcalf, Jessica L; Knight, Rob International journal of legal medicine. 26024793 2016 Jan;
Inflammation-associated microbiota in pediatric eosinophilic esophagitis. Benitez, Alain J; Hoffmann, Christian; Muir, Amanda B; Dods, Kara K; Spergel, Jonathan M; Bushman, Frederic D; Wang, Mei-Lun Microbiome 26034601 2015
Fast disease progression in simian HIV-infected female macaque is accompanied by a robust local inflammatory innate immune and microbial response. Ren, Wuze; Ma, Yingfei; Yang, Liying; Gettie, Agegnehu; Salas, January; Russell, Kasi; Blanchard, James; Davidow, Amy; Pei, Zhiheng; Chang, Theresa L; Cheng-Mayer, Cecilia AIDS (London, England). 26035329 2015 Jun 19;
Lungs, microbes and the developing neonate. Warner, Barbara B; Hamvas, Aaron Neonatology. 26044101 2015 June;
The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome. Davidovics, Zev H; Carter, Beth A; Luna, Ruth Ann; Hollister, Emily B; Shulman, Robert J; Versalovic, James JPEN. Journal of parenteral and enteral nutrition. 26059898 2016 11;
Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes. Alkanani, Aimon K; Hara, Naoko; Gottlieb, Peter A; Ir, Diana; Robertson, Charles E; Wagner, Brandie D; Frank, Daniel N; Zipris, Danny Diabetes. 26068542 2015 Oct;
Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort. Gall, Alevtina; Fero, Jutta; McCoy, Connor; Claywell, Brian C; Sanchez, Carissa A; Blount, Patricia L; Li, Xiaohong; Vaughan, Thomas L; Matsen, Frederick A; Reid, Brian J; Salama, Nina R PloS one. 26076489 2015 June 15;
Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9. Bryson, Alexandra L; Hwang, Young; Sherrill-Mix, Scott; Wu, Gary D; Lewis, James D; Black, Lindsay; Clark, Tyson A; Bushman, Frederic D mBio. 26081634 2015 June 16;
Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers. Feazel, Leah M; Santorico, Stephanie A; Robertson, Charles E; Bashraheil, Mahfudh; Scott, J Anthony G; Frank, Daniel N; Hammitt, Laura L PloS one. 26083474 2015;
Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. Chehoud, Christel; Albenberg, Lindsey G; Judge, Colleen; Hoffmann, Christian; Grunberg, Stephanie; Bittinger, Kyle; Baldassano, Robert N; Lewis, James D; Bushman, Frederic D; Wu, Gary D Inflammatory bowel diseases. 26083617 2015 Aug;
Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease. Vital, Marius; Harkema, Jack R; Rizzo, Mike; Tiedje, James; Brandenberger, Christina Journal of immunology research. 26090504 2015 April 16;
Engineering the gut microbiota to treat hyperammonemia. Shen, Ting-Chin David; Albenberg, Lindsey; Bittinger, Kyle; Chehoud, Christel; Chen, Ying-Yu; Judge, Colleen A; Chau, Lillian; Ni, Josephine; Sheng, Michael; Lin, Andrew; Wilkins, Benjamin J; Buza, Elizabeth L; Lewis, James D; Daikhin, Yevgeny; Nissim, Ilana; Yudkoff, Marc; Bushman, Frederic D; Wu, Gary D The Journal of clinical investigation. 26098218 2015 Jul 1;
Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome. Chumpitazi, B P; Cope, J L; Hollister, E B; Tsai, C M; McMeans, A R; Luna, R A; Versalovic, J; Shulman, R J Alimentary pharmacology & therapeutics. 26104013 2015 Aug;
Impact of neonatal intensive care bed configuration on rates of late-onset bacterial sepsis and methicillin-resistant Staphylococcus aureus colonization. Julian, Samuel; Burnham, Carey-Ann D; Sellenriek, Patricia; Shannon, William D; Hamvas, Aaron; Tarr, Phillip I; Warner, Barbara B Infection control and hospital epidemiology. 26108888 2015 Oct;
Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis. Kang, Dezhi; Shi, Baochen; Erfe, Marie C; Craft, Noah; Li, Huiying Science translational medicine. 26109103 2015 Jun 24;
Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants. Taft, Diana H; Ambalavanan, Namasivayam; Schibler, Kurt R; Yu, Zhuoteng; Newburg, David S; Deshmukh, Hitesh; Ward, Doyle V; Morrow, Ardythe L PloS one. 26110908 2015 Jun 25;
Using an in-vitro biofilm model to assess the virulence potential of bacterial vaginosis or non-bacterial vaginosis Gardnerella vaginalis isolates. Castro, Joana; Alves, Patrícia; Sousa, Cármen; Cereija, Tatiana; França, Ângela; Jefferson, Kimberly K; Cerca, Nuno Scientific reports. 26113465 2015 Jun 26;
Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nobel, Yael R; Cox, Laura M; Kirigin, Francis F; Bokulich, Nicholas A; Yamanishi, Shingo; Teitler, Isabel; Chung, Jennifer; Sohn, Jiho; Barber, Cecily M; Goldfarb, David S; Raju, Kartik; Abubucker, Sahar; Zhou, Yanjiao; Ruiz, Victoria E; Li, Huilin; Mitreva, Makedonka; Alekseyenko, Alexander V; Weinstock, George M; Sodergren, Erica; Blaser, Martin J Nature communications. 26123276 2015 Jun 30;
Compact graphical representation of phylogenetic data and metadata with GraPhlAn. Asnicar, Francesco; Weingart, George; Tickle, Timothy L; Huttenhower, Curtis; Segata, Nicola PeerJ. 26157614 2015;
Role of Autophagy in the Maintenance of Intestinal Homeostasis. Baxt, Leigh A; Xavier, Ramnik J Gastroenterology. 26170139 2015 Sep;
Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile. Schubert, Alyxandria M; Sinani, Hamide; Schloss, Patrick D mBio. 26173701 2015 Jul 14;
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. Sizova, Maria V; Chilaka, Amanda; Earl, Ashlee M; Doerfert, Sebastian N; Muller, Paul A; Torralba, Manolito; McCorrison, Jamison M; Durkin, A Scott; Nelson, Karen E; Epstein, Slava S Standards in genomic sciences. 26221418 2015;
The microbiome of uncontacted Amerindians. Clemente, Jose C; Pehrsson, Erica C; Blaser, Martin J; Sandhu, Kuldip; Gao, Zhan; Wang, Bin; Magris, Magda; Hidalgo, Glida; Contreras, Monica; Noya-Alarcón, Óscar; Lander, Orlana; McDonald, Jeremy; Cox, Mike; Walter, Jens; Oh, Phaik Lyn; Ruiz, Jean F; Rodriguez, Selena; Shen, Nan; Song, Se Jin; Metcalf, Jessica; Knight, Rob; Dantas, Gautam; Dominguez-Bello, M Gloria Science advances. 26229982 2015 Apr 3;
Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Beck, James M; Schloss, Patrick D; Venkataraman, Arvind; Twigg 3rd, Homer; Jablonski, Kathleen A; Bushman, Frederic D; Campbell, Thomas B; Charlson, Emily S; Collman, Ronald G; Crothers, Kristina; Curtis, Jeffrey L; Drews, Kimberly L; Flores, Sonia C; Fontenot, Andrew P; Foulkes, Mary A; Frank, Ian; Ghedin, Elodie; Huang, Laurence; Lynch, Susan V; Morris, Alison; Palmer, Brent E; Schmidt, Thomas M; Sodergren, Erica; Weinstock, George M; Young, Vincent B; Lung HIV Microbiome Project American journal of respiratory and critical care medicine. 26247840 2015 Dec 01;
The gut microbiota in human energy homeostasis and obesity. Rosenbaum, Michael; Knight, Rob; Leibel, Rudolph L Trends in endocrinology and metabolism: TEM. 26257300 2015 Sep;
Characterization of genetic loci that affect susceptibility to inflammatory bowel diseases in African Americans. Huang, Chengrui; Haritunians, Talin; Okou, David T; Cutler, David J; Zwick, Michael E; Taylor, Kent D; Datta, Lisa W; Maranville, Joseph C; Liu, Zhenqiu; Ellis, Shannon; Chopra, Pankaj; Alexander, Jonathan S; Baldassano, Robert N; Cross, Raymond K; Dassopoulos, Themistocles; Dhere, Tanvi A; Duerr, Richard H; Hanson, John S; Hou, Jason K; Hussain, Sunny Z; Isaacs, Kim L; Kachelries, Kelly E; Kader, Howard; Kappelman, Michael D; Katz, Jeffrey; Kellermayer, Richard; Kirschner, Barbara S; Kuemmerle, John F; Kumar, Archana; Kwon, John H; Lazarev, Mark; Mannon, Peter; Moulton, Dedrick E; Osuntokun, Bankole O; Patel, Ashish; Rioux, John D; Rotter, Jerome I; Saeed, Shehzad; Scherl, Ellen J; Silverberg, Mark S; Silverman, Ann; Targan, Stephan R; Valentine, John F; Wang, Ming-Hsi; Simpson, Claire L; Bridges, S Louis; Kimberly, Robert P; Rich, Stephen S; Cho, Judy H; Di Rienzo, Anna; Kao, Linda W H; McGovern, Dermot P B; Brant, Steven R; Kugathasan, Subra Gastroenterology. 26278503 2015 Nov;
Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts. Kelsen, Judith; Bittinger, Kyle; Pauly-Hubbard, Helen; Posivak, Leah; Grunberg, Stephanie; Baldassano, Robert; Lewis, James D; Wu, Gary D; Bushman, Frederic D Inflammatory bowel diseases. 26288001 2015 Dec;
Structure and function of the healthy pre-adolescent pediatric gut microbiome. Hollister, Emily B; Riehle, Kevin; Luna, Ruth Ann; Weidler, Erica M; Rubio-Gonzales, Michelle; Mistretta, Toni-Ann; Raza, Sabeen; Doddapaneni, Harsha V; Metcalf, Ginger A; Muzny, Donna M; Gibbs, Richard A; Petrosino, Joseph F; Shulman, Robert J; Versalovic, James Microbiome. 26306392 2015;
ConStrains identifies microbial strains in metagenomic datasets. Luo, Chengwei; Knight, Rob; Siljander, Heli; Knip, Mikael; Xavier, Ramnik J; Gevers, Dirk Nature biotechnology. 26344404 2015 Oct;
Early life dynamics of the human gut virome and bacterial microbiome in infants. Lim, Efrem S; Zhou, Yanjiao; Zhao, Guoyan; Bauer, Irma K; Droit, Lindsay; Ndao, I Malick; Warner, Barbara B; Tarr, Phillip I; Wang, David; Holtz, Lori R Nature medicine. 26366711 2015 Oct;
Host genetic variation impacts microbiome composition across human body sites. Blekhman, Ran; Goodrich, Julia K; Huang, Katherine; Sun, Qi; Bukowski, Robert; Bell, Jordana T; Spector, Timothy D; Keinan, Alon; Ley, Ruth E; Gevers, Dirk; Clark, Andrew G Genome biology. 26374288 2015 Sep 15;
MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Truong, Duy Tin; Franzosa, Eric A; Tickle, Timothy L; Scholz, Matthias; Weingart, George; Pasolli, Edoardo; Tett, Adrian; Huttenhower, Curtis; Segata, Nicola Nature methods. 26418763 2015 Oct;
Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Lewis, James D; Chen, Eric Z; Baldassano, Robert N; Otley, Anthony R; Griffiths, Anne M; Lee, Dale; Bittinger, Kyle; Bailey, Aubrey; Friedman, Elliot S; Hoffmann, Christian; Albenberg, Lindsey; Sinha, Rohini; Compher, Charlene; Gilroy, Erin; Nessel, Lisa; Grant, Amy; Chehoud, Christel; Li, Hongzhe; Wu, Gary D; Bushman, Frederic D Cell host & microbe. 26468751 2015 Oct 14;
The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Rogers, M A M; Aronoff, D M Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 26482265 2016 Feb;
Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study. Cleynen, Isabelle; Boucher, Gabrielle; Jostins, Luke; Schumm, L Philip; Zeissig, Sebastian; Ahmad, Tariq; Andersen, Vibeke; Andrews, Jane M; Annese, Vito; Brand, Stephan; Brant, Steven R; Cho, Judy H; Daly, Mark J; Dubinsky, Marla; Duerr, Richard H; Ferguson, Lynnette R; Franke, Andre; Gearry, Richard B; Goyette, Philippe; Hakonarson, Hakon; Halfvarson, Jonas; Hov, Johannes R; Huang, Hailang; Kennedy, Nicholas A; Kupcinskas, Limas; Lawrance, Ian C; Lee, James C; Satsangi, Jack; Schreiber, Stephan; Théâtre, Emilie; van der Meulen-de Jong, Andrea E; Weersma, Rinse K; Wilson, David C; International Inflammatory Bowel Disease Genetics Consortium; Parkes, Miles; Vermeire, Severine; Rioux, John D; Mansfield, John; Silverberg, Mark S; Radford-Smith, Graham; McGovern, Dermot P B; Barrett, Jeffrey C; Lees, Charlie W Lancet (London, England). 26490195 2016 Jan 9;
High Frequency of Detection by PCR of Viral Nucleic Acid in The Blood of Infants Presenting with Clinical Myocarditis. Simpson, Kathleen E; Storch, Gregory A; Lee, Caroline K; Ward, Kent E; Danon, Saar; Simon, Catherine M; Delaney, Jeffrey W; Tong, Alan; Canter, Charles E Pediatric cardiology. 26499513 2016 Feb;
mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. Davis, Curtis; Kota, Karthik; Baldhandapani, Venkat; Gong, Wei; Abubucker, Sahar; Becker, Eric; Martin, John; Wylie, Kristine M; Khetani, Radhika; Hudson, Matthew E; Weinstock, George M; Mitreva, Makedonka Journal of data mining in genomics & proteomics. 26500804 2015 Aug;
Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season. Wylie, Kristine M; Weinstock, George M; Storch, Gregory A Journal of the Pediatric Infectious Diseases Society. 26513823 2015 Dec;
Microbiome, a new dimension in cancer research. Neto, Antonio Galvao; Bradshaw, Azore-Dee; Pei, Zhiheng Annals of translational medicine. 26539446 2015 Sep;
Microfluidic Flow Cytometry for Single-Cell Protein Analysis. Wu, Meiye; Singh, Anup K Methods in molecular biology (Clifton, N.J.). 26542716 2015;
Global prevalence and distribution of genes and microorganisms involved in mercury methylation. Podar, Mircea; Gilmour, Cynthia C; Brandt, Craig C; Soren, Allyson; Brown, Steven D; Crable, Bryan R; Palumbo, Anthony V; Somenahally, Anil C; Elias, Dwayne A Science advances 26601305 2015 Oct
Nurturing the microbiome field. Schloss, Patrick Science (New York, N.Y.) 26612945 2015 Nov 27
Luminal Conversion and Immunoregulation by Probiotics. Ganesh, Bhanu Priya; Versalovic, James Frontiers in pharmacology. 26617521 2015;
The first microbial environment of infants born by C-section: the operating room microbes. Shin, Hakdong; Pei, Zhiheng; Martinez 2nd, Keith A; Rivera-Vinas, Juana I; Mendez, Keimari; Cavallin, Humberto; Dominguez-Bello, Maria G Microbiome. 26620712 2015 Dec 01;
Wham: Identifying Structural Variants of Biological Consequence. Kronenberg, Zev N; Osborne, Edward J; Cone, Kelsey R; Kennedy, Brett J; Domyan, Eric T; Shapiro, Michael D; Elde, Nels C; Yandell, Mark PLoS computational biology. 26625158 2015 Dec;
Engineering Values Into Genetic Engineering: A Proposed Analytic Framework for Scientific Social Responsibility. Sankar, Pamela L; Cho, Mildred K The American journal of bioethics : AJOB. 26632356 2015;
Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens. Zhou, Yanjiao; Wylie, Kristine M; El Feghaly, Rana E; Mihindukulasuriya, Kathie A; Elward, Alexis; Haslam, David B; Storch, Gregory A; Weinstock, George M Journal of clinical microbiology. 26637379 2016 Feb;
The microbiome quality control project: baseline study design and future directions. Sinha, Rashmi; Abnet, Christian C; White, Owen; Knight, Rob; Huttenhower, Curtis Genome biology. 26653756 2015;
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Kuleshov, Volodymyr; Jiang, Chao; Zhou, Wenyu; Jahanbani, Fereshteh; Batzoglou, Serafim; Snyder, Michael Nature biotechnology 26655498 2016 Jan
Microbial community assembly and metabolic function during mammalian corpse decomposition. Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob Science (New York, N.Y.). 26657285 2016 Jan 8;
Histamine H2 Receptor-Mediated Suppression of Intestinal Inflammation by Probiotic Lactobacillus reuteri. Gao, Chunxu; Major, Angela; Rendon, David; Lugo, Monica; Jackson, Vanessa; Shi, Zhongcheng; Mori-Akiyama, Yuko; Versalovic, James mBio. 26670383 2015 Dec 15;
Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma. Sankaranarayanan, Krithivasan; Ozga, Andrew T; Warinner, Christina; Tito, Raul Y; Obregon-Tito, Alexandra J; Xu, Jiawu; Gaffney, Patrick M; Jervis, Lori L; Cox, Derrell; Stephens, Lancer; Foster, Morris; Tallbull, Gloria; Spicer, Paul; Lewis, Cecil M Current biology : CB. 26671671 2015 Dec 21;
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. Kaminski, James; Gibson, Molly K; Franzosa, Eric A; Segata, Nicola; Dantas, Gautam; Huttenhower, Curtis PLoS computational biology 26682918 2015 Dec
Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Araya, Carlos L; Cenik, Can; Reuter, Jason A; Kiss, Gert; Pande, Vijay S; Snyder, Michael P; Greenleaf, William J Nature genetics. 26691984 2016 Feb;
HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria. Yang, Liying; Poles, Michael A; Fisch, Gene S; Ma, Yingfei; Nossa, Carlos; Phelan, Joan A; Pei, Zhiheng AIDS (London, England). 26731752 2016 Jan 02;
Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria. Abdelmaksoud, Abdallah A; Koparde, Vishal N; Sheth, Nihar U; Serrano, Myrna G; Glascock, Abigail L; Fettweis, Jennifer M; Strauss Iii, Jerome F; Buck, Gregory A; Jefferson, Kimberly K Microbiology (Reading, England). 26747455 2016 Jan 8;
Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium. Volkmann, Elizabeth R; Chang, Yu-Ling; Barroso, Nashla; Furst, Daniel E; Clements, Philip J; Gorn, Alan H; Roth, Bennett E; Conklin, Jeffrey L; Getzug, Terri; Borneman, James; McGovern, Dermot P B; Tong, Maomeng; Jacobs, Jonathan P; Braun, Jonathan Arthritis & rheumatology (Hoboken, N.J.). 26749064 2016 06;
A quantitative understanding of lac repressor's binding specificity and flexibility. Zuo, Zheng; Chang, Yiming; Stormo, Gary D Quantitative biology (Beijing, China). 26752632 2015 Jun 01;
Erratum to: The first microbial environment of infants born by C-section: the operating room microbes. Shin, Hakdong; Pei, Zhiheng; Martinez 2nd, Keith A; Rivera-Vinas, Juana I; Mendez, Keimari; Cavallin, Humberto; Dominguez-Bello, Maria G Microbiome. 26796629 2016 Jan 21;
Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Yassour, Moran; Lim, Mi Young; Yun, Hyun Sun; Tickle, Timothy L; Sung, Joohon; Song, Yun-Mi; Lee, Kayoung; Franzosa, Eric A; Morgan, Xochitl C; Gevers, Dirk; Lander, Eric S; Xavier, Ramnik J; Birren, Bruce W; Ko, GwangPyo; Huttenhower, Curtis Genome medicine 26884067 2016 Feb 17
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. Weiss, Sophie; Van Treuren, Will; Lozupone, Catherine; Faust, Karoline; Friedman, Jonathan; Deng, Ye; Xia, Li Charlie; Xu, Zhenjiang Zech; Ursell, Luke; Alm, Eric J; Birmingham, Amanda; Cram, Jacob A; Fuhrman, Jed A; Raes, Jeroen; Sun, Fengzhu; Zhou, Jizhong; Knight, Rob The ISME journal. 26905627 2016 Feb 23;
Can Metabolic Profiles Be Used as a Phenotypic Readout of the Genome to Enhance Precision Medicine? Contrepois, Kévin; Liang, Liang; Snyder, Michael Clinical chemistry. 26960666 2016 May;
Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study. Warner, Barbara B; Deych, Elena; Zhou, Yanjiao; Hall-Moore, Carla; Weinstock, George M; Sodergren, Erica; Shaikh, Nurmohammad; Hoffmann, Julie A; Linneman, Laura A; Hamvas, Aaron; Khanna, Geetika; Rouggly-Nickless, Lucina C; Ndao, I Malick; Shands, Berkley A; Escobedo, Marilyn; Sullivan, Janice E; Radmacher, Paula G; Shannon, William D; Tarr, Phillip I Lancet (London, England). 26969089 2016 May 07;
Microbiome and potential targets for chemoprevention of esophageal adenocarcinoma. Neto, Antonio Galvao; Whitaker, April; Pei, Zhiheng Seminars in oncology. 26970127 2016 Feb;
Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants. Ward, Doyle V; Scholz, Matthias; Zolfo, Moreno; Taft, Diana H; Schibler, Kurt R; Tett, Adrian; Segata, Nicola; Morrow, Ardythe L Cell reports. 26997279 2016 Mar 29;
Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation. Chehoud, Christel; Dryga, Anatoly; Hwang, Young; Nagy-Szakal, Dorottya; Hollister, Emily B; Luna, Ruth Ann; Versalovic, James; Kellermayer, Richard; Bushman, Frederic D mBio. 27025251 2016 Mar 29;
Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. Schloss, Patrick D; Jenior, Matthew L; Koumpouras, Charles C; Westcott, Sarah L; Highlander, Sarah K PeerJ. 27069806 2016;
Papillary urothelial carcinoma with squamous differentiation in association with human papilloma virus: case report and literature review. Guma, Sergei; Maglantay, Remegio; Lau, Ryan; Wieczorek, Rosemary; Melamed, Jonathan; Deng, Fang-Ming; Zhou, Ming; Makarov, Danil; Lee, Peng; Pincus, Matthew R; Pei, Zhi-Heng American journal of clinical and experimental urology. 27069958 2016;
Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility. Ward, Marc A; Pierre, Joseph F; Leal, Raquel F; Huang, Yong; Shogan, Benjamin; Dalal, Sushila R; Weber, Christopher R; Leone, Vanessa A; Musch, Mark W; An, Gary C; Rao, Mrinalini C; Rubin, David T; Raffals, Laura E; Antonopoulos, Dionysios A; Sogin, Mitch L; Hyman, Neil H; Alverdy, John C; Chang, Eugene B American journal of physiology. Gastrointestinal and liver physiology. 27079612 2016 06 01;
Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome. Perez Perez, Guillermo I; Gao, Zhan; Jourdain, Roland; Ramirez, Julia; Gany, Francesca; Clavaud, Cecile; Demaude, Julien; Breton, Lionel; Blaser, Martin J PloS one. 27088867 2016;
The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages. Mariano, Rachelle; Wuchty, Stefan; Vizoso-Pinto, Maria G; Häuser, Roman; Uetz, Peter Scientific reports. 27103053 2016 Apr 22;
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Vatanen, Tommi; Kostic, Aleksandar D; d'Hennezel, Eva; Siljander, Heli; Franzosa, Eric A; Yassour, Moran; Kolde, Raivo; Vlamakis, Hera; Arthur, Timothy D; Hämäläinen, Anu-Maaria; Peet, Aleksandr; Tillmann, Vallo; Uibo, Raivo; Mokurov, Sergei; Dorshakova, Natalya; Ilonen, Jorma; Virtanen, Suvi M; Szabo, Susanne J; Porter, Jeffrey A; Lähdesmäki, Harri; Huttenhower, Curtis; Gevers, Dirk; Cullen, Thomas W; Knip, Mikael; DIABIMMUNE Study Group; Xavier, Ramnik J Cell. 27133167 2016 May 5;
Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples. Rhee, Minsoung; Light, Yooli K; Meagher, Robert J; Singh, Anup K PloS one. 27144304 2016;
Cathelicidin suppresses lipid accumulation and hepatic steatosis by inhibition of the CD36 receptor. Hoang-Yen Tran, D; Hoang-Ngoc Tran, D; Mattai, S A; Sallam, T; Ortiz, C; Lee, E C; Robbins, L; Ho, S; Lee, J E; Fisseha, E; Shieh, C; Sideri, A; Shih, D Q; Fleshner, P; McGovern, D P B; Vu, M; Hing, T C; Bakirtzi, K; Cheng, M; Su, B; Law, I; Karagiannides, I; Targan, S R; Gallo, R L; Li, Z; Koon, H W International journal of obesity (2005). 27163748 2016 Sep;
Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. Blaser, Martin J; Cardon, Zoe G; Cho, Mildred K; Dangl, Jeffrey L; Donohue, Timothy J; Green, Jessica L; Knight, Rob; Maxon, Mary E; Northen, Trent R; Pollard, Katherine S; Brodie, Eoin L mBio. 27178263 2016 05 13;
Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Chu, Hiutung; Khosravi, Arya; Kusumawardhani, Indah P; Kwon, Alice H K; Vasconcelos, Anilton C; Cunha, Larissa D; Mayer, Anne E; Shen, Yue; Wu, Wei-Li; Kambal, Amal; Targan, Stephan R; Xavier, Ramnik J; Ernst, Peter B; Green, Douglas R; McGovern, Dermot P B; Virgin, Herbert W; Mazmanian, Sarkis K Science (New York, N.Y.). 27230380 2016 May 27;
Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot, Casey M; Young, Vincent B; Jansson, Janet K; Fredricks, David N; Borenstein, Elhanan mSystems 27239563 2016
Challenges for case-control studies with microbiome data. Brooks, J Paul Annals of epidemiology. 27255739 2016 05;
Prophages mediate defense against phage infection through diverse mechanisms. Bondy-Denomy, Joseph; Qian, Jason; Westra, Edze R; Buckling, Angus; Guttman, David S; Davidson, Alan R; Maxwell, Karen L The ISME journal. 27258950 2016 12;
STOPPING DECEPTIVE HEALTH CLAIMS: THE NEED FOR A PRIVATE RIGHT OF ACTION UNDER FEDERAL LAW. Hoffmann, Diane; Schwartz, Jack American journal of law & medicine. 27263263 2016;
Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis. Zackular, Joseph P; Baxter, Nielson T; Chen, Grace Y; Schloss, Patrick D mSphere. 27303681 2016 Jan-Feb;
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Yassour, Moran; Vatanen, Tommi; Siljander, Heli; Hämäläinen, Anu-Maaria; Härkönen, Taina; Ryhänen, Samppa J; Franzosa, Eric A; Vlamakis, Hera; Huttenhower, Curtis; Gevers, Dirk; Lander, Eric S; Knip, Mikael; DIABIMMUNE Study Group; Xavier, Ramnik J Science translational medicine. 27306663 2016 Jun 15;
Necrotizing enterocolitis and preterm infant gut bacteria. Warner, Barbara B; Tarr, Phillip I Seminars in fetal & neonatal medicine. 27343151 2016 12;
Gut bacteria and late-onset neonatal bloodstream infections in preterm infants. Tarr, Phillip I; Warner, Barbara B Seminars in fetal & neonatal medicine. 27345372 2016 12;
Oral microbiome diversity among Cheyenne and Arapaho individuals from Oklahoma. Ozga, Andrew T; Sankaranarayanan, Krithivasan; Tito, Raúl Y; Obregon-Tito, Alexandra J; Foster, Morris W; Tallbull, Gloria; Spicer, Paul; Warinner, Christina G; Lewis Jr, Cecil M American journal of physical anthropology. 27357925 2016 Oct;
Mobile genes in the human microbiome are structured from global to individual scales. Brito, I L; Yilmaz, S; Huang, K; Xu, L; Jupiter, S D; Jenkins, A P; Naisilisili, W; Tamminen, M; Smillie, C S; Wortman, J R; Birren, B W; Xavier, R J; Blainey, P C; Singh, A K; Gevers, D; Alm, E J Nature. 27409808 2016 07 21;
More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria. Srinivasan, Sujatha; Munch, Matthew M; Sizova, Maria V; Fiedler, Tina L; Kohler, Christina M; Hoffman, Noah G; Liu, Congzhou; Agnew, Kathy J; Marrazzo, Jeanne M; Epstein, Slava S; Fredricks, David N The Journal of infectious diseases. 27449870 2016 Aug 15;
GABA-producing Bifidobacterium dentium modulates visceral sensitivity in the intestine. Pokusaeva, K; Johnson, C; Luk, B; Uribe, G; Fu, Y; Oezguen, N; Matsunami, R K; Lugo, M; Major, A; Mori-Akiyama, Y; Hollister, E B; Dann, S M; Shi, X Z; Engler, D A; Savidge, T; Versalovic, J Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society. 27458085 2017 Jan;
Antibiotic perturbation of the preterm infant gut microbiome and resistome. Gasparrini, Andrew J; Crofts, Terence S; Gibson, Molly K; Tarr, Phillip I; Warner, Barbara B; Dantas, Gautam Gut microbes. 27472377 2016 09 02;
Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. Segal, Leopoldo N; Clemente, Jose C; Wu, Benjamin G; Wikoff, William R; Gao, Zhan; Li, Yonghua; Ko, Jane P; Rom, William N; Blaser, Martin J; Weiden, Michael D Thorax. 27486204 2017 Jan;
A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn's Disease and Human Gut Microbiome Composition. Li, Dalin; Achkar, Jean-Paul; Haritunians, Talin; Jacobs, Jonathan P; Hui, Ken Y; D'Amato, Mauro; Brand, Stephan; Radford-Smith, Graham; Halfvarson, Jonas; Niess, Jan-Hendrik; Kugathasan, Subra; Büning, Carsten; Schumm, L Philip; Klei, Lambertus; Ananthakrishnan, Ashwin; Aumais, Guy; Baidoo, Leonard; Dubinsky, Marla; Fiocchi, Claudio; Glas, Jürgen; Milgrom, Raquel; Proctor, Deborah D; Regueiro, Miguel; Simms, Lisa A; Stempak, Joanne M; Targan, Stephan R; Törkvist, Leif; Sharma, Yashoda; Devlin, Bernie; Borneman, James; Hakonarson, Hakon; Xavier, Ramnik J; Daly, Mark; Brant, Steven R; Rioux, John D; Silverberg, Mark S; Cho, Judy H; Braun, Jonathan; McGovern, Dermot P B; Duerr, Richard H Gastroenterology. 27492617 2016 Oct;
A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. Rivas, Manuel A; Graham, Daniel; Sulem, Patrick; Stevens, Christine; Desch, A Nicole; Goyette, Philippe; Gudbjartsson, Daniel; Jonsdottir, Ingileif; Thorsteinsdottir, Unnur; Degenhardt, Frauke; Mucha, Sören; Kurki, Mitja I; Li, Dalin; D'Amato, Mauro; Annese, Vito; Vermeire, Severine; Weersma, Rinse K; Halfvarson, Jonas; Paavola-Sakki, Paulina; Lappalainen, Maarit; Lek, Monkol; Cummings, Beryl; Tukiainen, Taru; Haritunians, Talin; Halme, Leena; Koskinen, Lotta L E; Ananthakrishnan, Ashwin N; Luo, Yang; Heap, Graham A; Visschedijk, Marijn C; UK IBD Genetics Consortium; NIDDK IBD Genetics Consortium; MacArthur, Daniel G; Neale, Benjamin M; Ahmad, Tariq; Anderson, Carl A; Brant, Steven R; Duerr, Richard H; Silverberg, Mark S; Cho, Judy H; Palotie, Aarno; Saavalainen, Päivi; Kontula, Kimmo; Färkkilä, Martti; McGovern, Dermot P B; Franke, Andre; Stefansson, Kari; Rioux, John D; Xavier, Ramnik J; Daly, Mark J; Barrett, J; de Lane, K; Edwards, C; Hart, A; Hawkey, C; Jostins, L; Kennedy, N; Lamb, C; Lee, J; Lees, C; Mansfield, J; Mathew, C; Mowatt, C; Newman, B; Nimmo, E; Parkes, M; Pollard, M; Prescott, N; Randall, J; Rice, D; Satsangi, J; Simmons, A; Tremelling, M; Uhlig, H; Wilson, D; Abraham, C; Achkar, J P; Bitton, A; Boucher, G; Croitoru, K; Fleshner, P; Glas, J; Kugathasan, S; Limbergen, J V; Milgrom, R; Proctor, D; Regueiro, M; Schumm, P L; Sharma, Y; Stempak, J M; Targan, S R; Wang, M H Nature communications. 27503255 2016 Aug 09;
The early infant gut microbiome varies in association with a maternal high-fat diet. Chu, Derrick M; Antony, Kathleen M; Ma, Jun; Prince, Amanda L; Showalter, Lori; Moller, Michelle; Aagaard, Kjersti M Genome medicine. 27503374 2016 08 09;
Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis. Gonzalez, Mercedes E; Schaffer, Julie V; Orlow, Seth J; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Blaser, Martin J Journal of the American Academy of Dermatology. 27543211 2016 Sep;
Butyrate and bioactive proteolytic form of Wnt-5a regulate colonic epithelial proliferation and spatial development. Uchiyama, Kazuhiko; Sakiyama, Toshio; Hasebe, Takumu; Musch, Mark W; Miyoshi, Hiroyuki; Nakagawa, Yasushi; He, Tong-Chuan; Lichtenstein, Lev; Naito, Yuji; Itoh, Yoshito; Yoshikawa, Toshikazu; Jabri, Bana; Stappenbeck, Thaddeus; Chang, Eugene B Scientific reports. 27561676 2016 Aug 26;
Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Gibson, Molly K; Wang, Bin; Ahmadi, Sara; Burnham, Carey-Ann D; Tarr, Phillip I; Warner, Barbara B; Dantas, Gautam Nature microbiology. 27572443 2016 Mar 07;
Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Segal, Leopoldo N; Clemente, Jose C; Tsay, Jun-Chieh J; Koralov, Sergei B; Keller, Brian C; Wu, Benjamin G; Li, Yonghua; Shen, Nan; Ghedin, Elodie; Morris, Alison; Diaz, Phillip; Huang, Laurence; Wikoff, William R; Ubeda, Carles; Artacho, Alejandro; Rom, William N; Sterman, Daniel H; Collman, Ronald G; Blaser, Martin J; Weiden, Michael D Nature microbiology. 27572644 2016;
Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Donati, Claudio; Zolfo, Moreno; Albanese, Davide; Tin Truong, Duy; Asnicar, Francesco; Iebba, Valerio; Cavalieri, Duccio; Jousson, Olivier; De Filippo, Carlotta; Huttenhower, Curtis; Segata, Nicola Nature microbiology. 27572971 2016 05 27;
Genetic Predictors of Benign Course of Ulcerative Colitis-A North American Inflammatory Bowel Disease Genetics Consortium Study. Kopylov, Uri; Boucher, Gabrielle; Waterman, Matti; Rivers, Claudia R; Patel, Mohini; Cho, Judy H; Colombel, Jean F; Duerr, Richard H; Binion, David; McGovern, Dermot P B; Schumm, Phillip P; Brant, Steven R; Silverberg, Mark S; Rioux, John D; Bitton, Alain Inflammatory bowel diseases. 27575496 2016 Oct;
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. Davison, Michelle; Treangen, Todd J; Koren, Sergey; Pop, Mihai; Bhaya, Devaki PloS one. 27611571 2016;
Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis. Robinson, Lloyd S; Perry, Justin; Lek, Sai; Wollam, Aye; Sodergren, Erica; Weinstock, George; Lewis, Warren G; Lewis, Amanda L Genome announcements. 27688326 2016 Sep 29;
Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women. Weimer, Cory M; Deitzler, Grace E; Robinson, Lloyd S; Park, SoEun; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G; Lewis, Amanda L Genome announcements. 27688327 2016 Sep 29;
Genome Sequences of 11 Human Vaginal Actinobacteria Strains. Lewis, Amanda L; Deitzler, Grace E; Ruiz, Maria J; Weimer, Cory; Park, SoEun; Robinson, Lloyd S; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G Genome announcements. 27688328 2016 Sep 29;
Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina. Deitzler, Grace E; Ruiz, Maria J; Weimer, Cory; Park, SoEun; Robinson, Lloyd; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Amanda L; Lewis, Warren G Genome announcements. 27688329 2016 Sep 29;
Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates. Deitzler, Grace E; Ruiz, Maria J; Lu, Wendy; Weimer, Cory; Park, SoEun; Robinson, Lloyd S; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G; Lewis, Amanda L Genome announcements. 27688330 2016 Sep 29;
A New Catalog of Microbiological Tools for Women's Infectious Disease Research. Lewis, Amanda L; Lewis, Warren G Genome announcements. 27688331 2016 Sep 29;
Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Brant, Steven R; Okou, David T; Simpson, Claire L; Cutler, David J; Haritunians, Talin; Bradfield, Jonathan P; Chopra, Pankaj; Prince, Jarod; Begum, Ferdouse; Kumar, Archana; Huang, Chengrui; Venkateswaran, Suresh; Datta, Lisa W; Wei, Zhi; Thomas, Kelly; Herrinton, Lisa J; Klapproth, Jan-Micheal A; Quiros, Antonio J; Seminerio, Jenifer; Liu, Zhenqiu; Alexander, Jonathan S; Baldassano, Robert N; Dudley-Brown, Sharon; Cross, Raymond K; Dassopoulos, Themistocles; Denson, Lee A; Dhere, Tanvi A; Dryden, Gerald W; Hanson, John S; Hou, Jason K; Hussain, Sunny Z; Hyams, Jeffrey S; Isaacs, Kim L; Kader, Howard; Kappelman, Michael D; Katz, Jeffry; Kellermayer, Richard; Kirschner, Barbara S; Kuemmerle, John F; Kwon, John H; Lazarev, Mark; Li, Ellen; Mack, David; Mannon, Peter; Moulton, Dedrick E; Newberry, Rodney D; Osuntokun, Bankole O; Patel, Ashish S; Saeed, Shehzad A; Targan, Stephan R; Valentine, John F; Wang, Ming-Hsi; Zonca, Martin; Rioux, John D; Duerr, Richard H; Silverberg, Mark S; Cho, Judy H; Hakonarson, Hakon; Zwick, Michael E; McGovern, Dermot P B; Kugathasan, Subra Gastroenterology. 27693347 2017 Jan;
Nat1 Deficiency Is Associated with Mitochondrial Dysfunction and Exercise Intolerance in Mice. Chennamsetty, Indumathi; Coronado, Michael; Contrepois, Kévin; Keller, Mark P; Carcamo-Orive, Ivan; Sandin, John; Fajardo, Giovanni; Whittle, Andrew J; Fathzadeh, Mohsen; Snyder, Michael; Reaven, Gerald; Attie, Alan D; Bernstein, Daniel; Quertermous, Thomas; Knowles, Joshua W Cell reports. 27705799 2016 Oct 4;
Ethical issues in microbiome research and medicine. Rhodes, Rosamond BMC medicine. 27729053 2016 Oct 12;
The TNF family member TL1A induces IL-22 secretion in committed human Th17 cells via IL-9 induction. Thomas, Lisa S; Targan, Stephan R; Tsuda, Masato; Yu, Qi T; Salumbides, Brenda C; Haritunians, Talin; Mengesha, Emebet; McGovern, Dermot P B; Michelsen, Kathrin S Journal of leukocyte biology. 27733581 2017 03;
HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences. Danaher, Robert J; Fouts, Derrick E; Chan, Agnes P; Choi, Yongwook; DePew, Jessica; McCorrison, Jamison M; Nelson, Karen E; Wang, Chunmei; Miller, Craig S Journal of neurovirology. 27739035 2017 Apr;
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Schirmer, Melanie; Smeekens, Sanne P; Vlamakis, Hera; Jaeger, Martin; Oosting, Marije; Franzosa, Eric A; Jansen, Trees; Jacobs, Liesbeth; Bonder, Marc Jan; Kurilshikov, Alexander; Fu, Jingyuan; Joosten, Leo A B; Zhernakova, Alexandra; Huttenhower, Curtis; Wijmenga, Cisca; Netea, Mihai G; Xavier, Ramnik J Cell. 27814509 2016 Nov 03;
HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS. Yu, Kun-Hsing; Hart, Steven N; Goldfeder, Rachel; Zhang, Qiangfeng Cliff; Parker, Stephen C J; Snyder, Michael Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 27897013 2016;
MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. Parikh, Hardik I; Koparde, Vishal N; Bradley, Steven P; Buck, Gregory A; Sheth, Nihar U BMC bioinformatics. 27905885 2016 Dec 01;
Effects of combined oral contraceptives, depot medroxyprogesterone acetate and the levonorgestrel-releasing intrauterine system on the vaginal microbiome. Brooks, J Paul; Edwards, David J; Blithe, Diana L; Fettweis, Jennifer M; Serrano, Myrna G; Sheth, Nihar U; Strauss 3rd, Jerome F; Buck, Gregory A; Jefferson, Kimberly K Contraception. 27913230 2016 Nov 29;
The balance of metagenomic elements shapes the skin microbiome in acne and health. Barnard, Emma; Shi, Baochen; Kang, Dezhi; Craft, Noah; Li, Huiying Scientific reports. 28000755 2016 12 21;
Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information. Li, Xiao; Dunn, Jessilyn; Salins, Denis; Zhou, Gao; Zhou, Wenyu; Schüssler-Fiorenza Rose, Sophia Miryam; Perelman, Dalia; Colbert, Elizabeth; Runge, Ryan; Rego, Shannon; Sonecha, Ria; Datta, Somalee; McLaughlin, Tracey; Snyder, Michael P PLoS biology. 28081144 2017 Jan;
Genome Sequence of Christensenella minuta DSM 22607T. Rosa, Bruce A; Hallsworth-Pepin, Kymberlie; Martin, John; Wollam, Aye; Mitreva, Makedonka Genome announcements. 28082495 2017 Jan 12;
Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Chu, Derrick M; Ma, Jun; Prince, Amanda L; Antony, Kathleen M; Seferovic, Maxim D; Aagaard, Kjersti M Nature medicine. 28112736 2017 Mar;
Myeloid ATG16L1 Facilitates Host-Bacteria Interactions in Maintaining Intestinal Homeostasis. Zhang, Hong; Zheng, Libo; McGovern, Dermot P B; Hamill, Ariel M; Ichikawa, Ryan; Kanazawa, Yoshitake; Luu, Justin; Kumagai, Kotaro; Cilluffo, Marianne; Fukata, Masayuki; Targan, Stephan R; Underhill, David M; Zhang, Xiaolan; Shih, David Q Journal of immunology (Baltimore, Md. : 1950). 28130498 2017 Mar 01;
Microbial strain-level population structure and genetic diversity from metagenomes. Truong, Duy Tin; Tett, Adrian; Pasolli, Edoardo; Huttenhower, Curtis; Segata, Nicola Genome research. 28167665 2017 Apr;
A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Levin, B J; Huang, Y Y; Peck, S C; Wei, Y; Martínez-Del Campo, A; Marks, J A; Franzosa, E A; Huttenhower, C; Balskus, E P Science (New York, N.Y.). 28183913 2017 02 10;
Dynamics of the human gut microbiome in inflammatory bowel disease. Halfvarson, Jonas; Brislawn, Colin J; Lamendella, Regina; Vázquez-Baeza, Yoshiki; Walters, William A; Bramer, Lisa M; D'Amato, Mauro; Bonfiglio, Ferdinando; McDonald, Daniel; Gonzalez, Antonio; McClure, Erin E; Dunklebarger, Mitchell F; Knight, Rob; Jansson, Janet K Nature microbiology. 28191884 2017 Feb 13;
Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Huang, Yong; Dalal, Sushila; Antonopoulos, Dionysios; Hubert, Nathaniel; Raffals, Laura H; Dolan, Kyle; Weber, Christopher; Messer, Jeannette S; Jabri, Bana; Bendelac, Albert; Eren, A Murat; Rubin, David T; Sogin, Mitch; Chang, Eugene B Inflammatory bowel diseases. 28221248 2017 03;
Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Huang, Yong; Dalal, Sushila; Antonopoulos, Dionysios; Hubert, Nathaniel; Raffals, Laura H; Dolan, Kyle; Weber, Christopher; Messer, Jeannette S; Jabri, Bana; Bendelac, Albert; Eren, A Murat; Rubin, David T; Sogin, Mitch; Chang, Eugene B Inflammatory bowel diseases. 28248733 2017 Feb 13;
Normalization and microbial differential abundance strategies depend upon data characteristics. Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal; Amir, Amnon; Bittinger, Kyle; Gonzalez, Antonio; Lozupone, Catherine; Zaneveld, Jesse R; Vázquez-Baeza, Yoshiki; Birmingham, Amanda; Hyde, Embriette R; Knight, Rob Microbiome. 28253908 2017 03 03;
Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Pammi, Mohan; Cope, Julia; Tarr, Phillip I; Warner, Barbara B; Morrow, Ardythe L; Mai, Volker; Gregory, Katherine E; Kroll, J Simon; McMurtry, Valerie; Ferris, Michael J; Engstrand, Lars; Lilja, Helene Engstrand; Hollister, Emily B; Versalovic, James; Neu, Josef Microbiome. 28274256 2017 03 09;
Bead mediated separation of microparticles in droplets. Wang, Sida; Sung, Ki-Joo; Lin, Xiaoxia Nina; Burns, Mark A PloS one 28282412 2017
Antibacterial and bioactive coatings on titanium implant surfaces. Kulkarni Aranya, Anupama; Pushalkar, Smruti; Zhao, Minglei; LeGeros, Racquel Z; Zhang, Yu; Saxena, Deepak Journal of biomedical materials research. Part A. 28380669 2017 Aug;
The protection role of Atg16l1 in CD11c+dendritic cells in murine colitis. Zhang, Hong; Zheng, Libo; Chen, Jeremy; Fukata, Masayuki; Ichikawa, Ryan; Shih, David Q; Zhang, Xiaolan Immunobiology. 28390705 2017 Jul;
Independence of gut bacterial content and neonatal necrotizing enterocolitis severity. Barron, Lauren K; Warner, Barbara B; Tarr, Phillip I; Shannon, William D; Deych, Elena; Warner, Brad W Journal of pediatric surgery. 28410788 2017 Jun;
Re: Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Misra, Ravi; Arebi, Naila Gastroenterology. 28478146 2017 06;
Early pregnancy vaginal microbiome trends and preterm birth. Stout, Molly J; Zhou, Yanjiao; Wylie, Kristine M; Tarr, Phillip I; Macones, George A; Tuuli, Methodius G American journal of obstetrics and gynecology. 28549981 2017 09;
Isolated Congenital Anosmia and CNGA2 Mutation. Sailani, M Reza; Jingga, Inlora; MirMazlomi, Seyed Hashem; Bitarafan, Fatemeh; Bernstein, Jonathan A; Snyder, Michael P; Garshasbi, Masoud Scientific reports. 28572688 2017 06 01;
Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance. Charepalli, Venkata; Reddivari, Lavanya; Radhakrishnan, Sridhar; Eriksson, Elisabeth; Xiao, Xia; Kim, Sung Woo; Shen, Frank; Vijay-Kumar, Matam; Li, Qunhua; Bhat, Vadiraja B; Knight, Rob; Vanamala, Jairam K P Cancer prevention research (Philadelphia, Pa.). 28576788 2017 Aug;
Vaginal Candida spp. genomes from women with vulvovaginal candidiasis. Bradford, L Latéy; Chibucos, Marcus C; Ma, Bing; Bruno, Vincent; Ravel, Jacques Pathogens and disease. 28582496 2017 08 31;
Dissecting the human microbiome with single-cell genomics. Tolonen, Andrew C; Xavier, Ramnik J Genome medicine. 28615076 2017 Jun 14;
A rare case of anal carcinosarcoma with human papilloma virus infection in both biphasic tumor elements: An immunohistochemical, molecular and ultrastructural study. Hickman, Richard A; Bradshaw, Azore-Dee; Cassai, Nicholas; Neto, Antonio Galvao; Zhou, David; Fu, Tinghao; Lee, Peng; Pei, Zhiheng; Wieczorek, Rosemary Papillomavirus research (Amsterdam, Netherlands). 28616595 2016 Dec;
Fine-mapping inflammatory bowel disease loci to single-variant resolution. Huang, Hailiang; Fang, Ming; Jostins, Luke; Umi?evi? Mirkov, Ma?a; Boucher, Gabrielle; Anderson, Carl A; Andersen, Vibeke; Cleynen, Isabelle; Cortes, Adrian; Crins, François; D'Amato, Mauro; Deffontaine, Valérie; Dmitrieva, Julia; Docampo, Elisa; Elansary, Mahmoud; Farh, Kyle Kai-How; Franke, Andre; Gori, Ann-Stephan; Goyette, Philippe; Halfvarson, Jonas; Haritunians, Talin; Knight, Jo; Lawrance, Ian C; Lees, Charlie W; Louis, Edouard; Mariman, Rob; Meuwissen, Theo; Mni, Myriam; Momozawa, Yukihide; Parkes, Miles; Spain, Sarah L; Théâtre, Emilie; Trynka, Gosia; Satsangi, Jack; van Sommeren, Suzanne; Vermeire, Severine; Xavier, Ramnik J; International Inflammatory Bowel Disease Genetics Consortium; Weersma, Rinse K; Duerr, Richard H; Mathew, Christopher G; Rioux, John D; McGovern, Dermot P B; Cho, Judy H; Georges, Michel; Daly, Mark J; Barrett, Jeffrey C Nature. 28658209 2017 Jul 13;
The Microbiome and Biomarkers for Necrotizing Enterocolitis: Are We Any Closer to Prediction? Rusconi, Brigida; Good, Misty; Warner, Barbara B The Journal of pediatrics. 28669607 2017 Oct;
Diacylglycerol kinase synthesized by commensal Lactobacillus reuteri diminishes protein kinase C phosphorylation and histamine-mediated signaling in the mammalian intestinal epithelium. Ganesh, B P; Hall, A; Ayyaswamy, S; Nelson, J W; Fultz, R; Major, A; Haag, A; Esparza, M; Lugo, M; Venable, S; Whary, M; Fox, J G; Versalovic, J Mucosal immunology. 28745328 2018 03;
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Bowers, Robert M; Kyrpides, Nikos C; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, T B K; Schulz, Frederik; Jarett, Jessica; Rivers, Adam R; Eloe-Fadrosh, Emiley A; Tringe, Susannah G; Ivanova, Natalia N; Copeland, Alex; Clum, Alicia; Becraft, Eric D; Malmstrom, Rex R; Birren, Bruce; Podar, Mircea; Bork, Peer; Weinstock, George M; Garrity, George M; Dodsworth, Jeremy A; Yooseph, Shibu; Sutton, Granger; Glöckner, Frank O; Gilbert, Jack A; Nelson, William C; Hallam, Steven J; Jungbluth, Sean P; Ettema, Thijs J G; Tighe, Scott; Konstantinidis, Konstantinos T; Liu, Wen-Tso; Baker, Brett J; Rattei, Thomas; Eisen, Jonathan A; Hedlund, Brian; McMahon, Katherine D; Fierer, Noah; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Tyson, Gene W; Rinke, Christian; Genome Standards Consortium; Lapidus, Alla; Meyer, Folker; Yilmaz, Pelin; Parks, Donovan H; Eren, A M; Schriml, Lynn; Banfield, Jillian F; Hugenholtz, Philip; Woyke, Tanja Nature biotechnology 28787424 2017 Aug 08
Community characteristics of the gut microbiomes of competitive cyclists. Petersen, Lauren M; Bautista, Eddy J; Nguyen, Hoan; Hanson, Blake M; Chen, Lei; Lek, Sai H; Sodergren, Erica; Weinstock, George M Microbiome. 28797298 2017 Aug 10;
Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. Yasuda, Koji; Hsu, Tiffany; Gallini, Carey A; Mclver, Lauren J; Schwager, Emma; Shi, Andy; DuLong, Casey R; Schwager, Randall N; Abu-Ali, Galeb S; Franzosa, Eric A; Garrett, Wendy S; Huttenhower, Curtis; Morgan, Xochitl C mSystems 28808691 2017
Human genetic variation and the gut microbiome in disease. Hall, Andrew Brantley; Tolonen, Andrew C; Xavier, Ramnik J Nature reviews. Genetics. 28824167 2017 11;
Association between statin use, the vaginal microbiome, and Gardnerella vaginalis vaginolysin-mediated cytotoxicity. Abdelmaksoud, Abdallah A; Girerd, Philippe H; Garcia, Erin M; Brooks, J Paul; Leftwich, Lauren M; Sheth, Nihar U; Bradley, Steven P; Serrano, Myrna G; Fettweis, Jennifer M; Huang, Bernice; Strauss 3rd, Jerome F; Buck, Gregory A; Jefferson, Kimberly K PloS one. 28846702 2017;
Strains, functions and dynamics in the expanded Human Microbiome Project. Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali; Crabtree, Jonathan; Orvis, Joshua; Hall, A Brantley; Brady, Arthur; Creasy, Heather H; McCracken, Carrie; Giglio, Michelle G; McDonald, Daniel; Franzosa, Eric A; Knight, Rob; White, Owen; Huttenhower, Curtis Nature. 28953883 2017 10 05;
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Sinha, Rashmi; Abu-Ali, Galeb; Vogtmann, Emily; Fodor, Anthony A; Ren, Boyu; Amir, Amnon; Schwager, Emma; Crabtree, Jonathan; Ma, Siyuan; Microbiome Quality Control Project Consortium; Abnet, Christian C; Knight, Rob; White, Owen; Huttenhower, Curtis Nature biotechnology. 28967885 2017 Nov;
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Olson, Nathan D; Treangen, Todd J; Hill, Christopher M; Cepeda-Espinoza, Victoria; Ghurye, Jay; Koren, Sergey; Pop, Mihai Briefings in bioinformatics. 28968737 2019 Jul 19;
Cultivation of Peptidiphaga gingivicola from subgingival plaque: The first representative of a novel genus of Actinomycetaceae. Beall, C J; Mokrzan, E M; Griffen, A L; Leys, E J Molecular oral microbiology 29105370 2018 02
Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation. Harmon, Brooke; Chylek, Lily A; Liu, Yanli; Mitra, Eshan D; Mahajan, Avanika; Saada, Edwin A; Schudel, Benjamin R; Holowka, David A; Baird, Barbara A; Wilson, Bridget S; Hlavacek, William S; Singh, Anup K Scientific reports. 29138425 2017 Nov 14;
A Bayesian method for detecting pairwise associations in compositional data. Schwager, Emma; Mallick, Himel; Ventz, Steffen; Huttenhower, Curtis PLoS computational biology. 29140991 2017 Nov;
A role for bacterial urease in gut dysbiosis and Crohn's disease. Ni, Josephine; Shen, Ting-Chin David; Chen, Eric Z; Bittinger, Kyle; Bailey, Aubrey; Roggiani, Manuela; Sirota-Madi, Alexandra; Friedman, Elliot S; Chau, Lillian; Lin, Andrew; Nissim, Ilana; Scott, Justin; Lauder, Abigail; Hoffmann, Christopher; Rivas, Gloriany; Albenberg, Lindsey; Baldassano, Robert N; Braun, Jonathan; Xavier, Ramnik J; Clish, Clary B; Yudkoff, Marc; Li, Hongzhe; Goulian, Mark; Bushman, Frederic D; Lewis, James D; Wu, Gary D Science translational medicine. 29141885 2017 Nov 15;
CSA13 inhibits colitis-associated intestinal fibrosis via a formyl peptide receptor like-1 mediated HMG-CoA reductase pathway. Xu, Chunlan; Ghali, Sally; Wang, Jiani; Shih, David Q; Ortiz, Christina; Mussatto, Caroline C; Lee, Elaine C; Tran, Diana H; Jacobs, Jonathan P; Lagishetty, Venu; Fleshner, Phillip; Robbins, Lori; Vu, Michelle; Hing, Tressia C; McGovern, Dermot P B; Koon, Hon Wai Scientific reports. 29180648 2017 Nov 27;
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Hall, Andrew Brantley; Yassour, Moran; Sauk, Jenny; Garner, Ashley; Jiang, Xiaofang; Arthur, Timothy; Lagoudas, Georgia K; Vatanen, Tommi; Fornelos, Nadine; Wilson, Robin; Bertha, Madeline; Cohen, Melissa; Garber, John; Khalili, Hamed; Gevers, Dirk; Ananthakrishnan, Ashwin N; Kugathasan, Subra; Lander, Eric S; Blainey, Paul; Vlamakis, Hera; Xavier, Ramnik J; Huttenhower, Curtis Genome medicine. 29183332 2017 Nov 28;
Experimental design and quantitative analysis of microbial community multiomics. Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, Curtis Genome biology. 29187204 2017 Nov 30;
bioBakery: a meta'omic analysis environment. McIver, Lauren J; Abu-Ali, Galeb; Franzosa, Eric A; Schwager, Randall; Morgan, Xochitl C; Waldron, Levi; Segata, Nicola; Huttenhower, Curtis Bioinformatics (Oxford, England). 29194469 2018 Apr 01;
Optimizing Selection of Biologics in Inflammatory Bowel Disease: Development of an Online Patient Decision Aid Using Conjoint Analysis. Almario, Christopher V; Keller, Michelle S; Chen, Michelle; Lasch, Karen; Ursos, Lyann; Shklovskaya, Julia; Melmed, Gil Y; Spiegel, Brennan M R The American journal of gastroenterology. 29206816 2018 01;
Enterotypes in the landscape of gut microbial community composition. Costea, Paul I; Hildebrand, Falk; Arumugam, Manimozhiyan; Bäckhed, Fredrik; Blaser, Martin J; Bushman, Frederic D; de Vos, Willem M; Ehrlich, S Dusko; Fraser, Claire M; Hattori, Masahira; Huttenhower, Curtis; Jeffery, Ian B; Knights, Dan; Lewis, James D; Ley, Ruth E; Ochman, Howard; O'Toole, Paul W; Quince, Christopher; Relman, David A; Shanahan, Fergus; Sunagawa, Shinichi; Wang, Jun; Weinstock, George M; Wu, Gary D; Zeller, Georg; Zhao, Liping; Raes, Jeroen; Knight, Rob; Bork, Peer Nature microbiology. 29255284 2018 Jan;
Quinones are growth factors for the human gut microbiota. Fenn, Kathrin; Strandwitz, Philip; Stewart, Eric J; Dimise, Eric; Rubin, Sarah; Gurubacharya, Shreya; Clardy, Jon; Lewis, Kim Microbiome 29262868 2017 Dec 20
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Schirmer, Melanie; Franzosa, Eric A; Lloyd-Price, Jason; McIver, Lauren J; Schwager, Randall; Poon, Tiffany W; Ananthakrishnan, Ashwin N; Andrews, Elizabeth; Barron, Gildardo; Lake, Kathleen; Prasad, Mahadev; Sauk, Jenny; Stevens, Betsy; Wilson, Robin G; Braun, Jonathan; Denson, Lee A; Kugathasan, Subra; McGovern, Dermot P B; Vlamakis, Hera; Xavier, Ramnik J; Huttenhower, Curtis Nature microbiology. 29311644 2018 03;
Stability of the human faecal microbiome in a cohort of adult men. Mehta, Raaj S; Abu-Ali, Galeb S; Drew, David A; Lloyd-Price, Jason; Subramanian, Ayshwarya; Lochhead, Paul; Joshi, Amit D; Ivey, Kerry L; Khalili, Hamed; Brown, Gordon T; DuLong, Casey; Song, Mingyang; Nguyen, Long H; Mallick, Himel; Rimm, Eric B; Izard, Jacques; Huttenhower, Curtis; Chan, Andrew T Nature microbiology. 29335554 2018 03;
Metatranscriptome of human faecal microbial communities in a cohort of adult men. Abu-Ali, Galeb S; Mehta, Raaj S; Lloyd-Price, Jason; Mallick, Himel; Branck, Tobyn; Ivey, Kerry L; Drew, David A; DuLong, Casey; Rimm, Eric; Izard, Jacques; Chan, Andrew T; Huttenhower, Curtis Nature microbiology. 29335555 2018 03;
Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. Piening, Brian D; Zhou, Wenyu; Contrepois, Kévin; Röst, Hannes; Gu Urban, Gucci Jijuan; Mishra, Tejaswini; Hanson, Blake M; Bautista, Eddy J; Leopold, Shana; Yeh, Christine Y; Spakowicz, Daniel; Banerjee, Imon; Chen, Cynthia; Kukurba, Kimberly; Perelman, Dalia; Craig, Colleen; Colbert, Elizabeth; Salins, Denis; Rego, Shannon; Lee, Sunjae; Zhang, Cheng; Wheeler, Jessica; Sailani, M Reza; Liang, Liang; Abbott, Charles; Gerstein, Mark; Mardinoglu, Adil; Smith, Ulf; Rubin, Daniel L; Pitteri, Sharon; Sodergren, Erica; McLaughlin, Tracey L; Weinstock, George M; Snyder, Michael P Cell systems. 29361466 2018 Feb 28;
Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis. Noyes, Noelle; Cho, Kyu-Chul; Ravel, Jacques; Forney, Larry J; Abdo, Zaid PloS one. 29364944 2018;
One-Way Particle Transport Using Oscillatory Flow in Asymmetric Traps. Lee, Jaesung; Burns, Mark A Small (Weinheim an der Bergstrasse, Germany). 29377529 2018 03;
Host genetic variation and its microbiome interactions within the Human Microbiome Project. Kolde, Raivo; Franzosa, Eric A; Rahnavard, Gholamali; Hall, Andrew Brantley; Vlamakis, Hera; Stevens, Christine; Daly, Mark J; Xavier, Ramnik J; Huttenhower, Curtis Genome medicine. 29378630 2018 Jan 29;
Carriage of Cronobacter sakazakii in the Very Preterm Infant Gut. Chandrasekaran, Sukantha; Burnham, Carey-Ann D; Warner, Barbara B; Tarr, Phillip I; Wylie, Todd N Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 29394356 2018 07 02;
Leveraging a relationship-based sexual health framework for sexual risk prevention in adolescent men in the United States. Hensel, Devon J; Bales, Casey L; Taylor, Julia F; Fortenberry, J Dennis Sexual health 29506642 2018 06
In situ cultivation of previously uncultivable microorganisms using the ichip. Berdy, Brittany; Spoering, Amy L; Ling, Losee L; Epstein, Slava S Nature protocols 29532802 2017 10
Personal Omics for Precision Health. Kellogg, Ryan A; Dunn, Jessilyn; Snyder, Michael P Circulation research. 29700064 2018 04 27;
Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications. Hall, Anne; Versalovic, James Journal of pediatric gastroenterology and nutrition. 29762384 2018 06;
Prevalence and Associations of Avascular Necrosis of the Hip in a Large Well-characterized Cohort of Patients With Inflammatory Bowel Disease. Rolston, Vineet S; Patel, Anish V; Learch, Thomas J; Li, Dalin; Karayev, Dmitry; Williams, Chadwick; Siddanthi, Madhavi L; Targan, Stephan R; Weisman, Michael H; McGovern, Dermot P B Journal of clinical rheumatology : practical reports on rheumatic & musculoskeletal diseases. 29794876 2019 Jan;
The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth. Chernikova, Diana A; Madan, Juliette C; Housman, Molly L; Zain-Ul-Abideen, Muhammad; Lundgren, Sara N; Morrison, Hilary G; Sogin, Mitchell L; Williams, Scott M; Moore, Jason H; Karagas, Margaret R; Hoen, Anne G Pediatric research. 29795209 2018 07;
Neurotransmitter modulation by the gut microbiota. Strandwitz, Philip Brain research. 29903615 2018 08 15;
PERFect: PERmutation Filtering test for microbiome data. Smirnova, Ekaterina; Huzurbazar, Snehalata; Jafari, Farhad Biostatistics (Oxford, England). 29917060 2019 10 01;
Are microbiome studies ready for hypothesis-driven research? Tripathi, Anupriya; Marotz, Clarisse; Gonzalez, Antonio; Vázquez-Baeza, Yoshiki; Song, Se Jin; Bouslimani, Amina; McDonald, Daniel; Zhu, Qiyun; Sanders, Jon G; Smarr, Larry; Dorrestein, Pieter C; Knight, Rob Current opinion in microbiology. 30059804 2018 08;
Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions. Liu, Chaoyue; Wright, Benjamin; Allen-Vercoe, Emma; Gu, Hong; Beiko, Robert Genome biology and evolution. 30137329 2018 09 01;
Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring. Jiang, Chao; Wang, Xin; Li, Xiyan; Inlora, Jingga; Wang, Ting; Liu, Qing; Snyder, Michael Cell. 30241608 2018 09 20;
Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota. Vital, Marius; Howe, Adina; Bergeron, Nathalie; Krauss, Ronald M; Jansson, Janet K; Tiedje, James M Applied and environmental microbiology. 30266729 2018 12 01;
Qiita: rapid, web-enabled microbiome meta-analysis. Gonzalez, Antonio; Navas-Molina, Jose A; Kosciolek, Tomasz; McDonald, Daniel; Vázquez-Baeza, Yoshiki; Ackermann, Gail; DeReus, Jeff; Janssen, Stefan; Swafford, Austin D; Orchanian, Stephanie B; Sanders, Jon G; Shorenstein, Joshua; Holste, Hannes; Petrus, Semar; Robbins-Pianka, Adam; Brislawn, Colin J; Wang, Mingxun; Rideout, Jai Ram; Bolyen, Evan; Dillon, Matthew; Caporaso, J Gregory; Dorrestein, Pieter C; Knight, Rob Nature methods. 30275573 2018 10;
Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. Schirmer, Melanie; Denson, Lee; Vlamakis, Hera; Franzosa, Eric A; Thomas, Sonia; Gotman, Nathan M; Rufo, Paul; Baker, Susan S; Sauer, Cary; Markowitz, James; Pfefferkorn, Marian; Oliva-Hemker, Maria; Rosh, Joel; Otley, Anthony; Boyle, Brendan; Mack, David; Baldassano, Robert; Keljo, David; LeLeiko, Neal; Heyman, Melvin; Griffiths, Anne; Patel, Ashish S; Noe, Joshua; Kugathasan, Subra; Walters, Thomas; Huttenhower, Curtis; Hyams, Jeffrey; Xavier, Ramnik J Cell host & microbe. 30308161 2018 10 10;
Association of plasma nitrite levels with obesity and metabolic syndrome in the Old Order Amish. Akram, F; Fuchs, D; Daue, M; Nijjar, G; Ryan, A; Benros, M E; Okusaga, O; Baca-Garcia, E; Brenner, L A; Lowry, C A; Ryan, K A; Pavlovich, M; Mitchell, B D; Snitker, S; Postolache, T T Obesity science & practice 30338117 2018 Oct
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Vatanen, Tommi; Franzosa, Eric A; Schwager, Randall; Tripathi, Surya; Arthur, Timothy D; Vehik, Kendra; Lernmark, Åke; Hagopian, William A; Rewers, Marian J; She, Jin-Xiong; Toppari, Jorma; Ziegler, Anette-G; Akolkar, Beena; Krischer, Jeffrey P; Stewart, Christopher J; Ajami, Nadim J; Petrosino, Joseph F; Gevers, Dirk; Lähdesmäki, Harri; Vlamakis, Hera; Huttenhower, Curtis; Xavier, Ramnik J Nature. 30356183 2018 10;
Species-level functional profiling of metagenomes and metatranscriptomes. Franzosa, Eric A; McIver, Lauren J; Rahnavard, Gholamali; Thompson, Luke R; Schirmer, Melanie; Weingart, George; Lipson, Karen Schwarzberg; Knight, Rob; Caporaso, J Gregory; Segata, Nicola; Huttenhower, Curtis Nature methods. 30377376 2018 11;
GABA-modulating bacteria of the human gut microbiota. Strandwitz, Philip; Kim, Ki Hyun; Terekhova, Darya; Liu, Joanne K; Sharma, Anukriti; Levering, Jennifer; McDonald, Daniel; Dietrich, David; Ramadhar, Timothy R; Lekbua, Asama; Mroue, Nader; Liston, Conor; Stewart, Eric J; Dubin, Marc J; Zengler, Karsten; Knight, Rob; Gilbert, Jack A; Clardy, Jon; Lewis, Kim Nature microbiology. 30531975 2019 03;
Gut microbiome structure and metabolic activity in inflammatory bowel disease. Franzosa, Eric A; Sirota-Madi, Alexandra; Avila-Pacheco, Julian; Fornelos, Nadine; Haiser, Henry J; Reinker, Stefan; Vatanen, Tommi; Hall, A Brantley; Mallick, Himel; McIver, Lauren J; Sauk, Jenny S; Wilson, Robin G; Stevens, Betsy W; Scott, Justin M; Pierce, Kerry; Deik, Amy A; Bullock, Kevin; Imhann, Floris; Porter, Jeffrey A; Zhernakova, Alexandra; Fu, Jingyuan; Weersma, Rinse K; Wijmenga, Cisca; Clish, Clary B; Vlamakis, Hera; Huttenhower, Curtis; Xavier, Ramnik J Nature microbiology. 30531976 2019 Feb;
Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis. Haberman, Yael; Schirmer, Melanie; Dexheimer, Phillip J; Karns, Rebekah; Braun, Tzipi; Kim, Mi-Ok; Walters, Thomas D; Baldassano, Robert N; Noe, Joshua D; Rosh, Joel; Markowitz, James; Crandall, Wallace V; Mack, David R; Griffiths, Anne M; Heyman, Melvin B; Baker, Susan S; Kellermayer, Richard; Moulton, Dedrick; Patel, Ashish S; Gulati, Ajay S; Steiner, Steven J; LeLeiko, Neal; Otley, Anthony; Oliva-Hemker, Maria; Ziring, David; Kirschner, Barbara S; Keljo, David J; Guthery, Stephen L; Cohen, Stanley A; Snapper, Scott; Evans, Jonathan; Dubinsky, Marla; Aronow, Bruce; Hyams, Jeffrey S; Kugathasan, Subra; Huttenhower, Curtis; Xavier, Ramnik J; Denson, Lee A Mucosal immunology. 30542108 2019 03;
HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. Schiffer, Lucas; Azhar, Rimsha; Shepherd, Lori; Ramos, Marcel; Geistlinger, Ludwig; Huttenhower, Curtis; Dowd, Jennifer B; Segata, Nicola; Waldron, Levi American journal of epidemiology. 30649166 2019 Jun 01;
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena; Zolfo, Moreno; Karcher, Nicolai; Armanini, Federica; Beghini, Francesco; Manghi, Paolo; Tett, Adrian; Ghensi, Paolo; Collado, Maria Carmen; Rice, Benjamin L; DuLong, Casey; Morgan, Xochitl C; Golden, Christopher D; Quince, Christopher; Huttenhower, Curtis; Segata, Nicola Cell. 30661755 2019 Jan 24;
Toward unrestricted use of public genomic data. Amann, Rudolf I; Baichoo, Shakuntala; Blencowe, Benjamin J; Bork, Peer; Borodovsky, Mark; Brooksbank, Cath; Chain, Patrick S G; Colwell, Rita R; Daffonchio, Daniele G; Danchin, Antoine; de Lorenzo, Victor; Dorrestein, Pieter C; Finn, Robert D; Fraser, Claire M; Gilbert, Jack A; Hallam, Steven J; Hugenholtz, Philip; Ioannidis, John P A; Jansson, Janet K; Kim, Jihyun F; Klenk, Hans-Peter; Klotz, Martin G; Knight, Rob; Konstantinidis, Konstantinos T; Kyrpides, Nikos C; Mason, Christopher E; McHardy, Alice C; Meyer, Folker; Ouzounis, Christos A; Patrinos, Aristides A N; Podar, Mircea; Pollard, Katherine S; Ravel, Jacques; Muñoz, Alejandro Reyes; Roberts, Richard J; Rosselló-Móra, Ramon; Sansone, Susanna-Assunta; Schloss, Patrick D; Schriml, Lynn M; Setubal, João C; Sorek, Rotem; Stevens, Rick L; Tiedje, James M; Turjanski, Adrian; Tyson, Gene W; Ussery, David W; Weinstock, George M; White, Owen; Whitman, William B; Xenarios, Ioannis Science (New York, N.Y.) 30679363 2019 01 25
Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn's remission patients despite temporal variations in microbial taxa, genomes, and proteomes. Blakeley-Ruiz, J Alfredo; Erickson, Alison R; Cantarel, Brandi L; Xiong, Weili; Adams, Rachel; Jansson, Janet K; Fraser, Claire M; Hettich, Robert L Microbiome. 30744677 2019 02 11;
2017 NIH-wide workshop report on ''The Human Microbiome: Emerging Themes at the Horizon of the 21st Century''. 2017 NIH-wide microbiome workshop writing team Microbiome. 30808401 2019 02 26;
Influence of Crohn's disease related polymorphisms in innate immune function on ileal microbiome. Li, Ellen; Zhang, Yuanhao; Tian, Xinyu; Wang, Xuefeng; Gathungu, Grace; Wolber, Ashley; Shiekh, Shehzad S; Sartor, R Balfour; Davidson, Nicholas O; Ciorba, Matthew A; Zhu, Wei; Nelson, Leah M; Robertson, Charles E; Frank, Daniel N PloS one. 30818349 2019;
Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics. Theis, Kevin R; Romero, Roberto; Winters, Andrew D; Greenberg, Jonathan M; Gomez-Lopez, Nardhy; Alhousseini, Ali; Bieda, Janine; Maymon, Eli; Pacora, Percy; Fettweis, Jennifer M; Buck, Gregory A; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Erez, Offer; Hassan, Sonia S American journal of obstetrics and gynecology. 30832984 2019 Mar;
Much ado about nothing: A qualitative study of the experiences of an average-risk population receiving results of exome sequencing. Rego, Shannon; Dagan-Rosenfeld, Orit; Bivona, Stephanie A; Snyder, Michael P; Ormond, Kelly E Journal of genetic counseling. 30835913 2019 Apr;
Relationship between vitamin D status and the vaginal microbiome during pregnancy. Jefferson, Kimberly K; Parikh, Hardik I; Garcia, Erin M; Edwards, David J; Serrano, Myrna G; Hewison, Martin; Shary, Judith R; Powell, Anna M; Hollis, Bruce W; Fettweis, Jennifer M; Strauss Iii, Jerome F; Buck, Gregory A; Wagner, Carol L Journal of perinatology : official journal of the California Perinatal Association. 30858609 2019 Jun;
Gene-Environment Interaction in the Era of Precision Medicine. Li, Jingjing; Li, Xiao; Zhang, Sai; Snyder, Michael Cell. 30901546 2019 03 21;
MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. Brown, Stuart M; Chen, Hao; Hao, Yuhan; Laungani, Bobby P; Ali, Thahmina A; Dong, Changsu; Lijeron, Carlos; Kim, Baekdoo; Wultsch, Claudia; Pei, Zhiheng; Krampis, Konstantinos GigaScience. 30942867 2019 04 01;
Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. Hollister, Emily B; Oezguen, Numan; Chumpitazi, Bruno P; Luna, Ruth Ann; Weidler, Erica M; Rubio-Gonzales, Michelle; Dahdouli, Mahmoud; Cope, Julia L; Mistretta, Toni-Ann; Raza, Sabeen; Metcalf, Ginger A; Muzny, Donna M; Gibbs, Richard A; Petrosino, Josep The Journal of molecular diagnostics : JMD 31005411 2019 May
A longitudinal big data approach for precision health. Schüssler-Fiorenza Rose, Sophia Miryam; Contrepois, Kévin; Moneghetti, Kegan J; Zhou, Wenyu; Mishra, Tejaswini; Mataraso, Samson; Dagan-Rosenfeld, Orit; Ganz, Ariel B; Dunn, Jessilyn; Hornburg, Daniel; Rego, Shannon; Perelman, Dalia; Ahadi, Sara; Sailani, M Reza; Zhou, Yanjiao; Leopold, Shana R; Chen, Jieming; Ashland, Melanie; Christle, Jeffrey W; Avina, Monika; Limcaoco, Patricia; Ruiz, Camilo; Tan, Marilyn; Butte, Atul J; Weinstock, George M; Slavich, George M; Sodergren, Erica; McLaughlin, Tracey L; Haddad, Francois; Snyder, Michael P Nature medicine. 31068711 2019 05;
Identifying Hospital Antimicrobial Resistance Targets via Robust Ranking. Brooks, J Paul; Dulá, José H; Pakyz, Amy L; Polk, Ronald E IISE transactions on healthcare systems engineering. 31098436 2017;
Impact of Herpes Simplex Virus Type 2 and Human Immunodeficiency Virus Dual Infection on Female Genital Tract Mucosal Immunity and the Vaginal Microbiome. Keller, Marla J; Huber, Ashley; Espinoza, Lilia; Serrano, Myrna G; Parikh, Hardik I; Buck, Gregory A; Gold, Jeremy A; Wu, Yiqun; Wang, Tao; Herold, Betsy C The Journal of infectious diseases 31111902 2019 07 31
The vaginal microbiome and preterm birth. Fettweis, Jennifer M; Serrano, Myrna G; Brooks, J Paul; Edwards, David J; Girerd, Philippe H; Parikh, Hardik I; Huang, Bernice; Arodz, Tom J; Edupuganti, Laahirie; Glascock, Abigail L; Xu, Jie; Jimenez, Nicole R; Vivadelli, Stephany C; Fong, Stephen S; Sheth, Nihar U; Jean, Sophonie; Lee, Vladimir; Bokhari, Yahya A; Lara, Ana M; Mistry, Shreni D; Duckworth 3rd, Robert A; Bradley, Steven P; Koparde, Vishal N; Orenda, X Valentine; Milton, Sarah H; Rozycki, Sarah K; Matveyev, Andrey V; Wright, Michelle L; Huzurbazar, Snehalata V; Jackson, Eugenie M; Smirnova, Ekaterina; Korlach, Jonas; Tsai, Yu-Chih; Dickinson, Molly R; Brooks, Jamie L; Drake, Jennifer I; Chaffin, Donald O; Sexton, Amber L; Gravett, Michael G; Rubens, Craig E; Wijesooriya, N Romesh; Hendricks-Muñoz, Karen D; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Buck, Gregory A Nature medicine. 31142849 2019 06;
Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy. Serrano, Myrna G; Parikh, Hardik I; Brooks, J Paul; Edwards, David J; Arodz, Tom J; Edupuganti, Laahirie; Huang, Bernice; Girerd, Philippe H; Bokhari, Yahya A; Bradley, Steven P; Brooks, Jamie L; Dickinson, Molly R; Drake, Jennifer I; Duckworth 3rd, Robert A; Fong, Stephen S; Glascock, Abigail L; Jean, Sophonie; Jimenez, Nicole R; Khoury, Joseph; Koparde, Vishal N; Lara, Ana M; Lee, Vladimir; Matveyev, Andrey V; Milton, Sarah H; Mistry, Shreni D; Rozycki, Sarah K; Sheth, Nihar U; Smirnova, Ekaterina; Vivadelli, Stephany C; Wijesooriya, N Romesh; Xu, Jie; Xu, Ping; Chaffin, Donald O; Sexton, Amber L; Gravett, Michael G; Rubens, Craig E; Hendricks-Muñoz, Karen D; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Fettweis, Jennifer M; Buck, Gregory A Nature medicine. 31142850 2019 06;
The Integrative Human Microbiome Project. Integrative HMP (iHMP) Research Network Consortium Nature. 31142853 2019 May;
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Lloyd-Price, Jason; Arze, Cesar; Ananthakrishnan, Ashwin N; Schirmer, Melanie; Avila-Pacheco, Julian; Poon, Tiffany W; Andrews, Elizabeth; Ajami, Nadim J; Bonham, Kevin S; Brislawn, Colin J; Casero, David; Courtney, Holly; Gonzalez, Antonio; Graeber, Thomas G; Hall, A Brantley; Lake, Kathleen; Landers, Carol J; Mallick, Himel; Plichta, Damian R; Prasad, Mahadev; Rahnavard, Gholamali; Sauk, Jenny; Shungin, Dmitry; Vázquez-Baeza, Yoshiki; White 3rd, Richard A; IBDMDB Investigators; Braun, Jonathan; Denson, Lee A; Jansson, Janet K; Knight, Rob; Kugathasan, Subra; McGovern, Dermot P B; Petrosino, Joseph F; Stappenbeck, Thaddeus S; Winter, Harland S; Clish, Clary B; Franzosa, Eric A; Vlamakis, Hera; Xavier, Ramnik J; Huttenhower, Curtis Nature. 31142855 2019 May;
Longitudinal multi-omics of host-microbe dynamics in prediabetes. Zhou, Wenyu; Sailani, M Reza; Contrepois, Kévin; Zhou, Yanjiao; Ahadi, Sara; Leopold, Shana R; Zhang, Martin J; Rao, Varsha; Avina, Monika; Mishra, Tejaswini; Johnson, Jethro; Lee-McMullen, Brittany; Chen, Songjie; Metwally, Ahmed A; Tran, Thi Dong Binh; Nguyen, Hoan; Zhou, Xin; Albright, Brandon; Hong, Bo-Young; Petersen, Lauren; Bautista, Eddy; Hanson, Blake; Chen, Lei; Spakowicz, Daniel; Bahmani, Amir; Salins, Denis; Leopold, Benjamin; Ashland, Melanie; Dagan-Rosenfeld, Orit; Rego, Shannon; Limcaoco, Patricia; Colbert, Elizabeth; Allister, Candice; Perelman, Dalia; Craig, Colleen; Wei, Eric; Chaib, Hassan; Hornburg, Daniel; Dunn, Jessilyn; Liang, Liang; Rose, Sophia Miryam Schüssler-Fiorenza; Kukurba, Kim; Piening, Brian; Rost, Hannes; Tse, David; McLaughlin, Tracey; Sodergren, Erica; Weinstock, George M; Snyder, Michael Nature. 31142858 2019 May;
The Cervicovaginal Microbiota-Host Interaction Modulates Chlamydia trachomatis Infection. Edwards, Vonetta L; Smith, Steven B; McComb, Elias J; Tamarelle, Jeanne; Ma, Bing; Humphrys, Michael S; Gajer, Pawel; Gwilliam, Kathleen; Schaefer, Alison M; Lai, Samuel K; Terplan, Mishka; Mark, Katrina S; Brotman, Rebecca M; Forney, Larry J; Bavoil, Patrik M; Ravel, Jacques mBio. 31409678 2019 Aug 13;
Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly. Ivey, Kerry L; Chan, Andrew T; Izard, Jacques; Cassidy, Aedin; Rogers, Geraint B; Rimm, Eric B mBio. 31551328 2019 Sep 24;
Nonoptimal Vaginal Microbiota After Azithromycin Treatment for Chlamydia trachomatis Infection. Tamarelle, Jeanne; Ma, Bing; Gajer, Pawel; Humphrys, Mike S; Terplan, Mishka; Mark, Katrina S; Thiébaut, Anne C M; Forney, Larry J; Brotman, Rebecca M; Delarocque-Astagneau, Elisabeth; Bavoil, Patrik M; Ravel, Jacques The Journal of infectious diseases. 31573603 2020 02 03;
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Tett, Adrian; Huang, Kun D; Asnicar, Francesco; Fehlner-Peach, Hannah; Pasolli, Edoardo; Karcher, Nicolai; Armanini, Federica; Manghi, Paolo; Bonham, Kevin; Zolfo, Moreno; De Filippis, Francesca; Magnabosco, Cara; Bonneau, Richard; Lusingu, John; Amuasi, John; Reinhard, Karl; Rattei, Thomas; Boulund, Fredrik; Engstrand, Lars; Zink, Albert; Collado, Maria Carmen; Littman, Dan R; Eibach, Daniel; Ercolini, Danilo; Rota-Stabelli, Omar; Huttenhower, Curtis; Maixner, Frank; Segata, Nicola Cell host & microbe. 31607556 2019 11 13;
Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains. Kirmiz, Nina; Galindo, Kadir; Cross, Karissa L; Luna, Estefani; Rhoades, Nicholas; Podar, Mircea; Flores, Gilberto E Applied and environmental microbiology. 31757822 2020 Jan 21;
Discordant transmission of bacteria and viruses from mothers to babies at birth. Maqsood, Rabia; Rodgers, Rachel; Rodriguez, Cynthia; Handley, Scott A; Ndao, I Malick; Tarr, Phillip I; Warner, Barbara B; Lim, Efrem S; Holtz, Lori R Microbiome 31823811 2019 12 10
Windows Into Human Health Through Wearables Data Analytics. Witt, Daniel; Kellogg, Ryan; Snyder, Michael; Dunn, Jessilyn Current opinion in biomedical engineering. 31832566 2019 Mar;
Personal aging markers and ageotypes revealed by deep longitudinal profiling. Ahadi, Sara; Zhou, Wenyu; Schüssler-Fiorenza Rose, Sophia Miryam; Sailani, M Reza; Contrepois, Kévin; Avina, Monika; Ashland, Melanie; Brunet, Anne; Snyder, Michael Nature medicine. 31932806 2020 01;
Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. Fornelos, Nadine; Franzosa, Eric A; Bishai, Jason; Annand, John W; Oka, Akihiko; Lloyd-Price, Jason; Arthur, Timothy D; Garner, Ashley; Avila-Pacheco, Julian; Haiser, Henry J; Tolonen, Andrew C; Porter, Jeffrey A; Clish, Clary B; Sartor, R Balfour; Huttenhower, Curtis; Vlamakis, Hera; Xavier, Ramnik J Nature microbiology. 31959971 2020 03;
Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Nguyen, Long H; Ma, Wenjie; Wang, Dong D; Cao, Yin; Mallick, Himel; Gerbaba, Teklu K; Lloyd-Price, Jason; Abu-Ali, Galeb; Hall, A Brantley; Sikavi, Daniel; Drew, David A; Mehta, Raaj S; Arze, Cesar; Joshi, Amit D; Yan, Yan; Branck, Tobyn; DuLong, Casey; Ivey, Kerry L; Ogino, Shuji; Rimm, Eric B; Song, Mingyang; Garrett, Wendy S; Izard, Jacques; Huttenhower, Curtis; Chan, Andrew T Gastroenterology. 31972239 2020 04;
Single-Cell Genomics and the Oral Microbiome. Balachandran, M; Cross, K L; Podar, M Journal of dental research 32091935 2020 06
Global chemical effects of the microbiome include new bile-acid conjugations. Quinn, Robert A; Melnik, Alexey V; Vrbanac, Alison; Fu, Ting; Patras, Kathryn A; Christy, Mitchell P; Bodai, Zsolt; Belda-Ferre, Pedro; Tripathi, Anupriya; Chung, Lawton K; Downes, Michael; Welch, Ryan D; Quinn, Melissa; Humphrey, Greg; Panitchpakdi, Morgan; Weldon, Kelly C; Aksenov, Alexander; da Silva, Ricardo; Avila-Pacheco, Julian; Clish, Clary; Bae, Sena; Mallick, Himel; Franzosa, Eric A; Lloyd-Price, Jason; Bussell, Robert; Thron, Taren; Nelson, Andrew T; Wang, Mingxun; Leszczynski, Eric; Vargas, Fernando; Gauglitz, Julia M; Meehan, Michael J; Gentry, Emily; Arthur, Timothy D; Komor, Alexis C; Poulsen, Orit; Boland, Brigid S; Chang, John T; Sandborn, William J; Lim, Meerana; Garg, Neha; Lumeng, Julie C; Xavier, Ramnik J; Kazmierczak, Barbara I; Jain, Ruchi; Egan, Marie; Rhee, Kyung E; Ferguson, David; Raffatellu, Manuela; Vlamakis, Hera; Haddad, Gabriel G; Siegel, Dionicio; Huttenhower, Curtis; Mazmanian, Sarkis K; Evans, Ronald M; Nizet, Victor; Knight, Rob; Dorrestein, Pieter C Nature. 32103176 2020 03;
Maternal activation of the EGFR prevents translocation of gut-residing pathogenic Escherichia coli in a model of late-onset neonatal sepsis. Knoop, Kathryn A; Coughlin, Paige E; Floyd, Alexandria N; Ndao, I Malick; Hall-Moore, Carla; Shaikh, Nurmohammad; Gasparrini, Andrew J; Rusconi, Brigida; Escobedo, Marilyn; Good, Misty; Warner, Barbara B; Tarr, Phillip I; Newberry, Rodney D Proceedings of the National Academy of Sciences of the United States of America. 32179676 2020 04 07;
Associations of Sleep Characteristics With Cognitive Function and Decline Among Older Adults. McSorley, V Eloesa; Bin, Yu Sun; Lauderdale, Diane S American journal of epidemiology. 32181824 2019 06 01;
Asymptomatic Bacterial Vaginosis Is Associated With Depletion of Mature Superficial Cells Shed From the Vaginal Epithelium. O'Hanlon, D Elizabeth; Gajer, Pawel; Brotman, Rebecca M; Ravel, Jacques Frontiers in cellular and infection microbiology. 32211347 2020;
MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data. Bangayan, Nathanael J; Shi, Baochen; Trinh, Jerry; Barnard, Emma; Kasimatis, Gabriela; Curd, Emily; Li, Huiying Microorganisms. 32397065 2020 May 08;
Complete Genome Sequences of Six Lactobacillus iners Strains Isolated from the Human Vagina. France, Michael T; Rutt, Lindsay; Narina, Shilpa; Arbaugh, Sarah; McComb, Elias; Humphrys, Mike S; Ma, Bing; Hayward, Matthew R; Costello, Elizabeth K; Relman, David A; Kwon, Douglas S; Ravel, Jacques Microbiology resource announcements. 32409537 2020 May 14;
Molecular Choreography of Acute Exercise. Contrepois, Kévin; Wu, Si; Moneghetti, Kegan J; Hornburg, Daniel; Ahadi, Sara; Tsai, Ming-Shian; Metwally, Ahmed A; Wei, Eric; Lee-McMullen, Brittany; Quijada, Jeniffer V; Chen, Songjie; Christle, Jeffrey W; Ellenberger, Mathew; Balliu, Brunilda; Taylor, Shalina; Durrant, Matthew G; Knowles, David A; Choudhry, Hani; Ashland, Melanie; Bahmani, Amir; Enslen, Brooke; Amsallem, Myriam; Kobayashi, Yukari; Avina, Monika; Perelman, Dalia; Schüssler-Fiorenza Rose, Sophia Miryam; Zhou, Wenyu; Ashley, Euan A; Montgomery, Stephen B; Chaib, Hassan; Haddad, Francois; Snyder, Michael P Cell. 32470399 2020 May 28;
PICRUSt2 for prediction of metagenome functions. Douglas, Gavin M; Maffei, Vincent J; Zaneveld, Jesse R; Yurgel, Svetlana N; Brown, James R; Taylor, Christopher M; Huttenhower, Curtis; Langille, Morgan G I Nature biotechnology. 32483366 2020 Jun;
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Karcher, Nicolai; Pasolli, Edoardo; Asnicar, Francesco; Huang, Kun D; Tett, Adrian; Manara, Serena; Armanini, Federica; Bain, Debbie; Duncan, Sylvia H; Louis, Petra; Zolfo, Moreno; Manghi, Paolo; Valles-Colomer, Mireia; Raffaetà, Roberta; Rota-Stabelli, Omar; Collado, Maria Carmen; Zeller, Georg; Falush, Daniel; Maixner, Frank; Walker, Alan W; Huttenhower, Curtis; Segata, Nicola Genome biology. 32513234 2020 06 08;
Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. Wagner, Justin; Kancherla, Jayaram; Braccia, Domenick; Matsumara, James; Felix, Victor; Crabtree, Jonathan; Mahurkar, Anup; Corrada Bravo, Héctor F1000Research 32742640 2020
Association of diet with circulating trimethylamine-N-oxide concentration. Hamaya, Rikuta; Ivey, Kerry L; Lee, Dong H; Wang, Molin; Li, Jun; Franke, Adrian; Sun, Qi; Rimm, Eric B The American journal of clinical nutrition. 32936862 2020 12 10;
Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. Sailani, M Reza; Metwally, Ahmed A; Zhou, Wenyu; Rose, Sophia Miryam Schüssler-Fiorenza; Ahadi, Sara; Contrepois, Kevin; Mishra, Tejaswini; Zhang, Martin Jinye; Kidzi?ski, ?ukasz; Chu, Theodore J; Snyder, Michael P Nature communications. 33004787 2020 10 01;
Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'. Tan, James Y; Wang, Sida; Dick, Gregory J; Young, Vincent B; Sherman, David H; Burns, Mark A; Lin, Xiaoxia N Integrative biology : quantitative biosciences from nano to macro. 33089329 2020 11 18;
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Nishiyama, Hiroki; Endo, Hisashi; Blanc-Mathieu, Romain; Ogata, Hiroyuki Microorganisms. 33121006 2020 Oct 27;
Genetic Variation in Toll-Like Receptor 5 and Colonization with Flagellated Bacterial Vaginosis-Associated Bacteria. Dela Cruz, Erin J; Fiedler, Tina L; Liu, Congzhou; Munch, Matthew M; Kohler, Christina M; Oot, Antoinette R; Wallis, Jacqueline M; Wang, Junhui; Frishman, Anna; Garcia, Kristina; Wiser, Andrew; Balkus, Jennifer E; Srinivasan, Sujatha; Golob, Jonathan L; Sycuro, Laura K; Marrazzo, Jeanne M; Hawn, Thomas R; Fredricks, David N Infection and immunity 33199356 2021 Feb 16
Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Münch, Philipp C; Franzosa, Eric A; Stecher, Bärbel; McHardy, Alice C; Huttenhower, Curtis Cell host & microbe. 33217332 2020 Nov 16;
VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. France, Michael T; Ma, Bing; Gajer, Pawel; Brown, Sarah; Humphrys, Michael S; Holm, Johanna B; Waetjen, L Elaine; Brotman, Rebecca M; Ravel, Jacques Microbiome. 33228810 2020 11 23;
Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis. Lee, Christina Y; Cheu, Ryan K; Lemke, Melissa M; Gustin, Andrew T; France, Michael T; Hampel, Benjamin; Thurman, Andrea R; Doncel, Gustavo F; Ravel, Jacques; Klatt, Nichole R; Arnold, Kelly B Nature communications 33262350 2020 Dec 01
HMPDACC: a Human Microbiome Project Multi-omic data resource. Creasy, Heather Huot; Felix, Victor; Aluvathingal, Jain; Crabtree, Jonathan; Ifeonu, Olukemi; Matsumura, James; McCracken, Carrie; Nickel, Lance; Orvis, Joshua; Schor, Mike; Giglio, Michelle; Mahurkar, Anup; White, Owen Nucleic acids research 33305317 2021 01 08
Fructan-sensitive children with irritable bowel syndrome have distinct gut microbiome signatures. Chumpitazi, Bruno P; Hoffman, Kristi L; Smith, Daniel P; McMeans, Ann R; Musaad, Salma; Versalovic, James; Petrosino, Joseph F; Shulman, Robert J Alimentary pharmacology & therapeutics. 33314183 2020 Dec 13;
Sequence Comparison of Vaginolysin from Different Gardnerella Species. Garcia, Erin M; Serrano, Myrna G; Edupuganti, Laahirie; Edwards, David J; Buck, Gregory A; Jefferson, Kimberly K Pathogens (Basel, Switzerland) 33498226 2021 Jan 20
The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. Wang, Dong D; Nguyen, Long H; Li, Yanping; Yan, Yan; Ma, Wenjie; Rinott, Ehud; Ivey, Kerry L; Shai, Iris; Willett, Walter C; Hu, Frank B; Rimm, Eric B; Stampfer, Meir J; Chan, Andrew T; Huttenhower, Curtis Nature medicine 33574608 2021 02
Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease. Somineni, Hari K; Nagpal, Sini; Venkateswaran, Suresh; Cutler, David J; Okou, David T; Haritunians, Talin; Simpson, Claire L; Begum, Ferdouse; Datta, Lisa W; Quiros, Antonio J; Seminerio, Jenifer; Mengesha, Emebet; Alexander, Jonathan S; Baldassano, Robert N; Dudley-Brown, Sharon; Cross, Raymond K; Dassopoulos, Themistocles; Denson, Lee A; Dhere, Tanvi A; Iskandar, Heba; Dryden, Gerald W; Hou, Jason K; Hussain, Sunny Z; Hyams, Jeffrey S; Isaacs, Kim L; Kader, Howard; Kappelman, Michael D; Katz, Jeffry; Kellermayer, Richard; Kuemmerle, John F; Lazarev, Mark; Li, Ellen; Mannon, Peter; Moulton, Dedrick E; Newberry, Rodney D; Patel, Ashish S; Pekow, Joel; Saeed, Shehzad A; Valentine, John F; Wang, Ming-Hsi; McCauley, Jacob L; Abreu, Maria T; Jester, Traci; Molle-Rios, Zarela; Palle, Sirish; Scherl, Ellen J; Kwon, John; Rioux, John D; Duerr, Richard H; Silverberg, Mark S; Zwick, Michael E; Stevens, Christine; Daly, Mark J; Cho, Judy H; Gibson, Greg; McGovern, Dermot P B; Brant, Steven R; Kugathasan, Subra American journal of human genetics 33600772 2021 03 04
Megasphaera lornae sp. nov., Megasphaera hutchinsoni sp. nov., and Megasphaera vaginalis sp. nov.: novel bacteria isolated from the female genital tract. Srinivasan, Sujatha; Beamer, May A; Fiedler, Tina L; Austin, Michele N; Sizova, Maria V; Strenk, Susan M; Agnew, Kathy J; Gowda, G A Nagana; Raftery, Daniel; Epstein, Slava S; Fredricks, David N; Hillier, Sharon L International journal of systematic and evolutionary microbiology 33616513 2019 Jun
Biogenic Amines Increase the Odds of Bacterial Vaginosis and Affect the Growth of and Lactic Acid Production by Vaginal Lactobacillus spp. Borgogna, Joanna-Lynn C; Shardell, Michelle D; Grace, Savannah G; Santori, Elisa K; Americus, Benjamin; Li, Zhong; Ulanov, Alexander; Forney, Larry; Nelson, Tiffanie M; Brotman, Rebecca M; Ravel, Jacques; Yeoman, Carl J Applied and environmental microbiology 33674429 2021 04 27
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Beghini, Francesco; McIver, Lauren J; Blanco-Míguez, Aitor; Dubois, Leonard; Asnicar, Francesco; Maharjan, Sagun; Mailyan, Ana; Manghi, Paolo; Scholz, Matthias; Thomas, Andrew Maltez; Valles-Colomer, Mireia; Weingart, George; Zhang, Yancong; Zolfo, Moreno; Huttenhower, Curtis; Franzosa, Eric A; Segata, Nicola eLife 33944776 2021 May 04
Wearable sensors enable personalized predictions of clinical laboratory measurements. Dunn, Jessilyn; Kidzinski, Lukasz; Runge, Ryan; Witt, Daniel; Hicks, Jennifer L; Schüssler-Fiorenza Rose, Sophia Miryam; Li, Xiao; Bahmani, Amir; Delp, Scott L; Hastie, Trevor; Snyder, Michael P Nature medicine 34031607 2021 Jun
Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome. Li, Yanping; Wang, Dong D; Satija, Ambika; Ivey, Kerry L; Li, Jun; Wilkinson, Jeremy E; Li, Ruifeng; Baden, Megu; Chan, Andrew T; Huttenhower, Curtis; Rimm, Eric B; Hu, Frank B; Sun, Qi The Journal of nutrition 34114015 2021 Jun 10
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. Ma, Wenjie; Nguyen, Long H; Song, Mingyang; Wang, Dong D; Franzosa, Eric A; Cao, Yin; Joshi, Amit; Drew, David A; Mehta, Raaj; Ivey, Kerry L; Strate, Lisa L; Giovannucci, Edward L; Izard, Jacques; Garrett, Wendy; Rimm, Eric B; Huttenhower, Curtis; Chan, Andrew T Genome medicine 34140026 2021 06 17
Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. Thänert, Robert; Thänert, Anna; Ou, Jocelyn; Bajinting, Adam; Burnham, Carey-Ann D; Engelstad, Holly J; Tecos, Maria E; Ndao, I Malick; Hall-Moore, Carla; Rouggly-Nickless, Colleen; Carl, Mike A; Rubin, Deborah C; Davidson, Nicholas O; Tarr, Phillip I; Warner, Barbara B; Dantas, Gautam; Warner, Brad W Gut microbes 34264786 2021 Jan-Dec
Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples? Brown, Sarah E; Robinson, Courtney K; Shardell, Michelle D; Holm, Johanna B; Ravel, Jacques; Ghanem, Khalil G; Brotman, Rebecca M Frontiers in cellular and infection microbiology 34268137 2021
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. Roodgar, Morteza; Good, Benjamin H; Garud, Nandita R; Martis, Stephen; Avula, Mohan; Zhou, Wenyu; Lancaster, Samuel M; Lee, Hayan; Babveyh, Afshin; Nesamoney, Sophia; Pollard, Katherine S; Snyder, Michael P Genome research 34301627 2021 08
The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. Sikavi, Daniel R; Nguyen, Long H; Haruki, Koichiro; Ugai, Tomotaka; Ma, Wenjie; Wang, Dong D; Thompson, Kelsey N; Yan, Yan; Branck, Tobyn; Wilkinson, Jeremy E; Akimoto, Naohiko; Zhong, Rong; Lau, Mai Chan; Mima, Kosuke; Kosumi, Keisuke; Morikawa, Teppei; Rimm, Eric B; Garrett, Wendy S; Izard, Jacques; Cao, Yin; Song, Mingyang; Huttenhower, Curtis; Ogino, Shuji; Chan, Andrew T Clinical and translational gastroenterology 34333506 2021 08 01
Vaginal microbiome Lactobacillus crispatus is heritable among European American women. Wright, Michelle L; Fettweis, Jennifer M; Eaves, Lindon J; Silberg, Judy L; Neale, Michael C; Serrano, Myrna G; Jimenez, Nicole R; Prom-Wormley, Elizabeth; Girerd, Philippe H; Borzelleca Jr, Joseph F; Jefferson, Kimberly K; Strauss 3rd, Jerome F; York, Timothy P; Buck, Gregory A Communications biology 34354222 2021 08 05
Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth. Pace, Ryan M; Chu, Derrick M; Prince, Amanda L; Ma, Jun; Seferovic, Maxim D; Aagaard, Kjersti M Med (New York, N.Y.) 34617072 2021 Sep 10
Metagenomic profiling of placental tissue suggests DNA virus infection of the placenta is rare. Witney, Adam A; Aller, Sean; Strang, Blair L The Journal of general virology 34723784 2021 11
Multivariable association discovery in population-scale meta-omics studies. Mallick, Himel; Rahnavard, Ali; McIver, Lauren J; Ma, Siyuan; Zhang, Yancong; Nguyen, Long H; Tickle, Timothy L; Weingart, George; Ren, Boyu; Schwager, Emma H; Chatterjee, Suvo; Thompson, Kelsey N; Wilkinson, Jeremy E; Subramanian, Ayshwarya; Lu, Yiren; Waldron, Levi; Paulson, Joseph N; Franzosa, Eric A; Bravo, Hector Corrada; Huttenhower, Curtis PLoS computational biology 34784344 2021 11
The vaginal microbiome in women of reproductive age with healthy weight versus overweight/obesity. Allen, Natalie G; Edupuganti, Laahirie; Edwards, David J; Jimenez, Nicole R; Buck, Gregory A; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Vaginal Microbiome Consortium; Wickham 3rd, Edmond P; Fettweis, Jennifer M Obesity (Silver Spring, Md.) 34806323 2022 01
Unique roles of vaginal Megasphaera phylotypes in reproductive health. Glascock, Abigail L; Jimenez, Nicole R; Boundy, Sam; Koparde, Vishal N; Brooks, J Paul; Edwards, David J; Strauss Iii, Jerome F; Jefferson, Kimberly K; Serrano, Myrna G; Buck, Gregory A; Fettweis, Jennifer M Microbial genomics 34898422 2021 12
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing. Zuo, Zheng; Chang, Yiming Kenny; Stormo, Gary D Briefings in functional genomics 34923581 2022 Apr 11
Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data. France, Michael T; Fu, Li; Rutt, Lindsay; Yang, Hongqiu; Humphrys, Michael S; Narina, Shilpa; Gajer, Pawel M; Ma, Bing; Forney, Larry J; Ravel, Jacques Genome biology 35232471 2022 Mar 01
Human gut bacteria produce ΤΗ17-modulating bile acid metabolites. Paik, Donggi; Yao, Lina; Zhang, Yancong; Bae, Sena; D'Agostino, Gabriel D; Zhang, Minghao; Kim, Eunha; Franzosa, Eric A; Avila-Pacheco, Julian; Bisanz, Jordan E; Rakowski, Christopher K; Vlamakis, Hera; Xavier, Ramnik J; Turnbaugh, Peter J; Longman, Randy S; Krout, Michael R; Clish, Clary B; Rastinejad, Fraydoon; Huttenhower, Curtis; Huh, Jun R; Devlin, A Sloan Nature 35296854 2022 03
Exerkines in health, resilience and disease. Chow, Lisa S; Gerszten, Robert E; Taylor, Joan M; Pedersen, Bente K; van Praag, Henriette; Trappe, Scott; Febbraio, Mark A; Galis, Zorina S; Gao, Yunling; Haus, Jacob M; Lanza, Ian R; Lavie, Carl J; Lee, Chih-Hao; Lucia, Alejandro; Moro, Cedric; Pandey, Ambarish; Robbins, Jeremy M; Stanford, Kristin I; Thackray, Alice E; Villeda, Saul; Watt, Matthew J; Xia, Ashley; Zierath, Juleen R; Goodpaster, Bret H; Snyder, Michael P Nature reviews. Endocrinology 35304603 2022 05
Associations Between Vaginal Bacteria and Bacterial Vaginosis Signs and Symptoms: A Comparative Study of Kenyan and American Women. Carter, Kayla A; Balkus, Jennifer E; Anzala, Omu; Kimani, Joshua; Hoffman, Noah G; Fiedler, Tina L; Mochache, Vernon; Fredricks, David N; McClelland, Raymond Scott; Srinivasan, Sujatha Frontiers in cellular and infection microbiology 35310847 2022
Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. Li, Yanping; Wang, Fenglei; Li, Jun; Ivey, Kerry L; Wilkinson, Jeremy E; Wang, Dong D; Li, Ruifeng; Liu, Gang; Eliassen, Heather A; Chan, Andrew T; Clish, Clary B; Huttenhower, Curtis; Hu, Frank B; Sun, Qi; Rimm, Eric B BMC microbiology 35350985 2022 03 29
Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants. Kaelin, Emily A; Rodriguez, Cynthia; Hall-Moore, Carla; Hoffmann, Julie A; Linneman, Laura A; Ndao, I Malick; Warner, Barbara B; Tarr, Phillip I; Holtz, Lori R; Lim, Efrem S Nature microbiology 35449461 2022 May
Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens. Brown, Sarah Elizabeth; He, Xin; Shardell, Michelle D; Ravel, Jacques; Ghanem, Khalil G; Zenilman, Jonathan M; Brotman, Rebecca M Sexually transmitted infections 35636931 2022 May 30
Progressive dysbiosis of human orodigestive microbiota along the sequence of gastroesophageal reflux, Barrett's esophagus and esophageal adenocarcinoma. Hao, Yuhan; Karaoz, Ulas; Yang, Liying; Yachimski, Patrick S; Tseng, Wenzhi; Nossa, Carlos W; Ye, Weimin; Tseng, Mengkao; Poles, Michael; Francois, Fritz; Traube, Morris; Brown, Stuart M; Chen, Yu; Torralba, Manolito; Peek, Richard M; Brodie, Eoin L; Pei, Zhiheng International journal of cancer 35751398 2022 Jun 24
High-sensitivity pattern discovery in large, paired multiomic datasets. Ghazi, Andrew R; Sucipto, Kathleen; Rahnavard, Ali; Franzosa, Eric A; McIver, Lauren J; Lloyd-Price, Jason; Schwager, Emma; Weingart, George; Moon, Yo Sup; Morgan, Xochitl C; Waldron, Levi; Huttenhower, Curtis Bioinformatics (Oxford, England) 35758795 2022 06 24
Complete Genome Sequences of Ezakiella coagulans C0061C1 and Fenollaria massiliensis C0061C2. France, Michael T; Clifford, Jack; Narina, Shilpa; Rutt, Lindsay; Ravel, Jacques Microbiology resource announcements 35861554 2022 Jul 21
Factors Associated With Incidence and Spontaneous Clearance of Molecular-Bacterial Vaginosis: Results From a Longitudinal Frequent-Sampling Observational Study. Tamarelle, Jeanne; Shardell, Michelle D; Ravel, Jacques; Brotman, Rebecca M Sexually transmitted diseases 35969846 2022 Sep 01
A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria. Yao, Lina; D'Agostino, Gabriel D; Park, Jinseok; Hang, Saiyu; Adhikari, Arijit A; Zhang, Yancong; Li, Wei; Avila-Pacheco, Julian; Bae, Sena; Clish, Clary B; Franzosa, Eric A; Huttenhower, Curtis; Huh, Jun R; Devlin, A Sloan Nature microbiology 35982310 2022 09
Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression. Delgado-Diaz, David Jose; Jesaveluk, Brianna; Hayward, Joshua A; Tyssen, David; Alisoltani, Arghavan; Potgieter, Matthys; Bell, Liam; Ross, Elizabeth; Iranzadeh, Arash; Allali, Imane; Dabee, Smritee; Barnabas, Shaun; Gamieldien, Hoyam; Blackburn, Jonathan M; Mulder, Nicola; Smith, Steven B; Edwards, Vonetta L; Burgener, Adam D; Bekker, Linda-Gail; Ravel, Jacques; Passmore, Jo-Ann S; Masson, Lindi; Hearps, Anna C; Tachedjian, Gilda Microbiome 36045402 2022 08 31
What is the FDA Going to Think?: Negotiating Values through Reflective and Strategic Category Work in Microbiome Science. Darling, Katherine W; Boyce, Angie M; Cho, Mildred K; Sankar, Pamela L Science, technology & human values 36119463 2015 Jan
Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients. Thompson, Dominique S; Fu, Chenlian; Gandhi, Tanmay; Fowler, J Christopher; Frueh, B Christopher; Weinstein, Benjamin L; Petrosino, Joseph; Hadden, Julia K; Carlson, Marianne; Coarfa, Cristian; Madan, Alok Progress in neuro-psychopharmacology & biological psychiatry 36122838 2023 Jan 10
Roles of the Microbiota of the Female Reproductive Tract in Gynecological and Reproductive Health. Zhu, Bin; Tao, Zhi; Edupuganti, Laahirie; Serrano, Myrna G; Buck, Gregory A Microbiology and molecular biology reviews : MMBR 36222685 2022 Dec 21
Persistence and In Vivo Evolution of Vaginal Bacterial Strains over a Multiyear Time Period. France, Michael; Ma, Bing; Ravel, Jacques mSystems 36413016 2022 Dec 20
Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth. Liao, Jingqiu; Shenhav, Liat; Urban, Julia A; Serrano, Myrna; Zhu, Bin; Buck, Gregory A; Korem, Tal bioRxiv : the preprint server for biology 36711990 2023 Jun 17
Does the Vaginal Microbiome Operate Differently by Race to Influence Risk of Precervical Cancer? Tossas, Katherine Y; Zhu, Bin; Perera, Robert A; Serrano, Myrna G; Sullivan, Stephanie; Sayeed, Sadia; Strauss 3rd, Jerome F; Winn, Robert A; Buck, Gregory A; Seewaldt, Victoria L Journal of women's health (2002) 36897755 2023 May
History of childhood physical abuse is associated with gut microbiota diversity among adult psychiatric inpatients. Rohr, Jessica C; Bourassa, Katelynn A; Thompson, Dominique S; Fowler, J Christopher; Frueh, B Christopher; Weinstein, Benjamin L; Petrosino, Joseph; Madan, Alok Journal of affective disorders 36933668 2023 Jun 15
The Microbiome and Big Data. Navas-Molina, Jose A; Hyde, Embriette R; Sanders, Jon; Knight, Rob Current opinion in systems biology 36937228 2017 Aug
High-resolution functional description of vaginal microbiomes in health and disease. Holm, Johanna B; France, Michael T; Gajer, Pawel; Ma, Bing; Brotman, Rebecca M; Shardell, Michelle; Forney, Larry; Ravel, Jacques bioRxiv : the preprint server for biology 36993583 2023 Mar 24
Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit. Schwartz, Drew J; Shalon, Nitan; Wardenburg, Kate; DeVeaux, Anna; Wallace, Meghan A; Hall-Moore, Carla; Ndao, I Malick; Sullivan, Janice E; Radmacher, Paula; Escobedo, Marilyn; Burnham, Carey-Ann D; Warner, Barbara B; Tarr, Phillip I; Dantas, Gautam Science translational medicine 37134153 2023 May 03
Investigating the impact of condomless vaginal intercourse and lubricant use on the vaginal metabolome: a pre-post observational study. Borgogna, Joanna-Lynn C; Grace, Savannah G; Holm, Johanna B; Aviles Zuniga, Tadeo; Kadriu, Herlin; He, Xin; McCoski, Sarah R; Ravel, Jacques; Brotman, Rebecca M; Yeoman, Carl J Sexually transmitted infections 37258272 2023 Nov
Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy. Lee, Christina Y; Diegel, Jenna; France, Michael T; Ravel, Jacques; Arnold, Kelly B PLoS computational biology 37566641 2023 Aug
Microdiversity of the vaginal microbiome is associated with preterm birth. Liao, Jingqiu; Shenhav, Liat; Urban, Julia A; Serrano, Myrna; Zhu, Bin; Buck, Gregory A; Korem, Tal Nature communications 37591872 2023 Aug 17
Profiling novel lateral gene transfer events in the human microbiome. Hsu, Tiffany Y; Nzabarushimana, Etienne; Wong, Dennis; Luo, Chengwei; Beiko, Robert G; Langille, Morgan; Huttenhower, Curtis; Nguyen, Long H; Franzosa, Eric A bioRxiv : the preprint server for biology 37609252 2023 Aug 14
Integrating compositional and functional content to describe vaginal microbiomes in health and disease. Holm, Johanna B; France, Michael T; Gajer, Pawel; Ma, Bing; Brotman, Rebecca M; Shardell, Michelle; Forney, Larry; Ravel, Jacques Microbiome 38031142 2023 Nov 30
Antibody Response to the Sneathia vaginalis Cytopathogenic Toxin A during Pregnancy. McCoy, Zion T; Serrano, Myrna G; Edupuganti, Laahirie; Spaine, Katherine M; Edwards, David J; Buck, Gregory A; Jefferson, Kimberly K ImmunoHorizons 38276916 2024 Jan 01
Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Zhou, Xin; Shen, Xiaotao; Johnson, Jethro S; Spakowicz, Daniel J; Agnello, Melissa; Zhou, Wenyu; Avina, Monica; Honkala, Alexander; Chleilat, Faye; Chen, Shirley Jingyi; Cha, Kexin; Leopold, Shana; Zhu, Chenchen; Chen, Lei; Lyu, Lin; Hornburg, Daniel; Wu, Si; Zhang, Xinyue; Jiang, Chao; Jiang, Liuyiqi; Jiang, Lihua; Jian, Ruiqi; Brooks, Andrew W; Wang, Meng; Contrepois, Kévin; Gao, Peng; Rose, Sophia Miryam Schüssler-Fiorenza; Tran, Thi Dong Binh; Nguyen, Hoan; Celli, Alessandra; Hong, Bo-Young; Bautista, Eddy J; Dorsett, Yair; Kavathas, Paula B; Zhou, Yanjiao; Sodergren, Erica; Weinstock, George M; Snyder, Michael P Cell host & microbe 38479397 2024 Mar 12

This page last reviewed on April 25, 2024