Human Microbiome Project (837)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
"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 LScience, technology & human values2015 Jan36119463
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, GildaMicrobiome2022 08 3136045402
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 SloanNature microbiology2022 0935982310
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 MSexually transmitted diseases2022 Sep 0135969846
Complete Genome Sequences of Ezakiella coagulans C0061C1 and Fenollaria massiliensis C0061C2.France, Michael T; Clifford, Jack; Narina, Shilpa; Rutt, Lindsay; Ravel, JacquesMicrobiology resource announcements2022 Jul 2135861554
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, CurtisBioinformatics (Oxford, England)2022 06 2435758795
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, ZhihengInternational journal of cancer2022 Jun 2435751398
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 MSexually transmitted infections2022 May 3035636931
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 SNature microbiology2022 May35449461
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 BBMC microbiology2022 03 2935350985
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, SujathaFrontiers in cellular and infection microbiology202235310847
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 PNature reviews. Endocrinology2022 0535304603
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 SloanNature2022 0335296854
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, JacquesGenome biology2022 Mar 0135232471
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing.Zuo, Zheng; Chang, Yiming Kenny; Stormo, Gary DBriefings in functional genomics2022 Apr 1134923581
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 MMicrobial genomics2021 1234898422
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 MObesity (Silver Spring, Md.)2022 0134806323
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, CurtisPLoS computational biology2021 1134784344
Metagenomic profiling of placental tissue suggests DNA virus infection of the placenta is rare.Witney, Adam A; Aller, Sean; Strang, Blair LThe Journal of general virology2021 1134723784
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 MMed (New York, N.Y.)2021 Sep 1034617072
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 ACommunications biology2021 08 0534354222
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 TClinical and translational gastroenterology2021 08 0134333506
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 PGenome research2021 0834301627
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 MFrontiers in cellular and infection microbiology202134268137
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 WGut microbes2021 Jan-Dec34264786
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 TGenome medicine2021 06 1734140026
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, QiThe Journal of nutrition2021 Jun 1034114015
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 PNature medicine2021 Jun34031607
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, NicolaeLife2021 May 0433944776
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 JApplied and environmental microbiology2021 04 2733674429
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 LInternational journal of systematic and evolutionary microbiology2019 Jun33616513
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, SubraAmerican journal of human genetics2021 03 0433600772
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, CurtisNature medicine2021 0233574608
Sequence Comparison of Vaginolysin from Different Gardnerella Species.Garcia, Erin M; Serrano, Myrna G; Edupuganti, Laahirie; Edwards, David J; Buck, Gregory A; Jefferson, Kimberly KPathogens (Basel, Switzerland)2021 Jan 2033498226
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 JAlimentary pharmacology & therapeutics.2020 Dec 13;33314183
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, OwenNucleic acids research2021 01 0833305317
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, JacquesMicrobiome.2020 11 23;33228810
Identification of Natural CRISPR Systems and Targets in the Human Microbiome.Münch, Philipp C; Franzosa, Eric A; Stecher, Bärbel; McHardy, Alice C; Huttenhower, CurtisCell host & microbe.2020 Nov 16;33217332
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 NInfection and immunity2021 Feb 1633199356
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut.Nishiyama, Hiroki; Endo, Hisashi; Blanc-Mathieu, Romain; Ogata, HiroyukiMicroorganisms.2020 Oct 27;33121006
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 NIntegrative biology : quantitative biosciences from nano to macro.2020 11 18;33089329
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 PNature communications.2020 10 01;33004787
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 BThe American journal of clinical nutrition.2020 12 10;32936862
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, HéctorF1000Research202032742640
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, NicolaGenome biology.2020 06 08;32513234
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 INature biotechnology.2020 Jun;32483366
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 PCell.2020 May 28;32470399
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, JacquesMicrobiology resource announcements.2020 May 14;32409537
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, HuiyingMicroorganisms.2020 May 08;32397065
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, JacquesFrontiers in cellular and infection microbiology.2020;32211347
Associations of Sleep Characteristics With Cognitive Function and Decline Among Older Adults.McSorley, V Eloesa; Bin, Yu Sun; Lauderdale, Diane SAmerican journal of epidemiology.2019 06 01;32181824
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 DProceedings of the National Academy of Sciences of the United States of America.2020 04 07;32179676
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 CNature.2020 03;32103176
Single-Cell Genomics and the Oral Microbiome.Balachandran, M; Cross, K L; Podar, MJournal of dental research2020 0632091935
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 TGastroenterology.2020 04;31972239
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 JNature microbiology.2020 03;31959971
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, MichaelNature medicine.2020 01;31932806
Windows Into Human Health Through Wearables Data Analytics.Witt, Daniel; Kellogg, Ryan; Snyder, Michael; Dunn, JessilynCurrent opinion in biomedical engineering.2019 Mar;31832566
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 RMicrobiome2019 12 1031823811
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 EApplied and environmental microbiology.2020 Jan 21;31757822
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, NicolaCell host & microbe.2019 11 13;31607556
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, JacquesThe Journal of infectious diseases.2020 02 03;31573603
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 BmBio.2019 Sep 24;31551328
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, JacquesmBio.2019 Aug 13;31409678
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, MichaelNature.2019 May;31142858
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, CurtisNature.2019 May;31142855
The Integrative Human Microbiome Project.Integrative HMP (iHMP) Research Network ConsortiumNature.2019 May;31142853
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 ANature medicine.2019 06;31142850
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 ANature medicine.2019 06;31142849
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 CThe Journal of infectious diseases2019 07 3131111902
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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, KonstantinosGigaScience.2019 04 01;30942867
Gene-Environment Interaction in the Era of Precision Medicine.Li, Jingjing; Li, Xiao; Zhang, Sai; Snyder, MichaelCell.2019 03 21;30901546
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 LJournal of perinatology : official journal of the California Perinatal Association.2019 Jun;30858609
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 EJournal of genetic counseling.2019 Apr;30835913
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 SAmerican journal of obstetrics and gynecology.2019 Mar;30832984
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 NPloS one.2019;30818349
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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 LMicrobiome.2019 02 11;30744677
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, IoannisScience (New York, N.Y.)2019 01 2530679363
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, NicolaCell.2019 Jan 24;30661755
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, LeviAmerican journal of epidemiology.2019 Jun 01;30649166
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 AMucosal immunology.2019 03;30542108
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 JNature microbiology.2019 Feb;30531976
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, KimNature microbiology.2019 03;30531975
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, CurtisNature methods.2018 11;30377376
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 JNature.2018 10;30356183
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 JCell host & microbe.2018 10 10;30308161
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, RobNature methods.2018 10;30275573
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 MApplied and environmental microbiology.2018 12 01;30266729
Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring.Jiang, Chao; Wang, Xin; Li, Xiyan; Inlora, Jingga; Wang, Ting; Liu, Qing; Snyder, MichaelCell.2018 09 20;30241608
Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions.Liu, Chaoyue; Wright, Benjamin; Allen-Vercoe, Emma; Gu, Hong; Beiko, RobertGenome biology and evolution.2018 09 01;30137329
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, RobCurrent opinion in microbiology.2018 08;30059804
PERFect: PERmutation Filtering test for microbiome data.Smirnova, Ekaterina; Huzurbazar, Snehalata; Jafari, FarhadBiostatistics (Oxford, England).2019 10 01;29917060
Neurotransmitter modulation by the gut microbiota.Strandwitz, PhilipBrain research.2018 08 15;29903615
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 GPediatric research.2018 07;29795209
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 BJournal of clinical rheumatology : practical reports on rheumatic & musculoskeletal diseases.2019 Jan;29794876
Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications.Hall, Anne; Versalovic, JamesJournal of pediatric gastroenterology and nutrition.2018 06;29762384
Personal Omics for Precision Health.Kellogg, Ryan A; Dunn, Jessilyn; Snyder, Michael PCirculation research.2018 04 27;29700064
In situ cultivation of previously uncultivable microorganisms using the ichip.Berdy, Brittany; Spoering, Amy L; Ling, Losee L; Epstein, Slava SNature protocols2017 1029532802
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 DennisSexual health2018 0629506642
Carriage of Cronobacter sakazakii in the Very Preterm Infant Gut.Chandrasekaran, Sukantha; Burnham, Carey-Ann D; Warner, Barbara B; Tarr, Phillip I; Wylie, Todd NClinical infectious diseases : an official publication of the Infectious Diseases Society of America.2018 07 02;29394356
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, CurtisGenome medicine.2018 Jan 29;29378630
One-Way Particle Transport Using Oscillatory Flow in Asymmetric Traps.Lee, Jaesung; Burns, Mark ASmall (Weinheim an der Bergstrasse, Germany).2018 03;29377529
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, ZaidPloS one.2018;29364944
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 PCell systems.2018 Feb 28;29361466
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, CurtisNature microbiology.2018 03;29335555
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 TNature microbiology.2018 03;29335554
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, CurtisNature microbiology.2018 03;29311644
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, PeerNature microbiology.2018 Jan;29255284
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 RThe American journal of gastroenterology.2018 01;29206816
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, CurtisBioinformatics (Oxford, England).2018 Apr 01;29194469
Experimental design and quantitative analysis of microbial community multiomics.Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, CurtisGenome biology.2017 Nov 30;29187204
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, CurtisGenome medicine.2017 Nov 28;29183332
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 WaiScientific reports.2017 Nov 27;29180648
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 DScience translational medicine.2017 Nov 15;29141885
A Bayesian method for detecting pairwise associations in compositional data.Schwager, Emma; Mallick, Himel; Ventz, Steffen; Huttenhower, CurtisPLoS computational biology.2017 Nov;29140991
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 KScientific reports.2017 Nov 14;29138425
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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, MihaiBriefings in bioinformatics.2019 Jul 19;28968737
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, CurtisNature biotechnology.2017 Nov;28967885
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, CurtisNature.2017 10 05;28953883
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 KPloS one.2017;28846702
Human genetic variation and the gut microbiome in disease.Hall, Andrew Brantley; Tolonen, Andrew C; Xavier, Ramnik JNature reviews. Genetics.2017 11;28824167
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 MMicrobiome.2017 Aug 10;28797298
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, TanjaNature biotechnology2017 Aug 0828787424
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, JMucosal immunology.2018 03;28745328
The Microbiome and Biomarkers for Necrotizing Enterocolitis: Are We Any Closer to Prediction?Rusconi, Brigida; Good, Misty; Warner, Barbara BThe Journal of pediatrics.2017 Oct;28669607
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 CNature.2017 Jul 13;28658209
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, RosemaryPapillomavirus research (Amsterdam, Netherlands).2016 Dec;28616595
Dissecting the human microbiome with single-cell genomics.Tolonen, Andrew C; Xavier, Ramnik JGenome medicine.2017 Jun 14;28615076
Vaginal Candida spp. genomes from women with vulvovaginal candidiasis.Bradford, L Latéy; Chibucos, Marcus C; Ma, Bing; Bruno, Vincent; Ravel, JacquesPathogens and disease.2017 08 31;28582496
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 PCancer prevention research (Philadelphia, Pa.).2017 Aug;28576788
Isolated Congenital Anosmia and CNGA2 Mutation.Sailani, M Reza; Jingga, Inlora; MirMazlomi, Seyed Hashem; Bitarafan, Fatemeh; Bernstein, Jonathan A; Snyder, Michael P; Garshasbi, MasoudScientific reports.2017 06 01;28572688
Early pregnancy vaginal microbiome trends and preterm birth.Stout, Molly J; Zhou, Yanjiao; Wylie, Kristine M; Tarr, Phillip I; Macones, George A; Tuuli, Methodius GAmerican journal of obstetrics and gynecology.2017 09;28549981
Re: Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease.Misra, Ravi; Arebi, NailaGastroenterology.2017 06;28478146
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 WJournal of pediatric surgery.2017 Jun;28410788
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, XiaolanImmunobiology.2017 Jul;28390705
Antibacterial and bioactive coatings on titanium implant surfaces.Kulkarni Aranya, Anupama; Pushalkar, Smruti; Zhao, Minglei; LeGeros, Racquel Z; Zhang, Yu; Saxena, DeepakJournal of biomedical materials research. Part A.2017 Aug;28380669
Bead mediated separation of microparticles in droplets.Wang, Sida; Sung, Ki-Joo; Lin, Xiaoxia Nina; Burns, Mark APloS one201728282412
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, JosefMicrobiome.2017 03 09;28274256
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, RobMicrobiome.2017 03 03;28253908
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 BInflammatory bowel diseases.2017 Feb 13;28248733
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 BInflammatory bowel diseases.2017 03;28221248
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 KNature microbiology.2017 Feb 13;28191884
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 PScience (New York, N.Y.).2017 02 10;28183913
Microbial strain-level population structure and genetic diversity from metagenomes.Truong, Duy Tin; Tett, Adrian; Pasolli, Edoardo; Huttenhower, Curtis; Segata, NicolaGenome research.2017 Apr;28167665
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 QJournal of immunology (Baltimore, Md. : 1950).2017 Mar 01;28130498
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 MNature medicine.2017 Mar;28112736
Genome Sequence of Christensenella minuta DSM 22607T.Rosa, Bruce A; Hallsworth-Pepin, Kymberlie; Martin, John; Wollam, Aye; Mitreva, MakedonkaGenome announcements.2017 Jan 12;28082495
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 PPLoS biology.2017 Jan;28081144
The balance of metagenomic elements shapes the skin microbiome in acne and health.Barnard, Emma; Shi, Baochen; Kang, Dezhi; Craft, Noah; Li, HuiyingScientific reports.2016 12 21;28000755
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 KContraception.2016 Nov 29;27913230
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 UBMC bioinformatics.2016 Dec 01;27905885
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, MichaelPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.2016;27897013
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 JCell.2016 Nov 03;27814509
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 SJournal of neurovirology.2017 Apr;27739035
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 SJournal of leukocyte biology.2017 03;27733581
Ethical issues in microbiome research and medicine.Rhodes, RosamondBMC medicine.2016 Oct 12;27729053
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 WCell reports.2016 Oct 4;27705799
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, SubraGastroenterology.2017 Jan;27693347
A New Catalog of Microbiological Tools for Women's Infectious Disease Research.Lewis, Amanda L; Lewis, Warren GGenome announcements.2016 Sep 29;27688331
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 LGenome announcements.2016 Sep 29;27688330
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 GGenome announcements.2016 Sep 29;27688329
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 GGenome announcements.2016 Sep 29;27688328
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 LGenome announcements.2016 Sep 29;27688327
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 LGenome announcements.2016 Sep 29;27688326
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.Davison, Michelle; Treangen, Todd J; Koren, Sergey; Pop, Mihai; Bhaya, DevakiPloS one.2016;27611571
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, AlainInflammatory bowel diseases.2016 Oct;27575496
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, NicolaNature microbiology.2016 05 27;27572971
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 DNature microbiology.2016;27572644
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, GautamNature microbiology.2016 Mar 07;27572443
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 BScientific reports.2016 Aug 26;27561676
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 JJournal of the American Academy of Dermatology.2016 Sep;27543211
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 MGenome medicine.2016 08 09;27503374
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 HNature communications.2016 Aug 09;27503255
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 HGastroenterology.2016 Oct;27492617
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 DThorax.2017 Jan;27486204
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, GautamGut microbes.2016 09 02;27472377
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, JNeurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society.2017 Jan;27458085
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 NThe Journal of infectious diseases.2016 Aug 15;27449870
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 JNature.2016 07 21;27409808
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 MAmerican journal of physical anthropology.2016 Oct;27357925
Gut bacteria and late-onset neonatal bloodstream infections in preterm infants.Tarr, Phillip I; Warner, Barbara BSeminars in fetal & neonatal medicine.2016 12;27345372
Necrotizing enterocolitis and preterm infant gut bacteria.Warner, Barbara B; Tarr, Phillip ISeminars in fetal & neonatal medicine.2016 12;27343151
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 JScience translational medicine.2016 Jun 15;27306663
Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis.Zackular, Joseph P; Baxter, Nielson T; Chen, Grace Y; Schloss, Patrick DmSphere.2016 Jan-Feb;27303681
STOPPING DECEPTIVE HEALTH CLAIMS: THE NEED FOR A PRIVATE RIGHT OF ACTION UNDER FEDERAL LAW.Hoffmann, Diane; Schwartz, JackAmerican journal of law & medicine.2016;27263263
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 LThe ISME journal.2016 12;27258950
Challenges for case-control studies with microbiome data.Brooks, J PaulAnnals of epidemiology.2016 05;27255739
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, ElhananmSystems.2016 Jan-Feb;27239563
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 KScience (New York, N.Y.).2016 May 27;27230380
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 LmBio.2016 05 13;27178263
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 WInternational journal of obesity (2005).2016 Sep;27163748
Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples.Rhee, Minsoung; Light, Yooli K; Meagher, Robert J; Singh, Anup KPloS one.2016;27144304
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 JCell.2016 May 5;27133167
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, PeterScientific reports.2016 Apr 22;27103053
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 JPloS one.2016;27088867
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 BAmerican journal of physiology. Gastrointestinal and liver physiology.2016 06 01;27079612
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-HengAmerican journal of clinical and experimental urology.2016;27069958
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 KPeerJ.2016;27069806
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 DmBio.2016 Mar 29;27025251
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 LCell reports.2016 Mar 29;26997279
Microbiome and potential targets for chemoprevention of esophageal adenocarcinoma.Neto, Antonio Galvao; Whitaker, April; Pei, ZhihengSeminars in oncology.2016 Feb;26970127
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 ILancet (London, England).2016 May 07;26969089
Can Metabolic Profiles Be Used as a Phenotypic Readout of the Genome to Enhance Precision Medicine?Contrepois, Kévin; Liang, Liang; Snyder, MichaelClinical chemistry.2016 May;26960666
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, RobThe ISME journal.2016 Feb 23;26905627
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 GMicrobiome.2016 Jan 21;26796629
A quantitative understanding of lac repressor's binding specificity and flexibility.Zuo, Zheng; Chang, Yiming; Stormo, Gary DQuantitative biology (Beijing, China).2015 Jun 01;26752632
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, JonathanArthritis & rheumatology (Hoboken, N.J.).2016 06;26749064
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 KMicrobiology (Reading, England).2016 Jan 8;26747455
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, ZhihengAIDS (London, England).2016 Jan 02;26731752
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 JNature genetics.2016 Feb;117-2526691984
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.Kaminski, James; Gibson, Molly K; Franzosa, Eric A; Segata, Nicola; Dantas, Gautam; Huttenhower, CurtisPLoS computational biology.2015 Dec;26682918
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 MCurrent biology : CB.2015 Dec 21;26671671
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, JamesmBio.2015 Dec 15;26670383
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, RobScience (New York, N.Y.).2016 Jan 8;158-6226657285
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.Kuleshov, Volodymyr; Jiang, Chao; Zhou, Wenyu; Jahanbani, Fereshteh; Batzoglou, Serafim; Snyder, MichaelNature biotechnology.2016 Jan;26655498
The microbiome quality control project: baseline study design and future directions.Sinha, Rashmi; Abnet, Christian C; White, Owen; Knight, Rob; Huttenhower, CurtisGenome biology.2015;26653756
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 MJournal of clinical microbiology.2016 Feb;26637379
Engineering Values Into Genetic Engineering: A Proposed Analytic Framework for Scientific Social Responsibility.Sankar, Pamela L; Cho, Mildred KThe American journal of bioethics : AJOB.2015;26632356
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, MarkPLoS computational biology.2015 Dec;26625158
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 GMicrobiome.2015 Dec 01;26620712
Luminal Conversion and Immunoregulation by Probiotics.Ganesh, Bhanu Priya; Versalovic, JamesFrontiers in pharmacology.2015;26617521
Nurturing the microbiome field.Schloss, PatrickScience (New York, N.Y.)2015 Nov 2726612945
Microfluidic Flow Cytometry for Single-Cell Protein Analysis.Wu, Meiye; Singh, Anup KMethods in molecular biology (Clifton, N.J.).2015;26542716
Microbiome, a new dimension in cancer research.Neto, Antonio Galvao; Bradshaw, Azore-Dee; Pei, ZhihengAnnals of translational medicine.2015 Sep;26539446
Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season.Wylie, Kristine M; Weinstock, George M; Storch, Gregory AJournal of the Pediatric Infectious Diseases Society.2015 Dec;e84-926513823
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, MakedonkaJournal of data mining in genomics & proteomics.2015 Aug;26500804
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 EPediatric cardiology.2016 Feb;26499513
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 WLancet (London, England).2016 Jan 9;156-6726490195
The influence of non-steroidal anti-inflammatory drugs on the gut microbiome.Rogers, M A M; Aronoff, D MClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.2016 Feb;178.e1-926482265
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 DCell host & microbe.2015 Oct 14;26468751
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, NicolaNature methods.2015 Oct;902-326418763
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 GGenome biology.2015 Sep 15;26374288
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 RNature medicine.2015 Oct;26366711
ConStrains identifies microbial strains in metagenomic datasets.Luo, Chengwei; Knight, Rob; Siljander, Heli; Knip, Mikael; Xavier, Ramnik J; Gevers, DirkNature biotechnology.2015 Oct;1045-5226344404
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, JamesMicrobiome.2015;26306392
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 DInflammatory bowel diseases.2015 Dec;26288001
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, SubraGastroenterology.2015 Nov;1575-8626278503
The gut microbiota in human energy homeostasis and obesity.Rosenbaum, Michael; Knight, Rob; Leibel, Rudolph LTrends in endocrinology and metabolism: TEM.2015 Sep;493-50126257300
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 ProjectAmerican journal of respiratory and critical care medicine.2015 Dec 01;26247840
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 GloriaScience advances.2015 Apr 3;26229982
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 SStandards in genomic sciences.2015;26221418
Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile.Schubert, Alyxandria M; Sinani, Hamide; Schloss, Patrick DmBio.2015 Jul 14;e0097426173701
Role of Autophagy in the Maintenance of Intestinal Homeostasis.Baxt, Leigh A; Xavier, Ramnik JGastroenterology.2015 Sep;553-6226170139
Compact graphical representation of phylogenetic data and metadata with GraPhlAn.Asnicar, Francesco; Weingart, George; Tickle, Timothy L; Huttenhower, Curtis; Segata, NicolaPeerJ.2015;26157614
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 JNature communications.2015 Jun 30;26123276
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, NunoScientific reports.2015 Jun 26;26113465
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 LPloS one.2015 Jun 25;e013060426110908
Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis.Kang, Dezhi; Shi, Baochen; Erfe, Marie C; Craft, Noah; Li, HuiyingScience translational medicine.2015 Jun 24;293ra10326109103
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 BInfection control and hospital epidemiology.2015 Oct;26108888
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 JAlimentary pharmacology & therapeutics.2015 Aug;418-2726104013
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 DThe Journal of clinical investigation.2015 Jul 1;2841-5026098218
Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease.Vital, Marius; Harkema, Jack R; Rizzo, Mike; Tiedje, James; Brandenberger, ChristinaJournal of immunology research.2015 April 16;26090504
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 DInflammatory bowel diseases.2015 Aug;1948-5626083617
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 LPloS one.2015;26083474
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 DmBio.2015 June 16;e0064826081634
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 RPloS one.2015 June 15;e012905526076489
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, DannyDiabetes.2015 Oct;3510-2026068542
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, JamesJPEN. Journal of parenteral and enteral nutrition.2016 11;26059898
Lungs, microbes and the developing neonate.Warner, Barbara B; Hamvas, AaronNeonatology.2015 June;337-4326044101
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, CeciliaAIDS (London, England).2015 Jun 19;F1-826035329
Carcass mass has little influence on the structure of gravesoil microbial communities.Weiss, Sophie; Carter, David O; Metcalf, Jessica L; Knight, RobInternational journal of legal medicine.2016 Jan;26024793
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 UAmerican journal of perinatology.2015 Nov;26007311
High-throughput sequencing technologies.Reuter, Jason A; Spacek, Damek V; Snyder, Michael PMolecular cell.2015 May 21;586-9726000844
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, PeterJournal of bacteriology.2015 Aug 1;2508-1625986902
An integrative view of microbiome-host interactions in inflammatory bowel diseases.Wlodarska, Marta; Kostic, Aleksandar D; Xavier, Ramnik JCell host & microbe.2015 May 13;577-9125974300
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 DInflammatory bowel diseases.2015 Aug;1786-9325970545
Identifying personal microbiomes using metagenomic codes.Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, CurtisProceedings of the National Academy of Sciences of the United States of America.2015 Jun 2;E2930-825964341
Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis.Segal, Leopoldo N; Blaser, Martin JThe Journal of pediatrics.2015 Jul;16-18.e125934071
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, CurtisNature reviews. Microbiology.2015 Jun;360-7225915636
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 BCell host & microbe.2015 May 13;681-925891358
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, CurtisGenome biology.2015 Apr 8;25887922
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 ABMC microbiology.2015 Mar 21;25880246
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, JiyoungPloS one.2015 Apr 15;e012459925874569
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 NmBio.2015 Apr 14;25873373
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 YCell.2015 Apr 9;264-7625860609
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 MGenome research.2015 May;679-8925858952
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, JamesThe American journal of gastroenterology.2015 Apr;25853207
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, HuiyingThe ISME journal.2015 Sep;2078-9325848871
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, HongzheBioinformatics (Oxford, England).2015 Aug 01;25819674
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 NThe Journal of allergy and clinical immunology.2015 Aug;25819063
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 CThe Journal of pediatrics.2015 Jul;138-47.e1-325818499
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 MNature communications.2015 Mar 25;25807110
Personal genomes, quantitative dynamic omics and personalized medicine.Mias, George I; Snyder, MichaelQuantitative biology.2013 Mar;71-9025798291
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, MichaelMolecular & cellular proteomics : MCP.2015 Jun;1684-9525787789
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 EPloS one.2015 Mar 5;e011863225741698
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 BInflammatory bowel diseases.2015 May;963-7225738379
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 CCell host & microbe.2015 Mar 11;385-9125732063
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 DPloS one.2015 Feb 17;e011773825689864
Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates.Ma, Jun; Purcell, Heidi; Showalter, Lori; Aagaard, Kjersti MAmerican journal of obstetrics and gynecology.2015 Apr;530.e1-825687567
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, FernandoPLoS genetics.2015 Feb;e100485025679959
Impact of allele-specific peptides in proteome quantification.Wu, Linfeng; Snyder, MichaelProteomics. Clinical applications.2015 Apr;432-625676416
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 JCell host & microbe.2015 Feb 11;260-7325662751
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 KAmerican journal of obstetrics and gynecology.2015 Jun;779.e1-779.e1325637842
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 WCell.2015 Jan 29;447-6025619688
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, PengAmerican journal of clinical and experimental urology.2014;25606580
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 DGastroenterology.2015 May;1087-10625597840
Asynchronous Magnetic Bead Rotation (AMBR) Microviscometer for Label-Free DNA Analysis.Li, Yunzi; Burke, David T; Kopelman, Raoul; Burns, Mark ABiosensors2014 Mar25587411
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 JGenome medicine.2014;25587358
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 JThe Journal of infectious diseases.2015 Jun 15;1895-90425583170
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, FolkerPLoS computational biology.2015 Jan;e100400825569221
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 DNature genetics.2015 Feb;172-925559196
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, KjerstiAmerican journal of obstetrics and gynecology.2015 May;653.e1-1625557210
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, ManfredScientific reports.2014;25519916
Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease.Esplin, Edward D; Oei, Ling; Snyder, Michael PPharmacogenomics.2014 Nov;1771-179025493570
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 EGenome medicine201425484919
Determining microbial products and identifying molecular targets in the human microbiome.Joice, Regina; Yasuda, Koji; Shafquat, Afrah; Morgan, Xochitl C; Huttenhower, CurtisCell metabolism.2014 Nov 4;731-4125440055
Beyond infectious disease: welcome to the era of population microbiology.Pincus, Matthew R; Pei, ZhihengClinics in laboratory medicine.2014 Dec;25439278
The changing landscape of the vaginal microbiome.Huang, Bernice; Fettweis, Jennifer M; Brooks, J Paul; Jefferson, Kimberly K; Buck, Gregory AClinics in laboratory medicine.2014 Dec;747-6125439274
Microbiome, innate immunity, and esophageal adenocarcinoma.Baghdadi, Jonathan; Chaudhary, Noami; Pei, Zhiheng; Yang, LiyingClinics in laboratory medicine.2014 Dec;721-3225439272
The interrelationships of the gut microbiome and inflammation in colorectal carcinogenesis.Cho, Margaret; Carter, Janell; Harari, Saul; Pei, ZhihengClinics in laboratory medicine.2014 Dec;699-71025439270
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 DGut.2014 Nov 26;25431456
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 ABMC bioinformatics.2014;25407910
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 CThe 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.2016;25394613
The gut microbiome in health and in disease.Shreiner, Andrew B; Kao, John Y; Young, Vincent BCurrent opinion in gastroenterology.2015 Jan;69-7525394236
Versatile on-demand droplet generation for controlled encapsulation.Rhee, Minsoung; Liu, Peng; Meagher, Robert J; Light, Yooli K; Singh, Anup KBiomicrofluidics.2014 May;25379072
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 MmBio.2014;e0186425370491
Spec-seq: determining protein-DNA-binding specificity by sequencing.Stormo, Gary D; Zuo, Zheng; Chang, Yiming KennyBriefings in functional genomics.2015 Jan;30-825362070
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 DApplied and environmental microbiology.2015 Jan;396-40425362056
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 JG3 (Bethesda, Md.).2014 Dec;2353-6325344410
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 MThe ISME journal.2015 Apr;832-4325343515
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 MThe ISME journal.2015 May;1130-4025343512
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 APloS one.2014;e11094325337710
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 LThe ISME journal.2015 Mar 17;25325381
Meta-analyses of human gut microbes associated with obesity and IBD.Walters, William A; Xu, Zech; Knight, RobFEBS letters.2014 Nov 17;25307765
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, OwenCell.2014 Oct 9;227-3025303518
Microbiology: An integrated view of the skin microbiome.Schloss, Patrick DNature2014 Oct 0225279916
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 RInternational forum of allergy & rhinology.2015 Jan;25278448
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 RJournal of clinical microbiology.2014 Dec;4260-625275005
The microbiome revolution.Blaser, Martin JThe Journal of clinical investigation.2014 Oct;4162-525271724
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 KLab on a chip.2014 Dec 7;4533-925270338
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 EAIDS research and human retroviruses.2014 Nov;1046-5425265254
MiRNA detection at single-cell resolution using microfluidic LNA flow-FISH.Wu, Meiye; Piccini, Matthew E; Singh, Anup KMethods in molecular biology (Clifton, N.J.).2014;245-6025218391
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 MBMC biology.2014;25212266
The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease.Integrative HMP (iHMP) Research Network ConsortiumCell host & microbe.2014 Sep 10;276-8925211071
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding.Zuo, Zheng; Stormo, Gary DGenetics.2014 Nov;1329-4325209146
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, JamesStandards in genomic sciences.2014 Jun 15;25197459
From deep sequencing to actual clones.D'Angelo, Sara; Kumar, Sandeep; Naranjo, Leslie; Ferrara, Fortunato; Kiss, Csaba; Bradbury, Andrew R MProtein engineering, design & selection : PEDS.2014 Oct;301-725183780
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 AScience (New York, N.Y.).2014 Aug 29;1048-5225170151
Probiotics: achieving a better regulatory fit.Hoffmann, Diane E; Fraser, Claire M; Palumbo, Francis; Ravel, Jacques; Rowthorn, Virginia; Schwartz, JackFood and drug law journal2014237-72, ii25163211
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, ZhihengAmerican journal of clinical and experimental urology2014 Apr 1557-6125126590
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 IProceedings of the National Academy of Sciences of the United States of America.2014 Aug 26;12522-725114261
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, DeepakInternational journal of oral science.2014 Dec;25105817
The Human Gut Microbiome as a Screening Tool for Colorectal Cancer.Zackular, Joseph P; Rogers, Mary A M; Ruffin 4th, Mack T; Schloss, Patrick DCancer prevention research (Philadelphia, Pa.)2014 Aug 7NULL25104642
Phylogenetics and the human microbiome.Matsen 4th, Frederick ASystematic biology.2015 Jan;e26-4125102857
Phase variation of poly-N-acetylglucosamine expression in Staphylococcus aureus.Brooks, Jamie L; Jefferson, Kimberly KPLoS pathogens.2014 Jul;e100429225077798
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)2014 Jul 29NULL25073854
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 AMicrobiome20141425071935
The dynamics of a family's gut microbiota reveal variations on a theme.Schloss, Patrick D; Iverson, Kathryn D; Petrosino, Joseph F; Schloss, Sarah JMicrobiome.2014;25061514
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 DGastroenterology.2014 Nov;1055-63.e825046162
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 ECell.2014 Jul 17;25036628
Serum profiling using protein microarrays to identify disease related antigens.Sharon, Donald; Snyder, MichaelMethods in molecular biology (Clifton, N.J.).2014;169-7825030927
Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution.Wu, Meiye; Singh, Anup KJournal of laboratory automation.2014 Dec;587-9225027027
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 SGut.2015 Jun;911-2025007816
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, JosephmBio2014e01390-1425006230
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 AThe Journal of clinical investigation.2014 Aug;3617-3325003194
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, SandraGenome biology2014R7624995464
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, RobFrontiers in microbiology.2014;24995004
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, SomyingBMC microbiology201417724989059
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 FProceedings of the National Academy of Sciences of the United States of America2014 Jul 89768-7324965364
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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 KGenome biology and evolution2014 Jul1772-8924951561
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Microbiome in reflux disorders and esophageal adenocarcinoma.Yang, Liying; Chaudhary, Noami; Baghdadi, Jonathan; Pei, ZhihengCancer journal (Sudbury, Mass.)2014 May-Jun207-1024855009
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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, CurtisProceedings of the National Academy of Sciences of the United States of America2014 Jun 3E2329-3824843156
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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 DmBio2014e01021-1424803517
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; BraThe ISME journal2014 Apr 29NULL24781901
Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data.Vital, Marius; Howe, Adina Chuang; Tiedje, James MmBio2014e0088924757212
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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, MirceaEnvironmental microbiology2014 Apr 17NULL24738594
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 SPloS one2014e8864524670812
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, HClinical infectious diseases : an official publication of the Infectious Diseases Society of America2014 May1211-824647013
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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 & microbe2014 Mar 12382-9224629344
Functional and phylogenetic assembly of microbial communities in the human microbiome.Shafquat, Afrah; Joice, Regina; Simmons, Sheri L; Huttenhower, CurtisTrends in microbiology2014 Mar 4NULL24618403
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The microbiome in inflammatory bowel disease: current status and the future ahead.Kostic, Aleksandar D; Xavier, Ramnik J; Gevers, DirkGastroenterology2014 May1489-9924560869
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, JacquesMicrobiome.2014;24558975
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 JPloS one2014e8939824551246
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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 EMicrobiome2014524529162
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, ZhihengJournal of virology2014 May4786-9724522917
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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 AG3 (Bethesda, Md.)2014 Apr561-7824496724
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, JAntonie van Leeuwenhoek2014 Mar579-9224488273
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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; DalaMicrobiome2013924451366
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 MMicrobiome2013824451334
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; AlvThe ISME journal2014 Jan 23NULL24451203
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 JMicrobiome20132924451163
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A brave new world: the lung microbiota in an era of change.Segal, Leopoldo N; Blaser, Martin JAnnals of the American Thoracic Society2014 JanS21-724437400
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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, JonathanPloS one2013e8070224260458
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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, MirceaProceedings of the National Academy of Sciences of the United States of America2013 Apr 25540-523509275
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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; TwiggAmerican journal of respiratory and critical care medicine2013 May 151067-7523491408
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Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes.Ballarini, Annalisa; Segata, Nicola; Huttenhower, Curtis; Jousson, OlivierPloS one2013e5576423409037
The human gut microbiome and body metabolism: implications for obesity and diabetes.Devaraj, Sridevi; Hemarajata, Peera; Versalovic, JamesClinical chemistry2013 Apr617-2823401286
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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, HuiyingThe Journal of investigative dermatology2013 Jan 2123337890
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 SScience (New York, N.Y.)2013 Mar 11084-823328391
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 EPLoS computational biology2013 Jane100286323326225
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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 JThe Journal of infectious diseases2013 Apr1105-1423300163
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'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 RHealth expectations : an international journal of public participation in health care and health policy2012 Dec 2823279082
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 MPloS one2012e5114623251439
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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; JansPloS one2012e4913823209564
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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 AAntimicrobial agents and chemotherapy2013 Jan261-823114757
"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 LBMC medical ethics20122823110633
Dietary issues in recurrent abdominal pain.Shulman, Robert JJournal of pediatric gastroenterology and nutrition2012 NovS40-223103654
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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 RScience translational medicine2012 Sep 26153ra13023019655
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Diverse CRISPRs evolving in human microbiomes.Rho, Mina; Wu, Yu-Wei; Tang, Haixu; Doak, Thomas G; Ye, YuzhenPLoS genetics2012e100244122719260
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, PatPLoS computational biology2012e100235822719234
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A framework for human microbiome research.Human Microbiome Project ConsortiumNature2012 Jun 14215-2122699610
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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, JacquesGenome biology2012R4222698087
A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community.Wang, Mingjie; Ye, Yuzhen; Tang, HaixuJournal of computational biology : a journal of computational molecular cell biology2012 Jun814-2522697249
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Understanding vaginal microbiome complexity from an ecological perspective.Hickey, Roxana J; Zhou, Xia; Pierson, Jacob D; Ravel, Jacques; Forney, Larry JTranslational research : the journal of laboratory and clinical medicine2012 Oct267-8222683415
The microbiome of the lung.Beck, James M; Young, Vincent B; Huffnagle, Gary BTranslational research : the journal of laboratory and clinical medicine2012 Oct258-6622683412
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 ANature biotechnology.2012 Jun;22678395
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 RayStandards in genomic sciences.2011 Dec 31;22675588
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, SalomonPloS one2012e3791922675498
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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 MPloS one2012e3693422655031
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Spatial and temporal variability of the human microbiota.Parfrey, L W; Knight, RClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases2012 Jul8-1122647040
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, RobRNA (New York, N.Y.)2012 Jul22645380
'Omics' of the mammalian gut--new insights into function.Lamendella, Regina; VerBerkmoes, Nathan; Jansson, Janet KCurrent opinion in biotechnology2012 Jun491-50022626866
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-JunPloS one2012e3694022615851
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, EllenPloS one2012e3713922606341
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 DennisPloS one2012e3629822606251
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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 AChemistry & biodiversity2012 May965-7622589096
Food and the gut microbiota in inflammatory bowel diseases: a critical connection.Albenberg, Lindsey G; Lewis, James D; Wu, Gary DCurrent opinion in gastroenterology2012 Jul314-2022573192
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, JohnPloS one2012e3600922558305
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, JacquesScience translational medicine2012 May 2132ra5222553250
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots.Matsen, Frederick A; Gallagher, AaronAlgorithms for molecular biology : AMB.2012 May 02;22549005
We are what we eat: how the diet of infants affects their gut microbiome.Pop, MihaiGenome biology201215222546514
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, RobThe Journal of allergy and clinical immunology2012 May1204-822541361
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 FPloS one2012e3547022532855
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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 FInfection and immunity2012 Jun2150-722493085
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, AndreasGenome biology2012R2322455878
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 JProceedings of the National Academy of Sciences of the United States of America2012 Apr 105809-1422451929
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, DavidNature medicine2012 Apr538-4622447074
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, AlexDatabase : the journal of biological databases and curation2012bas00322434837
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 CGenome research2012 Jun1107-1922434425
The impact of the gut microbiota on human health: an integrative view.Clemente, Jose C; Ursell, Luke K; Parfrey, Laura Wegener; Knight, RobCell.2012 Mar 16;22424233
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 TActa crystallographica. Section E, Structure reports online.2012 Mar 01;22412514
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, BabakActa crystallographica. Section E, Structure reports online.2012 Mar 01;22412406
The human microbiome: at the interface of health and disease.Cho, Ilseung; Blaser, Martin JNature reviews. Genetics2012 Apr260-7022411464
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, RobThe ISME journal.2012 Aug;1621-422402401
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 RHealth and quality of life outcomes20122522401607
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, EugenePloS one2012e3254522389708
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Of microbes and meals: the health consequences of dietary endotoxemia.Kelly, Caleb J; Colgan, Sean P; Frank, Daniel NNutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition.2012 Apr;22378797
Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, AndrePloS one2012e3159722355378
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Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus.Yang, Liying; Francois, Fritz; Pei, ZhihengClinical cancer research : an official journal of the American Association for Cancer Research2012 Apr 152138-4422344232
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, JamesJournal of pediatric gastroenterology and nutrition2012 Sep299-30722343914
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 NJournal of acquired immune deficiency syndromes (1999)2012 Jul 1299-30622343176
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 ScottThe Journal of clinical investigation2012 Mar 1974-8622326959
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; MartiThorax2012 May456-6322318161
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, NoahSoil biology & biochemistry2011 Jul1450-145522267877
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, JamesFASEB journal : official publication of the Federation of American Societies for Experimental Biology2012 May1960-922267340
Perturbation dynamics of the rumen microbiota in response to exogenous butyrate.Li, Robert W; Wu, Sitao; Baldwin 6th, Ransom L; Li, Weizhong; Li, CongjunPloS one2012e2939222253719
Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis.Feazel, Leah M; Robertson, Charles E; Ramakrishnan, Vijay R; Frank, Daniel NThe Laryngoscope2012 Feb467-7222253013
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, EInternational endodontic journal2012 Jun530-4122251411
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences.Soergel, David A W; Dey, Neelendu; Knight, Rob; Brenner, Steven EThe ISME journal2012 Jul1440-422237546
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, MihaiBriefings in bioinformatics2013 Mar213-2422199379
Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws.Smajs, David; Norris, Steven J; Weinstock, George MInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2012 Mar191-20222198325
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, NehaPloS one2011e2888622194940
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.Schloss, Patrick D; Gevers, Dirk; Westcott, Sarah LPloS one2011e2731022194782
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SitePainter: a tool for exploring biogeographical patterns.Gonzalez, Antonio; Stombaugh, Jesse; Lauber, Christian L; Fierer, Noah; Knight, RobBioinformatics (Oxford, England)2012 Feb 1436-822171330
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences.Wang, Xiaoyu; Cai, Yunpeng; Sun, Yijun; Knight, Rob; Mai, VolkerThe ISME journal2012 Jul1277-8022170430
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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, DanielNucleic acids research2012 JanD237-4122140108
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 CNucleic acids research2012 JanD571-922135293
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, PhilipThe ISME journal2012 Mar610-822134646
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The Human Microbiome Project: lessons from human genomics.Lewis Jr, Cecil M; Obregon-Tito, Alexandra; Tito, Raul Y; Foster, Morris W; Spicer, Paul GTrends in microbiology2012 Jan1-422112388
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment.Ye, YuzhenProceedings. IEEE International Conference on Bioinformatics and Biomedicine2011 Feb 4153-15722102981
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, DavidEmerging infectious diseases2011 Nov2050-222099095
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ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.Basu, Malay K; Selengut, Jeremy D; Haft, Daniel HBMC bioinformatics201143422070167
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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 HActa crystallographica. Section E, Structure reports online.2011 Sep 01;22058976
Saying privacy, meaning confidentiality.Schwab, Abraham P; Frank, Lily; Gligorov, NadaThe American journal of bioethics : AJOB2011 Nov44-522047127
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RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.Zhao, Yongan; Tang, Haixu; Ye, YuzhenBioinformatics (Oxford, England)2012 Jan 1125-622039206
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Microbiome and malignancy.Plottel, Claudia S; Blaser, Martin JCell host & microbe2011 Oct 20324-3522018233
Human-associated microbial signatures: examining their predictive value.Knights, Dan; Parfrey, Laura Wegener; Zaneveld, Jesse; Lozupone, Catherine; Knight, RobCell host & microbe.2011 Oct 20;22018228
Fluorescent labeling of antibody fragments using split GFP.Ferrara, Fortunato; Listwan, Pawel; Waldo, Geoffrey S; Bradbury, Andrew R MPloS one2011e2572721998685
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.Liu, Bo; Gibbons, Theodore; Ghodsi, Mohammad; Treangen, Todd; Pop, MihaiBMC genomics2011S421989143
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, ClaireBioinformatics (Oxford, England)2011 Dec 13242-921984758
Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies.Segata, Nicola; Huttenhower, CurtisPloS one2011e2470421931822
Bambus 2: scaffolding metagenomes.Koren, Sergey; Treangen, Todd J; Pop, MihaiBioinformatics (Oxford, England)2011 Nov 12964-7121926123
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 ICell host & microbe2011 Sep 15260-7221925113
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-HwaBiomicrofluidics.2011 Sep;21915241
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 SApplied and environmental microbiology2011 Nov7804-1421908640
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.Pirrung, Meg; Kennedy, Ryan; Caporaso, J Gregory; Stombaugh, Jesse; Wendel, Doug; Knight, RobBioinformatics (Oxford, England)2011 Nov 13067-921903626
WebMGA: a customizable web server for fast metagenomic sequence analysis.Wu, Sitao; Zhu, Zhengwei; Fu, Liming; Niu, Beifang; Li, WeizhongBMC genomics201144421899761
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, WadihThe New England journal of medicine2011 Sep 8892-90021899450
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; BusScience (New York, N.Y.)2011 Oct 7105-821885731
Antibiotic effects on bacterial profile in osteonecrosis of the jaw.Ji, X; Pushalkar, S; Li, Y; Glickman, R; Fleisher, K; Saxena, DOral diseases2012 Jan85-9521883710
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, RobTrends in microbiology2011 Oct472-8221872475
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 BPloS one2011e2278821829515
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-HwaAnalytical chemistry2011 Oct 17269-7521809842
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 BGut microbes2011 May-Jun145-5821804357
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, JizhongThe ISME journal2012 Feb259-7221796217
Investigating the biological and clinical significance of human dysbioses.Frank, Daniel N; Zhu, Wei; Sartor, R Balfour; Li, EllenTrends in microbiology2011 Sep427-3421775143
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 BFrontiers in microbiology201114421772835
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 TNature methods2011 Sep761-321765408
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 KLab on a chip2011 Aug 212673-921755095
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, SusGastroenterology2011 Nov1782-9121741921
Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown.Lladser, Manuel E; Gouet, Raul; Reeder, JensPloS one2011e2110521738613
DNACLUST: accurate and efficient clustering of phylogenetic marker genes.Ghodsi, Mohammadreza; Liu, Bo; Pop, MihaiBMC bioinformatics201127121718538
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 EThe ISME journal2012 Jan94-10321716311
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 RJournal of clinical gastroenterology2012 Feb138-4421716123
Metagenomic biomarker discovery and explanation.Segata, Nicola; Izard, Jacques; Waldron, Levi; Gevers, Dirk; Miropolsky, Larisa; Garrett, Wendy S; Huttenhower, CurtisGenome biology2011R6021702898
UCHIME improves sensitivity and speed of chimera detection.Edgar, Robert C; Haas, Brian J; Clemente, Jose C; Quince, Christopher; Knight, RobBioinformatics (Oxford, England)2011 Aug 152194-20021700674
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 WJournal of pediatric surgery2011 Jun1029-3321683193
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 TGut2012 Mar373-8421646247
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, RobGenome biology2011R5021624126
Mammalian Cell Sorting using ýýFACS.Cho, Sung Hwan; Chen, Chun Hao; Tsai, Frank S; Godin, Jessica; Lo, Yu-HwaConference on Lasers and Electro-optics : (CLEO). Conference on Lasers and Electro-optics2010 May 16CTuD121614147
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, BarbaraPloS one2011e1970921603636
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 LObesity (Silver Spring, Md.)2012 Apr738-4721593810
RAPSearch: a fast protein similarity search tool for short reads.Ye, Yuzhen; Choi, Jeong-Hyeon; Tang, HaixuBMC bioinformatics201115921575167
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 VNature reviews. Microbiology2011 Jun467-7721552286
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-SerrNature biotechnology2011 May415-2021552244
Boulder ALignment Editor (ALE): a web-based RNA alignment tool.Stombaugh, Jesse; Widmann, Jeremy; McDonald, Daniel; Knight, RobBioinformatics (Oxford, England)2011 Jun 151706-721546392
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 MAmerican journal of physical anthropology2011 Aug653-721541929
Development of the human gastrointestinal microbiota and insights from high-throughput sequencing.Dominguez-Bello, Maria Gloria; Blaser, Martin J; Ley, Ruth E; Knight, RobGastroenterology2011 May1713-921530737
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, VolkerBriefings in bioinformatics2012 Jan107-2121525143
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, NielsBMC ecology20111121524302
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes.Niu, Beifang; Zhu, Zhengwei; Fu, Limin; Wu, Sitao; Li, WeizhongBioinformatics (Oxford, England)2011 Jun 151704-521505035
Reliability and validity of a modified Bristol Stool Form Scale for children.Lane, Mariella M; Czyzewski, Danita I; Chumpitazi, Bruno P; Shulman, Robert JThe Journal of pediatrics2011 Sep437-441.e121489557
The mind-body-microbial continuum.Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J; Gordon, Jeffrey I; Knight, RobDialogues in clinical neuroscience201155-6221485746
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.Haft, Daniel H; Basu, Malay KumarJournal of bacteriology2011 Jun2745-5521478363
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, ChangyiWorld journal of surgery2011 Aug1693-921424870
Unravelling the effects of the environment and host genotype on the gut microbiome.Spor, Ayme; Koren, Omry; Ley, RuthNature reviews. Microbiology2011 Apr279-9021407244
Next generation sequence assembly with AMOS.Treangen, Todd J; Sommer, Dan D; Angly, Florent E; Koren, Sergey; Pop, MihaiCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]2011 MarUnit 11.821400694
Beyond natural antibodies: the power of in vitro display technologies.Bradbury, Andrew R M; Sidhu, Sachdev; Dubel, Stefan; McCafferty, JohnNature biotechnology2011 Mar245-5421390033
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.Wu, Yu-Wei; Ye, YuzhenJournal of computational biology : a journal of computational molecular cell biology2011 Mar523-3421385052
Host-associated and free-living phage communities differ profoundly in phylogenetic composition.Caporaso, J Gregory; Knight, Rob; Kelley, Scott TPloS one2011e1690021383980
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 RPloS one2011e1662621364937
Microdroplet-enabled highly parallel co-cultivation of microbial communities.Park, Jihyang; Kerner, Alissa; Burns, Mark A; Lin, Xiaoxia NinaPloS one2011e1701921364881
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 RGut2011 Aug1043-921317176
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 SCellular microbiology2011 Apr508-1721314883
Current concepts of the intestinal microbiota and the pathogenesis of infection.Wardwell, Leslie H; Huttenhower, Curtis; Garrett, Wendy SCurrent infectious disease reports2011 Feb28-3421308452
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, ShibuStandards in genomic sciences.2010 Mar 30;21304707
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 BPloS one2011e1622121283757
Inexact Local Alignment Search over Suffix Arrays.Ghodsi, Mohammadreza; Pop, MihaiProceedings. IEEE International Conference on Bioinformatics and Biomedicine2009 Nov 183-9721278916
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 BJournal of perinatology : official journal of the California Perinatal Association2011 Aug519-2321273988
Review Article: Recent advancements in optofluidic flow cytometer.Cho, Sung Hwan; Godin, Jessica M; Chen, Chun-Hao; Qiao, Wen; Lee, Hosuk; Lo, Yu-HwaBiomicrofluidics.2010 Dec 30;21267434
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 WayneFASEB journal : official publication of the Federation of American Societies for Experimental Biology2011 May1449-6021228220
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 AWorld journal of surgery2011 Aug1746-5021225260
Dielectrophoresis of Caenorhabditis elegans.Chuang, Han-Sheng; Raizen, David M; Lamb, Annesia; Dabbish, Nooreen; Bau, Haim HLab on a chip2011 Feb 21599-60421225036
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners.Haft, Daniel HBMC genomics20112121223593
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 AWorld journal of surgery2011 Aug1732-721221581
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; KnigGenome research2011 Mar494-50421212162
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, DeepakFEMS immunology and medical microbiology2011 Apr269-7721205002
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 JInfectious diseases in obstetrics and gynecology201073742521197076
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 DennisPloS one2010e1411621124791
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.Shah, Neethu; Tang, Haixu; Doak, Thomas G; Ye, YuzhenPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2011165-7621121044
Probiotics, enteric and diarrheal diseases, and global health.Preidis, Geoffrey A; Hill, Colin; Guerrant, Richard L; Ramakrishna, B S; Tannock, Gerald W; Versalovic, JamesGastroenterology2011 Jan8-1421075108
Digital MDA for enumeration of total nucleic acid contamination.Blainey, Paul C; Quake, Stephen RNucleic acids research2011 Mare1921071419
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 BPloS one2010e1360721042588
SmashCell: a software framework for the analysis of single-cell amplified genome sequences.Harrington, Eoghan D; Arumugam, Manimozhiyan; Raes, Jeroen; Bork, Peer; Relman, David ABioinformatics (Oxford, England)2010 Dec 12979-8020966005
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 HBiochemistry2010 Nov 3010117-3020961038
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, FredrikProceedings of the National Academy of Sciences of the United States of America2011 Mar 154592-820937873
Growth and Development Symposium: promoting healthier humans through healthier livestock: animal agriculture enters the metagenomics era.Frank, D NJournal of animal science2011 Mar835-4420935136
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 BApplied microbiology and biotechnology2010 Dec1333-4220931185
Lab-on-a-chip flow cytometer employing color-space-time coding.Cho, Sung Hwan; Qiao, Wen; Tsai, Frank S; Yamashita, Kenichi; Lo, Yu-HwaApplied physics letters.2010 Aug 30;20877655
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 one2010e1241120865041
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 BAmerican journal of physiology. Gastrointestinal and liver physiology2010 DecG1266-7520864653
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, EllenInflammatory bowel diseases2011 Jan179-8420839241
An algorithm for automated closure during assembly.Koren, Sergey; Miller, Jason R; Walenz, Brian P; Sutton, GrangerBMC bioinformatics201045720831800
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 JThe Journal of pediatrics2010 Oct594-720826285
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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, ZhihengWorld journal of gastroenterology : WJG2010 Sep 74135-4420806429
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.Reeder, Jens; Knight, RobNature methods2010 Sep668-920805793
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Quantitation of major human cutaneous bacterial and fungal populations.Gao, Zhan; Perez-Perez, Guillermo I; Chen, Yu; Blaser, Martin JJournal of clinical microbiology2010 Oct3575-8120702672
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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, NoahEnvironmental microbiology2010 Nov2885-9320545741
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 KBMC genomics201037520540756
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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, NoahFEMS microbiology letters2010 Jun80-620412303
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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-HwaLab on a chip2010 Jun 211567-7320379604
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Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.Wang, Gary P; Sherrill-Mix, Scott A; Chang, Kyong-Mi; Quince, Chris; Bushman, Frederic DJournal of virology2010 Jun6218-2820375170
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Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era.Preidis, Geoffrey A; Versalovic, JamesGastroenterology2009 May2015-3119462507
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