We Accelerate Discovery

You are here

Genotype-Tissue Expression (GTEx) (125)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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, MTranslational psychiatry.2015;e68726624926
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-ManuelJournal of the American Statistical Association.2015;975-98626617424
Joint Bayesian variable and graph selection for regression models with network-structured predictors.Peterson, Christine B; Stingo, Francesco C; Vannucci, MarinaStatistics in medicine.2016 Mar 30;1017-3126514925
A unified set-based test with adaptive filtering for gene-environment interaction analyses.Liu, Qianying; Chen, Lin S; Nicolae, Dan L; Pierce, Brandon LBiometrics.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, RoryBMC genomics.2015;26493208
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, ZhidongScientific reports.2015;26477495
Functional genomics bridges the gap between quantitative genetics and molecular biology.Lappalainen, TuuliGenome research.2015 Oct;1427-3126430152
BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS.Wen, Xiaoquan; Stephens, MatthewThe annals of applied statistics.2014;176-20326413181
The origins, determinants, and consequences of human mutations.Shendure, Jay; Akey, Joshua MScience (New York, N.Y.).2015 Sep 25;1478-8326404824
Tools and best practices for data processing in allelic expression analysis.Castel, Stephane E; Levy-Moonshine, Ami; Mohammadi, Pejman; Banks, Eric; Lappalainen, TuuliGenome biology.2015;26381377
WASP: allele-specific software for robust molecular quantitative trait locus discovery.van de Geijn, Bryce; McVicker, Graham; Gilad, Yoav; Pritchard, Jonathan KNature methods.2015 Nov;1061-326366987
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 TCell.2015 Aug 27;1039-5026300124
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 PGenome research.2015 Nov;1610-2126297486
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 KBMC 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 KyungNature genetics.2015 Sep;1091-826258848
A permutation approach for selecting the penalty parameter in penalized model selection.Sabourin, Jeremy A; Valdar, William; Nobel, Andrew BBiometrics.2015 Dec;1185-9426243050
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 TRICLHuman molecular genetics.2015 Sep 15;5356-6626138067
Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.Simmons, Sean; Peng, Jian; Bienkowska, Jadwiga; Berger, BonnieJournal of computational biology : a journal of computational molecular cell biology.2015 Aug;715-2826098139
Identification of causal genes for complex traits.Hormozdiari, Farhad; Kichaev, Gleb; Yang, Wen-Yun; Pasaniuc, Bogdan; Eskin, EleazarBioinformatics (Oxford, England).2015 Jun 15;i206-1326072484
Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure.Mimno, David; Blei, David M; Engelhardt, Barbara EProceedings of the National Academy of Sciences of the United States of America.2015 Jun 30;E3441-5026071445
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-HueiCell.2015 Jun 18;1592-60526052046
The projack: a resampling approach to correct for ranking bias in high-throughput studies.Zhou, Yi-Hui; Wright, Fred ABiostatistics (Oxford, England).2016 Jan;54-6426040912
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, BuhmAmerican journal of human genetics.2015 Jun 4;857-6826027500
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 TPLoS computational biology.2015 May;e100422025970446
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 GScience (New York, N.Y.).2015 May 8;666-925954003
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, RodericScience (New York, N.Y.).2015 May 8;660-525954002
Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.GTEx ConsortiumScience (New York, N.Y.).2015 May 8;648-6025954001
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, TuuliGenome research.2015 Jul;927-3625953952
The impact of human copy number variation on gene expression.Gamazon, Eric R; Stranger, Barbara EBriefings in functional genomics.2015 Apr 27;25922366
Cross-population joint analysis of eQTLs: fine mapping and functional annotation.Wen, Xiaoquan; Luca, Francesca; Pique-Regi, RogerPLoS genetics.2015 Apr;e100517625906321
Gene-Gene Interactions Detection Using a Two-stage Model.Wang, Zhanyong; Sul, Jae Hoon; Snir, Sagi; Lozano, Jose A; Eskin, EleazarJournal of computational biology : a journal of computational molecular cell biology.2015 Jun;563-7625871811
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, KariNature 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 BNature genetics.2015 May;544-925848752
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 ABioinformatics (Oxford, England).2015 Aug 1;2497-50425819081
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 JDatabase : the journal of biological databases and curation.2015;25818895
Bayesian model comparison in genetic association analysis: linear mixed modeling and SNP set testing.Wen, XiaoquanBiostatistics (Oxford, England).2015 Oct;701-1225796429
Hypothesis testing at the extremes: fast and robust association for high-throughput data.Zhou, Yi-Hui; Wright, Fred ABiostatistics (Oxford, England).2015 Jul;611-2525792622
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, LushengBMC genomics.2015;25765547
Efficient multiple-trait association and estimation of genetic correlation using the matrix-variate linear mixed model.Furlotte, Nicholas A; Eskin, EleazarGenetics.2015 May;59-6825724382
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues.Ernst, Jason; Kellis, ManolisNature biotechnology.2015 Apr;364-7625690853
Impact of allele-specific peptides in proteome quantification.Wu, Linfeng; Snyder, MichaelProteomics. Clinical applications.2015 Apr;432-625676416
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 ENature 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 RAmerican journal of human genetics.2015 Feb 5;318-2825640674
Memory efficient assembly of human genome.Hormozdiari, Farhad; Eskin, EleazarJournal of bioinformatics and computational biology.2015 Apr;25603998
(Epi)genomics approaches and their applications.Meissner, AlexanderMethods (San Diego, Calif.).2015 Jan 15;2-Jan25597875
A spatial haplotype copying model with applications to genotype imputation.Yang, Wen-Yun; Hormozdiari, Farhad; Eskin, Eleazar; Pasaniuc, BogdanJournal of computational biology : a journal of computational molecular cell biology.2015 May;451-6225526526
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 JAmerican journal of human genetics.2014 Nov 6;521-3425439722
Fine-mapping additive and dominant SNP effects using group-LASSO and fractional resample model averaging.Sabourin, Jeremy; Nobel, Andrew B; Valdar, WilliamGenetic epidemiology.2015 Feb;77-8825417853
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 PProceedings of the National Academy of Sciences of the United States of America.2014 Dec 2;17224-925413365
Structural architecture of SNP effects on complex traits.Gamazon, Eric R; Cox, Nancy J; Davis, Lea KAmerican journal of human genetics.2014 Nov 6;477-8925307299
Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies.Panousis, Nikolaos I; Gutierrez-Arcelus, Maria; Dermitzakis, Emmanouil T; Lappalainen, TuuliGenome 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 StephanieAmerican journal of respiratory and critical care medicine.2014 Sep 15;619-2725221879
Space Time Clustering and the Permutation Moments of Quadratic Form.Zhou, Yi-Hui; Mayhew, Gregory; Sun, Zhibin; Xu, Xiaolin; Zou, Fei; Wright, Fred AStat.2013 Jan 1;292-30225210205
Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk.Human molecular genetics.2015 Jan 1;285-9825168388
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 LThe American journal of psychiatry.2015 Jan;82-9325158072
Convergence of Sample Eigenvalues, Eigenvectors, and Principal Component Scores for Ultra-High Dimensional Data.Lee, Seunggeun; Zou, Fei; Wright, Fred ABiometrika2014 Jun484-49025143634
IRBIS: a systematic search for conserved complementarity.Pervouchine, Dmitri DRNA (New York, N.Y.).2014 Oct;1519-3125142064
Identification of genetic variants associated with alternative splicing using sQTLseekeR.Monlong, Jean; Calvo, Miquel; Ferreira, Pedro G; Guigo, RodericNature communications.2014;25140736
Identifying causal variants at loci with multiple signals of association.Hormozdiari, Farhad; Kostem, Emrah; Kang, Eun Yong; Pasaniuc, Bogdan; Eskin, EleazarGenetics.2014 Oct;497-50825104515
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.Mangul, Serghei; Caciula, Adrian; Al Seesi, Sahar; Brinza, Dumitru; M?ndoiu, Ion; Zelikovsky, AlexBMC genomics.2014;S725082147
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; SchadtMolecular systems biology201474325080494
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, SunaDiabetes.2014 Dec;4360-825008175
Accurate viral population assembly from ultra-deep sequencing data.Mangul, Serghei; Wu, Nicholas C; Mancuso, Nicholas; Zelikovsky, Alex; Sun, Ren; Eskin, EleazarBioinformatics (Oxford, England)2014 Jun 15i329-3724932001
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 ABMC genomics201447124927774
GWAS to Sequencing: Divergence in Study Design and Analysis.King, Christopher Ryan; Nicolae, Dan LGenes.2014;460-7624879455
Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation.Ha, Min Jin; Sun, WeiBiometrics2014 May 20NULL24845967
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 KyungGenetic epidemiology2014 May 2NULL24799323
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 RThe Journal of clinical investigation2014 Jun 22736-4924789909
Determining causality and consequence of expression quantitative trait loci.Battle, A; Montgomery, S BHuman genetics2014 Jun727-3524770875
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, CNature.2014 Apr 24;469-7624759409
Validating single-cell genomics for the study of renal development.Jain, Sanjay; Noordam, Michiel J; Hoshi, Masato; Vallania, Francesco L; Conrad, Donald FKidney international.2014 Nov;1049-5524759149
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, PauNature genetics2014 May430-724728292
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, AbProceedings of the National Academy of Sciences of the United States of America2014 Apr 225968-7324711425
Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies.Joo, Jong Wha J; Sul, Jae Hoon; Han, Buhm; Ye, Chun; Eskin, EleazarGenome biology2014 Apr 7R6124708878
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, Nature2014 Mar 20371-524646999
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; AnCancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology2014 Apr658-6924493630
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, EleazarPLoS genetics2014 Jane100402224415945
RNA-Seq optimization with eQTL gold standards.Ellis, Shannon E; Gupta, Simone; Ashar, Foram N; Bader, Joel S; West, Andrew B; Arking, Dan EBMC genomics201389224341889
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, PatriziaNature neuroscience2014 Jan121-3024270187
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; BlochPLoS genetics2013 Octe100386424204291
Quantitative allelic test-a fast test for very large association studies.Lee, Sang Mee; Karrison, Theodore G; Cox, Nancy J; Im, Hae KyungGenetic epidemiology2013 Dec831-924185610
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, DaphneGenome research2013 Nov 27NULL24092820
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; GuNature biotechnology2013 Nov1015-2224037425
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, MaNature2013 Sep 26506-1124037378
Efficiently identifying significant associations in genome-wide association studies.Kostem, Emrah; Eskin, EleazarJournal of computational biology : a journal of computational molecular cell biology.2013 Oct;817-3024033261
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 DGenome biology.2013;R7523889843
SCAN: a systems biology approach to pharmacogenomic discovery.Gamazon, Eric R; Huang, R Stephanie; Cox, Nancy JMethods in molecular biology (Clifton, N.J.)2013213-2423824859
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 ANature genetics2013 Aug852-923793028
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, WanqingBMC genomics201339523758991
Validation of Monte Carlo estimates of three-class ideal observer operating points for normal data.Edwards, Darrin CAcademic radiology2013 Jul908-1423747155
JOINT AND INDIVIDUAL VARIATION EXPLAINED (JIVE) FOR INTEGRATED ANALYSIS OF MULTIPLE DATA TYPES.Lock, Eric F; Hoadley, Katherine A; Marron, J S; Nobel, Andrew BThe annals of applied statistics2013 Mar 1523-54223745156
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 Genet2013 May 29580-523715323
A statistical framework for joint eQTL analysis in multiple tissues.Flutre, Timothee; Wen, Xiaoquan; Pritchard, Jonathan; Stephens, MatthewPLoS genetics2013 Maye100348623671422
eQTL Mapping Using RNA-seq Data.Sun, Wei; Hu, YijuanStatistics in biosciences2013 May 1198-21923667399
Marbled inflation from population structure in gene-based association studies with rare variants.Liu, Qianying; Nicolae, Dan L; Chen, Lin SGenetic epidemiology2013 Apr286-9223468125
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, SeirianGenome biology.2013;R2023442883
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 AJournal of the American Medical Informatics Association : JAMIA2013 Jul-Aug619-2923355459
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 SGenetics2013 Mar1003-1323288936
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 LJournal of the National Cancer Institute2013 Feb 20302-923243203
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, JunPLoS genetics2012e100310723236292
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 KPLoS genetics2012e100303623166509
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 LAmerican journal of human genetics2012 Dec 7977-8623159251
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 APLoS genetics2012e100299823133393
The GEM mapper: fast, accurate and versatile alignment by filtration.Marco-Sola, Santiago; Sammeth, Michael; Guigo, Roderic; Ribeca, PaoloNature methods2012 Dec1185-823103880
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 TGenome research2012 Dec2368-7522960374
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 JAmerican journal of human genetics2012 Sep 7466-7722958899
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 SGenetics2012 Aug1355-6522661325
Reprioritizing genetic associations in hit regions using LASSO-based resample model averaging.Valdar, William; Sabourin, Jeremy; Nobel, Andrew; Holmes, Christopher CGenetic epidemiology2012 Jul451-6222549815
Matrix eQTL: ultra fast eQTL analysis via large matrix operations.Shabalin, Andrey ABioinformatics (Oxford, England)2012 May 151353-822492648
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 JAmerican journal of human genetics2012 Apr 6591-822463877
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 KPloS one2012e3062922359548
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 KNature2012 Feb 16390-422307276
Computational tools for discovery and interpretation of expression quantitative trait loci.Wright, Fred A; Shabalin, Andrey A; Rusyn, IvanPharmacogenomics2012 Feb343-5222304583
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 KGenome biology2012R722293038
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 LMolecular psychiatry2013 Mar340-622212596
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 ABioinformatics (Oxford, England)2012 Feb 1451-222171328
Estimation of alternative splicing variability in human populations.Gonzalez-Porta, Mar; Calvo, Miquel; Sammeth, Michael; Guigo, RodericGenome research2012 Mar528-3822113879
Rare and common regulatory variation in population-scale sequenced human genomes.Montgomery, Stephen B; Lappalainen, Tuuli; Gutierrez-Arcelus, Maria; Dermitzakis, Emmanouil TPLoS genetics2011 Jule100214421811411
Phosphorylation of Spo0A by the histidine kinase KinD requires the lipoprotein med in Bacillus subtilis.Banse, Allison V; Hobbs, Errett C; Losick, RichardJournal of bacteriology2011 Aug3949-5521622736
Copy number polymorphisms and anticancer pharmacogenomics.Gamazon, Eric R; Huang, R Stephanie; Dolan, M Eileen; Cox, Nancy JGenome biology2011R4621609475
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 ConsortiumNature genetics2011 Jun561-421572415
A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci.Gamazon, Eric R; Nicolae, Dan L; Cox, Nancy JPLoS genetics2011e100129221304891
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors.Walter, Vonn; Nobel, Andrew B; Wright, Fred ABioinformatics (Oxford, England)2011 Mar 1678-8521183584
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 ABMC genomics201057420955544
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 WPharmacogenomics2010 Aug1127-3620704464


Up to Top