Genotype-Tissue Expression Program (GTEx)
Genotype-Tissue Expression Program (GTEx)
Program Publications
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date |
|---|---|---|---|---|---|
| Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. | eGTEx Project | Nature genetics | 29019975 | Nat Genet | 2017 Dec |
| The impact of sex on gene expression across human tissues. | Oliva M, Muñoz-Aguirre M, Kim-Hellmuth S, Wucher V, Gewirtz ADH, Cotter DJ, Parsana P, Kasela S, Balliu B, Viñuela A, Castel SE, Mohammadi P, Aguet F, Zou Y, Khramtsova EA, Skol AD, Garrido-Martín D, Reverter F, Brown A, Evans P, Gamazon ER, Payne A, Bonazzola R, Barbeira AN, Hamel AR, Martinez-Perez A, Soria JM, GTEx Consortium, Pierce BL, Stephens M, Eskin E, Dermitzakis ET, Segrè AV, Im HK, Engelhardt BE, Ardlie KG, Montgomery SB, Battle AJ, Lappalainen T, Guigó R, Stranger BE | Science (New York, N.Y.) | 32913072 | Science | 2020 Sep 11 |
| Determinants of telomere length across human tissues. | Demanelis K, Jasmine F, Chen LS, Chernoff M, Tong L, Delgado D, Zhang C, Shinkle J, Sabarinathan M, Lin H, Ramirez E, Oliva M, Kim-Hellmuth S, Stranger BE, Lai TP, Aviv A, Ardlie KG, Aguet F, Ahsan H, GTEx Consortium, Doherty JA, Kibriya MG, Pierce BL | Science (New York, N.Y.) | 32913074 | Science | 2020 Sep 11 |
| Transcriptomic signatures across human tissues identify functional rare genetic variation. | Ferraro NM, Strober BJ, Einson J, Abell NS, Aguet F, Barbeira AN, Brandt M, Bucan M, Castel SE, Davis JR, Greenwald E, Hess GT, Hilliard AT, Kember RL, Kotis B, Park Y, Peloso G, Ramdas S, Scott AJ, Smail C, Tsang EK, Zekavat SM, Ziosi M, Aradhana, TOPMed Lipids Working Group, Ardlie KG, Assimes TL, Bassik MC, Brown CD, Correa A, Hall I, Im HK, Li X, Natarajan P, GTEx Consortium, Lappalainen T, Mohammadi P, Montgomery SB, Battle A | Science (New York, N.Y.) | 32913073 | Science | 2020 Sep 11 |
| Cell type-specific genetic regulation of gene expression across human tissues. | Kim-Hellmuth S, Aguet F, Oliva M, Muñoz-Aguirre M, Kasela S, Wucher V, Castel SE, Hamel AR, Viñuela A, Roberts AL, Mangul S, Wen X, Wang G, Barbeira AN, Garrido-Martín D, Nadel BB, Zou Y, Bonazzola R, Quan J, Brown A, Martinez-Perez A, Soria JM, GTEx Consortium, Getz G, Dermitzakis ET, Small KS, Stephens M, Xi HS, Im HK, Guigó R, Segrè AV, Stranger BE, Ardlie KG, Lappalainen T | Science (New York, N.Y.) | 32913075 | Science | 2020 Sep 11 |
| The GTEx Consortium atlas of genetic regulatory effects across human tissues. | GTEx Consortium | Science (New York, N.Y.) | 32913098 | Science | 2020 Sep 11 |
| PhenomeXcan: Mapping the genome to the phenome through the transcriptome. | Pividori M, Rajagopal PS, Barbeira A, Liang Y, Melia O, Bastarache L, Park Y, Consortium G, Wen X, Im HK | Science advances | 32917697 | Sci Adv | 2020 Sep |
| Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. | Rizzardi LF, Hickey PF, Rodriguez DiBlasi V, Tryggvadóttir R, Callahan CM, Idrizi A, Hansen KD, Feinberg AP | Nature neuroscience | 30643296 | Nat Neurosci | 2019 Feb |
| Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits. | Rizzardi LF, Hickey PF, Idrizi A, Tryggvadóttir R, Callahan CM, Stephens KE, Taverna SD, Zhang H, Ramazanoglu S, GTEx Consortium, Hansen KD, Feinberg AP | Genome biology | 33888138 | Genome Biol | 2021 Apr 22 |
| A Quantitative Proteome Map of the Human Body. | Jiang L, Wang M, Lin S, Jian R, Li X, Chan J, Dong G, Fang H, Robinson AE, GTEx Consortium, Snyder MP | Cell | 32916130 | Cell | 2020 Oct 1 |
| Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. | Cenik C, Cenik ES, Byeon GW, Grubert F, Candille SI, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H, Ricci E, Snyder MP | Genome research | 26297486 | Genome Res | 2015 Nov |
| RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data. | Wang M, Jiang L, Jian R, Chan JY, Liu Q, Snyder MP, Tang H | Bioinformatics (Oxford, England) | 33098413 | Bioinformatics | 2021 May 5 |
| AdaTiSS: a novel data-Adaptive robust method for identifying Tissue Specificity Scores. | Wang M, Jiang L, Snyder MP | Bioinformatics (Oxford, England) | 34146104 | Bioinformatics | 2021 Dec 7 |
| Impact of allele-specific peptides in proteome quantification. | Wu L, Snyder M | Proteomics. Clinical applications | 25676416 | Proteomics Clin Appl | 2015 Apr |
| A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. | Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, DeLuca DS, Peter-Demchok J, Gelfand ET, Guan P, Korzeniewski GE, Lockhart NC, Rabiner CA, Rao AK, Robinson KL, Roche NV, Sawyer SJ, Segrè AV, Shive CE, Smith AM, Sobin LH, Undale AH, Valentino KM, Vaught J, Young TR, Moore HM, GTEx Consortium | Biopreservation and biobanking | 26484571 | Biopreserv Biobank | 2015 Oct |
| An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. | Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E | Genome research | 30606742 | Genome Res | 2019 Feb |
| Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. | Madabhushi R, Gao F, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, Yamakawa H, Pao PC, Stott RT, Gjoneska E, Nott A, Cho S, Kellis M, Tsai LH | Cell | 26052046 | Cell | 2015 Jun 18 |
| Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. | GTEx Consortium | Science (New York, N.Y.) | 25954001 | Science | 2015 May 8 |
| Genetic drivers of m(6)A methylation in human brain, lung, heart and muscle. | Xiong X, Hou L, Park YP, Molinie B, GTEx Consortium, Gregory RI, Kellis M | Nature genetics | 34211177 | Nat Genet | 2021 Aug |
| Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. | Ernst J, Kellis M | Nature biotechnology | 25690853 | Nat Biotechnol | 2015 Apr |
| Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. | Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, Zhao Y, Mobbs CV, Schadt EE, Zhu J, Tu Z, GTEx Consortium | Scientific reports | 26477495 | Sci Rep | 2015 Oct 19 |
| N(6)-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. | Wang Y, Li Y, Yue M, Wang J, Kumar S, Wechsler-Reya RJ, Zhang Z, Ogawa Y, Kellis M, Duester G, Zhao JC | Nature neuroscience | 29335608 | Nat Neurosci | 2018 Feb |
| Targeted bisulfite sequencing of the dynamic DNA methylome. | Ziller MJ, Stamenova EK, Gu H, Gnirke A, Meissner A | Epigenetics & chromatin | 27980681 | Epigenetics Chromatin | 2016 |
| Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. | Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, Zhao Y, Mobbs CV, Schadt EE, Zhu J, Tu Z, GTEx Consortium | Scientific reports | 26795431 | Sci Rep | 2016 Jan 21 |
| High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human. | Wang X, He L, Goggin SM, Saadat A, Wang L, Sinnott-Armstrong N, Claussnitzer M, Kellis M | Nature communications | 30568279 | Nat Commun | 2018 Dec 19 |
| Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. | Gamazon ER, Segrè AV, van de Bunt M, Wen X, Xi HS, Hormozdiari F, Ongen H, Konkashbaev A, Derks EM, Aguet F, Quan J, GTEx Consortium, Nicolae DL, Eskin E, Kellis M, Getz G, McCarthy MI, Dermitzakis ET, Cox NJ, Ardlie KG | Nature genetics | 29955180 | Nat Genet | 2018 Jul |
| Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. | Yang F, Wang J, GTEx Consortium, Pierce BL, Chen LS | Genome research | 29021290 | Genome Res | 2017 Nov |
| Dynamic landscape and regulation of RNA editing in mammals. | Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, 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 A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB | Nature | 29022589 | Nature | 2017 Oct 11 |
| Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. | Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M | Nature biotechnology | 27701403 | Nat Biotechnol | 2016 Nov |
| Regulatory genomic circuitry of human disease loci by integrative epigenomics. | Boix CA, James BT, Park YP, Meuleman W, Kellis M | Nature | 33536621 | Nature | 2021 Feb |
| HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. | Ward LD, Kellis M | Nucleic acids research | 26657631 | Nucleic Acids Res | 2016 Jan 4 |
| Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. | Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A | Science (New York, N.Y.) | 30139913 | Science | 2018 Sep 28 |
| The impact of rare variation on gene expression across tissues. | Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD, 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 IM, Battle A, Montgomery SB | Nature | 29022581 | Nature | 2017 Oct 11 |
| Landscape of X chromosome inactivation across human tissues. | Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, 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 T, Regev A, Ardlie KG, Hacohen N, MacArthur DG | Nature | 29022598 | Nature | 2017 Oct 11 |
| Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. | Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, GTEx Consortium, Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG | Science (New York, N.Y.) | 25954003 | Science | 2015 May 8 |
| Sharing and Specificity of Co-expression Networks across 35 Human Tissues. | Pierson E, GTEx Consortium, Koller D, Battle A, Mostafavi S, Ardlie KG, Getz G, Wright FA, Kellis M, Volpi S, Dermitzakis ET | PLoS computational biology | 25970446 | PLoS Comput Biol | 2015 May |
| Co-expression networks reveal the tissue-specific regulation of transcription and splicing. | Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, GTEx Consortium, Engelhardt BE, Battle A | Genome research | 29021288 | Genome Res | 2017 Nov |
| Evidence of reduced recombination rate in human regulatory domains. | Liu Y, Sarkar A, Kheradpour P, Ernst J, Kellis M | Genome biology | 29058599 | Genome Biol | 2017 Oct 20 |
| Joint profiling of DNA methylation and chromatin architecture in single cells. | Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, Ren B | Nature methods | 31384045 | Nat Methods | 2019 Oct |
| (Epi)genomics approaches and their applications. | Meissner A | Methods (San Diego, Calif.) | 25597875 | Methods | 2015 Jan 15 |
| Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases. | Li Y, Kellis M | Nucleic acids research | 27407109 | Nucleic Acids Res | 2016 Oct 14 |
| Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease. | Hou L, Xiong X, Park Y, Boix C, James B, Sun N, He L, Patel A, Zhang Z, Molinie B, Van Wittenberghe N, Steelman S, Nusbaum C, Aguet F, Ardlie KG, Kellis M | Nature genetics | 37770633 | Nat Genet | 2023 Oct |
| Genetic determinants of telomere length and risk of common cancers: a Mendelian randomization study. | Zhang C, Doherty JA, Burgess S, Hung RJ, Lindström S, Kraft P, Gong J, Amos CI, Sellers TA, Monteiro AN, Chenevix-Trench G, Bickeböller H, Risch A, Brennan P, Mckay JD, Houlston RS, Landi MT, Timofeeva MN, Wang Y, Heinrich J, Kote-Jarai Z, Eeles RA, Muir K, Wiklund F, Grönberg H, Berndt SI, Chanock SJ, Schumacher F, Haiman CA, Henderson BE, Amin Al Olama A, Andrulis IL, Hopper JL, Chang-Claude J, John EM, Malone KE, Gammon MD, Ursin G, Whittemore AS, Hunter DJ, Gruber SB, Knight JA, Hou L, Le Marchand L, Newcomb PA, Hudson TJ, Chan AT, Li L, Woods MO, Ahsan H, Pierce BL, GECCO and GAME-ON Network: CORECT, DRIVE, ELLIPSE, FOCI, and TRICL | Human molecular genetics | 26138067 | Hum Mol Genet | 2015 Sep 15 |
| Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx. | Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS | American journal of human genetics | 27040689 | Am J Hum Genet | 2016 Apr 7 |
| A study of telomere length, arsenic exposure, and arsenic toxicity in a Bangladeshi cohort. | Zhang C, Kibriya MG, Jasmine F, Roy S, Gao J, Sabarinathan M, Shinkle J, Delgado D, Ahmed A, Islam T, Eunus M, Islam MT, Hasan R, Graziano JH, Ahsan H, Pierce BL | Environmental research | 29567420 | Environ Res | 2018 Jul |
| The association between telomere length and mortality in Bangladesh. | Dean SG, Zhang C, Gao J, Roy S, Shinkle J, Sabarinathan M, Argos M, Tong L, Ahmed A, Islam MT, Islam T, Rakibuz-Zaman M, Sarwar G, Shahriar H, Rahman M, Yunus M, Graziano JH, Chen LS, Jasmine F, Kibriya MG, Ahsan H, Pierce BL | Aging | 28630379 | Aging (Albany NY) | 2017 Jun 15 |
| DNA methylation correlates of chronological age in diverse human tissue types. | Jain N, Li JL, Tong L, Jasmine F, Kibriya MG, Demanelis K, Oliva M, Chen LS, Pierce BL | Epigenetics & chromatin | 39118140 | Epigenetics Chromatin | 2024 Aug 8 |
| Genetically Increased Telomere Length and Aging-Related Traits in the U.K. Biobank. | Demanelis K, Tong L, Pierce BL | The journals of gerontology. Series A, Biological sciences and medical sciences | 31603979 | J Gerontol A Biol Sci Med Sci | 2021 Jan 1 |
| Sex-Specific and Time-Varying Associations Between Cigarette Smoking and Telomere Length Among Older Adults. | Zhang C, Lauderdale DS, Pierce BL | American journal of epidemiology | 27856448 | Am J Epidemiol | 2016 Dec 15 |
| The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans. | Delgado DA, Zhang C, Gleason K, Demanelis K, Chen LS, Gao J, Roy S, Shinkle J, Sabarinathan M, Argos M, Tong L, Ahmed A, Islam T, Rakibuz-Zaman M, Sarwar G, Shahriar H, Rahman M, Yunus M, Doherty JA, Jasmine F, Kibriya MG, Ahsan H, Pierce BL | Human genetics | 30536049 | Hum Genet | 2019 Jan |
| Mendelian randomization studies of cancer risk: a literature review. | Pierce BL, Kraft P, Zhang C | Current epidemiology reports | 30034993 | Curr Epidemiol Rep | 2018 Jun |
| Genome-wide association study of telomere length among South Asians identifies a second RTEL1 association signal. | Delgado DA, Zhang C, Chen LS, Gao J, Roy S, Shinkle J, Sabarinathan M, Argos M, Tong L, Ahmed A, Islam T, Rakibuz-Zaman M, Sarwar G, Shahriar H, Rahman M, Yunus M, Jasmine F, Kibriya MG, Ahsan H, Pierce BL | Journal of medical genetics | 29151059 | J Med Genet | 2018 Jan |
| Novel Luminex Assay for Telomere Repeat Mass Does Not Show Well Position Effects Like qPCR. | Kibriya MG, Jasmine F, Roy S, Ahsan H, Pierce BL | PloS one | 27182778 | PLoS One | 2016 |
| Telomere length measurement by a novel Luminex-based assay: a blinded comparison to Southern blot. | Pierce BL, Jasmine F, Roy S, Zhang C, Aviv A, Hunt SC, Ahsan H, Kibriya MG | International journal of molecular epidemiology and genetics | 27186324 | Int J Mol Epidemiol Genet | 2016 |
| DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. | Oliva M, Demanelis K, Lu Y, Chernoff M, Jasmine F, Ahsan H, Kibriya MG, Chen LS, Pierce BL | Nature genetics | 36510025 | Nat Genet | 2023 Jan |
| Characterization of DNA methylation clock algorithms applied to diverse tissue types. | Richardson M, Brandt C, Jain N, Li JL, Demanelis K, Jasmine F, Kibriya MG, Tong L, Pierce BL | Aging | 39754638 | Aging (Albany NY) | 2025 Jan 3 |
| Genetic Determinants of Reduced Arsenic Metabolism Efficiency in the 10q24.32 Region Are Associated With Reduced AS3MT Expression in Multiple Human Tissue Types. | Chernoff M, Tong L, Demanelis K, Vander Griend D, Ahsan H, Pierce BL | Toxicological sciences : an official journal of the Society of Toxicology | 32433756 | Toxicol Sci | 2020 Aug 1 |
| A novel pooled-sample multiplex luminex assay for high-throughput measurement of relative telomere length. | Jasmine F, Shinkle J, Sabarinathan M, Ahsan H, Pierce BL, Kibriya MG | American journal of human biology : the official journal of the Human Biology Council | 29527774 | Am J Hum Biol | 2018 Jul |
| The association of cigarette smoking with DNA methylation and gene expression in human tissue samples. | Li JL, Jain N, Tamayo LI, Tong L, Jasmine F, Kibriya MG, Demanelis K, Oliva M, Chen LS, Pierce BL | American journal of human genetics | 38490207 | Am J Hum Genet | 2024 Apr 4 |
| DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. | Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA | Nature genetics | 23793028 | Nat Genet | 2013 Aug |
| Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. | Nadel BB, Oliva M, Shou BL, Mitchell K, Ma F, Montoya DJ, Mouton A, Kim-Hellmuth S, Stranger BE, Pellegrini M, Mangul S | Briefings in bioinformatics | 34346485 | Brief Bioinform | 2021 Nov 5 |
| Accurate and fast multiple-testing correction in eQTL studies. | Sul JH, Raj T, de Jong S, de Bakker PI, Raychaudhuri S, Ophoff RA, Stranger BE, Eskin E, Han B | American journal of human genetics | 26027500 | Am J Hum Genet | 2015 Jun 4 |
| Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. | Barbeira AN, Bonazzola R, Gamazon ER, Liang Y, Park Y, Kim-Hellmuth S, Wang G, Jiang Z, Zhou D, Hormozdiari F, Liu B, Rao A, Hamel AR, Pividori MD, Aguet F, GTEx GWAS Working Group, Bastarache L, Jordan DM, Verbanck M, Do R, GTEx Consortium, Stephens M, Ardlie K, McCarthy M, Montgomery SB, Segrè AV, Brown CD, Lappalainen T, Wen X, Im HK | Genome biology | 33499903 | Genome Biol | 2021 Jan 26 |
| Fine-mapping and QTL tissue-sharing information improves the reliability of causal gene identification. | Barbeira AN, Melia OJ, Liang Y, Bonazzola R, Wang G, Wheeler HE, Aguet F, Ardlie KG, Wen X, Im HK | Genetic epidemiology | 32964524 | Genet Epidemiol | 2020 Sep 10 |
| RNA editing underlies genetic risk of common inflammatory diseases. | Li Q, Gloudemans MJ, Geisinger JM, Fan B, Aguet F, Sun T, Ramaswami G, Li YI, Ma JB, Pritchard JK, Montgomery SB, Li JB | Nature | 35922514 | Nature | 2022 Aug |
| Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse. | Babak T, DeVeale B, Tsang EK, Zhou Y, Li X, Smith KS, Kukurba KR, Zhang R, Li JB, van der Kooy D, Montgomery SB, Fraser HB | Nature genetics | 25848752 | Nat Genet | 2015 May |
| 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 A, Brown CD, Engelhardt BE, Montgomery SB | Nature | 29022597 | Nature | 2017 Oct 11 |
| Detecting Sources of Transcriptional Heterogeneity in Large-Scale RNA-Seq Data Sets. | Searle BC, Gittelman RM, Manor O, Akey JM | Genetics | 27729424 | Genetics | 2016 Dec |
| The origins, determinants, and consequences of human mutations. | Shendure J, Akey JM | Science (New York, N.Y.) | 26404824 | Science | 2015 Sep 25 |
| Landscape of human protein-coding somatic mutations across tissues and individuals. | Xu H, Bierman R, Akey D, Koers C, Comi T, McWhite C, Akey JM | bioRxiv : the preprint server for biology | 39829890 | bioRxiv | 2025 Jan 8 |
| A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets. | Moon S, Akey JM | Genome research | 27197222 | Genome Res | 2016 Jun |
| Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression. | McCoy RC, Wakefield J, Akey JM | Cell | 28235201 | Cell | 2017 Feb 23 |
| Blood pressure-associated polymorphism controls ARHGAP42 expression via serum response factor DNA binding. | Bai X, Mangum KD, Dee RA, Stouffer GA, Lee CR, Oni-Orisan A, Patterson C, Schisler JC, Viera AJ, Taylor JM, Mack CP | The Journal of clinical investigation | 28112683 | J Clin Invest | 2017 Feb 1 |
| A genome-wide association study yields five novel thyroid cancer risk loci. | Gudmundsson J, Thorleifsson G, Sigurdsson JK, Stefansdottir L, Jonasson JG, Gudjonsson SA, Gudbjartsson DF, Masson G, Johannsdottir H, Halldorsson GH, Stacey SN, Helgason H, Sulem P, Senter L, He H, Liyanarachchi S, Ringel MD, Aguillo E, Panadero A, Prats E, Garcia-Castaño A, De Juan A, Rivera F, Xu L, Kiemeney LA, Eyjolfsson GI, Sigurdardottir O, Olafsson I, Kristvinsson H, Netea-Maier RT, Jonsson T, Mayordomo JI, Plantinga TS, Hjartarson H, Hrafnkelsson J, Sturgis EM, Thorsteinsdottir U, Rafnar T, de la Chapelle A, Stefansson K | Nature communications | 28195142 | Nat Commun | 2017 Feb 14 |
| Low Baseline Pulmonary Levels of Cytotoxic Lymphocytes as a Predisposing Risk Factor for Severe COVID-19. | Duijf PHG | mSystems | 32873611 | mSystems | 2020 Sep 1 |
| Mitochondrial GWAS and association of nuclear - mitochondrial epistasis with BMI in T1DM patients. | Ludwig-Słomczyńska AH, Seweryn MT, Kapusta P, Pitera E, Handelman SK, Mantaj U, Cyganek K, Gutaj P, Dobrucka Ł, Wender-Ożegowska E, Małecki MT, Wołkow PP | BMC medical genomics | 32635923 | BMC Med Genomics | 2020 Jul 7 |
| Mitochondrial-nuclear epistasis underlying phenotypic variation in breast cancer pathology. | Bushel PR, Ward J, Burkholder A, Li J, Anchang B | Scientific reports | 35082309 | Sci Rep | 2022 Jan 26 |
| A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients. | Degener MJF, van Cruchten RTP, Otero BA, Wang ET, Wansink DG, 't Hoen PAC | NAR genomics and bioinformatics | 35274098 | NAR Genom Bioinform | 2022 Mar |
| Non-linear interactions between candidate genes of myocardial infarction revealed in mRNA expression profiles. | Hartmann K, Seweryn M, Handelman SK, Rempała GA, Sadee W | BMC genomics | 27640124 | BMC Genomics | 2016 Sep 17 |
| Detection of human adaptation during the past 2000 years. | Field Y, Boyle EA, Telis N, Gao Z, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, Pritchard JK | Science (New York, N.Y.) | 27738015 | Science | 2016 Nov 11 |
| RNA splicing is a primary link between genetic variation and disease. | Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, Pritchard JK | Science (New York, N.Y.) | 27126046 | Science | 2016 Apr 29 |
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| Two olfactory receptors-OR2A4/7 and OR51B5-differentially affect epidermal proliferation and differentiation. | Tsai T, Veitinger S, Peek I, Busse D, Eckardt J, Vladimirova D, Jovancevic N, Wojcik S, Gisselmann G, Altmüller J, Ständer S, Luger T, Paus R, Cheret J, Hatt H | Experimental dermatology | 27315375 | Exp Dermatol | 2017 Jan |
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| Clinical and Genome-Wide Analysis of Cisplatin-Induced Peripheral Neuropathy in Survivors of Adult-Onset Cancer. | Dolan ME, El Charif O, Wheeler HE, Gamazon ER, Ardeshir-Rouhani-Fard S, Monahan P, Feldman DR, Hamilton RJ, Vaughn DJ, Beard CJ, Fung C, Kim J, Fossa SD, Hertz DL, Mushiroda T, Kubo M, Einhorn LH, Cox NJ, Travis LB, Platinum Study Group | Clinical cancer research : an official journal of the American Association for Cancer Research | 28611204 | Clin Cancer Res | 2017 Oct 1 |
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| Rare variants with large effects provide functional insights into the pathology of migraine subtypes, with and without aura. | Bjornsdottir G, Chalmer MA, Stefansdottir L, Skuladottir AT, Einarsson G, Andresdottir M, Beyter D, Ferkingstad E, Gretarsdottir S, Halldorsson BV, Halldorsson GH, Helgadottir A, Helgason H, Hjorleifsson Eldjarn G, Jonasdottir A, Jonasdottir A, Jonsdottir I, Knowlton KU, Nadauld LD, Lund SH, Magnusson OT, Melsted P, Moore KHS, Oddsson A, Olason PI, Sigurdsson A, Stefansson OA, Saemundsdottir J, Sveinbjornsson G, Tragante V, Unnsteinsdottir U, Walters GB, Zink F, Rødevand L, Andreassen OA, Igland J, Lie RT, Haavik J, Banasik K, Brunak S, Didriksen M, T Bruun M, Erikstrup C, Kogelman LJA, Nielsen KR, Sørensen E, Pedersen OB, Ullum H, DBDS Genetic Consortium, Masson G, Thorsteinsdottir U, Olesen J, Ludvigsson P, Thorarensen O, Bjornsdottir A, Sigurdardottir GR, Sveinsson OA, Ostrowski SR, Holm H, Gudbjartsson DF, Thorleifsson G, Sulem P, Stefansson H, Thorgeirsson TE, Hansen TF, Stefansson K | Nature genetics | 37884687 | Nat Genet | 2023 Nov |
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| Genome-wide analyses characterize shared heritability among cancers and identify novel cancer susceptibility regions. | Lindström S, Wang L, Feng H, Majumdar A, Huo S, Macdonald J, Harrison T, Turman C, Chen H, Mancuso N, Bammler T, Breast Cancer Association Consortium (BCAC), Gallinger S, Gruber SB, Gunter MJ, Le Marchand L, Moreno V, Offit K, Colorectal Transdisciplinary Study (CORECT), Colon Cancer Family Registry Study (CCFR), Genetics And Epidemiology Of Colorectal Cancer Consortium (GECCO), De Vivo I, O'Mara TA, Spurdle AB, Tomlinson I, Endometrial Cancer Association Consortium (ECAC), Fitzgerald R, Gharahkhani P, Gockel I, Jankowski J, Macgregor S, Schumacher J, Barnholtz-Sloan J, Bondy ML, Houlston RS, Jenkins RB, Melin B, Wrensch M, Brennan P, Christiani DC, Johansson M, Mckay J, Aldrich MC, Amos CI, Landi MT, Tardon A, International Lung Cancer Consortium (ILCCO), Bishop DT, Demenais F, Goldstein AM, Iles MM, Kanetsky PA, Law MH, Ovarian Cancer Association Consortium (OCAC), Amundadottir LT, Stolzenberg-Solomon R, Wolpin BM, Pancreatic Cancer Cohort Consortium (Panscan), Klein A, Petersen G, Risch H, Pancreatic Cancer Case-Control Consortium (Panc4), The PRACTICAL Consortium, Chanock SJ, Purdue MP, Scelo G, Pharoah P, Kar S, Hung RJ, Pasaniuc B, Kraft P | Journal of the National Cancer Institute | 36929942 | J Natl Cancer Inst | 2023 Jun 8 |
| Human endogenous retroviruses of the HERV-K (HML-2) family are expressed in the brain of healthy individuals and modify the composition of the brain-infiltrating immune cells. | Nevalainen T, Autio A, Hurme M | Heliyon | 37920490 | Heliyon | 2023 Nov |
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| Statistical tests for detecting variance effects in quantitative trait studies. | Dumitrascu B, Darnell G, Ayroles J, Engelhardt BE | Bioinformatics (Oxford, England) | 29982387 | Bioinformatics | 2019 Jan 15 |
| Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. | McDowell IC, Barrera A, D'Ippolito AM, Vockley CM, Hong LK, Leichter SM, Bartelt LC, Majoros WH, Song L, Safi A, Koçak DD, Gersbach CA, Hartemink AJ, Crawford GE, Engelhardt BE, Reddy TE | Genome research | 30097539 | Genome Res | 2018 Sep |
| Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease. | de Goede OM, Nachun DC, Ferraro NM, Gloudemans MJ, Rao AS, Smail C, Eulalio TY, Aguet F, Ng B, Xu J, Barbeira AN, Castel SE, Kim-Hellmuth S, Park Y, Scott AJ, Strober BJ, GTEx Consortium, Brown CD, Wen X, Hall IM, Battle A, Lappalainen T, Im HK, Ardlie KG, Mostafavi S, Quertermous T, Kirkegaard K, Montgomery SB | Cell | 33864768 | Cell | 2021 May 13 |
| Transposable elements are the primary source of novelty in primate gene regulation. | Trizzino M, Park Y, Holsbach-Beltrame M, Aracena K, Mika K, Caliskan M, Perry GH, Lynch VJ, Brown CD | Genome research | 28855262 | Genome Res | 2017 Oct |
| Sparse multi-output Gaussian processes for online medical time series prediction. | Cheng LF, Dumitrascu B, Darnell G, Chivers C, Draugelis M, Li K, Engelhardt BE | BMC medical informatics and decision making | 32641134 | BMC Med Inform Decis Mak | 2020 Jul 8 |
| Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci. | Pashos EE, Park Y, Wang X, Raghavan A, Yang W, Abbey D, Peters DT, Arbelaez J, Hernandez M, Kuperwasser N, Li W, Lian Z, Liu Y, Lv W, Lytle-Gabbin SL, Marchadier DH, Rogov P, Shi J, Slovik KJ, Stylianou IM, Wang L, Yan R, Zhang X, Kathiresan S, Duncan SA, Mikkelsen TS, Morrisey EE, Rader DJ, Brown CD, Musunuru K | Cell stem cell | 28388432 | Cell Stem Cell | 2017 Apr 6 |
| Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure. | Mimno D, Blei DM, Engelhardt BE | Proceedings of the National Academy of Sciences of the United States of America | 26071445 | Proc Natl Acad Sci U S A | 2015 Jun 30 |
| Increased burden of deleterious variants in essential genes in autism spectrum disorder. | Ji X, Kember RL, Brown CD, Bućan M | Proceedings of the National Academy of Sciences of the United States of America | 27956632 | Proc Natl Acad Sci U S A | 2016 Dec 27 |
| Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension. | Surendran P, Drenos F, Young R, Warren H, Cook JP, Manning AK, Grarup N, Sim X, Barnes DR, Witkowska K, Staley JR, Tragante V, Tukiainen T, Yaghootkar H, Masca N, Freitag DF, Ferreira T, Giannakopoulou O, Tinker A, Harakalova M, Mihailov E, Liu C, Kraja AT, Fallgaard Nielsen S, Rasheed A, Samuel M, Zhao W, Bonnycastle LL, Jackson AU, Narisu N, Swift AJ, Southam L, Marten J, Huyghe JR, Stančáková A, Fava C, Ohlsson T, Matchan A, Stirrups KE, Bork-Jensen J, Gjesing AP, Kontto J, Perola M, Shaw-Hawkins S, Havulinna AS, Zhang H, Donnelly LA, Groves CJ, Rayner NW, Neville MJ, Robertson NR, Yiorkas AM, Herzig KH, Kajantie E, Zhang W, Willems SM, Lannfelt L, Malerba G, Soranzo N, Trabetti E, Verweij N, Evangelou E, Moayyeri A, Vergnaud AC, Nelson CP, Poveda A, Varga TV, Caslake M, de Craen AJ, Trompet S, Luan J, Scott RA, Harris SE, Liewald DC, Marioni R, Menni C, Farmaki AE, Hallmans G, Renström F, Huffman JE, Hassinen M, Burgess S, Vasan RS, Felix JF, CHARGE-Heart Failure Consortium, Uria-Nickelsen M, Malarstig A, Reily DF, Hoek M, Vogt T, Lin H, Lieb W, EchoGen Consortium, Traylor M, Markus HF, METASTROKE Consortium, Highland HM, Justice AE, Marouli E, GIANT Consortium, Lindström J, Uusitupa M, Komulainen P, Lakka TA, Rauramaa R, Polasek O, Rudan I, Rolandsson O, Franks PW, Dedoussis G, Spector TD, EPIC-InterAct Consortium, Jousilahti P, Männistö S, Deary IJ, Starr JM, Langenberg C, Wareham NJ, Brown MJ, Dominiczak AF, Connell JM, Jukema JW, Sattar N, Ford I, Packard CJ, Esko T, Mägi R, Metspalu A, de Boer RA, van der Meer P, van der Harst P, Lifelines Cohort Study, Gambaro G, Ingelsson E, Lind L, de Bakker PI, Numans ME, Brandslund I, Christensen C, Petersen ER, Korpi-Hyövälti E, Oksa H, Chambers JC, Kooner JS, Blakemore AI, Franks S, Jarvelin MR, Husemoen LL, Linneberg A, Skaaby T, Thuesen B, Karpe F, Tuomilehto J, Doney AS, Morris AD, Palmer CN, Holmen OL, Hveem K, Willer CJ, Tuomi T, Groop L, Käräjämäki A, Palotie A, Ripatti S, Salomaa V, Alam DS, Shafi Majumder AA, Di Angelantonio E, Chowdhury R, McCarthy MI, Poulter N, Stanton AV, Sever P, Amouyel P, Arveiler D, Blankenberg S, Ferrières J, Kee F, Kuulasmaa K, Müller-Nurasyid M, Veronesi G, Virtamo J, Deloukas P, Wellcome Trust Case Control Consortium, Elliott P, Understanding Society Scientific Group, Zeggini E, Kathiresan S, Melander O, Kuusisto J, Laakso M, Padmanabhan S, Porteous D, Hayward C, Scotland G, Collins FS, Mohlke KL, Hansen T, Pedersen O, Boehnke M, Stringham HM, EPIC-CVD Consortium, Frossard P, Newton-Cheh C, CHARGE+ Exome Chip Blood Pressure Consortium, Tobin MD, Nordestgaard BG, T2D-GENES Consortium, GoT2DGenes Consortium, ExomeBP Consortium, CHD Exome+ Consortium, Caulfield MJ, Mahajan A, Morris AP, Tomaszewski M, Samani NJ, Saleheen D, Asselbergs FW, Lindgren CM, Danesh J, Wain LV, Butterworth AS, Howson JM, Munroe PB | Nature genetics | 27618447 | Nat Genet | 2016 Oct |
| Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering. | Gao C, McDowell IC, Zhao S, Brown CD, Engelhardt BE | PLoS computational biology | 27467526 | PLoS Comput Biol | 2016 Jul |
| A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. | Gallagher MD, Posavi M, Huang P, Unger TL, Berlyand Y, Gruenewald AL, Chesi A, Manduchi E, Wells AD, Grant SFA, Blobel GA, Brown CD, Chen-Plotkin AS | American journal of human genetics | 29056226 | Am J Hum Genet | 2017 Nov 2 |
| Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1. | Guo C, Ludvik AE, Arlotto ME, Hayes MG, Armstrong LL, Scholtens DM, Brown CD, Newgard CB, Becker TC, Layden BT, Lowe WL, Reddy TE | Nature communications | 25648650 | Nat Commun | 2015 Feb 4 |
| Detecting differential growth of microbial populations with Gaussian process regression. | Tonner PD, Darnell CL, Engelhardt BE, Schmid AK | Genome research | 27864351 | Genome Res | 2017 Feb |
| Genetic association with B-cell acute lymphoblastic leukemia in allogeneic transplant patients differs by age and sex. | Clay-Gilmour AI, Hahn T, Preus LM, Onel K, Skol A, Hungate E, Zhu Q, Haiman CA, Stram DO, Pooler L, Sheng X, Yan L, Liu Q, Hu Q, Liu S, Battaglia S, Zhu X, Block AW, Sait SNJ, Karaesmen E, Rizvi A, Weisdorf DJ, Ambrosone CB, Tritchler D, Ellinghaus E, Ellinghaus D, Stanulla M, Clavel J, Orsi L, Spellman S, Pasquini MC, McCarthy PL, Sucheston-Campbell LE | Blood advances | 29296818 | Blood Adv | 2017 Sep 12 |
| Structural architecture of SNP effects on complex traits. | Gamazon ER, Cox NJ, Davis LK | American journal of human genetics | 25307299 | Am J Hum Genet | 2014 Nov 6 |
| Genetic resilience to amyloid related cognitive decline. | Hohman TJ, Dumitrescu L, Cox NJ, Jefferson AL, Alzheimer’s Neuroimaging Initiative | Brain imaging and behavior | 27743375 | Brain Imaging Behav | 2017 Apr |
| Variants in WFS1 and Other Mendelian Deafness Genes Are Associated with Cisplatin-Associated Ototoxicity. | Wheeler HE, Gamazon ER, Frisina RD, Perez-Cervantes C, El Charif O, Mapes B, Fossa SD, Feldman DR, Hamilton RJ, Vaughn DJ, Beard CJ, Fung C, Kollmannsberger C, Kim J, Mushiroda T, Kubo M, Ardeshir-Rouhani-Fard S, Einhorn LH, Cox NJ, Dolan ME, Travis LB | Clinical cancer research : an official journal of the American Association for Cancer Research | 28039263 | Clin Cancer Res | 2017 Jul 1 |
| Gene and MicroRNA Perturbations of Cellular Response to Pemetrexed Implicate Biological Networks and Enable Imputation of Response in Lung Adenocarcinoma. | Gamazon ER, Trendowski MR, Wen Y, Wing C, Delaney SM, Huh W, Wong S, Cox NJ, Dolan ME | Scientific reports | 29335598 | Sci Rep | 2018 Jan 15 |
| SCAN: a systems biology approach to pharmacogenomic discovery. | Gamazon ER, Huang RS, Cox NJ | Methods in molecular biology (Clifton, N.J.) | 23824859 | Methods Mol Biol | 2013 |
| SCAN database: facilitating integrative analyses of cytosine modification and expression QTL. | Zhang W, Gamazon ER, Zhang X, Konkashbaev A, Liu C, Szilágyi KL, Dolan ME, Cox NJ | Database : the journal of biological databases and curation | 25818895 | Database (Oxford) | 2015 |
| Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. | Barbeira AN, Dickinson SP, Bonazzola R, Zheng J, Wheeler HE, Torres JM, Torstenson ES, Shah KP, Garcia T, Edwards TL, Stahl EA, Huckins LM, GTEx Consortium, Nicolae DL, Cox NJ, Im HK | Nature communications | 29739930 | Nat Commun | 2018 May 8 |
| Genome-wide interrogation of longitudinal FEV1 in children with asthma. | Wu K, Gamazon ER, Im HK, Geeleher P, White SR, Solway J, Clemmer GL, Weiss ST, Tantisira KG, Cox NJ, Ratain MJ, Huang RS | American journal of respiratory and critical care medicine | 25221879 | Am J Respir Crit Care Med | 2014 Sep 15 |
| Poly-omic prediction of complex traits: OmicKriging. | Wheeler HE, Aquino-Michaels K, Gamazon ER, Trubetskoy VV, Dolan ME, Huang RS, Cox NJ, Im HK | Genetic epidemiology | 24799323 | Genet Epidemiol | 2014 Jul |
| Cross-tissue and tissue-specific eQTLs: partitioning the heritability of a complex trait. | Torres JM, Gamazon ER, Parra EJ, Below JE, Valladares-Salgado A, Wacher N, Cruz M, Hanis CL, Cox NJ | American journal of human genetics | 25439722 | Am J Hum Genet | 2014 Nov 6 |
| The genetic architecture of type 2 diabetes. | Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, Ma C, Fontanillas P, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Tajes JF, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H, Huyghe JR, van de Bunt M, Pearson RD, Kumar A, Müller-Nurasyid M, Grarup N, Stringham HM, Gamazon ER, Lee J, Chen Y, Scott RA, Below JE, Chen P, Huang J, Go MJ, Stitzel ML, Pasko D, Parker SCJ, Varga TV, Green T, Beer NL, Day-Williams AG, Ferreira T, Fingerlin T, Horikoshi M, Hu C, Huh I, Ikram MK, Kim BJ, Kim Y, Kim YJ, Kwon MS, Lee J, Lee S, Lin KH, Maxwell TJ, Nagai Y, Wang X, Welch RP, Yoon J, Zhang W, Barzilai N, Voight BF, Han BG, Jenkinson CP, Kuulasmaa T, Kuusisto J, Manning A, Ng MCY, Palmer ND, Balkau B, Stančáková A, Abboud HE, Boeing H, Giedraitis V, Prabhakaran D, Gottesman O, Scott J, Carey J, Kwan P, Grant G, Smith JD, Neale BM, Purcell S, Butterworth AS, Howson JMM, Lee HM, Lu Y, Kwak SH, Zhao W, Danesh J, Lam VKL, Park KS, Saleheen D, So WY, Tam CHT, Afzal U, Aguilar D, Arya R, Aung T, Chan E, Navarro C, Cheng CY, Palli D, Correa A, Curran JE, Rybin D, Farook VS, Fowler SP, Freedman BI, Griswold M, Hale DE, Hicks PJ, Khor CC, Kumar S, Lehne B, Thuillier D, Lim WY, Liu J, van der Schouw YT, Loh M, Musani SK, Puppala S, Scott WR, Yengo L, Tan ST, Taylor HA Jr, Thameem F, Wilson G Sr, Wong TY, Njølstad PR, Levy JC, Mangino M, Bonnycastle LL, Schwarzmayr T, Fadista J, Surdulescu GL, Herder C, Groves CJ, Wieland T, Bork-Jensen J, Brandslund I, Christensen C, Koistinen HA, Doney ASF, Kinnunen L, Esko T, Farmer AJ, Hakaste L, Hodgkiss D, Kravic J, Lyssenko V, Hollensted M, Jørgensen ME, Jørgensen T, Ladenvall C, Justesen JM, Käräjämäki A, Kriebel J, Rathmann W, Lannfelt L, Lauritzen T, Narisu N, Linneberg A, Melander O, Milani L, Neville M, Orho-Melander M, Qi L, Qi Q, Roden M, Rolandsson O, Swift A, Rosengren AH, Stirrups K, Wood AR, Mihailov E, Blancher C, Carneiro MO, Maguire J, Poplin R, Shakir K, Fennell T, DePristo M, de Angelis MH, Deloukas P, Gjesing AP, Jun G, Nilsson P, Murphy J, Onofrio R, Thorand B, Hansen T, Meisinger C, Hu FB, Isomaa B, Karpe F, Liang L, Peters A, Huth C, O'Rahilly SP, Palmer CNA, Pedersen O, Rauramaa R, Tuomilehto J, Salomaa V, Watanabe RM, Syvänen AC, Bergman RN, Bharadwaj D, Bottinger EP, Cho YS, Chandak GR, Chan JCN, Chia KS, Daly MJ, Ebrahim SB, Langenberg C, Elliott P, Jablonski KA, Lehman DM, Jia W, Ma RCW, Pollin TI, Sandhu M, Tandon N, Froguel P, Barroso I, Teo YY, Zeggini E, Loos RJF, Small KS, Ried JS, DeFronzo RA, Grallert H, Glaser B, Metspalu A, Wareham NJ, Walker M, Banks E, Gieger C, Ingelsson E, Im HK, Illig T, Franks PW, Buck G, Trakalo J, Buck D, Prokopenko I, Mägi R, Lind L, Farjoun Y, Owen KR, Gloyn AL, Strauch K, Tuomi T, Kooner JS, Lee JY, Park T, Donnelly P, Morris AD, Hattersley AT, Bowden DW, Collins FS, Atzmon G, Chambers JC, Spector TD, Laakso M, Strom TM, Bell GI, Blangero J, Duggirala R, Tai ES, McVean G, Hanis CL, Wilson JG, Seielstad M, Frayling TM, Meigs JB, Cox NJ, Sladek R, Lander ES, Gabriel S, Burtt NP, Mohlke KL, Meitinger T, Groop L, Abecasis G, Florez JC, Scott LJ, Morris AP, Kang HM, Boehnke M, Altshuler D, McCarthy MI | Nature | 27398621 | Nature | 2016 Aug 4 |
| Integrated analysis of genetic variation and gene expression reveals novel variant for increased warfarin dose requirement in African Americans. | Hernandez W, Gamazon ER, Aquino-Michaels K, Smithberger E, O'Brien TJ, Harralson AF, Tuck M, Barbour A, Cavallari LH, Perera MA | Journal of thrombosis and haemostasis : JTH | 28135054 | J Thromb Haemost | 2017 Apr |
| Novel genetic predictors of venous thromboembolism risk in African Americans. | Hernandez W, Gamazon ER, Smithberger E, O'Brien TJ, Harralson AF, Tuck M, Barbour A, Kittles RA, Cavallari LH, Perera MA | Blood | 26888256 | Blood | 2016 Apr 14 |
| Allele-specific expression reveals interactions between genetic variation and environment. | Knowles DA, Davis JR, Edgington H, Raj A, Favé MJ, Zhu X, Potash JB, Weissman MM, Shi J, Levinson DF, Awadalla P, Mostafavi S, Montgomery SB, Battle A | Nature methods | 28530654 | Nat Methods | 2017 Jul |
| On Using Local Ancestry to Characterize the Genetic Architecture of Human Traits: Genetic Regulation of Gene Expression in Multiethnic or Admixed Populations. | Zhong Y, Perera MA, Gamazon ER | American journal of human genetics | 31104770 | Am J Hum Genet | 2019 Jun 6 |
| Integrating predicted transcriptome from multiple tissues improves association detection. | Barbeira AN, Pividori M, Zheng J, Wheeler HE, Nicolae DL, Im HK | PLoS genetics | 30668570 | PLoS Genet | 2019 Jan |
| Analysis of Genetically Regulated Gene Expression Identifies a Prefrontal PTSD Gene, SNRNP35, Specific to Military Cohorts. | Huckins LM, Chatzinakos C, Breen MS, Hartmann J, Klengel T, da Silva Almeida AC, Dobbyn A, Girdhar K, Hoffman GE, Klengel C, Logue MW, Lori A, Maihofer AX, Morrison FG, Nguyen HT, Park Y, Ruderfer D, Sloofman LG, van Rooij SJH, PTSD Working Group of Psychiatric Genomics Consortium, Baker DG, Chen CY, Cox N, Duncan LE, Geyer MA, Glatt SJ, Im HK, Risbrough VB, Smoller JW, Stein DJ, Yehuda R, Liberzon I, Koenen KC, Jovanovic T, Kellis M, Miller MW, Bacanu SA, Nievergelt CM, Buxbaum JD, Sklar P, Ressler KJ, Stahl EA, Daskalakis NP | Cell reports | 32492425 | Cell Rep | 2020 Jun 2 |
| Quantitative allelic test--a fast test for very large association studies. | Lee SM, Karrison TG, Cox NJ, Im HK | Genetic epidemiology | 24185610 | Genet Epidemiol | 2013 Dec |
| The impact of human copy number variation on gene expression. | Gamazon ER, Stranger BE | Briefings in functional genomics | 25922366 | Brief Funct Genomics | 2015 Sep |
| Obesity-associated variants within FTO form long-range functional connections with IRX3. | Smemo S, Tena JJ, Kim KH, Gamazon ER, Sakabe NJ, Gómez-Marín C, Aneas I, Credidio FL, Sobreira DR, Wasserman NF, Lee JH, Puviindran V, Tam D, Shen M, Son JE, Vakili NA, Sung HK, Naranjo S, Acemel RD, Manzanares M, Nagy A, Cox NJ, Hui CC, Gomez-Skarmeta JL, Nóbrega MA | Nature | 24646999 | Nature | 2014 Mar 20 |
| A unified set-based test with adaptive filtering for gene-environment interaction analyses. | Liu Q, Chen LS, Nicolae DL, Pierce BL | Biometrics | 26496228 | Biometrics | 2016 Jun |
| A reference panel of 64,976 haplotypes for genotype imputation. | McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K, Luo Y, Sidore C, Kwong A, Timpson N, Koskinen S, Vrieze S, Scott LJ, Zhang H, Mahajan A, Veldink J, Peters U, Pato C, van Duijn CM, Gillies CE, Gandin I, Mezzavilla M, Gilly A, Cocca M, Traglia M, Angius A, Barrett JC, Boomsma D, Branham K, Breen G, Brummett CM, Busonero F, Campbell H, Chan A, Chen S, Chew E, Collins FS, Corbin LJ, Smith GD, Dedoussis G, Dorr M, Farmaki AE, Ferrucci L, Forer L, Fraser RM, Gabriel S, Levy S, Groop L, Harrison T, Hattersley A, Holmen OL, Hveem K, Kretzler M, Lee JC, McGue M, Meitinger T, Melzer D, Min JL, Mohlke KL, Vincent JB, Nauck M, Nickerson D, Palotie A, Pato M, Pirastu N, McInnis M, Richards JB, Sala C, Salomaa V, Schlessinger D, Schoenherr S, Slagboom PE, Small K, Spector T, Stambolian D, Tuke M, Tuomilehto J, Van den Berg LH, Van Rheenen W, Volker U, Wijmenga C, Toniolo D, Zeggini E, Gasparini P, Sampson MG, Wilson JF, Frayling T, de Bakker PI, Swertz MA, McCarroll S, Kooperberg C, Dekker A, Altshuler D, Willer C, Iacono W, Ripatti S, Soranzo N, Walter K, Swaroop A, Cucca F, Anderson CA, Myers RM, Boehnke M, McCarthy MI, Durbin R, Haplotype Reference Consortium | Nature genetics | 27548312 | Nat Genet | 2016 Oct |
| Bid maintains mitochondrial cristae structure and function and protects against cardiac disease in an integrative genomics study. | Salisbury-Ruf CT, Bertram CC, Vergeade A, Lark DS, Shi Q, Heberling ML, Fortune NL, Okoye GD, Jerome WG, Wells QS, Fessel J, Moslehi J, Chen H, Roberts LJ 2nd, Boutaud O, Gamazon ER, Zinkel SS | eLife | 30281024 | Elife | 2018 Oct 3 |
| GWAS to Sequencing: Divergence in Study Design and Analysis. | King CR, Nicolae DL | Genes | 24879455 | Genes (Basel) | 2014 May 28 |
| Genetic variation associated with euphorigenic effects of d-amphetamine is associated with diminished risk for schizophrenia and attention deficit hyperactivity disorder. | Hart AB, Gamazon ER, Engelhardt BE, Sklar P, Kähler AK, Hultman CM, Sullivan PF, Neale BM, Faraone SV, Psychiatric Genomics Consortium: ADHD Subgroup, de Wit H, Cox NJ, Palmer AA | Proceedings of the National Academy of Sciences of the United States of America | 24711425 | Proc Natl Acad Sci U S A | 2014 Apr 22 |
| Estimating and accounting for unobserved covariates in high-dimensional correlated data. | McKennan C, Nicolae D | Journal of the American Statistical Association | 35615339 | J Am Stat Assoc | 2022 |
| Partitioning the heritability of Tourette syndrome and obsessive compulsive disorder reveals differences in genetic architecture. | Davis LK, Yu D, Keenan CL, Gamazon ER, Konkashbaev AI, Derks EM, Neale BM, Yang J, Lee SH, Evans P, Barr CL, Bellodi L, Benarroch F, Berrio GB, Bienvenu OJ, Bloch MH, Blom RM, Bruun RD, Budman CL, Camarena B, Campbell D, Cappi C, Cardona Silgado JC, Cath DC, Cavallini MC, Chavira DA, Chouinard S, Conti DV, Cook EH, Coric V, Cullen BA, Deforce D, Delorme R, Dion Y, Edlund CK, Egberts K, Falkai P, Fernandez TV, Gallagher PJ, Garrido H, Geller D, Girard SL, Grabe HJ, Grados MA, Greenberg BD, Gross-Tsur V, Haddad S, Heiman GA, Hemmings SM, Hounie AG, Illmann C, Jankovic J, Jenike MA, Kennedy JL, King RA, Kremeyer B, Kurlan R, Lanzagorta N, Leboyer M, Leckman JF, Lennertz L, Liu C, Lochner C, Lowe TL, Macciardi F, McCracken JT, McGrath LM, Mesa Restrepo SC, Moessner R, Morgan J, Muller H, Murphy DL, Naarden AL, Ochoa WC, Ophoff RA, Osiecki L, Pakstis AJ, Pato MT, Pato CN, Piacentini J, Pittenger C, Pollak Y, Rauch SL, Renner TJ, Reus VI, Richter MA, Riddle MA, Robertson MM, Romero R, Rosàrio MC, Rosenberg D, Rouleau GA, Ruhrmann S, Ruiz-Linares A, Sampaio AS, Samuels J, Sandor P, Sheppard B, Singer HS, Smit JH, Stein DJ, Strengman E, Tischfield JA, Valencia Duarte AV, Vallada H, Van Nieuwerburgh F, Veenstra-Vanderweele J, Walitza S, Wang Y, Wendland JR, Westenberg HG, Shugart YY, Miguel EC, McMahon W, Wagner M, Nicolini H, Posthuma D, Hanna GL, Heutink P, Denys D, Arnold PD, Oostra BA, Nestadt G, Freimer NB, Pauls DL, Wray NR, Stewart SE, Mathews CA, Knowles JA, Cox NJ, Scharf JM | PLoS genetics | 24204291 | PLoS Genet | 2013 Oct |
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| 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 EM, Zwinderman AH, Gamazon ER | Behavior genetics | 28185111 | Behav Genet | 2017 May |
| 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 H, Halpern J, Kibriya MG, Pierce BL, Tong L, Gamazon E, McGuire V, Felberg A, Shi J, Jasmine F, Roy S, Brutus R, Argos M, Melkonian S, Chang-Claude J, Andrulis I, Hopper JL, John EM, Malone K, Ursin G, Gammon MD, Thomas DC, Seminara D, Casey G, Knight JA, Southey MC, Giles GG, Santella RM, Lee E, Conti D, Duggan D, Gallinger S, Haile R, Jenkins M, Lindor NM, Newcomb P, Michailidou K, Apicella C, Park DJ, Peto J, Fletcher O, dos Santos Silva I, Lathrop M, Hunter DJ, Chanock SJ, Meindl A, Schmutzler RK, Müller-Myhsok B, Lochmann M, Beckmann L, Hein R, Makalic E, Schmidt DF, Bui QM, Stone J, Flesch-Janys D, Dahmen N, Nevanlinna H, Aittomäki K, Blomqvist C, Hall P, Czene K, Irwanto A, Liu J, Rahman N, Turnbull C, Familial Breast Cancer Study, Dunning AM, Pharoah P, Waisfisz Q, Meijers-Heijboer H, Uitterlinden AG, Rivadeneira F, Nicolae D, Easton DF, Cox NJ, Whittemore AS | Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology | 24493630 | Cancer Epidemiol Biomarkers Prev | 2014 Apr |
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| A variant at 9p21.3 functionally implicates CDKN2B in paediatric B-cell precursor acute lymphoblastic leukaemia aetiology. | Hungate EA, Vora SR, Gamazon ER, Moriyama T, Best T, Hulur I, Lee Y, Evans TJ, Ellinghaus E, Stanulla M, Rudant J, Orsi L, Clavel J, Milne E, Scott RJ, Pui CH, Cox NJ, Loh ML, Yang JJ, Skol AD, Onel K | Nature communications | 26868379 | Nat Commun | 2016 Feb 12 |
| Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration. | Parsana P, Amend SR, Hernandez J, Pienta KJ, Battle A | BMC cancer | 28651527 | BMC Cancer | 2017 Jun 26 |
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| A tiered, Bayesian approach to estimating of population variability for regulatory decision-making. | Chiu WA, Wright FA, Rusyn I | ALTEX | 27960008 | ALTEX | 2017 |
