Publications Search by Program
Search Result
The search results on this publication page are automated on a monthly schedule based on acknowledgment of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
Genotype-Tissue Expression (GTEx) (375)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Hypotheses on a tree: new error rates and testing strategies. | Bogomolov, Marina; Peterson, Christine B; Benjamini, Yoav; Sabatti, Chiara | Biometrika | 2021 Sep | 575-590 | 36825068 |
| Day-night and seasonal variation of human gene expression across tissues. | Wucher, Valentin; Sodaei, Reza; Amador, Raziel; Irimia, Manuel; Guigó, Roderic | PLoS biology | 2023 Feb | e3001986 | 36745672 |
| DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. | Oliva, Meritxell; Demanelis, Kathryn; Lu, Yihao; Chernoff, Meytal; Jasmine, Farzana; Ahsan, Habibul; Kibriya, Muhammad G; Chen, Lin S; Pierce, Brandon L | Nature genetics | 2022 Dec 12 | 36510025 | |
| Leveraging pleiotropy for joint analysis of genome-wide association studies with per trait interpretations. | Taraszka, Kodi; Zaitlen, Noah; Eskin, Eleazar | PLoS genetics | 2022 Nov | 36342933 | |
| RNA editing underlies genetic risk of common inflammatory diseases. | Li, Qin; Gloudemans, Michael J; Geisinger, Jonathan M; Fan, Boming; Aguet, François; Sun, Tao; Ramaswami, Gokul; Li, Yang I; Ma, Jin-Biao; Pritchard, Jonathan K; Montgomery, Stephen B; Li, Jin Billy | Nature | 2022 08 | 35922514 | |
| Identification of human mitochondrial RNA cleavage sites and candidate RNA processing factors. | Carbajosa, Guillermo; Ali, Aminah T; Hodgkinson, Alan | BMC biology | 2022 07 22 | 35869520 | |
| Estimating and accounting for unobserved covariates in high-dimensional correlated data. | McKennan, Chris; Nicolae, Dan | Journal of the American Statistical Association | 2022 | 35615339 | |
| A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients. | Degener, Max J F; van Cruchten, Remco T P; Otero, Brittney A; Wang, Eric T; Wansink, Derick G; 't Hoen, Peter A C | NAR genomics and bioinformatics | 2022 Mar | 35274098 | |
| Mitochondrial-nuclear epistasis underlying phenotypic variation in breast cancer pathology. | Bushel, Pierre R; Ward, James; Burkholder, Adam; Li, Jianying; Anchang, Benedict | Scientific reports | 2022 01 26 | 35082309 | |
| A de novo paradigm for male infertility. | Oud, M S; Smits, R M; Smith, H E; Mastrorosa, F K; Holt, G S; Houston, B J; de Vries, P F; Alobaidi, B K S; Batty, L E; Ismail, H; Greenwood, J; Sheth, H; Mikulasova, A; Astuti, G D N; Gilissen, C; McEleny, K; Turner, H; Coxhead, J; Cockell, S; Braat, D D | Nature communications | 2022 Jan 10 | 154 | 35013161 |
| Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease. | Fairbrother-Browne, Aine; Ali, Aminah T; Reynolds, Regina H; Garcia-Ruiz, Sonia; Zhang, David; Chen, Zhongbo; Ryten, Mina; Hodgkinson, Alan | Communications biology | 2021 Nov 04 | 34737414 | |
| Identifying causal variants by fine mapping across multiple studies. | LaPierre, Nathan; Taraszka, Kodi; Huang, Helen; He, Rosemary; Hormozdiari, Farhad; Eskin, Eleazar | PLoS genetics | 2021 Sep | 34543273 | |
| Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. | Võsa, Urmo; Claringbould, Annique; Westra, Harm-Jan; Bonder, Marc Jan; Deelen, Patrick; Zeng, Biao; Kirsten, Holger; Saha, Ashis; Kreuzhuber, Roman; Yazar, Seyhan; Brugge, Harm; Oelen, Roy; de Vries, Dylan H; van der Wijst, Monique G P; Kasela, Silva; Per | Nature genetics | 2021 09 | 34475573 | |
| Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. | Nadel, Brian B; Oliva, Meritxell; Shou, Benjamin L; Mitchell, Keith; Ma, Feiyang; Montoya, Dennis J; Mouton, Alice; Kim-Hellmuth, Sarah; Stranger, Barbara E; Pellegrini, Matteo; Mangul, Serghei | Briefings in bioinformatics | 2021 11 05 | 34346485 | |
| Mapping the miRNA-mRNA Interactome in Human Hepatocytes and Identification of Functional mirSNPs in Pharmacogenes. | Powell, Nicholas R; Zhao, Harrison; Ipe, Joseph; Liu, Yunlong; Skaar, Todd C | Clinical pharmacology and therapeutics | 2021 10 | 34314509 | |
| Genetic drivers of m6A methylation in human brain, lung, heart and muscle. | Xiong, Xushen; Hou, Lei; Park, Yongjin P; Molinie, Benoit; GTEx Consortium; Gregory, Richard I; Kellis, Manolis | Nature genetics | 2021 Jul 01 | 34211177 | |
| Feasibility of predicting allele specific expression from DNA sequencing using machine learning. | Zhang, Zhenhua; van Dijk, Freerk; de Klein, Niek; van Gijn, Mariëlle E; Franke, Lude H; Sinke, Richard J; Swertz, Morris A; van der Velde, K Joeri | Scientific reports | 2021 May 19 | 34012022 | |
| Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease. | de Goede, Olivia M; Nachun, Daniel C; Ferraro, Nicole M; Gloudemans, Michael J; Rao, Abhiram S; Smail, Craig; Eulalio, Tiffany Y; Aguet, François; Ng, Bernard; Xu, Jishu; Barbeira, Alvaro N; Castel, Stephane E; Kim-Hellmuth, Sarah; Park, YoSon; Scott, Alexandra J; Strober, Benjamin J; GTEx Consortium; Brown, Christopher D; Wen, Xiaoquan; Hall, Ira M; Battle, Alexis; Lappalainen, Tuuli; Im, Hae Kyung; Ardlie, Kristin G; Mostafavi, Sara; Quertermous, Thomas; Kirkegaard, Karla; Montgomery, Stephen B | Cell | 2021 05 13 | 33864768 | |
| Day-night and seasonal variation of human gene expression across tissues. | Wucher, Valentin; Sodaei, Reza; Amador, Raziel; Irimia, Manuel; Guigó, Roderic | bioRxiv : the preprint server for biology | 2021 Mar 01 | 33688644 | |
| Regulatory genomic circuitry of human disease loci by integrative epigenomics. | Boix, Carles A; James, Benjamin T; Park, Yongjin P; Meuleman, Wouter; Kellis, Manolis | Nature | 2021 02 | 33536621 | |
| Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. | Garrido-Martín, Diego; Borsari, Beatrice; Calvo, Miquel; Reverter, Ferran; Guigó, Roderic | Nature communications | 2021 02 01 | 33526779 | |
| Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. | Barbeira, Alvaro N; Bonazzola, Rodrigo; Gamazon, Eric R; Liang, Yanyu; Park, YoSon; Kim-Hellmuth, Sarah; Wang, Gao; Jiang, Zhuoxun; Zhou, Dan; Hormozdiari, Farhad; Liu, Boxiang; Rao, Abhiram; Hamel, Andrew R; Pividori, Milton D; Aguet, François; GTEx GWAS | Genome biology | 2021 01 26 | 33499903 | |
| Alterations observed in the interferon α and β signaling pathway in MDD patients are marginally influenced by cis-acting alleles. | Magri, Chiara; Giacopuzzi, Edoardo; Sacco, Chiara; Bocchio-Chiavetto, Luisella; Minelli, Alessandra; Gennarelli, Massimo | Scientific reports | 2021 01 12 | 33436853 | |
| Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability. | Lagou, Vasiliki; Mägi, Reedik; Hottenga, Jouke- Jan; Grallert, Harald; Perry, John R B; Bouatia-Naji, Nabila; Marullo, Letizia; Rybin, Denis; Jansen, Rick; Min, Josine L; Dimas, Antigone S; Ulrich, Anna; Zudina, Liudmila; Gådin, Jesper R; Jiang, Longda; Faggian, Alessia; Bonnefond, Amélie; Fadista, Joao; Stathopoulou, Maria G; Isaacs, Aaron; Willems, Sara M; Navarro, Pau; Tanaka, Toshiko; Jackson, Anne U; Montasser, May E; O'Connell, Jeff R; Bielak, Lawrence F; Webster, Rebecca J; Saxena, Richa; Stafford, Jeanette M; Pourcain, Beate St; Timpson, Nicholas J; Salo, Perttu; Shin, So-Youn; Amin, Najaf; Smith, Albert V; Li, Guo; Verweij, Niek; Goel, Anuj; Ford, Ian; Johnson, Paul C D; Johnson, Toby; Kapur, Karen; Thorleifsson, Gudmar; Strawbridge, Rona J; Rasmussen-Torvik, Laura J; Esko, Tõnu; Mihailov, Evelin; Fall, Tove; Fraser, Ross M; Mahajan, Anubha; Kanoni, Stavroula; Giedraitis, Vilmantas; Kleber, Marcus E; Silbernagel, Günther; Meyer, Julia; Müller-Nurasyid, Martina; Ganna, Andrea; Sarin, Antti-Pekka; Yengo, Loic; Shungin, Dmitry; Luan, Jian'an; Horikoshi, Momoko; An, Ping; Sanna, Serena; Boettcher, Yvonne; Rayner, N William; Nolte, Ilja M; Zemunik, Tatijana; Iperen, Erik van; Kovacs, Peter; Hastie, Nicholas D; Wild, Sarah H; McLachlan, Stela; Campbell, Susan; Polasek, Ozren; Carlson, Olga; Egan, Josephine; Kiess, Wieland; Willemsen, Gonneke; Kuusisto, Johanna; Laakso, Markku; Dimitriou, Maria; Hicks, Andrew A; Rauramaa, Rainer; Bandinelli, Stefania; Thorand, Barbara; Liu, Yongmei; Miljkovic, Iva; Lind, Lars; Doney, Alex; Perola, Markus; Hingorani, Aroon; Kivimaki, Mika; Kumari, Meena; Bennett, Amanda J; Groves, Christopher J; Herder, Christian; Koistinen, Heikki A; Kinnunen, Leena; Faire, Ulf de; Bakker, Stephan J L; Uusitupa, Matti; Palmer, Colin N A; Jukema, J Wouter; Sattar, Naveed; Pouta, Anneli; Snieder, Harold; Boerwinkle, Eric; Pankow, James S; Magnusson, Patrik K; Krus, Ulrika; Scapoli, Chiara; de Geus, Eco J C N; Blüher, Matthias; Wolffenbuttel, Bruce H R; Province, Michael A; Abecasis, Goncalo R; Meigs, James B; Hovingh, G Kees; Lindström, Jaana; Wilson, James F; Wright, Alan F; Dedoussis, George V; Bornstein, Stefan R; Schwarz, Peter E H; Tönjes, Anke; Winkelmann, Bernhard R; Boehm, Bernhard O; März, Winfried; Metspalu, Andres; Price, Jackie F; Deloukas, Panos; Körner, Antje; Lakka, Timo A; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Bergman, Richard N; Tuomilehto, Jaakko; Wareham, Nicholas J; Langenberg, Claudia; Männistö, Satu; Franks, Paul W; Hayward, Caroline; Vitart, Veronique; Kaprio, Jaakko; Visvikis-Siest, Sophie; Balkau, Beverley; Altshuler, David; Rudan, Igor; Stumvoll, Michael; Campbell, Harry; van Duijn, Cornelia M; Gieger, Christian; Illig, Thomas; Ferrucci, Luigi; Pedersen, Nancy L; Pramstaller, Peter P; Boehnke, Michael; Frayling, Timothy M; Shuldiner, Alan R; Peyser, Patricia A; Kardia, Sharon L R; Palmer, Lyle J; Penninx, Brenda W; Meneton, Pierre; Harris, Tamara B; Navis, Gerjan; Harst, Pim van der; Smith, George Davey; Forouhi, Nita G; Loos, Ruth J F; Salomaa, Veikko; Soranzo, Nicole; Boomsma, Dorret I; Groop, Leif; Tuomi, Tiinamaija; Hofman, Albert; Munroe, Patricia B; Gudnason, Vilmundur; Siscovick, David S; Watkins, Hugh; Lecoeur, Cecile; Vollenweider, Peter; Franco-Cereceda, Anders; Eriksson, Per; Jarvelin, Marjo-Riitta; Stefansson, Kari; Hamsten, Anders; Nicholson, George; Karpe, Fredrik; Dermitzakis, Emmanouil T; Lindgren, Cecilia M; McCarthy, Mark I; Froguel, Philippe; Kaakinen, Marika A; Lyssenko, Valeriya; Watanabe, Richard M; Ingelsson, Erik; Florez, Jose C; Dupuis, Josée; Barroso, Inês; Morris, Andrew P; Prokopenko, Inga; Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) | Nature communications | 2021 01 05 | 33402679 | |
| RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data. | Wang, Meng; Jiang, Lihua; Jian, Ruiqi; Chan, Joanne Y; Liu, Qing; Snyder, Michael P; Tang, Hua | Bioinformatics (Oxford, England) | 2021 May 05 | 33098413 | |
| Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data. | Deutelmoser, Heike; Scherer, Dominique; Brenner, Hermann; Waldenberger, Melanie; INTERVAL study; Suhre, Karsten; Kastenmüller, Gabi; Lorenzo Bermejo, Justo | Briefings in bioinformatics | 2021 Jul 20 | 33063116 | |
| Pleiotropic Locus 15q24.1 Reveals a Gender-Specific Association with Neovascular but Not Atrophic Age-Related Macular Degeneration (AMD). | Kiel, Christina; Strunz, Tobias; International Amd Genomics Consortium Project Manager Susan Blanton Iamdgc; Grassmann, Felix; Weber, Bernhard H F | Cells. | 2020 10 08; | 33050031 | |
| Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. | Viñuela, Ana; Varshney, Arushi; van de Bunt, Martijn; Prasad, Rashmi B; Asplund, Olof; Bennett, Amanda; Boehnke, Michael; Brown, Andrew A; Erdos, Michael R; Fadista, João; Hansson, Ola; Hatem, Gad; Howald, Cédric; Iyengar, Apoorva K; Johnson, Paul; Krus, | Nature communications. | 2020 09 30; | 32999275 | |
| Fine-mapping and QTL tissue-sharing information improves the reliability of causal gene identification. | Barbeira, Alvaro N; Melia, Owen J; Liang, Yanyu; Bonazzola, Rodrigo; Wang, Gao; Wheeler, Heather E; Aguet, François; Ardlie, Kristin G; Wen, Xiaoquan; Im, Hae K | Genetic epidemiology. | 2020 Sep 10; | 32964524 | |
| PhenomeXcan: Mapping the genome to the phenome through the transcriptome. | Pividori, Milton; Rajagopal, Padma S; Barbeira, Alvaro; Liang, Yanyu; Melia, Owen; Bastarache, Lisa; Park, YoSon; Consortium, GTEx; Wen, Xiaoquan; Im, Hae K | Science advances | 2020 09 | 32917697 | |
| A Quantitative Proteome Map of the Human Body. | Jiang, Lihua; Wang, Meng; Lin, Shin; Jian, Ruiqi; Li, Xiao; Chan, Joanne; Dong, Guanlan; Fang, Huaying; Robinson, Aaron E; GTEx Consortium; Snyder, Michael P | Cell. | 2020 Oct 01; | 32916130 | |
| Genome-wide association study identifies novel single nucleotide polymorphisms having age-specific effect on prostate-specific antigen levels. | Li, Weiqiang; Bicak, Mesude; Sjoberg, Daniel D; Vertosick, Emily; Dahlin, Anders; Melander, Olle; Ulmert, David; Lilja, Hans; Klein, Robert J | The Prostate. | 2020 Dec; | 32914890 | |
| The GTEx Consortium atlas of genetic regulatory effects across human tissues. | GTEx Consortium | Science (New York, N.Y.). | 2020 09 11; | 32913098 | |
| Cell type-specific genetic regulation of gene expression across human tissues. | Kim-Hellmuth, Sarah; Aguet, François; Oliva, Meritxell; Muñoz-Aguirre, Manuel; Kasela, Silva; Wucher, Valentin; Castel, Stephane E; Hamel, Andrew R; Viñuela, Ana; Roberts, Amy L; Mangul, Serghei; Wen, Xiaoquan; Wang, Gao; Barbeira, Alvaro N; Garrido-Martí | Science (New York, N.Y.). | 2020 09 11; | 32913075 | |
| Determinants of telomere length across human tissues. | Demanelis, Kathryn; Jasmine, Farzana; Chen, Lin S; Chernoff, Meytal; Tong, Lin; Delgado, Dayana; Zhang, Chenan; Shinkle, Justin; Sabarinathan, Mekala; Lin, Hannah; Ramirez, Eduardo; Oliva, Meritxell; Kim-Hellmuth, Sarah; Stranger, Barbara E; Lai, Tsung-Po | Science (New York, N.Y.). | 2020 09 11; | 32913074 | |
| Transcriptomic signatures across human tissues identify functional rare genetic variation. | Ferraro, Nicole M; Strober, Benjamin J; Einson, Jonah; Abell, Nathan S; Aguet, Francois; Barbeira, Alvaro N; Brandt, Margot; Bucan, Maja; Castel, Stephane E; Davis, Joe R; Greenwald, Emily; Hess, Gaelen T; Hilliard, Austin T; Kember, Rachel L; Kotis, Benc | Science (New York, N.Y.). | 2020 09 11; | 32913073 | |
| The impact of sex on gene expression across human tissues. | Oliva, Meritxell; Muñoz-Aguirre, Manuel; Kim-Hellmuth, Sarah; Wucher, Valentin; Gewirtz, Ariel D H; Cotter, Daniel J; Parsana, Princy; Kasela, Silva; Balliu, Brunilda; Viñuela, Ana; Castel, Stephane E; Mohammadi, Pejman; Aguet, François; Zou, Yuxin; Khram | Science (New York, N.Y.). | 2020 09 11; | 32913072 | |
| A vast resource of allelic expression data spanning human tissues. | Castel, Stephane E; Aguet, François; Mohammadi, Pejman; GTEx Consortium; Ardlie, Kristin G; Lappalainen, Tuuli | Genome biology. | 2020 Sep 11; | 32912332 | |
| Metalign: efficient alignment-based metagenomic profiling via containment min hash. | LaPierre, Nathan; Alser, Mohammed; Eskin, Eleazar; Koslicki, David; Mangul, Serghei | Genome biology. | 2020 09 10; | 32912225 | |
| Low Baseline Pulmonary Levels of Cytotoxic Lymphocytes as a Predisposing Risk Factor for Severe COVID-19. | Duijf, Pascal H G | mSystems. | 2020 Sep 01; | 32873611 | |
| Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia. | Bustamante-Marin, Ximena M; Horani, Amjad; Stoyanova, Mihaela; Charng, Wu-Lin; Bottier, Mathieu; Sears, Patrick R; Yin, Wei-Ning; Daniels, Leigh Anne; Bowen, Hailey; Conrad, Donald F; Knowles, Michael R; Ostrowski, Lawrence E; Zariwala, Maimoona A; Dutche | PLoS genetics. | 2020 08; | 32764743 | |
| A limited set of transcriptional programs define major cell types. | Breschi, Alessandra; Muñoz-Aguirre, Manuel; Wucher, Valentin; Davis, Carrie A; Garrido-Martín, Diego; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D; Vlasova, Anna; Dobin, Alexander; Zaleski, Chris; Drenkow, Jorg; Danyko, Cassidy; Scavelli, Alexandr | Genome research. | 2020 Jul; | 32759341 | |
| DCAF1 regulates Treg senescence via the ROS axis during immunological aging. | Guo, Zengli; Wang, Gang; Wu, Bing; Chou, Wei-Chun; Cheng, Liang; Zhou, Chenlin; Lou, Jitong; Wu, Di; Su, Lishan; Zheng, Junnian; Ting, Jenny P-Y; Wan, Yisong Y | The Journal of clinical investigation. | 2020 Nov 02; | 32730228 | |
| An enhanced machine learning tool for cis-eQTL mapping with regularization and confounder adjustments. | Yan, Kang K; Zhao, Hongyu; Wu, Joseph T; Pang, Herbert | Genetic epidemiology | 2020 Nov | 32700329 | |
| Sparse multi-output Gaussian processes for online medical time series prediction. | Cheng, Li-Fang; Dumitrascu, Bianca; Darnell, Gregory; Chivers, Corey; Draugelis, Michael; Li, Kai; Engelhardt, Barbara E | BMC medical informatics and decision making. | 2020 Jul 08; | 32641134 | |
| Baseline pulmonary levels of CD8+ T cells and NK cells inversely correlate with expression of the SARS-CoV-2 entry receptor ACE2. | Duijf, Pascal H G | bioRxiv : the preprint server for biology. | 2020 May 05; | 32511391 | |
| Analysis of Genetically Regulated Gene Expression Identifies a Prefrontal PTSD Gene, SNRNP35, Specific to Military Cohorts. | Huckins, Laura M; Chatzinakos, Chris; Breen, Michael S; Hartmann, Jakob; Klengel, Torsten; da Silva Almeida, Ana C; Dobbyn, Amanda; Girdhar, Kiran; Hoffman, Gabriel E; Klengel, Claudia; Logue, Mark W; Lori, Adriana; Maihofer, Adam X; Morrison, Filomene G; | Cell reports. | 2020 Jun 02; | 32492425 | |
| Genetic Determinants of Reduced Arsenic Metabolism Efficiency in the 10q24.32 Region Are Associated With Reduced AS3MT Expression in Multiple Human Tissue Types. | Chernoff, Meytal; Tong, Lin; Demanelis, Kathryn; Vander Griend, Donald; Ahsan, Habib; Pierce, Brandon L | Toxicological sciences : an official journal of the Society of Toxicology | 2020 08 01 | 32433756 | |
| Analysis of mitochondrial m1A/G RNA modification reveals links to nuclear genetic variants and associated disease processes. | Ali, Aminah Tasnim; Idaghdour, Youssef; Hodgkinson, Alan | Communications biology | 2020 03 27 | 32221480 | |
| A TESTING BASED APPROACH TO THE DISCOVERY OF DIFFERENTIALLY CORRELATED VARIABLE SETS. | Bodwin, By Kelly; Zhang, Kai; Nobel, Andrew | The annals of applied statistics. | 2018 Jun; | 31871518 | |
| Community Extraction in Multilayer Networks with Heterogeneous Community Structure. | Wilson, James D; Palowitch, John; Bhamidi, Shankar; Nobel, Andrew B | Journal of machine learning research : JMLR. | 2017; | 31871433 | |
| Leveraging allelic imbalance to refine fine-mapping for eQTL studies. | Zou, Jennifer; Hormozdiari, Farhad; Jew, Brandon; Castel, Stephane E; Lappalainen, Tuuli; Ernst, Jason; Sul, Jae Hoon; Eskin, Eleazar | PLoS genetics. | 2019 12; | 31834882 | |
| Identification of genetic variants in CFAP221 as a cause of primary ciliary dyskinesia. | Bustamante-Marin, Ximena M; Shapiro, Adam; Sears, Patrick R; Charng, Wu-Lin; Conrad, Donald F; Leigh, Margaret W; Knowles, Michael R; Ostrowski, Lawrence E; Zariwala, Maimoona A | Journal of human genetics. | 2020 Jan; | 31636325 | |
| Rare mutations in the complement regulatory gene CSMD1 are associated with male and female infertility. | Lee, Arthur S; Rusch, Jannette; Lima, Ana C; Usmani, Abul; Huang, Ni; Lepamets, Maarja; Vigh-Conrad, Katinka A; Worthington, Ronald E; Mägi, Reedik; Wu, Xiaobo; Aston, Kenneth I; Atkinson, John P; Carrell, Douglas T; Hess, Rex A; O'Bryan, Moira K; Conrad, Donald F | Nature communications. | 2019 Oct 11; | 31604923 | |
| Genetically Increased Telomere Length and Aging-Related Traits in the U.K. Biobank. | Demanelis, Kathryn; Tong, Lin; Pierce, Brandon L | The journals of gerontology. Series A, Biological sciences and medical sciences | 2021 01 01 | 31603979 | |
| Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences. | Colbran, Laura L; Gamazon, Eric R; Zhou, Dan; Evans, Patrick; Cox, Nancy J; Capra, John A | Nature ecology & evolution. | 2019 Oct 07; | 31591491 | |
| Joint profiling of DNA methylation and chromatin architecture in single cells. | Li, Guoqiang; Liu, Yaping; Zhang, Yanxiao; Kubo, Naoki; Yu, Miao; Fang, Rongxin; Kellis, Manolis; Ren, Bing | Nature methods. | 2019 Oct; | 31384045 | |
| Identifying causal variants and genes using functional genomics in specialized cell types and contexts. | Liu, Boxiang; Montgomery, Stephen B | Human genetics. | 2020 Jan; | 31317254 | |
| Selection-adjusted inference: an application to confidence intervals for cis-eQTL effect sizes. | Panigrahi, Snigdha; Zhu, Junjie; Sabatti, Chiara | Biostatistics (Oxford, England) | 2021 01 28 | 31301173 | |
| Unified single-cell analysis of testis gene regulation and pathology in five mouse strains. | Jung, Min; Wells, Daniel; Rusch, Jannette; Ahmad, Suhaira; Marchini, Jonathan; Myers, Simon R; Conrad, Donald F | eLife. | 2019 Jun 25; | 31237565 | |
| Challenges and recommendations to improve the installability and archival stability of omics computational tools. | Mangul, Serghei; Mosqueiro, Thiago; Abdill, Richard J; Duong, Dat; Mitchell, Keith; Sarwal, Varuni; Hill, Brian; Brito, Jaqueline; Littman, Russell Jared; Statz, Benjamin; Lam, Angela Ka-Mei; Dayama, Gargi; Grieneisen, Laura; Martin, Lana S; Flint, Jonathan; Eskin, Eleazar; Blekhman, Ran | PLoS biology. | 2019 06; | 31220077 | |
| MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples. | LaPierre, Nathan; Mangul, Serghei; Alser, Mohammed; Mandric, Igor; Wu, Nicholas C; Koslicki, David; Eskin, Eleazar | BMC genomics. | 2019 Jun 06; | 31167634 | |
| Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms. | Liu, Boxiang; Calton, Melissa A; Abell, Nathan S; Benchorin, Gillie; Gloudemans, Michael J; Chen, Ming; Hu, Jane; Li, Xin; Balliu, Brunilda; Bok, Dean; Montgomery, Stephen B; Vollrath, Douglas | Communications biology. | 2019; | 31123710 | |
| On Using Local Ancestry to Characterize the Genetic Architecture of Human Traits: Genetic Regulation of Gene Expression in Multiethnic or Admixed Populations. | Zhong, Yizhen; Perera, Minoli A; Gamazon, Eric R | American journal of human genetics. | 2019 Jun 06; | 31104770 | |
| Multi-tissue transcriptome analyses identify genetic mechanisms underlying neuropsychiatric traits. | Gamazon, Eric R; Zwinderman, Aeilko H; Cox, Nancy J; Denys, Damiaan; Derks, Eske M | Nature genetics. | 2019 06; | 31086352 | |
| Opportunities and challenges for transcriptome-wide association studies. | Wainberg, Michael; Sinnott-Armstrong, Nasa; Mancuso, Nicholas; Barbeira, Alvaro N; Knowles, David A; Golan, David; Ermel, Raili; Ruusalepp, Arno; Quertermous, Thomas; Hao, Ke; Björkegren, Johan L M; Im, Hae Kyung; Pasaniuc, Bogdan; Rivas, Manuel A; Kundaje, Anshul | Nature genetics. | 2019 04; | 30926968 | |
| Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data. | Fernández-Tajes, Juan; Gaulton, Kyle J; van de Bunt, Martijn; Torres, Jason; Thurner, Matthias; Mahajan, Anubha; Gloyn, Anna L; Lage, Kasper; McCarthy, Mark I | Genome medicine. | 2019 03 26; | 30914061 | |
| Significance-based community detection in weighted networks. | Palowitch, John; Bhamidi, Shankar; Nobel, Andrew B | Journal of machine learning research : JMLR. | 2018 Apr; | 30853860 | |
| Improving the usability and archival stability of bioinformatics software. | Mangul, Serghei; Martin, Lana S; Eskin, Eleazar; Blekhman, Ran | Genome biology. | 2019 02 27; | 30813962 | |
| Nuclear genetic regulation of the human mitochondrial transcriptome. | Ali, Aminah T; Boehme, Lena; Carbajosa, Guillermo; Seitan, Vlad C; Small, Kerrin S; Hodgkinson, Alan | eLife. | 2019 Feb 18; | 30775970 | |
| Integrating predicted transcriptome from multiple tissues improves association detection. | Barbeira, Alvaro N; Pividori, Milton; Zheng, Jiamao; Wheeler, Heather E; Nicolae, Dan L; Im, Hae Kyung | PLoS genetics. | 2019 01; | 30668570 | |
| Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. | Rizzardi, Lindsay F; Hickey, Peter F; Rodriguez DiBlasi, Varenka; Tryggvadóttir, Rakel; Callahan, Colin M; Idrizi, Adrian; Hansen, Kasper D; Feinberg, Andrew P | Nature neuroscience. | 2019 Feb; | 30643296 | |
| False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors. | Saha, Ashis; Battle, Alexis | F1000Research. | 2018; | 30613398 | |
| An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. | Zhang, Zhizhuo; Chng, Kern Rei; Lingadahalli, Shreyas; Chen, Zikai; Liu, Mei Hui; Do, Huy Hoang; Cai, Shaojiang; Rinaldi, Nicola; Poh, Huay Mei; Li, Guoliang; Sung, Ying Ying; Heng, Charlie L; Core, Leighton J; Tan, Si Kee; Ruan, Xiaoan; Lis, John T; Kellis, Manolis; Ruan, Yijun; Sung, Wing-Kin; Cheung, Edwin | Genome research. | 2019 02; | 30606742 | |
| Population structure in genetic studies: Confounding factors and mixed models. | Sul, Jae Hoon; Martin, Lana S; Eskin, Eleazar | PLoS genetics. | 2018 12; | 30589851 | |
| Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables. | Giacopuzzi, Edoardo; Gennarelli, Massimo; Sacco, Chiara; Filippini, Alice; Mingardi, Jessica; Magri, Chiara; Barbon, Alessandro | BMC genomics. | 2018 Dec 27; | 30587120 | |
| High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human. | Wang, Xinchen; He, Liang; Goggin, Sarah M; Saadat, Alham; Wang, Li; Sinnott-Armstrong, Nasa; Claussnitzer, Melina; Kellis, Manolis | Nature communications | 2018 12 19 | 30568279 | |
| The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans. | Delgado, Dayana A; Zhang, Chenan; Gleason, Kevin; Demanelis, Kathryn; Chen, Lin S; Gao, Jianjun; Roy, Shantanu; Shinkle, Justin; Sabarinathan, Mekala; Argos, Maria; Tong, Lin; Ahmed, Alauddin; Islam, Tariqul; Rakibuz-Zaman, Muhammad; Sarwar, Golam; Shahriar, Hasan; Rahman, Mahfuzar; Yunus, Muhammad; Doherty, Jennifer A; Jasmine, Farzana; Kibriya, Muhammad G; Ahsan, Habibul; Pierce, Brandon L | Human genetics. | 2019 Jan; | 30536049 | |
| Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. | Urbut, Sarah M; Wang, Gao; Carbonetto, Peter; Stephens, Matthew | Nature genetics. | 2019 01; | 30478440 | |
| Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions. | Duong, Dat; Ahmad, Wasi Uddin; Eskin, Eleazar; Chang, Kai-Wei; Li, Jingyi Jessica | Journal of computational biology : a journal of computational molecular cell biology. | 2019 Jan; | 30383443 | |
| Bid maintains mitochondrial cristae structure and function and protects against cardiac disease in an integrative genomics study. | Salisbury-Ruf, Christi T; Bertram, Clinton C; Vergeade, Aurelia; Lark, Daniel S; Shi, Qiong; Heberling, Marlene L; Fortune, Niki L; Okoye, G Donald; Jerome, W Gray; Wells, Quinn S; Fessel, Josh; Moslehi, Javid; Chen, Heidi; Roberts 2nd, L Jackson; Boutaud, Olivier; Gamazon, Eric R; Zinkel, Sandra S | eLife. | 2018 10 03; | 30281024 | |
| Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies. | Wu, Yue; Hormozdiari, Farhad; Joo, Jong Wha J; Eskin, Eleazar | Journal of computational biology : a journal of computational molecular cell biology. | 2019 Nov; | 30272994 | |
| BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference. | Rahmani, Elior; Schweiger, Regev; Shenhav, Liat; Wingert, Theodora; Hofer, Ira; Gabel, Eilon; Eskin, Eleazar; Halperin, Eran | Genome biology. | 2018 09 21; | 30241486 | |
| A Comprehensive Map of Genetic Variation in the World's Largest Ethnic Group-Han Chinese. | Chiang, Charleston W K; Mangul, Serghei; Robles, Christopher; Sankararaman, Sriram | Molecular biology and evolution. | 2018 11 01; | 30169787 | |
| Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci. | Liu, Boxiang; Pjanic, Milos; Wang, Ting; Nguyen, Trieu; Gloudemans, Michael; Rao, Abhiram; Castano, Victor G; Nurnberg, Sylvia; Rader, Daniel J; Elwyn, Susannah; Ingelsson, Erik; Montgomery, Stephen B; Miller, Clint L; Quertermous, Thomas | American journal of human genetics. | 2018 09 06; | 30146127 | |
| Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. | Onuchic, Vitor; Lurie, Eugene; Carrero, Ivenise; Pawliczek, Piotr; Patel, Ronak Y; Rozowsky, Joel; Galeev, Timur; Huang, Zhuoyi; Altshuler, Robert C; Zhang, Zhizhuo; Harris, R Alan; Coarfa, Cristian; Ashmore, Lillian; Bertol, Jessica W; Fakhouri, Walid D; Yu, Fuli; Kellis, Manolis; Gerstein, Mark; Milosavljevic, Aleksandar | Science (New York, N.Y.). | 2018 Aug 23; | 30139913 | |
| Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. | Castel, Stephane E; Cervera, Alejandra; Mohammadi, Pejman; Aguet, François; Reverter, Ferran; Wolman, Aaron; Guigo, Roderic; Iossifov, Ivan; Vasileva, Ana; Lappalainen, Tuuli | Nature genetics. | 2018 Sep; | 30127527 | |
| Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. | McDowell, Ian C; Barrera, Alejandro; D'Ippolito, Anthony M; Vockley, Christopher M; Hong, Linda K; Leichter, Sarah M; Bartelt, Luke C; Majoros, William H; Song, Lingyun; Safi, Alexias; Koçak, D Dewran; Gersbach, Charles A; Hartemink, Alexander J; Crawford, Gregory E; Engelhardt, Barbara E; Reddy, Timothy E | Genome research. | 2018 09; | 30097539 | |
| Bi-allelic Recessive Loss-of-Function Variants in FANCM Cause Non-obstructive Azoospermia. | Kasak, Laura; Punab, Margus; Nagirnaja, Liina; Grigorova, Marina; Minajeva, Ave; Lopes, Alexandra M; Punab, Anna Maria; Aston, Kenneth I; Carvalho, Filipa; Laasik, Eve; Smith, Lee B; GEMINI Consortium; Conrad, Donald F; Laan, Maris | American journal of human genetics. | 2018 08 02; | 30075111 | |
| Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. | Jaffe, Andrew E; Straub, Richard E; Shin, Joo Heon; Tao, Ran; Gao, Yuan; Collado-Torres, Leonardo; Kam-Thong, Tony; Xi, Hualin S; Quan, Jie; Chen, Qiang; Colantuoni, Carlo; Ulrich, William S; Maher, Brady J; Deep-Soboslay, Amy; BrainSeq Consortium; Cross, Alan J; Brandon, Nicholas J; Leek, Jeffrey T; Hyde, Thomas M; Kleinman, Joel E; Weinberger, Daniel R | Nature neuroscience. | 2018 08; | 30050107 | |
| Mendelian randomization studies of cancer risk: a literature review. | Pierce, Brandon L; Kraft, Peter; Zhang, Chenan | Current epidemiology reports. | 2018 Jun; | 30034993 | |
| Statistical tests for detecting variance effects in quantitative trait studies. | Dumitrascu, Bianca; Darnell, Gregory; Ayroles, Julien; Engelhardt, Barbara E | Bioinformatics (Oxford, England). | 2019 01 15; | 29982387 | |
| Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. | Gamazon, Eric R; Segrè, Ayellet V; van de Bunt, Martijn; Wen, Xiaoquan; Xi, Hualin S; Hormozdiari, Farhad; Ongen, Halit; Konkashbaev, Anuar; Derks, Eske M; Aguet, François; Quan, Jie; GTEx Consortium; Nicolae, Dan L; Eskin, Eleazar; Kellis, Manolis; Getz, Gad; McCarthy, Mark I; Dermitzakis, Emmanouil T; Cox, Nancy J; Ardlie, Kristin G | Nature genetics. | 2018 07; | 29955180 | |
| Finding associated variants in genome-wide association studies on multiple traits. | Gai, Lisa; Eskin, Eleazar | Bioinformatics (Oxford, England). | 2018 07 01; | 29949991 | |
| Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits. | Hormozdiari, Farhad; Gazal, Steven; van de Geijn, Bryce; Finucane, Hilary K; Ju, Chelsea J-T; Loh, Po-Ru; Schoech, Armin; Reshef, Yakir; Liu, Xuanyao; O'Connor, Luke; Gusev, Alexander; Eskin, Eleazar; Price, Alkes L | Nature genetics. | 2018 07; | 29942083 | |
| Towards a complete map of the human long non-coding RNA transcriptome. | Uszczynska-Ratajczak, Barbara; Lagarde, Julien; Frankish, Adam; Guigó, Roderic; Johnson, Rory | Nature reviews. Genetics. | 2018 Sep; | 29795125 | |
| An Association Mapping Framework To Account for Potential Sex Difference in Genetic Architectures. | Kang, Eun Yong; Lee, Cue Hyunkyu; Furlotte, Nicholas A; Joo, Jong Wha J; Kostem, Emrah; Zaitlen, Noah; Eskin, Eleazar; Han, Buhm | Genetics. | 2018 07; | 29752291 | |
| Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia. | Olde Loohuis, Loes M; Mangul, Serghei; Ori, Anil P S; Jospin, Guillaume; Koslicki, David; Yang, Harry Taegyun; Wu, Timothy; Boks, Marco P; Lomen-Hoerth, Catherine; Wiedau-Pazos, Martina; Cantor, Rita M; de Vos, Willem M; Kahn, René S; Eskin, Eleazar; Ophoff, Roel A | Translational psychiatry. | 2018 05 10; | 29743478 | |
| Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. | Barbeira, Alvaro N; Dickinson, Scott P; Bonazzola, Rodrigo; Zheng, Jiamao; Wheeler, Heather E; Torres, Jason M; Torstenson, Eric S; Shah, Kaanan P; Garcia, Tzintzuni; Edwards, Todd L; Stahl, Eli A; Huckins, Laura M; GTEx Consortium; Nicolae, Dan L; Cox, Nancy J; Im, Hae Kyung | Nature communications. | 2018 05 08; | 29739930 | |
| A Genome-Wide Association Study of Diabetic Kidney Disease in Subjects With Type 2 Diabetes. | van Zuydam, Natalie R; Ahlqvist, Emma; Sandholm, Niina; Deshmukh, Harshal; Rayner, N William; Abdalla, Moustafa; Ladenvall, Claes; Ziemek, Daniel; Fauman, Eric; Robertson, Neil R; McKeigue, Paul M; Valo, Erkka; Forsblom, Carol; Harjutsalo, Valma; Finnish Diabetic Nephropathy Study (FinnDiane); Perna, Annalisa; Rurali, Erica; Marcovecchio, M Loredana; Igo Jr, Robert P; Salem, Rany M; Perico, Norberto; Lajer, Maria; Käräjämäki, Annemari; Imamura, Minako; Kubo, Michiaki; Takahashi, Atsushi; Sim, Xueling; Liu, Jianjun; van Dam, Rob M; Jiang, Guozhi; Tam, Claudia H T; Luk, Andrea O Y; Lee, Heung Man; Lim, Cadmon K P; Szeto, Cheuk Chun; So, Wing Yee; Chan, Juliana C N; Hong Kong Diabetes Registry Theme-based Research Scheme Project Group; Ang, Su Fen; Dorajoo, Rajkumar; Wang, Ling; Clara, Tan Si Hua; McKnight, Amy-Jayne; Duffy, Seamus; Warren 3 and Genetics of Kidneys in Diabetes (GoKinD) Study Group; Pezzolesi, Marcus G; GENIE (GEnetics of Nephropathy an International Effort) Consortium; Marre, Michel; Gyorgy, Beata; Hadjadj, Samy; Hiraki, Linda T; Diabetes Control and Complications Trial (DCCT)/Epidemiology of Diabetes Interventions and Complications (EDIC) Research Group; Ahluwalia, Tarunveer S; Almgren, Peter; Schulz, Christina-Alexandra; Orho-Melander, Marju; Linneberg, Allan; Christensen, Cramer; Witte, Daniel R; Grarup, Niels; Brandslund, Ivan; Melander, Olle; Paterson, Andrew D; Tregouet, David; Maxwell, Alexander P; Lim, Su Chi; Ma, Ronald C W; Tai, E Shyong; Maeda, Shiro; Lyssenko, Valeriya; Tuomi, Tiinamaija; Krolewski, Andrzej S; Rich, Stephen S; Hirschhorn, Joel N; Florez, Jose C; Dunger, David; Pedersen, Oluf; Hansen, Torben; Rossing, Peter; Remuzzi, Giuseppe; SUrrogate markers for Micro- and Macrovascular hard endpoints for Innovative diabetes Tools (SUMMIT) Consortium; Brosnan, Mary Julia; Palmer, Colin N A; Groop, Per-Henrik; Colhoun, Helen M; Groop, Leif C; McCarthy, Mark I | Diabetes. | 2018 07; | 29703844 | |
| A study of telomere length, arsenic exposure, and arsenic toxicity in a Bangladeshi cohort. | Zhang, Chenan; Kibriya, Muhammad G; Jasmine, Farzana; Roy, Shantanu; Gao, Jianjun; Sabarinathan, Mekala; Shinkle, Justin; Delgado, Dayana; Ahmed, Alauddin; Islam, Tariqul; Eunus, Mahbubul; Islam, Md Tariqul; Hasan, Rabiul; Graziano, Joseph H; Ahsan, Habibul; Pierce, Brandon L | Environmental research. | 2018 07; | 29567420 | |
| ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. | Mangul, Serghei; Yang, Harry Taegyun; Strauli, Nicolas; Gruhl, Franziska; Porath, Hagit T; Hsieh, Kevin; Chen, Linus; Daley, Timothy; Christenson, Stephanie; Wesolowska-Andersen, Agata; Spreafico, Roberto; Rios, Cydney; Eng, Celeste; Smith, Andrew D; Hernandez, Ryan D; Ophoff, Roel A; Santana, Jose Rodriguez; Levanon, Erez Y; Woodruff, Prescott G; Burchard, Esteban; Seibold, Max A; Shifman, Sagiv; Eskin, Eleazar; Zaitlen, Noah | Genome biology. | 2018 Feb 15; | 29548336 | |
| A novel pooled-sample multiplex luminex assay for high-throughput measurement of relative telomere length. | Jasmine, Farzana; Shinkle, Justin; Sabarinathan, Mekala; Ahsan, Habibul; Pierce, Brandon L; Kibriya, Muhammad G | American journal of human biology : the official journal of the Human Biology Council. | 2018 Mar 12; | 29527774 | |
| HT-eQTL: integrative expression quantitative trait loci analysis in a large number of human tissues. | Li, Gen; Jima, Dereje; Wright, Fred A; Nobel, Andrew B | BMC bioinformatics. | 2018 03 09; | 29523079 | |
| The effects of death and post-mortem cold ischemia on human tissue transcriptomes. | Ferreira, Pedro G; Muñoz-Aguirre, Manuel; Reverter, Ferran; Sá Godinho, Caio P; Sousa, Abel; Amadoz, Alicia; Sodaei, Reza; Hidalgo, Marta R; Pervouchine, Dmitri; Carbonell-Caballero, Jose; Nurtdinov, Ramil; Breschi, Alessandra; Amador, Raziel; Oliveira, Patrícia; Çubuk, Cankut; Curado, João; Aguet, François; Oliveira, Carla; Dopazo, Joaquin; Sammeth, Michael; Ardlie, Kristin G; Guigó, Roderic | Nature communications. | 2018 02 13; | 29440659 | |
| Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci. | Thurner, Matthias; van de Bunt, Martijn; Torres, Jason M; Mahajan, Anubha; Nylander, Vibe; Bennett, Amanda J; Gaulton, Kyle J; Barrett, Amy; Burrows, Carla; Bell, Christopher G; Lowe, Robert; Beck, Stephan; Rakyan, Vardhman K; Gloyn, Anna L; McCarthy, Mark I | eLife. | 2018 02 07; | 29412141 | |
| Bipolar disorder with binge eating behavior: a genome-wide association study implicates PRR5-ARHGAP8. | McElroy, Susan L; Winham, Stacey J; Cuellar-Barboza, Alfredo B; Colby, Colin L; Ho, Ada Man-Choi; Sicotte, Hugues; Larrabee, Beth R; Crow, Scott; Frye, Mark A; Biernacka, Joanna M | Translational psychiatry. | 2018 Feb 02; | 29391396 | |
| Genetic variation in theNEIL2DNA glycosylase gene is associated with oxidative DNA damage inBRCA2mutation carriers. | Benítez-Buelga, Carlos; Baquero, Juan Miguel; Vaclova, Tereza; Fernández, Victoria; Martín, Paloma; Inglada-Perez, Lucia; Urioste, Miguel; Osorio, Ana; Benítez, Javier | Oncotarget. | 2017 Dec 29; | 29383107 | |
| Clustering gene expression time series data using an infinite Gaussian process mixture model. | McDowell, Ian C; Manandhar, Dinesh; Vockley, Christopher M; Schmid, Amy K; Reddy, Timothy E; Engelhardt, Barbara E | PLoS computational biology. | 2018 01; | 29337990 | |
| N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. | Wang, Yang; Li, Yue; Yue, Minghui; Wang, Jun; Kumar, Sandeep; Wechsler-Reya, Robert J; Zhang, Zhaolei; Ogawa, Yuya; Kellis, Manolis; Duester, Gregg; Zhao, Jing Crystal | Nature neuroscience. | 2018 02; | 29335608 | |
| Gene and MicroRNA Perturbations of Cellular Response to Pemetrexed Implicate Biological Networks and Enable Imputation of Response in Lung Adenocarcinoma. | Gamazon, Eric R; Trendowski, Matthew R; Wen, Yujia; Wing, Claudia; Delaney, Shannon M; Huh, Won; Wong, Shan; Cox, Nancy J; Dolan, M Eileen | Scientific reports. | 2018 Jan 15; | 29335598 | |
| Genetic association with B-cell acute lymphoblastic leukemia in allogeneic transplant patients differs by age and sex. | Clay-Gilmour, Alyssa I; Hahn, Theresa; Preus, Leah M; Onel, Kenan; Skol, Andrew; Hungate, Eric; Zhu, Qianqian; Haiman, Christopher A; Stram, Daniel O; Pooler, Loreall; Sheng, Xin; Yan, Li; Liu, Qian; Hu, Qiang; Liu, Song; Battaglia, Sebastiano; Zhu, Xiaochun; Block, AnneMarie W; Sait, Sheila N J; Karaesmen, Ezgi; Rizvi, Abbas; Weisdorf, Daniel J; Ambrosone, Christine B; Tritchler, David; Ellinghaus, Eva; Ellinghaus, David; Stanulla, Martin; Clavel, Jacqueline; Orsi, Laurent; Spellman, Stephen; Pasquini, Marcelo C; McCarthy, Philip L; Sucheston-Campbell, Lara E | Blood advances. | 2017 Sep 12; | 29296818 | |
| Impact of regulatory variation across human iPSCs and differentiated cells. | Banovich, Nicholas E; Li, Yang I; Raj, Anil; Ward, Michelle C; Greenside, Peyton; Calderon, Diego; Tung, Po Yuan; Burnett, Jonathan E; Myrthil, Marsha; Thomas, Samantha M; Burrows, Courtney K; Romero, Irene Gallego; Pavlovic, Bryan J; Kundaje, Anshul; Pritchard, Jonathan K; Gilad, Yoav | Genome research. | 2018 01; | 29208628 | |
| Cohort-specific imputation of gene expression improves prediction of warfarin dose for African Americans. | Gottlieb, Assaf; Daneshjou, Roxana; DeGorter, Marianne; Bourgeois, Stephane; Svensson, Peter J; Wadelius, Mia; Deloukas, Panos; Montgomery, Stephen B; Altman, Russ B | Genome medicine. | 2017 Nov 24; | 29178968 | |
| Genome-wide association study of telomere length among South Asians identifies a second RTEL1 association signal. | Delgado, Dayana A; Zhang, Chenan; Chen, Lin S; Gao, Jianjun; Roy, Shantanu; Shinkle, Justin; Sabarinathan, Mekala; Argos, Maria; Tong, Lin; Ahmed, Alauddin; Islam, Tariqul; Rakibuz-Zaman, Muhammad; Sarwar, Golam; Shahriar, Hasan; Rahman, Mahfuzar; Yunus, Mohammad; Jasmine, Farzana; Kibriya, Muhammad G; Ahsan, Habibul; Pierce, Brandon L | Journal of medical genetics. | 2018 Jan; | 29151059 | |
| Genome-wide association study identifies a novel locus for cannabis dependence. | Agrawal, A; Chou, Y-L; Carey, C E; Baranger, D A A; Zhang, B; Sherva, R; Wetherill, L; Kapoor, M; Wang, J-C; Bertelsen, S; Anokhin, A P; Hesselbrock, V; Kramer, J; Lynskey, M T; Meyers, J L; Nurnberger, J I; Rice, J P; Tischfield, J; Bierut, L J; Degenhardt, L; Farrer, L A; Gelernter, J; Hariri, A R; Heath, A C; Kranzler, H R; Madden, P A F; Martin, N G; Montgomery, G W; Porjesz, B; Wang, T; Whitfield, J B; Edenberg, H J; Foroud, T; Goate, A M; Bogdan, R; Nelson, E C | Molecular psychiatry. | 2017 Nov 07; | 29112194 | |
| High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. | Lagarde, Julien; Uszczynska-Ratajczak, Barbara; Carbonell, Silvia; Pérez-Lluch, Sílvia; Abad, Amaya; Davis, Carrie; Gingeras, Thomas R; Frankish, Adam; Harrow, Jennifer; Guigo, Roderic; Johnson, Rory | Nature genetics. | 2017 Dec; | 29106417 | |
| Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate. | Jasinska, Anna J; Zelaya, Ivette; Service, Susan K; Peterson, Christine B; Cantor, Rita M; Choi, Oi-Wa; DeYoung, Joseph; Eskin, Eleazar; Fairbanks, Lynn A; Fears, Scott; Furterer, Allison E; Huang, Yu S; Ramensky, Vasily; Schmitt, Christopher A; Svardal, Hannes; Jorgensen, Matthew J; Kaplan, Jay R; Villar, Diego; Aken, Bronwen L; Flicek, Paul; Nag, Rishi; Wong, Emily S; Blangero, John; Dyer, Thomas D; Bogomolov, Marina; Benjamini, Yoav; Weinstock, George M; Dewar, Ken; Sabatti, Chiara; Wilson, Richard K; Jentsch, J David; Warren, Wesley; Coppola, Giovanni; Woods, Roger P; Freimer, Nelson B | Nature genetics. | 2017 Dec; | 29083405 | |
| Estimation of cis-eQTL effect sizes using a log of linear model. | Palowitch, John; Shabalin, Andrey; Zhou, Yi-Hui; Nobel, Andrew B; Wright, Fred A | Biometrics. | 2017 Oct 26; | 29073327 | |
| Evidence of reduced recombination rate in human regulatory domains. | Liu, Yaping; Sarkar, Abhishek; Kheradpour, Pouya; Ernst, Jason; Kellis, Manolis | Genome biology. | 2017 Oct 20; | 29058599 | |
| Bayesian Partition Models for Identifying Expression Quantitative Trait Loci. | Jiang, Bo; Liu, Jun S | Journal of the American Statistical Association. | 2015; | 29056798 | |
| A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. | Gallagher, Michael D; Posavi, Marijan; Huang, Peng; Unger, Travis L; Berlyand, Yosef; Gruenewald, Analise L; Chesi, Alessandra; Manduchi, Elisabetta; Wells, Andrew D; Grant, Struan F A; Blobel, Gerd A; Brown, Christopher D; Chen-Plotkin, Alice S | American journal of human genetics. | 2017 Nov 02; | 29056226 | |
| An empirical Bayes approach for multiple tissue eQTL analysis. | Li, Gen; Shabalin, Andrey A; Rusyn, Ivan; Wright, Fred A; Nobel, Andrew B | Biostatistics (Oxford, England). | 2017 Sep 25; | 29029013 | |
| Landscape of X chromosome inactivation across human tissues. | Tukiainen, Taru; Villani, Alexandra-Chloé; Yen, Angela; Rivas, Manuel A; Marshall, Jamie L; Satija, Rahul; Aguirre, Matt; Gauthier, Laura; Fleharty, Mark; Kirby, Andrew; Cummings, Beryl B; Castel, Stephane E; Karczewski, Konrad J; Aguet, François; Byrnes, Andrea; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)?Analysis Working Group; Statistical Methods groups?Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site?NDRI; Biospecimen Collection Source Site?RPCI; Biospecimen Core Resource?VARI; Brain Bank Repository?University of Miami Brain Endowment Bank; Leidos Biomedical?Project Management; ELSI Study; Genome Browser Data Integration &Visualization?EBI; Genome Browser Data Integration &Visualization?UCSC Genomics Institute, University of California Santa Cruz; Lappalainen, Tuuli; Regev, Aviv; Ardlie, Kristin G; Hacohen, Nir; MacArthur, Daniel G | Nature. | 2017 Oct 11; | 29022598 | |
| Genetic effects on gene expression across human tissues. | GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)?Analysis Working Group; Statistical Methods groups?Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site?NDRI; Biospecimen Collection Source Site?RPCI; Biospecimen Core Resource?VARI; Brain Bank Repository?University of Miami Brain Endowment Bank; Leidos Biomedical?Project Management; ELSI Study; Genome Browser Data Integration &Visualization?EBI; Genome Browser Data Integration &Visualization?UCSC Genomics Institute, University of California Santa Cruz; Lead analysts:; Laboratory, Data Analysis &Coordinating Center (LDACC):; NIH program management:; Biospecimen collection:; Pathology:; eQTL manuscript working group:; Battle, Alexis; Brown, Christopher D; Engelhardt, Barbara E; Montgomery, Stephen B | Nature. | 2017 Oct 11; | 29022597 | |
| Dynamic landscape and regulation of RNA editing in mammals. | Tan, Meng How; Li, Qin; Shanmugam, Raghuvaran; Piskol, Robert; Kohler, Jennefer; Young, Amy N; Liu, Kaiwen Ivy; Zhang, Rui; Ramaswami, Gokul; Ariyoshi, Kentaro; Gupte, Ankita; Keegan, Liam P; George, Cyril X; Ramu, Avinash; Huang, Ni; Pollina, Elizabeth A; Leeman, Dena S; Rustighi, Alessandra; Goh, Y P Sharon; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)?Analysis Working Group; Statistical Methods groups?Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site?NDRI; Biospecimen Collection Source Site?RPCI; Biospecimen Core Resource?VARI; Brain Bank Repository?University of Miami Brain Endowment Bank; Leidos Biomedical?Project Management; ELSI Study; Genome Browser Data Integration &Visualization?EBI; Genome Browser Data Integration &Visualization?UCSC Genomics Institute, University of California Santa Cruz; Chawla, Ajay; Del Sal, Giannino; Peltz, Gary; Brunet, Anne; Conrad, Donald F; Samuel, Charles E; O'Connell, Mary A; Walkley, Carl R; Nishikura, Kazuko; Li, Jin Billy | Nature. | 2017 Oct 11; | 29022589 | |
| The impact of rare variation on gene expression across tissues. | Li, Xin; Kim, Yungil; Tsang, Emily K; Davis, Joe R; Damani, Farhan N; Chiang, Colby; Hess, Gaelen T; Zappala, Zachary; Strober, Benjamin J; Scott, Alexandra J; Li, Amy; Ganna, Andrea; Bassik, Michael C; Merker, Jason D; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)?Analysis Working Group; Statistical Methods groups?Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site?NDRI; Biospecimen Collection Source Site?RPCI; Biospecimen Core Resource?VARI; Brain Bank Repository?University of Miami Brain Endowment Bank; Leidos Biomedical?Project Management; ELSI Study; Genome Browser Data Integration &Visualization?EBI; Genome Browser Data Integration &Visualization?UCSC Genomics Institute, University of California Santa Cruz; Hall, Ira M; Battle, Alexis; Montgomery, Stephen B | Nature. | 2017 10 11; | 29022581 | |
| Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. | Yang, Fan; Wang, Jiebiao; GTEx Consortium; Pierce, Brandon L; Chen, Lin S | Genome research. | 2017 Nov; | 29021290 | |
| Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. | Mohammadi, Pejman; Castel, Stephane E; Brown, Andrew A; Lappalainen, Tuuli | Genome research. | 2017 Nov; | 29021289 | |
| Co-expression networks reveal the tissue-specific regulation of transcription and splicing. | Saha, Ashis; Kim, Yungil; Gewirtz, Ariel D H; Jo, Brian; Gao, Chuan; McDowell, Ian C; GTEx Consortium; Engelhardt, Barbara E; Battle, Alexis | Genome research. | 2017 Nov; | 29021288 | |
| Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. | eGTEx Project | Nature genetics. | 2017 Dec; | 29019975 | |
| Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. | McAllister, Kimberly; Mechanic, Leah E; Amos, Christopher; Aschard, Hugues; Blair, Ian A; Chatterjee, Nilanjan; Conti, David; Gauderman, W James; Hsu, Li; Hutter, Carolyn M; Jankowska, Marta M; Kerr, Jacqueline; Kraft, Peter; Montgomery, Stephen B; Mukherjee, Bhramar; Papanicolaou, George J; Patel, Chirag J; Ritchie, Marylyn D; Ritz, Beate R; Thomas, Duncan C; Wei, Peng; Witte, John S | American journal of epidemiology. | 2017 Oct 01; | 28978193 | |
| Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions. | Ritchie, Marylyn D; Davis, Joe R; Aschard, Hugues; Battle, Alexis; Conti, David; Du, Mengmeng; Eskin, Eleazar; Fallin, M Daniele; Hsu, Li; Kraft, Peter; Moore, Jason H; Pierce, Brandon L; Bien, Stephanie A; Thomas, Duncan C; Wei, Peng; Montgomery, Stephen B | American journal of epidemiology. | 2017 Oct 01; | 28978191 | |
| A genome-wide association study of LCH identifies a variant inSMAD6associated with susceptibility. | Peckham-Gregory, Erin C; Chakraborty, Rikhia; Scheurer, Michael E; Belmont, John W; Abhyankar, Harshal; Sengal, Amel G; Scull, Brooks P; Eckstein, Olive; Zinn, Daniel J; Mayer, Louisa; Shih, Albert; Merad, Miriam; Parsons, D Williams; McClain, Kenneth L; Lupo, Philip J; Allen, Carl E | Blood. | 2017 11 16; | 28935696 | |
| Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes. | Duong, Dat; Gai, Lisa; Snir, Sagi; Kang, Eun Yong; Han, Buhm; Sul, Jae Hoon; Eskin, Eleazar | Bioinformatics (Oxford, England). | 2017 Jul 15; | 28881962 | |
| Transposable elements are the primary source of novelty in primate gene regulation. | Trizzino, Marco; Park, YoSon; Holsbach-Beltrame, Marcia; Aracena, Katherine; Mika, Katelyn; Caliskan, Minal; Perry, George H; Lynch, Vincent J; Brown, Christopher D | Genome research. | 2017 10; | 28855262 | |
| Eigenvalue significance testing for genetic association. | Zhou, Yi-Hui; Marron, J S; Wright, Fred A | Biometrics. | 2018 06; | 28853138 | |
| A Loss-of-Function Splice Acceptor Variant in IGF2 Is Protective for Type 2 Diabetes. | Mercader, Josep M; Liao, Rachel G; Bell, Avery D; Dymek, Zachary; Estrada, Karol; Tukiainen, Taru; Huerta-Chagoya, Alicia; Moreno-Macías, Hortensia; Jablonski, Kathleen A; Hanson, Robert L; Walford, Geoffrey A; Moran, Ignasi; Chen, Ling; Agarwala, Vineeta; Ordoñez-Sánchez, María Luisa; Rodríguez-Guillen, Rosario; Rodríguez-Torres, Maribel; Segura-Kato, Yayoi; García-Ortiz, Humberto; Centeno-Cruz, Federico; Barajas-Olmos, Francisco; Caulkins, Lizz; Puppala, Sobha; Fontanillas, Pierre; Williams, Amy L; Bonàs-Guarch, Sílvia; Hartl, Chris; Ripke, Stephan; Diabetes Prevention Program Research Group; Tooley, Katherine; Lane, Jacqueline; Zerrweck, Carlos; Martínez-Hernández, Angélica; Córdova, Emilio J; Mendoza-Caamal, Elvia; Contreras-Cubas, Cecilia; González-Villalpando, María E; Cruz-Bautista, Ivette; Muñoz-Hernández, Liliana; Gómez-Velasco, Donaji; Alvirde, Ulises; Henderson, Brian E; Wilkens, Lynne R; Le Marchand, Loic; Arellano-Campos, Olimpia; Riba, Laura; Harden, Maegan; Broad Genomics Platform; Gabriel, Stacey; T2D-GENES Consortium; Abboud, Hanna E; Cortes, Maria L; Revilla-Monsalve, Cristina; Islas-Andrade, Sergio; Soberon, Xavier; Curran, Joanne E; Jenkinson, Christopher P; DeFronzo, Ralph A; Lehman, Donna M; Hanis, Craig L; Bell, Graeme I; Boehnke, Michael; Blangero, John; Duggirala, Ravindranath; Saxena, Richa; MacArthur, Daniel; Ferrer, Jorge; McCarroll, Steven A; Torrents, David; Knowler, William C; Baier, Leslie J; Burtt, Noel; González-Villalpando, Clicerio; Haiman, Christopher A; Aguilar-Salinas, Carlos A; Tusié-Luna, Teresa; Flannick, Jason; Jacobs, Suzanne B R; Orozco, Lorena; Altshuler, David; Florez, Jose C; SIGMA T2D Genetics Consortium | Diabetes. | 2017 11; | 28838971 | |
| A Standardized Approach for Multispecies Purification of Mammalian Male Germ Cells by Mechanical Tissue Dissociation and Flow Cytometry. | Lima, Ana C; Jung, Min; Rusch, Jannette; Usmani, Abul; Lopes, Alexandra M; Conrad, Donald F | Journal of visualized experiments : JoVE. | 2017 07 12; | 28745623 | |
| 10 Years of GWAS Discovery: Biology, Function, and Translation. | Visscher, Peter M; Wray, Naomi R; Zhang, Qian; Sklar, Pamela; McCarthy, Mark I; Brown, Matthew A; Yang, Jian | American journal of human genetics. | 2017 Jul 06; | 28686856 | |
| How to Map the Genetic Basis for Conditions that are Comorbid with Male Infertility. | Nagirnaja, Liina; Vigh-Conrad, Katinka; Conrad, Donald F | Seminars in reproductive medicine. | 2017 05; | 28658705 | |
| Female Genomics: Infertility and Overall Health. | Joshi, Nikhil; Chan, Jessica L | Seminars in reproductive medicine. | 2017 05; | 28658704 | |
| Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration. | Parsana, Princy; Amend, Sarah R; Hernandez, James; Pienta, Kenneth J; Battle, Alexis | BMC cancer. | 2017 Jun 26; | 28651527 | |
| Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues. | Zhang, Mingfeng; Lykke-Andersen, Soren; Zhu, Bin; Xiao, Wenming; Hoskins, Jason W; Zhang, Xijun; Rost, Lauren M; Collins, Irene; Bunt, Martijn van de; Jia, Jinping; Parikh, Hemang; Zhang, Tongwu; Song, Lei; Jermusyk, Ashley; Chung, Charles C; Zhu, Bin; Zhou, Weiyin; Matters, Gail L; Kurtz, Robert C; Yeager, Meredith; Jensen, Torben Heick; Brown, Kevin M; Ongen, Halit; Bamlet, William R; Murray, Bradley A; McCarthy, Mark I; Chanock, Stephen J; Chatterjee, Nilanjan; Wolpin, Brian M; Smith, Jill P; Olson, Sara H; Petersen, Gloria M; Shi, Jianxin; Amundadottir, Laufey | Gut. | 2017 Jun 20; | 28634199 | |
| The association between telomere length and mortality in Bangladesh. | Dean, Samantha G; Zhang, Chenan; Gao, Jianjun; Roy, Shantanu; Shinkle, Justin; Sabarinathan, Mekala; Argos, Maria; Tong, Lin; Ahmed, Alauddin; Islam, Md Tariqul; Islam, Tariqul; Rakibuz-Zaman, Muhammad; Sarwar, Golam; Shahriar, Hasan; Rahman, Mahfuzar; Yunus, Md; Graziano, Joseph H; Chen, Lin S; Jasmine, Farzana; Kibriya, Muhammad G; Ahsan, Habibul; Pierce, Brandon L | Aging. | 2017 Jun 15; | 28630379 | |
| Clinical and Genome-Wide Analysis of Cisplatin-Induced Peripheral Neuropathy in Survivors of Adult-Onset Cancer. | Dolan, M Eileen; El Charif, Omar; Wheeler, Heather E; Gamazon, Eric R; Ardeshir-Rouhani-Fard, Shirin; Monahan, Patrick; Feldman, Darren R; Hamilton, Robert J; Vaughn, David J; Beard, Clair J; Fung, Chunkit; Kim, Jeri; Fossa, Sophie D; Hertz, Daniel L; Mushiroda, Taisei; Kubo, Michiaki; Einhorn, Lawrence H; Cox, Nancy J; Travis, Lois B; Platinum Study Group | Clinical cancer research : an official journal of the American Association for Cancer Research. | 2017 Oct 01; | 28611204 | |
| Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve. | Yang, Bo; Zhou, Wei; Jiao, Jiao; Nielsen, Jonas B; Mathis, Michael R; Heydarpour, Mahyar; Lettre, Guillaume; Folkersen, Lasse; Prakash, Siddharth; Schurmann, Claudia; Fritsche, Lars; Farnum, Gregory A; Lin, Maoxuan; Othman, Mohammad; Hornsby, Whitney; Driscoll, Anisa; Levasseur, Alexandra; Thomas, Marc; Farhat, Linda; Dubé, Marie-Pierre; Isselbacher, Eric M; Franco-Cereceda, Anders; Guo, Dong-Chuan; Bottinger, Erwin P; Deeb, G Michael; Booher, Anna; Kheterpal, Sachin; Chen, Y Eugene; Kang, Hyun Min; Kitzman, Jacob; Cordell, Heather J; Keavney, Bernard D; Goodship, Judith A; Ganesh, Santhi K; Abecasis, Gonçalo; Eagle, Kim A; Boyle, Alan P; Loos, Ruth J F; Eriksson, Per; Tardif, Jean-Claude; Brummett, Chad M; Milewicz, Dianna M; Body, Simon C; Willer, Cristen J | Nature communications. | 2017 May 25; | 28541271 | |
| Allele-specific expression reveals interactions between genetic variation and environment. | Knowles, David A; Davis, Joe R; Edgington, Hilary; Raj, Anil; Favé, Marie-Julie; Zhu, Xiaowei; Potash, James B; Weissman, Myrna M; Shi, Jianxin; Levinson, Douglas F; Awadalla, Philip; Mostafavi, Sara; Montgomery, Stephen B; Battle, Alexis | Nature methods. | 2017 Jul; | 28530654 | |
| Widespread Allelic Heterogeneity in Complex Traits. | Hormozdiari, Farhad; Zhu, Anthony; Kichaev, Gleb; Ju, Chelsea J-T; Segrè, Ayellet V; Joo, Jong Wha J; Won, Hyejung; Sankararaman, Sriram; Pasaniuc, Bogdan; Shifman, Sagiv; Eskin, Eleazar | American journal of human genetics. | 2017 May 04; | 28475861 | |
| veqtl-mapper: variance association mapping for molecular phenotypes. | Brown, Andrew Anand | Bioinformatics (Oxford, England). | 2017 Sep 01; | 28449110 | |
| Reproducible RNA-seq analysis using recount2. | Collado-Torres, Leonardo; Nellore, Abhinav; Kammers, Kai; Ellis, Shannon E; Taub, Margaret A; Hansen, Kasper D; Jaffe, Andrew E; Langmead, Ben; Leek, Jeffrey T | Nature biotechnology. | 2017 04 11; | 28398307 | |
| Population- and individual-specific regulatory variation in Sardinia. | Pala, Mauro; Zappala, Zachary; Marongiu, Mara; Li, Xin; Davis, Joe R; Cusano, Roberto; Crobu, Francesca; Kukurba, Kimberly R; Gloudemans, Michael J; Reinier, Frederic; Berutti, Riccardo; Piras, Maria G; Mulas, Antonella; Zoledziewska, Magdalena; Marongiu, | Nature genetics. | 2017 May; | 28394350 | |
| Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci. | Pashos, Evanthia E; Park, YoSon; Wang, Xiao; Raghavan, Avanthi; Yang, Wenli; Abbey, Deepti; Peters, Derek T; Arbelaez, Juan; Hernandez, Mayda; Kuperwasser, Nicolas; Li, Wenjun; Lian, Zhaorui; Liu, Ying; Lv, Wenjian; Lytle-Gabbin, Stacey L; Marchadier, Dawn H; Rogov, Peter; Shi, Jianting; Slovik, Katherine J; Stylianou, Ioannis M; Wang, Li; Yan, Ruilan; Zhang, Xiaolan; Kathiresan, Sekar; Duncan, Stephen A; Mikkelsen, Tarjei S; Morrisey, Edward E; Rader, Daniel J; Brown, Christopher D; Musunuru, Kiran | Cell stem cell. | 2017 Apr 06; | 28388432 | |
| The impact of structural variation on human gene expression. | Chiang, Colby; Scott, Alexandra J; Davis, Joe R; Tsang, Emily K; Li, Xin; Kim, Yungil; Hadzic, Tarik; Damani, Farhan N; Ganel, Liron; GTEx Consortium; Montgomery, Stephen B; Battle, Alexis; Conrad, Donald F; Hall, Ira M | Nature genetics. | 2017 May; | 28369037 | |
| A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk. | Manning, Alisa (see original citation for additional authors) | Diabetes. | 2017 Jul; | 28341696 | |
| PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4. | Salsman, Jayme; Stathakis, Alex; Parker, Ellen; Chung, Dudley; Anthes, Livia E; Koskowich, Kara L; Lahsaee, Sara; Gaston, Daniel; Kukurba, Kimberly R; Smith, Kevin S; Chute, Ian C; Léger, Daniel; Frost, Laura D; Montgomery, Stephen B; Lewis, Stephen M; Es | Scientific reports. | 2017 Mar 23; | 28332630 | |
| Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. | Pulido-Quetglas, Carlos; Aparicio-Prat, Estel; Arnan, Carme; Polidori, Taisia; Hermoso, Toni; Palumbo, Emilio; Ponomarenko, Julia; Guigo, Roderic; Johnson, Rory | PLoS computational biology. | 2017 03; | 28253259 | |
| Whole-transcriptome sequencing in blood provides a diagnosis of spinal muscular atrophy with progressive myoclonic epilepsy. | Kernohan, Kristin D; Frésard, Laure; Zappala, Zachary; Hartley, Taila; Smith, Kevin S; Wagner, Justin; Xu, Hongbin; McBride, Arran; Bourque, Pierre R; Consortium, Care Rare Canada; Bennett, Steffany A L; Dyment, David A; Boycott, Kym M; Montgomery, Stephen B; Warman Chardon, Jodi | Human mutation. | 2017 06; | 28251733 | |
| Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation. | Rahmani, Elior; Zaitlen, Noah; Baran, Yael; Eng, Celeste; Hu, Donglei; Galanter, Joshua; Oh, Sam; Burchard, Esteban G; Eskin, Eleazar; Zou, James; Halperin, Eran | Nature methods. | 2017 Feb 28; | 28245214 | |
| Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression. | McCoy, Rajiv C; Wakefield, Jon; Akey, Joshua M | Cell. | 2017 02 23; | 28235201 | |
| Pathway-wide association study identifies five shared pathways associated with schizophrenia in three ancestral distinct populations. | Liu, C; Bousman, C A; Pantelis, C; Skafidas, E; Zhang, D; Yue, W; Everall, I P | Translational psychiatry. | 2017 Feb 21; | 28221366 | |
| A genome-wide association study yields five novel thyroid cancer risk loci. | Gudmundsson, Julius; Thorleifsson, Gudmar; Sigurdsson, Jon K; Stefansdottir, Lilja; Jonasson, Jon G; Gudjonsson, Sigurjon A; Gudbjartsson, Daniel F; Masson, Gisli; Johannsdottir, Hrefna; Halldorsson, Gisli H; Stacey, Simon N; Helgason, Hannes; Sulem, Patr | Nature communications. | 2017 Feb 14; | 28195142 | |
| MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets. | Fort, Alexandre; Panousis, Nikolaos I; Garieri, Marco; Antonarakis, Stylianos E; Lappalainen, Tuuli; Dermitzakis, Emmanouil T; Delaneau, Olivier | Bioinformatics (Oxford, England). | 2017 Jun 15; | 28186259 | |
| The Relation Between Inflation in Type-I and Type-II Error Rate and Population Divergence in Genome-Wide Association Analysis of Multi-Ethnic Populations. | Derks, E M; Zwinderman, A H; Gamazon, E R | Behavior genetics. | 2017 May; | 28185111 | |
| Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results. | Khramtsova, Ekaterina A; Stranger, Barbara E | Bioinformatics (Oxford, England). | 2017 02 01; | 28172529 | |
| Integrated analysis of genetic variation and gene expression reveals novel variant for increased warfarin dose requirement in African Americans. | Hernandez, W; Gamazon, E R; Aquino-Michaels, K; Smithberger, E; O'Brien, T J; Harralson, A F; Tuck, M; Barbour, A; Cavallari, L H; Perera, M A | Journal of thrombosis and haemostasis : JTH. | 2017 04; | 28135054 | |
| Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice. | Carrat, Gaelle R; Hu, Ming; Nguyen-Tu, Marie-Sophie; Chabosseau, Pauline; Gaulton, Kyle J; van de Bunt, Martijn; Siddiq, Afshan; Falchi, Mario; Thurner, Matthias; Canouil, Mickaël; Pattou, Francois; Leclerc, Isabelle; Pullen, Timothy J; Cane, Matthew C; P | American journal of human genetics. | 2017 Feb 02; | 28132686 | |
| Simultaneous Modeling of Disease Status and Clinical Phenotypes To Increase Power in Genome-Wide Association Studies. | Bilow, Michael; Crespo, Fernando; Pan, Zhicheng; Eskin, Eleazar; Eyheramendy, Susana | Genetics. | 2017 Mar; | 28132020 | |
| Regulatory Variants Modulate Protein Kinase C ? (PRKCA) Gene Expression in Human Heart. | Li, Liang; Zhang, Lizhi; Binkley, Philip F; Sadee, Wolfgang; Wang, Danxin | Pharmaceutical research. | 2017 Aug; | 28120175 | |
| Blood pressure-associated polymorphism controls ARHGAP42 expression via serum response factor DNA binding. | Bai, Xue; Mangum, Kevin D; Dee, Rachel A; Stouffer, George A; Lee, Craig R; Oni-Orisan, Akinyemi; Patterson, Cam; Schisler, Jonathan C; Viera, Anthony J; Taylor, Joan M; Mack, Christopher P | The Journal of clinical investigation. | 2017 Feb 01; | 28112683 | |
| Non-Coding Loss-of-Function Variation in Human Genomes. | Zappala, Zachary; Montgomery, Stephen B | Human heredity. | 2016; | 28076858 | |
| Variants in WFS1 and other Mendelian deafness genes are associated with cisplatin-associated ototoxicity. | Wheeler, Heather E; Gamazon, Eric R; Frisina, Robert; Perez-Cervantes, Carlos; El Charif, Omar; Mapes, Brandon; Fossa, Sophie D; Feldman, Darren; Hamilton, Robert; Vaughn, David J; Beard, Clair; Fung, Chunkit; Kollmannsberger, Christian; Kim, Jeri; Mushir | Clinical cancer research : an official journal of the American Association for Cancer Research. | 2016 Dec 30; | 28039263 | |
| Targeted bisulfite sequencing of the dynamic DNA methylome. | Ziller, Michael J; Stamenova, Elena K; Gu, Hongcang; Gnirke, Andreas; Meissner, Alexander | Epigenetics & chromatin. | 2016; | 27980681 | |
| A tiered, Bayesian approach to estimating of population variability for regulatory decision-making. | Chiu, Weihsueh A; Wright, Fred A; Rusyn, Ivan | ALTEX. | 2016 Dec 13; | 27960008 | |
| Increased burden of deleterious variants in essential genes in autism spectrum disorder. | Ji, Xiao; Kember, Rachel L; Brown, Christopher D; Bu?an, Maja | Proceedings of the National Academy of Sciences of the United States of America. | 2016 12 27; | 27956632 | |
| Genomic Characterization of Metformin Hepatic Response. | Luizon, Marcelo R; Eckalbar, Walter L; Wang, Yao; Jones, Stacy L; Smith, Robin P; Laurance, Megan; Lin, Lawrence; Gallins, Paul J; Etheridge, Amy S; Wright, Fred; Zhou, Yihui; Molony, Cliona; Innocenti, Federico; Yee, Sook Wah; Giacomini, Kathleen M; Ahit | PLoS genetics. | 2016 Nov; | 27902686 | |
| Alpha-2 macroglobulin in Alzheimer's disease: a marker of neuronal injury through the RCAN1 pathway. | Varma, V R; Varma, S; An, Y; Hohman, T J; Seddighi, S; Casanova, R; Beri, A; Dammer, E B; Seyfried, N T; Pletnikova, O; Moghekar, A; Wilson, M R; Lah, J J; O'Brien, R J; Levey, A I; Troncoso, J C; Albert, M S; Thambisetty, M | Molecular psychiatry. | 2017 Jan; | 27872486 | |
| Integrating GWAS and Co-expression Network Data Identifies Bone Mineral Density Genes SPTBN1 and MARK3 and an Osteoblast Functional Module. | Calabrese, Gina M; Mesner, Larry D; Stains, Joseph P; Tommasini, Steven M; Horowitz, Mark C; Rosen, Clifford J; Farber, Charles R | Cell systems. | 2017 Jan 25; | 27866947 | |
| Colocalization of GWAS and eQTL Signals Detects Target Genes. | Hormozdiari, Farhad; van de Bunt, Martijn; Segrè, Ayellet V; Li, Xiao; Joo, Jong Wha J; Bilow, Michael; Sul, Jae Hoon; Sankararaman, Sriram; Pasaniuc, Bogdan; Eskin, Eleazar | American journal of human genetics. | 2016 Dec 01; | 27866706 | |
| Detecting differential growth of microbial populations with Gaussian process regression. | Tonner, Peter D; Darnell, Cynthia L; Engelhardt, Barbara E; Schmid, Amy K | Genome research. | 2017 Feb; | 27864351 | |
| Multiplex shRNA Screening of Germ Cell Development by in Vivo Transfection of Mouse Testis. | Ho, Nicholas R Y; Usmani, Abul R; Yin, Yan; Ma, Liang; Conrad, Donald F | G3 (Bethesda, Md.). | 2017 Jan 05; | 27856695 | |
| Sex-Specific and Time-Varying Associations Between Cigarette Smoking and Telomere Length Among Older Adults. | Zhang, Chenan; Lauderdale, Diane S; Pierce, Brandon L | American journal of epidemiology. | 2016 Dec 15; | 27856448 | |
| Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues. | Wheeler, Heather E; Shah, Kaanan P; Brenner, Jonathon; Garcia, Tzintzuni; Aquino-Michaels, Keston; GTEx Consortium; Cox, Nancy J; Nicolae, Dan L; Im, Hae Kyung | PLoS genetics. | 2016 Nov; | 27835642 | |
| Controlling the Rate of GWAS False Discoveries. | Brzyski, Damian; Peterson, Christine B; Sobczyk, Piotr; Candès, Emmanuel J; Bogdan, Malgorzata; Sabatti, Chiara | Genetics. | ; | 27784720 | |
| Genome-wide significance testing of variation from single case exomes. | Wilfert AB, Chao KR, Kaushal M, Jain S, Zollner S, Adams DR, Conrad DF. | Nat Genet | 2016 Oct | 27776118 | |
| Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure. | Joo, Jong Wha J; Kang, Eun Yong; Org, Elin; Furlotte, Nick; Parks, Brian; Hormozdiari, Farhad; Lusis, Aldons J; Eskin, Eleazar | Genetics. | 2016 Dec; | 27770036 | |
| Discovering SNPs Regulating Human Gene Expression Using Allele Specific Expression from RNA-Seq Data. | Kang, Eun Yong; Martin, Lisa; Mangul, Serghei; Isvilanonda, Warin; Zou, Jennifer; Ben-David, Eyal; Han, Buhm; Lusis, Aldons J; Shifman, Sagiv; Eskin, Eleazar | Genetics. | 2016 Oct 07; | 27765809 | |
| Chromosome conformation elucidates regulatory relationships in developing human brain. | Won, Hyejung; de la Torre-Ubieta, Luis; Stein, Jason L; Parikshak, Neelroop N; Huang, Jerry; Opland, Carli K; Gandal, Michael J; Sutton, Gavin J; Hormozdiari, Farhad; Lu, Daning; Lee, Changhoon; Eskin, Eleazar; Voineagu, Irina; Ernst, Jason; Geschwind, Da | Nature. | 2016 Oct 19; | 27760116 | |
| Genetic resilience to amyloid related cognitive decline. | Hohman, Timothy J; Dumitrescu, Logan; Cox, Nancy J; Jefferson, Angela L; Alzheimer?s Neuroimaging Initiative | Brain imaging and behavior. | 2017 Apr; | 27743375 | |
| Detection of human adaptation during the past 2000 years. | Field, Yair; Boyle, Evan A; Telis, Natalie; Gao, Ziyue; Gaulton, Kyle J; Golan, David; Yengo, Loic; Rocheleau, Ghislain; Froguel, Philippe; McCarthy, Mark I; Pritchard, Jonathan K | Science (New York, N.Y.). | ; | 27738015 | |
| Detecting Sources of Transcriptional Heterogeneity in Large-Scale RNA-Seq Data Sets. | Searle, Brian C; Gittelman, Rachel M; Manor, Ohad; Akey, Joshua M | Genetics. | 2016 Dec; | 27729424 | |
| Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. | Ernst, Jason; Melnikov, Alexandre; Zhang, Xiaolan; Wang, Li; Rogov, Peter; Mikkelsen, Tarjei S; Kellis, Manolis | Nature biotechnology. | 2016 Nov; | 27701403 | |
| IL1RL1 asthma risk variants regulate airway type 2 inflammation. | Gordon, Erin D; Palandra, Joe; Wesolowska-Andersen, Agata; Ringel, Lando; Rios, Cydney L; Lachowicz-Scroggins, Marrah E; Sharp, Louis Z; Everman, Jamie L; MacLeod, Hannah J; Lee, Jae W; Mason, Robert J; Matthay, Michael A; Sheldon, Richard T; Peters, Mich | JCI insight. | 2016 Sep 08; | 27699235 | |
| Non-linear interactions between candidate genes of myocardial infarction revealed in mRNA expression profiles. | Hartmann, Katherine; Seweryn, Micha?; Handleman, Samuel K; Rempa?a, Grzegorz A; Sadee, Wolfgang | BMC genomics. | 2016 Sep 17; | 27640124 | |
| Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension. | Surendran, Praveen (see original citation for additional authors) | Nature genetics. | 2016 10; | 27618447 | |
| Rare variant phasing and haplotypic expression from RNA sequencing with phASER. | Castel, Stephane E; Mohammadi, Pejman; Chung, Wendy K; Shen, Yufeng; Lappalainen, Tuuli | Nature communications. | 2016 Sep 08; | 27605262 | |
| REDIportal: a comprehensive database of A-to-I RNA editing events in humans. | Picardi, Ernesto; D'Erchia, Anna Maria; Lo Giudice, Claudio; Pesole, Graziano | Nucleic acids research. | 2017 Jan 04; | 27587585 | |
| Multispecies Purification of Testicular Germ Cells. | Lima, Ana C; Jung, Min; Rusch, Jannette; Usmani, Abul; Lopes, Alexandra; Conrad, Donald F | Biology of reproduction. | 2016 Aug 24; | 27557646 | |
| A reference panel of 64,976 haplotypes for genotype imputation. | McCarthy, Shane; Das, Sayantan; Kretzschmar, Warren; Delaneau, Olivier; Wood, Andrew R; Teumer, Alexander; Kang, Hyun Min; Fuchsberger, Christian; Danecek, Petr; Sharp, Kevin; Luo, Yang; Sidore, Carlo; Kwong, Alan; Timpson, Nicholas; Koskinen, Seppo; Vrieze, Scott; Scott, Laura J; Zhang, He; Mahajan, Anubha; Veldink, Jan; Peters, Ulrike; Pato, Carlos; van Duijn, Cornelia M; Gillies, Christopher E; Gandin, Ilaria; Mezzavilla, Massimo; Gilly, Arthur; Cocca, Massimiliano; Traglia, Michela; Angius, Andrea; Barrett, Jeffrey C; Boomsma, Dorrett; Branham, Kari; Breen, Gerome; Brummett, Chad M; Busonero, Fabio; Campbell, Harry; Chan, Andrew; Chen, Sai; Chew, Emily; Collins, Francis S; Corbin, Laura J; Smith, George Davey; Dedoussis, George; Dorr, Marcus; Farmaki, Aliki-Eleni; Ferrucci, Luigi; Forer, Lukas; Fraser, Ross M; Gabriel, Stacey; Levy, Shawn; Groop, Leif; Harrison, Tabitha; Hattersley, Andrew; Holmen, Oddgeir L; Hveem, Kristian; Kretzler, Matthias; Lee, James C; McGue, Matt; Meitinger, Thomas; Melzer, David; Min, Josine L; Mohlke, Karen L; Vincent, John B; Nauck, Matthias; Nickerson, Deborah; Palotie, Aarno; Pato, Michele; Pirastu, Nicola; McInnis, Melvin; Richards, J Brent; Sala, Cinzia; Salomaa, Veikko; Schlessinger, David; Schoenherr, Sebastian; Slagboom, P Eline; Small, Kerrin; Spector, Timothy; Stambolian, Dwight; Tuke, Marcus; Tuomilehto, Jaakko; Van den Berg, Leonard H; Van Rheenen, Wouter; Volker, Uwe; Wijmenga, Cisca; Toniolo, Daniela; Zeggini, Eleftheria; Gasparini, Paolo; Sampson, Matthew G; Wilson, James F; Frayling, Timothy; de Bakker, Paul I W; Swertz, Morris A; McCarroll, Steven; Kooperberg, Charles; Dekker, Annelot; Altshuler, David; Willer, Cristen; Iacono, William; Ripatti, Samuli; Soranzo, Nicole; Walter, Klaudia; Swaroop, Anand; Cucca, Francesco; Anderson, Carl A; Myers, Richard M; Boehnke, Michael; McCarthy, Mark I; Durbin, Richard; Haplotype Reference Consortium | Nature genetics. | 2016 10; | 27548312 | |
| Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. | Brinkmeyer-Langford, Candice L; Guan, Jinting; Ji, Guoli; Cai, James J | Frontiers in aging neuroscience. | 2016; | 27536236 | |
| Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). | Lagarde, Julien; Uszczynska-Ratajczak, Barbara; Santoyo-Lopez, Javier; Gonzalez, Jose Manuel; Tapanari, Electra; Mudge, Jonathan M; Steward, Charles A; Wilming, Laurens; Tanzer, Andrea; Howald, Cédric; Chrast, Jacqueline; Vela-Boza, Alicia; Rueda, Antonio; Lopez-Domingo, Francisco J; Dopazo, Joaquin; Reymond, Alexandre; Guigó, Roderic; Harrow, Jennifer | Nature communications. | 2016 Aug 17; | 27531712 | |
| Loss of Function of GALNT2 Lowers High-Density Lipoproteins in Humans, Nonhuman Primates, and Rodents. | Khetarpal, Sumeet A; Schjoldager, Katrine T; Christoffersen, Christina; Raghavan, Avanthi; Edmondson, Andrew C; Reutter, Heiko M; Ahmed, Bouhouche; Ouazzani, Reda; Peloso, Gina M; Vitali, Cecilia; Zhao, Wei; Somasundara, Amritha Varshini Hanasoge; Millar, John S; Park, YoSon; Fernando, Gayani; Livanov, Valentin; Choi, Seungbum; Noé, Eric; Patel, Pritesh; Ho, Siew Peng; Myocardial Infarction Exome Sequencing Study; Kirchgessner, Todd G; Wandall, Hans H; Hansen, Lars; Bennett, Eric P; Vakhrushev, Sergey Y; Saleheen, Danish; Kathiresan, Sekar; Brown, Christopher D; Abou Jamra, Rami; LeGuern, Eric; Clausen, Henrik; Rader, Daniel J | Cell metabolism. | 2016 Aug 09; | 27508872 | |
| Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering. | Gao, Chuan; McDowell, Ian C; Zhao, Shiwen; Brown, Christopher D; Engelhardt, Barbara E | PLoS computational biology. | 2016 Jul; | 27467526 | |
| Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases. | Li, Yue; Kellis, Manolis | Nucleic acids research. | 2016 Oct 14; | 27407109 | |
| The genetic architecture of type 2 diabetes. | Nature. | 2016 Aug 4; | 27398621 | ||
| Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder. | Hou, Liping; Bergen, Sarah E; Akula, Nirmala; Song, Jie; Hultman, Christina M; Landén, Mikael; Adli, Mazda; Alda, Martin; Ardau, Raffaella; Arias, Bárbara; Aubry, Jean-Michel; Backlund, Lena; Badner, Judith A; Barrett, Thomas B; Bauer, Michael; Baune, Ber | Human molecular genetics. | 2016 Aug 01; | 27329760 | |
| Two olfactory receptors-OR2A4/7 and OR51B5-differentially affect epidermal proliferation and differentiation. | Tsai, Teresa; Veitinger, Sophie; Peek, Irina; Busse, Daniela; Eckardt, Josephine; Vladimirova, Dilyana; Jovancevic, Nikolina; Wojcik, Sebastian; Gisselmann, Günter; Altmüller, Janine; Ständer, Sonja; Luger, Thomas; Paus, Ralf; Cheret, Jeremy; Hatt, Hanns | Experimental dermatology. | 2017 01; | 27315375 | |
| Using genomic annotations increases statistical power to detect eGenes. | Duong, Dat; Zou, Jennifer; Hormozdiari, Farhad; Sul, Jae Hoon; Ernst, Jason; Han, Buhm; Eskin, Eleazar | Bioinformatics (Oxford, England). | 2016 Jun 15; | 27307612 | |
| Imputing Phenotypes for Genome-wide Association Studies. | Hormozdiari, Farhad; Kang, Eun Yong; Bilow, Michael; Ben-David, Eyal; Vulpe, Chris; McLachlan, Stela; Lusis, Aldons J; Han, Buhm; Eskin, Eleazar | American journal of human genetics. | 2016 Jul 7; | 27292110 | |
| Fast and Accurate Construction of Confidence Intervals for Heritability. | Schweiger, Regev; Kaufman, Shachar; Laaksonen, Reijo; Kleber, Marcus E; März, Winfried; Eskin, Eleazar; Rosset, Saharon; Halperin, Eran | American journal of human genetics. | 2016 Jun 2; | 27259052 | |
| Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. | Wen, Xiaoquan; Lee, Yeji; Luca, Francesca; Pique-Regi, Roger | American journal of human genetics. | 2016 Jun 2; | 27236919 | |
| Defining the Phenotype and Assessing Severity in Phosphoglucomutase-1 Deficiency. | Wong, Sunnie Yan-Wai; Beamer, Lesa J; Gadomski, Therese; Honzik, Tomas; Mohamed, Miski; Wortmann, Saskia B; Brocke Holmefjord, Katja S; Mork, Marit; Bowling, Francis; Sykut-Cegielska, Jolanta; Koch, Dieter; Ackermann, Amanda; Stanley, Charles A; Rymen, Da | The Journal of pediatrics. | 2016 Aug; | 27206562 | |
| Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. | Lan, Xun; Pritchard, Jonathan K | Science (New York, N.Y.). | 2016 May 20; | 27199432 | |
| A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets. | Moon, Sunjin; Akey, Joshua M | Genome research. | 2016 Jun; | 27197222 | |
| Impact of the X Chromosome and sex on regulatory variation. | Kukurba, Kimberly R; Parsana, Princy; Balliu, Brunilda; Smith, Kevin S; Zappala, Zachary; Knowles, David A; Favé, Marie-Julie; Davis, Joe R; Li, Xin; Zhu, Xiaowei; Potash, James B; Weissman, Myrna M; Shi, Jianxin; Kundaje, Anshul; Levinson, Douglas F; Awadalla, Philip; Mostafavi, Sara; Battle, Alexis; Montgomery, Stephen B | Genome research. | 2016 Jun; | 27197214 | |
| ForestPMPlot: A Flexible Tool for Visualizing Heterogeneity Between Studies in Meta-analysis. | Kang, Eun Yong; Park, Yurang; Li, Xiao; Segrè, Ayellet V; Han, Buhm; Eskin, Eleazar | G3 (Bethesda, Md.). | 2016 07 07; | 27194809 | |
| Telomere length measurement by a novel Luminex-based assay: a blinded comparison to Southern blot. | Pierce, Brandon L; Jasmine, Farzana; Roy, Shantanu; Zhang, Chenan; Aviv, Abraham; Hunt, Steven C; Ahsan, Habibul; Kibriya, Muhammad G | International journal of molecular epidemiology and genetics. | 2016; | 27186324 | |
| Novel Luminex Assay for Telomere Repeat Mass Does Not Show Well Position Effects Like qPCR. | Kibriya, Muhammad G; Jasmine, Farzana; Roy, Shantanu; Ahsan, Habibul; Pierce, Brandon L | PloS one. | 2016; | 27182778 | |
| Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for Bipolar Disorder. | Peterson, Christine B; Service, Susan K; Jasinska, Anna J; Gao, Fuying; Zelaya, Ivette; Teshiba, Terri M; Bearden, Carrie E; Cantor, Rita M; Reus, Victor I; Macaya, Gabriel; López-Jaramillo, Carlos; Bogomolov, Marina; Benjamini, Yoav; Eskin, Eleazar; Coppola, Giovanni; Freimer, Nelson B; Sabatti, Chiara | PLoS genetics. | 2016 May; | 27176483 | |
| A human-specific AS3MT isoform and BORCS7 are molecular risk factors in the 10q24.32 schizophrenia-associated locus. | Li, Ming; Jaffe, Andrew E; Straub, Richard E; Tao, Ran; Shin, Joo Heon; Wang, Yanhong; Chen, Qiang; Li, Chao; Jia, Yankai; Ohi, Kazutaka; Maher, Brady J; Brandon, Nicholas J; Cross, Alan; Chenoweth, Joshua G; Hoeppner, Daniel J; Wei, Huijun; Hyde, Thomas M; McKay, Ronald; Kleinman, Joel E; Weinberger, Daniel R | Nature medicine. | 2016 06; | 27158905 | |
| TreeQTL: hierarchical error control for eQTL findings. | Peterson, C B; Bogomolov, M; Benjamini, Y; Sabatti, C | Bioinformatics (Oxford, England). | 2016 Apr 19; | 27153635 | |
| Functional Characterization of DNA Methylation in the Oligodendrocyte Lineage. | Moyon, Sarah; Huynh, Jimmy L; Dutta, Dipankar; Zhang, Fan; Ma, Dan; Yoo, Seungyeul; Lawrence, Rebecca; Wegner, Michael; John, Gareth R; Emery, Ben; Lubetzki, Catherine; Franklin, Robin J M; Fan, Guoping; Zhu, Jun; Dupree, Jeffrey L; Casaccia, Patrizia | Cell reports. | 2016 Apr 13; | 27149841 | |
| RNA splicing is a primary link between genetic variation and disease. | Li, Yang I; van de Geijn, Bryce; Raj, Anil; Knowles, David A; Petti, Allegra A; Golan, David; Gilad, Yoav; Pritchard, Jonathan K | Science (New York, N.Y.). | 2016 Apr 29; | 27126046 | |
| Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx. | Wang, Jiebiao; Gamazon, Eric R; Pierce, Brandon L; Stranger, Barbara E; Im, Hae Kyung; Gibbons, Robert D; Cox, Nancy J; Nicolae, Dan L; Chen, Lin S | American journal of human genetics. | 2016 Apr 7; | 27040689 | |
| Multiple testing correction in linear mixed models. | Joo, Jong Wha J; Hormozdiari, Farhad; Han, Buhm; Eskin, Eleazar | Genome biology. | 2016; | 27039378 | |
| Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies. | Rahmani, Elior; Zaitlen, Noah; Baran, Yael; Eng, Celeste; Hu, Donglei; Galanter, Joshua; Oh, Sam; Burchard, Esteban G; Eskin, Eleazar; Zou, James; Halperin, Eran | Nature methods. | 2016 May; | 27018579 | |
| Molecular insights into the OGG1 gene, a cancer risk modifier in BRCA1 and BRCA2 mutations carriers. | Benitez-Buelga, Carlos; Vaclová, Tereza; Ferreira, Sofia; Urioste, Miguel; Inglada-Perez, Lucia; Soberón, Nora; Blasco, Maria A; Osorio, Ana; Benitez, Javier | Oncotarget. | 2016 May 03; | 27015555 | |
| Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models. | Sul, Jae Hoon; Bilow, Michael; Yang, Wen-Yun; Kostem, Emrah; Furlotte, Nick; He, Dan; Eskin, Eleazar | PLoS genetics. | 2016 Mar; | 26943367 | |
| Novel genetic predictors of venous thromboembolism risk in African Americans. | Hernandez, Wenndy; Gamazon, Eric R; Smithberger, Erin; O'Brien, Travis J; Harralson, Arthur F; Tuck, Matthew; Barbour, April; Kittles, Rick A; Cavallari, Larisa H; Perera, Minoli A | Blood. | 2016 Apr 14; | 26888256 | |
| A variant at 9p21.3 functionally implicates CDKN2B in paediatric B-cell precursor acute lymphoblastic leukaemia aetiology. | Hungate, Eric A; Vora, Sapana R; Gamazon, Eric R; Moriyama, Takaya; Best, Timothy; Hulur, Imge; Lee, Younghee; Evans, Tiffany-Jane; Ellinghaus, Eva; Stanulla, Martin; Rudant, Jéremie; Orsi, Laurent; Clavel, Jacqueline; Milne, Elizabeth; Scott, Rodney J; Pui, Ching-Hon; Cox, Nancy J; Loh, Mignon L; Yang, Jun J; Skol, Andrew D; Onel, Kenan | Nature communications. | 2016; | 26868379 | |
| Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication. | Long, Quan; Argmann, Carmen; Houten, Sander M; Huang, Tao; Peng, Siwu; Zhao, Yong; Tu, Zhidong; GTEx Consortium; Zhu, Jun | Genome medicine. | 2016; | 26856537 | |
| Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. | Yang, Jialiang; Huang, Tao; Petralia, Francesca; Long, Quan; Zhang, Bin; Argmann, Carmen; Zhao, Yong; Mobbs, Charles V; Schadt, Eric E; Zhu, Jun; Tu, Zhidong; GTEx Consortium | Scientific reports. | 2016 Jan 21; | 26795431 | |
| An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants. | Davis, Joe R; Fresard, Laure; Knowles, David A; Pala, Mauro; Bustamante, Carlos D; Battle, Alexis; Montgomery, Stephen B | American journal of human genetics. | 2016 Jan 7; | 26749306 | |
| Insertion of an SVA-E retrotransposon into the CASP8 gene is associated with protection against prostate cancer. | Stacey, Simon N; Kehr, Birte; Gudmundsson, Julius; Zink, Florian; Jonasdottir, Aslaug; Gudjonsson, Sigurjon A; Sigurdsson, Asgeir; Halldorsson, Bjarni V; Agnarsson, Bjarni A; Benediktsdottir, Kristrun R; Aben, Katja K H; Vermeulen, Sita H; Cremers, Ruben G; Panadero, Angeles; Helfand, Brian T; Cooper, Phillip R; Donovan, Jenny L; Hamdy, Freddie C; Jinga, Viorel; Okamoto, Ichiro; Jonasson, Jon G; Tryggvadottir, Laufey; Johannsdottir, Hrefna; Kristinsdottir, Anna M; Masson, Gisli; Magnusson, Olafur T; Iordache, Paul D; Helgason, Agnar; Helgason, Hannes; Sulem, Patrick; Gudbjartsson, Daniel F; Kong, Augustine; Jonsson, Eirikur; Barkardottir, Rosa B; Einarsson, Gudmundur V; Rafnar, Thorunn; Thorsteinsdottir, Unnur; Mates, Ioan N; Neal, David E; Catalona, William J; Mayordomo, José I; Kiemeney, Lambertus A; Thorleifsson, Gudmar; Stefansson, Kari | Human molecular genetics. | 2016 Mar 1; | 26740556 | |
| Common variants on 17q25 and gene-gene interactions conferring risk of schizophrenia in Han Chinese population and regulating gene expressions in human brain. | Guan, L; Wang, Q; Wang, L; Wu, B; Chen, Y; Liu, F; Ye, F; Zhang, T; Li, K; Yan, B; Lu, C; Su, L; Jin, G; Wang, H; Tian, H; Wang, L; Chen, Z; Wang, Y; Chen, J; Yuan, Y; Cong, W; Zheng, J; Wang, J; Xu, X; Liu, H; Xiao, W; Han, C; Zhang, Y; Jia, F; Qiao, X; Genetic REsearch on schizophrenia neTwork-China and Netherland (GREAT-CN); Zhang, D; Zhang, M; Ma, H | Molecular psychiatry. | 2016 09; | 26728569 | |
| HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. | Ward, Lucas D; Kellis, Manolis | Nucleic acids research | 2016 Jan 04 | 26657631 | |
| Many Phenotypes Without Many False Discoveries: Error Controlling Strategies for Multitrait Association Studies. | Peterson, Christine B; Bogomolov, Marina; Benjamini, Yoav; Sabatti, Chiara | Genetic epidemiology. | 2016 Jan; | 26626037 | |
| Proteasome system dysregulation and treatment resistance mechanisms in major depressive disorder. | Minelli, A; Magri, C; Barbon, A; Bonvicini, C; Segala, M; Congiu, C; Bignotti, S; Milanesi, E; Trabucchi, L; Cattane, N; Bortolomasi, M; Gennarelli, M | Translational psychiatry. | 2015; | e687 | 26624926 |
| Transcript Expression Data from Human Islets Links Regulatory Signals from Genome-Wide Association Studies for Type 2 Diabetes and Glycemic Traits to Their Downstream Effectors. | van de Bunt, Martijn; Manning Fox, Jocelyn E; Dai, Xiaoqing; Barrett, Amy; Grey, Caleb; Li, Lei; Bennett, Amanda J; Johnson, Paul R; Rajotte, Raymond V; Gaulton, Kyle J; Dermitzakis, Emmanouil T; MacDonald, Patrick E; McCarthy, Mark I; Gloyn, Anna L | PLoS genetics. | 2015 Dec; | 26624892 | |
| IsoDOT Detects Differential RNA-isoform Expression/Usage with respect to a Categorical or Continuous Covariate with High Sensitivity and Specificity. | Sun, Wei; Liu, Yufeng; Crowley, James J; Chen, Ting-Hued; Zhou, Hua; Chu, Haitao; Huang, Shunping; Kuan, Pei-Fen; Li, Yuan; Miller, Darla R; Shaw, Ginger D; Wu, Yichao; Zhabotynsky, Vasyl; McMillan, Leonard; Zou, Fei; Sullivan, Patrick F; de Villena, Fernando Pardo-Manuel | Journal of the American Statistical Association. | 2015; | 975-986 | 26617424 |
| ORegAnno 3.0: a community-driven resource for curated regulatory annotation. | Lesurf, Robert; Cotto, Kelsy C; Wang, Grace; Griffith, Malachi; Kasaian, Katayoon; Jones, Steven J M; Montgomery, Stephen B; Griffith, Obi L; Open Regulatory Annotation Consortium | Nucleic acids research. | 2016 Jan 4; | 26578589 | |
| Joint Bayesian variable and graph selection for regression models with network-structured predictors. | Peterson, Christine B; Stingo, Francesco C; Vannucci, Marina | Statistics in medicine. | 2016 Mar 30; | 1017-31 | 26514925 |
| A unified set-based test with adaptive filtering for gene-environment interaction analyses. | Liu, Qianying; Chen, Lin S; Nicolae, Dan L; Pierce, Brandon L | Biometrics. | 2015 Oct 23; | 26496228 | |
| DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs. | Aparicio-Prat, Estel; Arnan, Carme; Sala, Ilaria; Bosch, Núria; Guigó, Roderic; Johnson, Rory | BMC genomics. | 2015; | 26493208 | |
| A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. | Carithers, Latarsha J; Ardlie, Kristin; Barcus, Mary; Branton, Philip A; Britton, Angela; Buia, Stephen A; Compton, Carolyn C; DeLuca, David S; Peter-Demchok, Joanne; Gelfand, Ellen T; Guan, Ping; Korzeniewski, Greg E; Lockhart, Nicole C; Rabiner, Chana A | Biopreservation and biobanking | 2015 Oct | 311-9 | 26484571 |
| Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. | Yang, Jialiang; Huang, Tao; Petralia, Francesca; Long, Quan; Zhang, Bin; Argmann, Carmen; Zhao, Yong; Mobbs, Charles V; GTEx Consortium; Schadt, Eric E; Zhu, Jun; Tu, Zhidong | Scientific reports. | 2015; | 26477495 | |
| Functional genomics bridges the gap between quantitative genetics and molecular biology. | Lappalainen, Tuuli | Genome research. | 2015 Oct; | 1427-31 | 26430152 |
| BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS. | Wen, Xiaoquan; Stephens, Matthew | The annals of applied statistics. | 2014; | 176-203 | 26413181 |
| The origins, determinants, and consequences of human mutations. | Shendure, Jay; Akey, Joshua M | Science (New York, N.Y.). | 2015 Sep 25; | 1478-83 | 26404824 |
| Tools and best practices for data processing in allelic expression analysis. | Castel, Stephane E; Levy-Moonshine, Ami; Mohammadi, Pejman; Banks, Eric; Lappalainen, Tuuli | Genome biology. | 2015; | 26381377 | |
| WASP: allele-specific software for robust molecular quantitative trait locus discovery. | van de Geijn, Bryce; McVicker, Graham; Gilad, Yoav; Pritchard, Jonathan K | Nature methods. | 2015 Nov; | 1061-3 | 26366987 |
| Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. | Waszak, Sebastian M; Delaneau, Olivier; Gschwind, Andreas R; Kilpinen, Helena; Raghav, Sunil K; Witwicki, Robert M; Orioli, Andrea; Wiederkehr, Michael; Panousis, Nikolaos I; Yurovsky, Alisa; Romano-Palumbo, Luciana; Planchon, Alexandra; Bielser, Deborah; Padioleau, Ismael; Udin, Gilles; Thurnheer, Sarah; Hacker, David; Hernandez, Nouria; Reymond, Alexandre; Deplancke, Bart; Dermitzakis, Emmanouil T | Cell. | 2015 Aug 27; | 1039-50 | 26300124 |
| Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. | Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W; Grubert, Fabian; Candille, Sophie I; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L; Tang, Hua; Ricci, Emiliano; Snyder, Michael P | Genome research. | 2015 Nov; | 1610-21 | 26297486 |
| A robust blood gene expression-based prognostic model for castration-resistant prostate cancer. | Wang, Li; Gong, Yixuan; Chippada-Venkata, Uma; Heck, Matthias Michael; Retz, Margitta; Nawroth, Roman; Galsky, Matthew; Tsao, Che-Kai; Schadt, Eric; de Bono, Johann; Olmos, David; Zhu, Jun; Oh, William K | BMC medicine. | 2015; | 26297150 | |
| A gene-based association method for mapping traits using reference transcriptome data. | Gamazon, Eric R; Wheeler, Heather E; Shah, Kaanan P; Mozaffari, Sahar V; Aquino-Michaels, Keston; Carroll, Robert J; Eyler, Anne E; Denny, Joshua C; GTEx Consortium; Nicolae, Dan L; Cox, Nancy J; Im, Hae Kyung | Nature genetics. | 2015 Sep; | 1091-8 | 26258848 |
| A permutation approach for selecting the penalty parameter in penalized model selection. | Sabourin, Jeremy A; Valdar, William; Nobel, Andrew B | Biometrics. | 2015 Dec; | 1185-94 | 26243050 |
| Rare double sex and mab-3-related transcription factor 1 regulatory variants in severe spermatogenic failure. | Lima, A C; Carvalho, F; Gonçalves, J; Fernandes, S; Marques, P I; Sousa, M; Barros, A; Seixas, S; Amorim, A; Conrad, D F; Lopes, A M | Andrology. | 2015 Sep; | 26139570 | |
| Genetic determinants of telomere length and risk of common cancers: a Mendelian randomization study. | Zhang, Chenan; Doherty, Jennifer A; Burgess, Stephen; Hung, Rayjean J; Lindström, Sara; Kraft, Peter; Gong, Jian; Amos, Christopher I; Sellers, Thomas A; Monteiro, Alvaro N A; Chenevix-Trench, Georgia; Bickeböller, Heike; Risch, Angela; Brennan, Paul; Mckay, James D; Houlston, Richard S; Landi, Maria Teresa; Timofeeva, Maria N; Wang, Yufei; Heinrich, Joachim; Kote-Jarai, Zsofia; Eeles, Rosalind A; Muir, Ken; Wiklund, Fredrik; Grönberg, Henrik; Berndt, Sonja I; Chanock, Stephen J; Schumacher, Fredrick; Haiman, Christopher A; Henderson, Brian E; Amin Al Olama, Ali; Andrulis, Irene L; Hopper, John L; Chang-Claude, Jenny; John, Esther M; Malone, Kathleen E; Gammon, Marilie D; Ursin, Giske; Whittemore, Alice S; Hunter, David J; Gruber, Stephen B; Knight, Julia A; Hou, Lifang; Le Marchand, Loic; Newcomb, Polly A; Hudson, Thomas J; Chan, Andrew T; Li, Li; Woods, Michael O; Ahsan, Habibul; Pierce, Brandon L; GECCO and GAME-ON Network: CORECT, DRIVE, ELLIPSE, FOCI, and TRICL | Human molecular genetics. | 2015 Sep 15; | 5356-66 | 26138067 |
| Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. | Simmons, Sean; Peng, Jian; Bienkowska, Jadwiga; Berger, Bonnie | Journal of computational biology : a journal of computational molecular cell biology. | 2015 Aug; | 715-28 | 26098139 |
| Identification of causal genes for complex traits. | Hormozdiari, Farhad; Kichaev, Gleb; Yang, Wen-Yun; Pasaniuc, Bogdan; Eskin, Eleazar | Bioinformatics (Oxford, England). | 2015 Jun 15; | i206-13 | 26072484 |
| Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure. | Mimno, David; Blei, David M; Engelhardt, Barbara E | Proceedings of the National Academy of Sciences of the United States of America. | 2015 Jun 30; | E3441-50 | 26071445 |
| Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. | Madabhushi, Ram; Gao, Fan; Pfenning, Andreas R; Pan, Ling; Yamakawa, Satoko; Seo, Jinsoo; Rueda, Richard; Phan, Trongha X; Yamakawa, Hidekuni; Pao, Ping-Chieh; Stott, Ryan T; Gjoneska, Elizabeta; Nott, Alexi; Cho, Sukhee; Kellis, Manolis; Tsai, Li-Huei | Cell. | 2015 Jun 18; | 1592-605 | 26052046 |
| The projack: a resampling approach to correct for ranking bias in high-throughput studies. | Zhou, Yi-Hui; Wright, Fred A | Biostatistics (Oxford, England). | 2016 Jan; | 54-64 | 26040912 |
| Accurate and fast multiple-testing correction in eQTL studies. | Sul, Jae Hoon; Raj, Towfique; de Jong, Simone; de Bakker, Paul I W; Raychaudhuri, Soumya; Ophoff, Roel A; Stranger, Barbara E; Eskin, Eleazar; Han, Buhm | American journal of human genetics. | 2015 Jun 4; | 857-68 | 26027500 |
| Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides. | Nikolskiy, Igor; Conrad, Donald F; Chun, Sung; Fay, Justin C; Cheverud, James M; Lawson, Heather A | BMC genomics. | 2015 May 28; | 26016481 | |
| Sharing and Specificity of Co-expression Networks across 35 Human Tissues. | Pierson, Emma; GTEx Consortium; Koller, Daphne; Battle, Alexis; Mostafavi, Sara; Ardlie, Kristin G; Getz, Gad; Wright, Fred A; Kellis, Manolis; Volpi, Simona; Dermitzakis, Emmanouil T | PLoS computational biology. | 2015 May; | e1004220 | 25970446 |
| Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. | Rivas, Manuel A; Pirinen, Matti; Conrad, Donald F; Lek, Monkol; Tsang, Emily K; Karczewski, Konrad J; Maller, Julian B; Kukurba, Kimberly R; DeLuca, David S; Fromer, Menachem; Ferreira, Pedro G; Smith, Kevin S; Zhang, Rui; Zhao, Fengmei; Banks, Eric; Poplin, Ryan; Ruderfer, Douglas M; Purcell, Shaun M; Tukiainen, Taru; Minikel, Eric V; Stenson, Peter D; Cooper, David N; Huang, Katharine H; Sullivan, Timothy J; Nedzel, Jared; GTEx Consortium; Geuvadis Consortium; Bustamante, Carlos D; Li, Jin Billy; Daly, Mark J; Guigo, Roderic; Donnelly, Peter; Ardlie, Kristin; Sammeth, Michael; Dermitzakis, Emmanouil T; McCarthy, Mark I; Montgomery, Stephen B; Lappalainen, Tuuli; MacArthur, Daniel G | Science (New York, N.Y.). | 2015 May 8; | 666-9 | 25954003 |
| Human genomics. The human transcriptome across tissues and individuals. | Melé, Marta; Ferreira, Pedro G; Reverter, Ferran; DeLuca, David S; Monlong, Jean; Sammeth, Michael; Young, Taylor R; Goldmann, Jakob M; Pervouchine, Dmitri D; Sullivan, Timothy J; Johnson, Rory; Segrè, Ayellet V; Djebali, Sarah; Niarchou, Anastasia; GTEx Consortium; Wright, Fred A; Lappalainen, Tuuli; Calvo, Miquel; Getz, Gad; Dermitzakis, Emmanouil T; Ardlie, Kristin G; Guigó, Roderic | Science (New York, N.Y.). | 2015 May 8; | 660-5 | 25954002 |
| Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. | GTEx Consortium | Science (New York, N.Y.). | 2015 May 8; | 648-60 | 25954001 |
| The landscape of genomic imprinting across diverse adult human tissues. | Baran, Yael; Subramaniam, Meena; Biton, Anne; Tukiainen, Taru; Tsang, Emily K; Rivas, Manuel A; Pirinen, Matti; Gutierrez-Arcelus, Maria; Smith, Kevin S; Kukurba, Kim R; Zhang, Rui; Eng, Celeste; Torgerson, Dara G; Urbanek, Cydney; GTEx Consortium; Li, Jin Billy; Rodriguez-Santana, Jose R; Burchard, Esteban G; Seibold, Max A; MacArthur, Daniel G; Montgomery, Stephen B; Zaitlen, Noah A; Lappalainen, Tuuli | Genome research. | 2015 Jul; | 927-36 | 25953952 |
| The impact of human copy number variation on gene expression. | Gamazon, Eric R; Stranger, Barbara E | Briefings in functional genomics. | 2015 Apr 27; | 25922366 | |
| Cross-population joint analysis of eQTLs: fine mapping and functional annotation. | Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger | PLoS genetics. | 2015 Apr; | e1005176 | 25906321 |
| Gene-Gene Interactions Detection Using a Two-stage Model. | Wang, Zhanyong; Sul, Jae Hoon; Snir, Sagi; Lozano, Jose A; Eskin, Eleazar | Journal of computational biology : a journal of computational molecular cell biology. | 2015 Jun; | 563-76 | 25871811 |
| New basal cell carcinoma susceptibility loci. | Stacey, Simon N; Helgason, Hannes; Gudjonsson, Sigurjon A; Thorleifsson, Gudmar; Zink, Florian; Sigurdsson, Asgeir; Kehr, Birte; Gudmundsson, Julius; Sulem, Patrick; Sigurgeirsson, Bardur; Benediktsdottir, Kristrun R; Thorisdottir, Kristin; Ragnarsson, Rafn; Fuentelsaz, Victoria; Corredera, Cristina; Gilaberte, Yolanda; Grasa, Matilde; Planelles, Dolores; Sanmartin, Onofre; Rudnai, Peter; Gurzau, Eugene; Koppova, Kvetoslava; Nexø, Bjørn A; Tjønneland, Anne; Overvad, Kim; Jonasson, Jon G; Tryggvadottir, Laufey; Johannsdottir, Hrefna; Kristinsdottir, Anna M; Stefansson, Hreinn; Masson, Gisli; Magnusson, Olafur T; Halldorsson, Bjarni V; Kong, Augustine; Rafnar, Thorunn; Thorsteinsdottir, Unnur; Vogel, Ulla; Kumar, Rajiv; Nagore, Eduardo; Mayordomo, José I; Gudbjartsson, Daniel F; Olafsson, Jon H; Stefansson, Kari | Nature communications. | 2015; | 25855136 | |
| Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse. | Babak, Tomas; DeVeale, Brian; Tsang, Emily K; Zhou, Yiqi; Li, Xin; Smith, Kevin S; Kukurba, Kim R; Zhang, Rui; Li, Jin Billy; van der Kooy, Derek; Montgomery, Stephen B; Fraser, Hunter B | Nature genetics. | 2015 May; | 544-9 | 25848752 |
| Assessing allele-specific expression across multiple tissues from RNA-seq read data. | Pirinen, Matti; Lappalainen, Tuuli; Zaitlen, Noah A; GTEx Consortium; Dermitzakis, Emmanouil T; Donnelly, Peter; McCarthy, Mark I; Rivas, Manuel A | Bioinformatics (Oxford, England). | 2015 Aug 1; | 2497-504 | 25819081 |
| SCAN database: facilitating integrative analyses of cytosine modification and expression QTL. | Zhang, Wei; Gamazon, Eric R; Zhang, Xu; Konkashbaev, Anuar; Liu, Cong; Szilágyi, Keely L; Dolan, M Eileen; Cox, Nancy J | Database : the journal of biological databases and curation. | 2015; | 25818895 | |
| The Genotype-Tissue Expression (GTEx) Project: Linking Clinical Data with Molecular Analysis to Advance Personalized Medicine. | Keen, Judy C; Moore, Helen M | Journal of personalized medicine. | 2015 Feb 05; | 25809799 | |
| Bayesian model comparison in genetic association analysis: linear mixed modeling and SNP set testing. | Wen, Xiaoquan | Biostatistics (Oxford, England). | 2015 Oct; | 701-12 | 25796429 |
| Hypothesis testing at the extremes: fast and robust association for high-throughput data. | Zhou, Yi-Hui; Wright, Fred A | Biostatistics (Oxford, England). | 2015 Jul; | 611-25 | 25792622 |
| A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits. | Zhu, Jun; Chen, Congying; Yang, Bin; Guo, Yuanmei; Ai, Huashui; Ren, Jun; Peng, Zhiyu; Tu, Zhidong; Yang, Xia; Meng, Qingying; Friend, Stephen; Huang, Lusheng | BMC genomics. | 2015; | 25765547 | |
| Efficient multiple-trait association and estimation of genetic correlation using the matrix-variate linear mixed model. | Furlotte, Nicholas A; Eskin, Eleazar | Genetics. | 2015 May; | 59-68 | 25724382 |
| Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. | Ernst, Jason; Kellis, Manolis | Nature biotechnology. | 2015 Apr; | 364-76 | 25690853 |
| Impact of allele-specific peptides in proteome quantification. | Wu, Linfeng; Snyder, Michael | Proteomics. Clinical applications. | 2015 Apr; | 432-6 | 25676416 |
| Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1. | Guo, Cong; Ludvik, Anton E; Arlotto, Michelle E; Hayes, M Geoffrey; Armstrong, Loren L; Scholtens, Denise M; Brown, Christopher D; Newgard, Christopher B; Becker, Thomas C; Layden, Brian T; Lowe, William L; Reddy, Timothy E | Nature communications. | 2015; | 25648650 | |
| Gene expression in transformed lymphocytes reveals variation in endomembrane and HLA pathways modifying cystic fibrosis pulmonary phenotypes. | O'Neal, Wanda K; Gallins, Paul; Pace, Rhonda G; Dang, Hong; Wolf, Whitney E; Jones, Lisa C; Guo, XueLiang; Zhou, Yi-Hui; Madar, Vered; Huang, Jinyan; Liang, Liming; Moffatt, Miriam F; Cutting, Garry R; Drumm, Mitchell L; Rommens, Johanna M; Strug, Lisa J; Sun, Wei; Stonebraker, Jaclyn R; Wright, Fred A; Knowles, Michael R | American journal of human genetics. | 2015 Feb 5; | 318-28 | 25640674 |
| Memory efficient assembly of human genome. | Hormozdiari, Farhad; Eskin, Eleazar | Journal of bioinformatics and computational biology. | 2015 Apr; | 25603998 | |
| (Epi)genomics approaches and their applications. | Meissner, Alexander | Methods (San Diego, Calif.). | 2015 Jan 15; | 2-Jan | 25597875 |
| A spatial haplotype copying model with applications to genotype imputation. | Yang, Wen-Yun; Hormozdiari, Farhad; Eskin, Eleazar; Pasaniuc, Bogdan | Journal of computational biology : a journal of computational molecular cell biology. | 2015 May; | 451-62 | 25526526 |
| Cross-tissue and tissue-specific eQTLs: partitioning the heritability of a complex trait. | Torres, Jason M; Gamazon, Eric R; Parra, Esteban J; Below, Jennifer E; Valladares-Salgado, Adan; Wacher, Niels; Cruz, Miguel; Hanis, Craig L; Cox, Nancy J | American journal of human genetics. | 2014 Nov 6; | 521-34 | 25439722 |
| Fine-mapping additive and dominant SNP effects using group-LASSO and fractional resample model averaging. | Sabourin, Jeremy; Nobel, Andrew B; Valdar, William | Genetic epidemiology. | 2015 Feb; | 77-88 | 25417853 |
| Comparison of the transcriptional landscapes between human and mouse tissues. | Lin, Shin; Lin, Yiing; Nery, Joseph R; Urich, Mark A; Breschi, Alessandra; Davis, Carrie A; Dobin, Alexander; Zaleski, Christopher; Beer, Michael A; Chapman, William C; Gingeras, Thomas R; Ecker, Joseph R; Snyder, Michael P | Proceedings of the National Academy of Sciences of the United States of America. | 2014 Dec 2; | 17224-9 | 25413365 |
| Structural architecture of SNP effects on complex traits. | Gamazon, Eric R; Cox, Nancy J; Davis, Lea K | American journal of human genetics. | 2014 Nov 6; | 477-89 | 25307299 |
| Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies. | Panousis, Nikolaos I; Gutierrez-Arcelus, Maria; Dermitzakis, Emmanouil T; Lappalainen, Tuuli | Genome biology. | 2014; | 25239376 | |
| Genome-wide interrogation of longitudinal FEV1 in children with asthma. | Wu, Kehua; Gamazon, Eric R; Im, Hae Kyung; Geeleher, Paul; White, Steven R; Solway, Julian; Clemmer, George L; Weiss, Scott T; Tantisira, Kelan G; Cox, Nancy J; Ratain, Mark J; Huang, R Stephanie | American journal of respiratory and critical care medicine. | 2014 Sep 15; | 619-27 | 25221879 |
| Space Time Clustering and the Permutation Moments of Quadratic Form. | Zhou, Yi-Hui; Mayhew, Gregory; Sun, Zhibin; Xu, Xiaolin; Zou, Fei; Wright, Fred A | Stat. | 2013 Jan 1; | 292-302 | 25210205 |
| Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk. | Human molecular genetics. | 2015 Jan 1; | 285-98 | 25168388 | |
| Cross-disorder genome-wide analyses suggest a complex genetic relationship between Tourette's syndrome and OCD. | Yu, Dongmei; Mathews, Carol A; Scharf, Jeremiah M; Neale, Benjamin M; Davis, Lea K; Gamazon, Eric R; Derks, Eske M; Evans, Patrick; Edlund, Christopher K; Crane, Jacquelyn; Fagerness, Jesen A; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L; Bellodi, Laura; Benarroch, Fortu; Berrio, Gabriel Bedoya; Bienvenu, O Joseph; Black, Donald W; Bloch, Michael H; Brentani, Helena; Bruun, Ruth D; Budman, Cathy L; Camarena, Beatriz; Campbell, Desmond D; Cappi, Carolina; Silgado, Julio C Cardona; Cavallini, Maria C; Chavira, Denise A; Chouinard, Sylvain; Cook, Edwin H; Cookson, M R; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L; Girard, Simon L; Grabe, Hans J; Grados, Marco A; Greenberg, Benjamin D; Gross-Tsur, Varda; Grunblatt, Edna; Hardy, John; Heiman, Gary A; Hemmings, Sian M J; Herrera, Luis D; Hezel, Dianne M; Hoekstra, Pieter J; Jankovic, Joseph; Kennedy, James L; King, Robert A; Konkashbaev, Anuar I; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T; Mesa Restrepo, Sandra C; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L; Naarden, Allan L; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A; Pakstis, Andrew J; Pato, Michele T; Pato, Carlos N; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L; Renner, Tobias; Reus, Victor I; Richter, Margaret A; Riddle, Mark A; Robertson, Mary M; Romero, Roxana; Rosario, Maria C; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S; Samuels, Jack; Sandor, Paul; Service, Susan K; Sheppard, Brooke; Singer, Harvey S; Smit, Jan H; Stein, Dan J; Strengman, Eric; Tischfield, Jay A; Turiel, Maurizio; Valencia Duarte, Ana V; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R; Westenberg, Herman G M; Shugart, Yin Yao; Hounie, Ana G; Miguel, Euripedes C; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C; McMahon, William; Posthuma, Danielle; Oostra, Ben A; Nestadt, Gerald; Rouleau, Guy A; Purcell, Shaun; Jenike, Michael A; Heutink, Peter; Hanna, Gregory L; Conti, David V; Arnold, Paul D; Freimer, Nelson B; Stewart, S Evelyn; Knowles, James A; Cox, Nancy J; Pauls, David L | The American journal of psychiatry. | 2015 Jan; | 82-93 | 25158072 |
| Convergence of Sample Eigenvalues, Eigenvectors, and Principal Component Scores for Ultra-High Dimensional Data. | Lee, Seunggeun; Zou, Fei; Wright, Fred A | Biometrika | 2014 Jun | 484-490 | 25143634 |
| IRBIS: a systematic search for conserved complementarity. | Pervouchine, Dmitri D | RNA (New York, N.Y.). | 2014 Oct; | 1519-31 | 25142064 |
| Identification of genetic variants associated with alternative splicing using sQTLseekeR. | Monlong, Jean; Calvo, Miquel; Ferreira, Pedro G; Guigo, Roderic | Nature communications. | 2014; | 25140736 | |
| Identifying causal variants at loci with multiple signals of association. | Hormozdiari, Farhad; Kostem, Emrah; Kang, Eun Yong; Pasaniuc, Bogdan; Eskin, Eleazar | Genetics. | 2014 Oct; | 497-508 | 25104515 |
| Transcriptome assembly and quantification from Ion Torrent RNA-Seq data. | Mangul, Serghei; Caciula, Adrian; Al Seesi, Sahar; Brinza, Dumitru; M?ndoiu, Ion; Zelikovsky, Alex | BMC genomics. | 2014; | S7 | 25082147 |
| Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases. | Narayanan, Manikandan; Huynh, Jimmy L; Wang, Kai; Yang, Xia; Yoo, Seungyeul; McElwee, Joshua; Zhang, Bin; Zhang, Chunsheng; Lamb, John R; Xie, Tao; Suver, Christine; Molony, Cliona; Melquist, Stacey; Johnson, Andrew D; Fan, Guoping; Stone, David J; Schadt | Molecular systems biology | 2014 | 743 | 25080494 |
| Putative cis-regulatory drivers in colorectal cancer. | Ongen, Halit; Andersen, Claus L; Bramsen, Jesper B; Oster, Bodil; Rasmussen, Mads H; Ferreira, Pedro G; Sandoval, Juan; Vidal, Enrique; Whiffin, Nicola; Planchon, Alexandra; Padioleau, Ismael; Bielser, Deborah; Romano, Luciana; Tomlinson, Ian; Houlston, Richard S; Esteller, Manel; Orntoft, Torben F; Dermitzakis, Emmanouil T | Nature. | 2014 Aug 07; | 25079323 | |
| Fine mapping and functional studies of risk variants for type 1 diabetes at chromosome 16p13.13. | Tomlinson 4th, M Joseph; Pitsillides, Achilleas; Pickin, Rebecca; Mika, Matthew; Keene, Keith L; Hou, Xuanlin; Mychaleckyj, Josyf; Chen, Wei-Min; Concannon, Patrick; Onengut-Gumuscu, Suna | Diabetes. | 2014 Dec; | 4360-8 | 25008175 |
| Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. | Zhang, Xiaoling; Gierman, Hinco J; Levy, Daniel; Plump, Andrew; Dobrin, Radu; Goring, Harald H H; Curran, Joanne E; Johnson, Matthew P; Blangero, John; Kim, Stuart K; O'Donnell, Christopher J; Emilsson, Valur; Johnson, Andrew D | BMC genomics. | 2014 Jun 27; | 24973796 | |
| Accurate viral population assembly from ultra-deep sequencing data. | Mangul, Serghei; Wu, Nicholas C; Mancuso, Nicholas; Zelikovsky, Alex; Sun, Ren; Eskin, Eleazar | Bioinformatics (Oxford, England) | 2014 Jun 15 | i329-37 | 24932001 |
| Allele-specific expression and eQTL analysis in mouse adipose tissue. | Hasin-Brumshtein, Yehudit; Hormozdiari, Farhad; Martin, Lisa; van Nas, Atila; Eskin, Eleazar; Lusis, Aldons J; Drake, Thomas A | BMC genomics | 2014 | 471 | 24927774 |
| GWAS to Sequencing: Divergence in Study Design and Analysis. | King, Christopher Ryan; Nicolae, Dan L | Genes. | 2014; | 460-76 | 24879455 |
| Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation. | Ha, Min Jin; Sun, Wei | Biometrics | 2014 May 20 | NULL | 24845967 |
| Poly-Omic Prediction of Complex Traits: OmicKriging. | Wheeler, Heather E; Aquino-Michaels, Keston; Gamazon, Eric R; Trubetskoy, Vassily V; Dolan, M Eileen; Huang, R Stephanie; Cox, Nancy J; Im, Hae Kyung | Genetic epidemiology | 2014 May 2 | NULL | 24799323 |
| Bicc1 is a genetic determinant of osteoblastogenesis and bone mineral density. | Mesner, Larry D; Ray, Brianne; Hsu, Yi-Hsiang; Manichaikul, Ani; Lum, Eric; Bryda, Elizabeth C; Rich, Stephen S; Rosen, Clifford J; Criqui, Michael H; Allison, Matthew; Budoff, Matthew J; Clemens, Thomas L; Farber, Charles R | The Journal of clinical investigation | 2014 Jun 2 | 2736-49 | 24789909 |
| Determining causality and consequence of expression quantitative trait loci. | Battle, A; Montgomery, S B | Human genetics | 2014 Jun | 727-35 | 24770875 |
| Guidelines for investigating causality of sequence variants in human disease. | MacArthur, D G; Manolio, T A; Dimmock, D P; Rehm, H L; Shendure, J; Abecasis, G R; Adams, D R; Altman, R B; Antonarakis, S E; Ashley, E A; Barrett, J C; Biesecker, L G; Conrad, D F; Cooper, G M; Cox, N J; Daly, M J; Gerstein, M B; Goldstein, D B; Hirschhorn, J N; Leal, S M; Pennacchio, L A; Stamatoyannopoulos, J A; Sunyaev, S R; Valle, D; Voight, B F; Winckler, W; Gunter, C | Nature. | 2014 Apr 24; | 469-76 | 24759409 |
| Validating single-cell genomics for the study of renal development. | Jain, Sanjay; Noordam, Michiel J; Hoshi, Masato; Vallania, Francesco L; Conrad, Donald F | Kidney international. | 2014 Nov; | 1049-55 | 24759149 |
| Heritability and genomics of gene expression in peripheral blood. | Wright, Fred A; Sullivan, Patrick F; Brooks, Andrew I; Zou, Fei; Sun, Wei; Xia, Kai; Madar, Vered; Jansen, Rick; Chung, Wonil; Zhou, Yi-Hui; Abdellaoui, Abdel; Batista, Sandra; Butler, Casey; Chen, Guanhua; Chen, Ting-Huei; D'Ambrosio, David; Gallins, Pau | Nature genetics | 2014 May | 430-7 | 24728292 |
| Genetic variation associated with euphorigenic effects of d-amphetamine is associated with diminished risk for schizophrenia and attention deficit hyperactivity disorder. | Hart, Amy B; Gamazon, Eric R; Engelhardt, Barbara E; Sklar, Pamela; Kahler, Anna K; Hultman, Christina M; Sullivan, Patrick F; Neale, Benjamin M; Faraone, Stephen V; Psychiatric Genomics Consortium: ADHD Subgroup; de Wit, Harriet; Cox, Nancy J; Palmer, Ab | Proceedings of the National Academy of Sciences of the United States of America | 2014 Apr 22 | 5968-73 | 24711425 |
| Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies. | Joo, Jong Wha J; Sul, Jae Hoon; Han, Buhm; Ye, Chun; Eskin, Eleazar | Genome biology | 2014 Apr 7 | R61 | 24708878 |
| Obesity-associated variants within FTO form long-range functional connections with IRX3. | Smemo, Scott; Tena, Juan J; Kim, Kyoung-Han; Gamazon, Eric R; Sakabe, Noboru J; Gomez-Marin, Carlos; Aneas, Ivy; Credidio, Flavia L; Sobreira, Debora R; Wasserman, Nora F; Lee, Ju Hee; Puviindran, Vijitha; Tam, Davis; Shen, Michael; Son, Joe Eun; Vakili, | Nature | 2014 Mar 20 | 371-5 | 24646999 |
| A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age. | Ahsan, Habibul; Halpern, Jerry; Kibriya, Muhammad G; Pierce, Brandon L; Tong, Lin; Gamazon, Eric; McGuire, Valerie; Felberg, Anna; Shi, Jianxin; Jasmine, Farzana; Roy, Shantanu; Brutus, Rachelle; Argos, Maria; Melkonian, Stephanie; Chang-Claude, Jenny; An | Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology | 2014 Apr | 658-69 | 24493630 |
| Meta-analysis identifies gene-by-environment interactions as demonstrated in a study of 4,965 mice. | Kang, Eun Yong; Han, Buhm; Furlotte, Nicholas; Joo, Jong Wha J; Shih, Diana; Davis, Richard C; Lusis, Aldons J; Eskin, Eleazar | PLoS genetics | 2014 Jan | e1004022 | 24415945 |
| RNA-Seq optimization with eQTL gold standards. | Ellis, Shannon E; Gupta, Simone; Ashar, Foram N; Bader, Joel S; West, Andrew B; Arking, Dan E | BMC genomics | 2013 | 892 | 24341889 |
| Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing. | Mostafavi, S; Battle, A; Zhu, X; Potash, J B; Weissman, M M; Shi, J; Beckman, K; Haudenschild, C; McCormick, C; Mei, R; Gameroff, M J; Gindes, H; Adams, P; Goes, F S; Mondimore, F M; MacKinnon, D F; Notes, L; Schweizer, B; Furman, D; Montgomery, S B; Urban, A E; Koller, D; Levinson, D F | Molecular psychiatry. | 2014 Dec; | 24296977 | |
| Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains. | Huynh, Jimmy L; Garg, Paras; Thin, Tin Htwe; Yoo, Seungyeul; Dutta, Ranjan; Trapp, Bruce D; Haroutunian, Vahram; Zhu, Jun; Donovan, Michael J; Sharp, Andrew J; Casaccia, Patrizia | Nature neuroscience | 2014 Jan | 121-30 | 24270187 |
| Partitioning the heritability of Tourette syndrome and obsessive compulsive disorder reveals differences in genetic architecture. | Davis, Lea K; Yu, Dongmei; Keenan, Clare L; Gamazon, Eric R; Konkashbaev, Anuar I; Derks, Eske M; Neale, Benjamin M; Yang, Jian; Lee, S Hong; Evans, Patrick; Barr, Cathy L; Bellodi, Laura; Benarroch, Fortu; Berrio, Gabriel Bedoya; Bienvenu, Oscar J; Bloch | PLoS genetics | 2013 Oct | e1003864 | 24204291 |
| Quantitative allelic test-a fast test for very large association studies. | Lee, Sang Mee; Karrison, Theodore G; Cox, Nancy J; Im, Hae Kyung | Genetic epidemiology | 2013 Dec | 831-9 | 24185610 |
| Reduced burden of very large and rare CNVs in bipolar affective disorder. | Grozeva, Detelina; Kirov, George; Conrad, Donald F; Barnes, Chris P; Hurles, Matthew; Owen, Michael J; O'Donovan, Michael C; Craddock, Nick | Bipolar disorders. | 2013 Dec; | 24127788 | |
| Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. | Battle, Alexis; Mostafavi, Sara; Zhu, Xiaowei; Potash, James B; Weissman, Myrna M; McCormick, Courtney; Haudenschild, Christian D; Beckman, Kenneth B; Shi, Jianxin; Mei, Rui; Urban, Alexander E; Montgomery, Stephen B; Levinson, Douglas F; Koller, Daphne | Genome research | 2013 Nov 27 | NULL | 24092820 |
| Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. | 't Hoen, Peter A C; Friedlander, Marc R; Almlof, Jonas; Sammeth, Michael; Pulyakhina, Irina; Anvar, Seyed Yahya; Laros, Jeroen F J; Buermans, Henk P J; Karlberg, Olof; Brannvall, Mathias; GEUVADIS Consortium; den Dunnen, Johan T; van Ommen, Gert-Jan B; Gu | Nature biotechnology | 2013 Nov | 1015-22 | 24037425 |
| Transcriptome and genome sequencing uncovers functional variation in humans. | Lappalainen, Tuuli; Sammeth, Michael; Friedlander, Marc R; 't Hoen, Peter A C; Monlong, Jean; Rivas, Manuel A; Gonzalez-Porta, Mar; Kurbatova, Natalja; Griebel, Thasso; Ferreira, Pedro G; Barann, Matthias; Wieland, Thomas; Greger, Liliana; van Iterson, Ma | Nature | 2013 Sep 26 | 506-11 | 24037378 |
| Efficiently identifying significant associations in genome-wide association studies. | Kostem, Emrah; Eskin, Eleazar | Journal of computational biology : a journal of computational molecular cell biology. | 2013 Oct; | 817-30 | 24033261 |
| Gene expression changes with age in skin, adipose tissue, blood and brain. | Glass, Daniel; Viñuela, Ana; Davies, Matthew N; Ramasamy, Adaikalavan; Parts, Leopold; Knowles, David; Brown, Andrew A; Hedman, Asa K; Small, Kerrin S; Buil, Alfonso; Grundberg, Elin; Nica, Alexandra C; Di Meglio, Paola; Nestle, Frank O; Ryten, Mina; UK Brain Expression consortium; MuTHER consortium; Durbin, Richard; McCarthy, Mark I; Deloukas, Panagiotis; Dermitzakis, Emmanouil T; Weale, Michael E; Bataille, Veronique; Spector, Tim D | Genome biology. | 2013; | R75 | 23889843 |
| SCAN: a systems biology approach to pharmacogenomic discovery. | Gamazon, Eric R; Huang, R Stephanie; Cox, Nancy J | Methods in molecular biology (Clifton, N.J.) | 2013 | 213-24 | 23824859 |
| DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. | Mercer, Tim R; Edwards, Stacey L; Clark, Michael B; Neph, Shane J; Wang, Hao; Stergachis, Andrew B; John, Sam; Sandstrom, Richard; Li, Guoliang; Sandhu, Kuljeet S; Ruan, Yijun; Nielsen, Lars K; Mattick, John S; Stamatoyannopoulos, John A | Nature genetics | 2013 Aug | 852-9 | 23793028 |
| A genome-wide integrative study of microRNAs in human liver. | Gamazon, Eric R; Innocenti, Federico; Wei, Rongrong; Wang, Libo; Zhang, Min; Mirkov, Snezana; Ramirez, Jacqueline; Huang, R Stephanie; Cox, Nancy J; Ratain, Mark J; Liu, Wanqing | BMC genomics | 2013 | 395 | 23758991 |
| Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. | Gamazon, Eric R; Huang, R Stephanie; Dolan, M Eileen; Cox, Nancy J; Im, Hae Kyung | Frontiers in genetics. | 2012; | 23755062 | |
| Validation of Monte Carlo estimates of three-class ideal observer operating points for normal data. | Edwards, Darrin C | Academic radiology | 2013 Jul | 908-14 | 23747155 |
| JOINT AND INDIVIDUAL VARIATION EXPLAINED (JIVE) FOR INTEGRATED ANALYSIS OF MULTIPLE DATA TYPES. | Lock, Eric F; Hoadley, Katherine A; Marron, J S; Nobel, Andrew B | The annals of applied statistics | 2013 Mar 1 | 523-542 | 23745156 |
| The Genotype-Tissue Expression (GTEx) project. | Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N, Foster B, Moser M, Karasik E, Gillard B, Ramsey K, Sullivan S, Bridge J, Magazine H, Syron J, Fleming J, Siminoff L, Traino H, et al. | Nat Genet | 2013 May 29 | 580-5 | 23715323 |
| A statistical framework for joint eQTL analysis in multiple tissues. | Flutre, Timothee; Wen, Xiaoquan; Pritchard, Jonathan; Stephens, Matthew | PLoS genetics | 2013 May | e1003486 | 23671422 |
| eQTL Mapping Using RNA-seq Data. | Sun, Wei; Hu, Yijuan | Statistics in biosciences | 2013 May 1 | 198-219 | 23667399 |
| Marbled inflation from population structure in gene-based association studies with rare variants. | Liu, Qianying; Nicolae, Dan L; Chen, Lin S | Genetic epidemiology | 2013 Apr | 286-92 | 23468125 |
| Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. | Ferreira, Pedro G; Patalano, Solenn; Chauhan, Ritika; Ffrench-Constant, Richard; Gabaldón, Toni; Guigó, Roderic; Sumner, Seirian | Genome biology. | 2013; | R20 | 23442883 |
| Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. | Lee, Younghee; Li, Haiquan; Li, Jianrong; Rebman, Ellen; Achour, Ikbel; Regan, Kelly E; Gamazon, Eric R; Chen, James L; Yang, Xinan Holly; Cox, Nancy J; Lussier, Yves A | Journal of the American Medical Informatics Association : JAMIA | 2013 Jul-Aug | 619-29 | 23355459 |
| Modeling causality for pairs of phenotypes in system genetics. | Neto, Elias Chaibub; Broman, Aimee T; Keller, Mark P; Attie, Alan D; Zhang, Bin; Zhu, Jun; Yandell, Brian S | Genetics | 2013 Mar | 1003-13 | 23288936 |
| Trans-population analysis of genetic mechanisms of ethnic disparities in neuroblastoma survival. | Gamazon, Eric R; Pinto, Navin; Konkashbaev, Anuar; Im, Hae Kyung; Diskin, Sharon J; London, Wendy B; Maris, John M; Dolan, M Eileen; Cox, Nancy J; Cohn, Susan L | Journal of the National Cancer Institute | 2013 Feb 20 | 302-9 | 23243203 |
| Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets. | Tu, Zhidong; Keller, Mark P; Zhang, Chunsheng; Rabaglia, Mary E; Greenawalt, Danielle M; Yang, Xia; Wang, I-Ming; Dai, Hongyue; Bruss, Matthew D; Lum, Pek Y; Zhou, Yun-Ping; Kemp, Daniel M; Kendziorski, Christina; Yandell, Brian S; Attie, Alan D; Schadt, Eric E; Zhu, Jun | PLoS genetics | 2012 | e1003107 | 23236292 |
| Controls of nucleosome positioning in the human genome. | Gaffney, Daniel J; McVicker, Graham; Pai, Athma A; Fondufe-Mittendorf, Yvonne N; Lewellen, Noah; Michelini, Katelyn; Widom, Jonathan; Gilad, Yoav; Pritchard, Jonathan K | PLoS genetics | 2012 | e1003036 | 23166509 |
| An exponential combination procedure for set-based association tests in sequencing studies. | Chen, Lin S; Hsu, Li; Gamazon, Eric R; Cox, Nancy J; Nicolae, Dan L | American journal of human genetics | 2012 Dec 7 | 977-86 | 23159251 |
| Variants affecting exon skipping contribute to complex traits. | Lee, Younghee; Gamazon, Eric R; Rebman, Ellen; Lee, Yeunsook; Lee, Sanghyuk; Dolan, M Eileen; Cox, Nancy J; Lussier, Yves A | PLoS genetics | 2012 | e1002998 | 23133393 |
| The GEM mapper: fast, accurate and versatile alignment by filtration. | Marco-Sola, Santiago; Sammeth, Michael; Guigo, Roderic; Ribeca, Paolo | Nature methods | 2012 Dec | 1185-8 | 23103880 |
| Sex-biased genetic effects on gene regulation in humans. | Dimas, Antigone S; Nica, Alexandra C; Montgomery, Stephen B; Stranger, Barbara E; Raj, Towfique; Buil, Alfonso; Giger, Thomas; Lappalainen, Tuuli; Gutierrez-Arcelus, Maria; MuTHER Consortium; McCarthy, Mark I; Dermitzakis, Emmanouil T | Genome research | 2012 Dec | 2368-75 | 22960374 |
| Genetic risk factors for type 2 diabetes: a trans-regulatory genetic architecture? | Elbein, Steven C; Gamazon, Eric R; Das, Swapan K; Rasouli, Neda; Kern, Philip A; Cox, Nancy J | American journal of human genetics | 2012 Sep 7 | 466-77 | 22958899 |
| Mapping cis- and trans-regulatory effects across multiple tissues in twins. | Grundberg, Elin; Small, Kerrin S; Hedman, Åsa K; Nica, Alexandra C; Buil, Alfonso; Keildson, Sarah; Bell, Jordana T; Yang, Tsun-Po; Meduri, Eshwar; Barrett, Amy; Nisbett, James; Sekowska, Magdalena; Wilk, Alicja; Shin, So-Youn; Glass, Daniel; Travers, Mary; Min, Josine L; Ring, Sue; Ho, Karen; Thorleifsson, Gudmar; Kong, Augustine; Thorsteindottir, Unnur; Ainali, Chrysanthi; Dimas, Antigone S; Hassanali, Neelam; Ingle, Catherine; Knowles, David; Krestyaninova, Maria; Lowe, Christopher E; Di Meglio, Paola; Montgomery, Stephen B; Parts, Leopold; Potter, Simon; Surdulescu, Gabriela; Tsaprouni, Loukia; Tsoka, Sophia; Bataille, Veronique; Durbin, Richard; Nestle, Frank O; O'Rahilly, Stephen; Soranzo, Nicole; Lindgren, Cecilia M; Zondervan, Krina T; Ahmadi, Kourosh R; Schadt, Eric E; Stefansson, Kari; Smith, George Davey; McCarthy, Mark I; Deloukas, Panos; Dermitzakis, Emmanouil T; Spector, Tim D; Multiple Tissue Human Expression Resource (MuTHER) Consortium | Nature genetics. | 2012 Oct; | 22941192 | |
| Quantile-based permutation thresholds for quantitative trait loci hotspots. | Neto, Elias Chaibub; Keller, Mark P; Broman, Andrew F; Attie, Alan D; Jansen, Ritsert C; Broman, Karl W; Yandell, Brian S | Genetics | 2012 Aug | 1355-65 | 22661325 |
| Reprioritizing genetic associations in hit regions using LASSO-based resample model averaging. | Valdar, William; Sabourin, Jeremy; Nobel, Andrew; Holmes, Christopher C | Genetic epidemiology | 2012 Jul | 451-62 | 22549815 |
| Matrix eQTL: ultra fast eQTL analysis via large matrix operations. | Shabalin, Andrey A | Bioinformatics (Oxford, England) | 2012 May 15 | 1353-8 | 22492648 |
| On sharing quantitative trait GWAS results in an era of multiple-omics data and the limits of genomic privacy. | Im, Hae Kyung; Gamazon, Eric R; Nicolae, Dan L; Cox, Nancy J | American journal of human genetics | 2012 Apr 6 | 591-8 | 22463877 |
| Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. | Veyrieras, Jean-Baptiste; Gaffney, Daniel J; Pickrell, Joseph K; Gilad, Yoav; Stephens, Matthew; Pritchard, Jonathan K | PloS one | 2012 | e30629 | 22359548 |
| DNaseýýýI sensitivity QTLs are a major determinant of human expression variation. | Degner, Jacob F; Pai, Athma A; Pique-Regi, Roger; Veyrieras, Jean-Baptiste; Gaffney, Daniel J; Pickrell, Joseph K; De Leon, Sherryl; Michelini, Katelyn; Lewellen, Noah; Crawford, Gregory E; Stephens, Matthew; Gilad, Yoav; Pritchard, Jonathan K | Nature | 2012 Feb 16 | 390-4 | 22307276 |
| Computational tools for discovery and interpretation of expression quantitative trait loci. | Wright, Fred A; Shabalin, Andrey A; Rusyn, Ivan | Pharmacogenomics | 2012 Feb | 343-52 | 22304583 |
| Dissecting the regulatory architecture of gene expression QTLs. | Gaffney, Daniel J; Veyrieras, Jean-Baptiste; Degner, Jacob F; Pique-Regi, Roger; Pai, Athma A; Crawford, Gregory E; Stephens, Matthew; Gilad, Yoav; Pritchard, Jonathan K | Genome biology | 2012 | R7 | 22293038 |
| Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants. | Gamazon, E R; Badner, J A; Cheng, L; Zhang, C; Zhang, D; Cox, N J; Gershon, E S; Kelsoe, J R; Greenwood, T A; Nievergelt, C M; Chen, C; McKinney, R; Shilling, P D; Schork, N J; Smith, E N; Bloss, C S; Nurnberger, J I; Edenberg, H J; Foroud, T; Koller, D L | Molecular psychiatry | 2013 Mar | 340-6 | 22212596 |
| seeQTL: a searchable database for human eQTLs. | Xia, Kai; Shabalin, Andrey A; Huang, Shunping; Madar, Vered; Zhou, Yi-Hui; Wang, Wei; Zou, Fei; Sun, Wei; Sullivan, Patrick F; Wright, Fred A | Bioinformatics (Oxford, England) | 2012 Feb 1 | 451-2 | 22171328 |
| Estimation of alternative splicing variability in human populations. | Gonzalez-Porta, Mar; Calvo, Miquel; Sammeth, Michael; Guigo, Roderic | Genome research | 2012 Mar | 528-38 | 22113879 |
| Rare and common regulatory variation in population-scale sequenced human genomes. | Montgomery, Stephen B; Lappalainen, Tuuli; Gutierrez-Arcelus, Maria; Dermitzakis, Emmanouil T | PLoS genetics | 2011 Jul | e1002144 | 21811411 |
| Phosphorylation of Spo0A by the histidine kinase KinD requires the lipoprotein med in Bacillus subtilis. | Banse, Allison V; Hobbs, Errett C; Losick, Richard | Journal of bacteriology | 2011 Aug | 3949-55 | 21622736 |
| Copy number polymorphisms and anticancer pharmacogenomics. | Gamazon, Eric R; Huang, R Stephanie; Dolan, M Eileen; Cox, Nancy J | Genome biology | 2011 | R46 | 21609475 |
| Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. | Small, Kerrin S; Hedman, Asa K; Grundberg, Elin; Nica, Alexandra C; Thorleifsson, Gudmar; Kong, Augustine; Thorsteindottir, Unnur; Shin, So-Youn; Richards, Hannah B; GIANT Consortium; MAGIC Investigators; DIAGRAM Consortium; Soranzo, Nicole; Ahmadi, Kourosh R; Lindgren, Cecilia M; Stefansson, Kari; Dermitzakis, Emmanouil T; Deloukas, Panos; Spector, Timothy D; McCarthy, Mark I; MuTHER Consortium | Nature genetics | 2011 Jun | 561-4 | 21572415 |
| A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. | Gamazon, Eric R; Nicolae, Dan L; Cox, Nancy J | PLoS genetics | 2011 | e1001292 | 21304891 |
| DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors. | Walter, Vonn; Nobel, Andrew B; Wright, Fred A | Bioinformatics (Oxford, England) | 2011 Mar 1 | 678-85 | 21183584 |
| Heading down the wrong pathway: on the influence of correlation within gene sets. | Gatti, Daniel M; Barry, William T; Nobel, Andrew B; Rusyn, Ivan; Wright, Fred A | BMC genomics | 2010 | 574 | 20955544 |
| Toxicogenetics: population-based testing of drug and chemical safety in mouse models. | Rusyn, Ivan; Gatti, Daniel M; Wiltshire, Timothy; Wilshire, Timothy; Kleeberger, Steven R; Threadgill, David W | Pharmacogenomics | 2010 Aug | 1127-36 | 20704464 |
| Quantification of population structure using correlated SNPs by shrinkage principal components. | Zou, Fei; Lee, Seunggeun; Knowles, Michael R; Wright, Fred A | Human heredity. | 2010; | 20413978 |