Genotype-Tissue Expression Program (GTEx)
Genotype-Tissue Expression Program (GTEx)
Program Publications
Publications Search by Program
Search Results
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date | PubMedLink |
|---|---|---|---|---|---|---|
| Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. | eGTEx Project | Nature genetics | 29019975 | Nat Genet | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29019975 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32913074 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32913072 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32913075 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33888138 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32913073 |
| The GTEx Consortium atlas of genetic regulatory effects across human tissues. | GTEx Consortium | Science (New York, N.Y.) | 32913098 | Science | 2020 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/32913098 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32917697 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30643296 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32916130 |
| Impact of allele-specific peptides in proteome quantification. | Wu L, Snyder M | Proteomics. Clinical applications | 25676416 | Proteomics Clin Appl | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25676416 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34146104 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33098413 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26297486 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27701403 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29021290 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29022598 |
| Targeted bisulfite sequencing of the dynamic DNA methylome. | Ziller MJ, Stamenova EK, Gu H, Gnirke A, Meissner A | Epigenetics & chromatin | 27980681 | Epigenetics Chromatin | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27980681 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26484571 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25954003 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30139913 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30568279 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26657631 |
| Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. | Ernst J, Kellis M | Nature biotechnology | 25690853 | Nat Biotechnol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25690853 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26795431 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34211177 |
| (Epi)genomics approaches and their applications. | Meissner A | Methods (San Diego, Calif.) | 25597875 | Methods | 2015 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/25597875 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26052046 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25954001 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29021288 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29022581 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29022589 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29335608 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33536621 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29058599 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27407109 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26477495 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30606742 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31384045 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29955180 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25970446 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37770633 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27856448 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30536049 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27182778 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27186324 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29527774 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29567420 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36510025 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28630379 |
| Mendelian randomization studies of cancer risk: a literature review. | Pierce BL, Kraft P, Zhang C | Current epidemiology reports | 30034993 | Curr Epidemiol Rep | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30034993 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38490207 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26138067 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31603979 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27040689 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29151059 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39118140 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32433756 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39754638 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23793028 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26027500 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34346485 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33499903 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32964524 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25848752 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35922514 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27729424 |
| Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression. | McCoy RC, Wakefield J, Akey JM | Cell | 28235201 | Cell | 2017 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/28235201 |
| The origins, determinants, and consequences of human mutations. | Shendure J, Akey JM | Science (New York, N.Y.) | 26404824 | Science | 2015 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/26404824 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29022597 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27197222 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39829890 |
| Pathway-wide association study identifies five shared pathways associated with schizophrenia in three ancestral distinct populations. | Liu C, Bousman CA, Pantelis C, Skafidas E, Zhang D, Yue W, Everall IP | Translational psychiatry | 28221366 | Transl Psychiatry | 2017 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/28221366 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28611204 |
| Bayesian model comparison in genetic association analysis: linear mixed modeling and SNP set testing. | Wen X | Biostatistics (Oxford, England) | 25796429 | Biostatistics | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25796429 |
| A statistical framework for joint eQTL analysis in multiple tissues. | Flutre T, Wen X, Pritchard J, Stephens M | PLoS genetics | 23671422 | PLoS Genet | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23671422 |
| A Loss-of-Function Splice Acceptor Variant in IGF2 Is Protective for Type 2 Diabetes. | Mercader JM, Liao RG, Bell AD, Dymek Z, Estrada K, Tukiainen T, Huerta-Chagoya A, Moreno-Macías H, Jablonski KA, Hanson RL, Walford GA, Moran I, Chen L, Agarwala V, Ordoñez-Sánchez ML, Rodríguez-Guillen R, Rodríguez-Torres M, Segura-Kato Y, García-Ortiz H, Centeno-Cruz F, Barajas-Olmos F, Caulkins L, Puppala S, Fontanillas P, Williams AL, Bonàs-Guarch S, Hartl C, Ripke S, Diabetes Prevention Program Research Group, Tooley K, Lane J, Zerrweck C, Martínez-Hernández A, Córdova EJ, Mendoza-Caamal E, Contreras-Cubas C, González-Villalpando ME, Cruz-Bautista I, Muñoz-Hernández L, Gómez-Velasco D, Alvirde U, Henderson BE, Wilkens LR, Le Marchand L, Arellano-Campos O, Riba L, Harden M, Broad Genomics Platform, Gabriel S, T2D-GENES Consortium, Abboud HE, Cortes ML, Revilla-Monsalve C, Islas-Andrade S, Soberon X, Curran JE, Jenkinson CP, DeFronzo RA, Lehman DM, Hanis CL, Bell GI, Boehnke M, Blangero J, Duggirala R, Saxena R, MacArthur D, Ferrer J, McCarroll SA, Torrents D, Knowler WC, Baier LJ, Burtt N, González-Villalpando C, Haiman CA, Aguilar-Salinas CA, Tusié-Luna T, Flannick J, Jacobs SBR, Orozco L, Altshuler D, Florez JC, SIGMA T2D Genetics Consortium | Diabetes | 28838971 | Diabetes | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28838971 |
| Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication. | Long Q, Argmann C, Houten SM, Huang T, Peng S, Zhao Y, Tu Z, GTEx Consortium, Zhu J | Genome medicine | 26856537 | Genome Med | 2016 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/26856537 |
| Low baseline pulmonary levels of cytotoxic lymphocytes as a predisposing risk factor for severe COVID-19. | Duijf PHG | bioRxiv : the preprint server for biology | 32511391 | bioRxiv | 2020 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/32511391 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32635923 |
| Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. | Wen X, Lee Y, Luca F, Pique-Regi R | American journal of human genetics | 27236919 | Am J Hum Genet | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27236919 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36929942 |
| SPARCL1 Accelerates Symptom Onset in Alzheimer's Disease and Influences Brain Structure and Function During Aging. | Seddighi S, Varma VR, An Y, Varma S, Beason-Held LL, Tanaka T, Kitner-Triolo MH, Kraut MA, Davatzikos C, Thambisetty M | Journal of Alzheimer's disease : JAD | 29154276 | J Alzheimers Dis | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29154276 |
| Multiregion transcriptomic profiling of the primate brain reveals signatures of aging and the social environment. | Chiou KL, DeCasien AR, Rees KP, Testard C, Spurrell CH, Gogate AA, Pliner HA, Tremblay S, Mercer A, Whalen CJ, Negrón-Del Valle JE, Janiak MC, Bauman Surratt SE, González O, Compo NR, Stock MK, Ruiz-Lambides AV, Martínez MI, Cayo Biobank Research Unit, Wilson MA, Melin AD, Antón SC, Walker CS, Sallet J, Newbern JM, Starita LM, Shendure J, Higham JP, Brent LJN, Montague MJ, Platt ML, Snyder-Mackler N | Nature neuroscience | 36424430 | Nat Neurosci | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36424430 |
| 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 | 26728569 | Mol Psychiatry | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26728569 |
| Insertion of an SVA-E retrotransposon into the CASP8 gene is associated with protection against prostate cancer. | Stacey SN, Kehr B, Gudmundsson J, Zink F, Jonasdottir A, Gudjonsson SA, Sigurdsson A, Halldorsson BV, Agnarsson BA, Benediktsdottir KR, Aben KK, Vermeulen SH, Cremers RG, Panadero A, Helfand BT, Cooper PR, Donovan JL, Hamdy FC, Jinga V, Okamoto I, Jonasson JG, Tryggvadottir L, Johannsdottir H, Kristinsdottir AM, Masson G, Magnusson OT, Iordache PD, Helgason A, Helgason H, Sulem P, Gudbjartsson DF, Kong A, Jonsson E, Barkardottir RB, Einarsson GV, Rafnar T, Thorsteinsdottir U, Mates IN, Neal DE, Catalona WJ, Mayordomo JI, Kiemeney LA, Thorleifsson G, Stefansson K | Human molecular genetics | 26740556 | Hum Mol Genet | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26740556 |
| Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. | Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ | Frontiers in aging neuroscience | 27536236 | Front Aging Neurosci | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27536236 |
| A human-specific AS3MT isoform and BORCS7 are molecular risk factors in the 10q24.32 schizophrenia-associated locus. | Li M, Jaffe AE, Straub RE, Tao R, Shin JH, Wang Y, Chen Q, Li C, Jia Y, Ohi K, Maher BJ, Brandon NJ, Cross A, Chenoweth JG, Hoeppner DJ, Wei H, Hyde TM, McKay R, Kleinman JE, Weinberger DR | Nature medicine | 27158905 | Nat Med | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27158905 |
| Molecular insights into the OGG1 gene, a cancer risk modifier in BRCA1 and BRCA2 mutations carriers. | Benitez-Buelga C, Vaclová T, Ferreira S, Urioste M, Inglada-Perez L, Soberón N, Blasco MA, Osorio A, Benitez J | Oncotarget | 27015555 | Oncotarget | 2016 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/27015555 |
| Regulatory Variants Modulate Protein Kinase C α (PRKCA) Gene Expression in Human Heart. | Li L, Zhang L, Binkley PF, Sadee W, Wang D | Pharmaceutical research | 28120175 | Pharm Res | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28120175 |
| Genetic variation in the NEIL2 DNA glycosylase gene is associated with oxidative DNA damage in BRCA2 mutation carriers. | Benítez-Buelga C, Baquero JM, Vaclova T, Fernández V, Martín P, Inglada-Perez L, Urioste M, Osorio A, Benítez J | Oncotarget | 29383107 | Oncotarget | 2017 Dec 29 | https://www.ncbi.nlm.nih.gov/pubmed/29383107 |
| A genome-wide association study of LCH identifies a variant in SMAD6 associated with susceptibility. | Peckham-Gregory EC, Chakraborty R, Scheurer ME, Belmont JW, Abhyankar H, Sengal AG, Scull BP, Eckstein O, Zinn DJ, Mayer L, Shih A, Merad M, Parsons DW, McClain KL, Lupo PJ, Allen CE | Blood | 28935696 | Blood | 2017 Nov 16 | https://www.ncbi.nlm.nih.gov/pubmed/28935696 |
| Rare variant phasing and haplotypic expression from RNA sequencing with phASER. | Castel SE, Mohammadi P, Chung WK, Shen Y, Lappalainen T | Nature communications | 27605262 | Nat Commun | 2016 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/27605262 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27640124 |
| Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. | Jaffe AE, Straub RE, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-Soboslay A, BrainSeq Consortium, Cross AJ, Brandon NJ, Leek JT, Hyde TM, Kleinman JE, Weinberger DR | Nature neuroscience | 30050107 | Nat Neurosci | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30050107 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27126046 |
| Nuclear genetic regulation of the human mitochondrial transcriptome. | Ali AT, Boehme L, Carbajosa G, Seitan VC, Small KS, Hodgkinson A | eLife | 30775970 | Elife | 2019 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/30775970 |
| Low Baseline Pulmonary Levels of Cytotoxic Lymphocytes as a Predisposing Risk Factor for Severe COVID-19. | Duijf PHG | mSystems | 32873611 | mSystems | 2020 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/32873611 |
| An enhanced machine learning tool for cis-eQTL mapping with regularization and confounder adjustments. | Yan KK, Zhao H, Wu JT, Pang H | Genetic epidemiology | 32700329 | Genet Epidemiol | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32700329 |
| Herpesviruses and their genetic diversity in the blood virome of healthy individuals: effect of aging. | Autio A, Kettunen J, Nevalainen T, Kimura B, Hurme M | Immunity & ageing : I & A | 35279192 | Immun Ageing | 2022 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/35279192 |
| Germline rare deleterious variant load alters cancer risk, age of onset and tumor characteristics. | Esai Selvan M, Onel K, Gnjatic S, Klein RJ, Gümüş ZH | NPJ precision oncology | 36707626 | NPJ Precis Oncol | 2023 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/36707626 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37920490 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37884687 |
| Adipose tissue eQTL meta-analysis reveals the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits. | Brotman SM, El-Sayed Moustafa JS, Guan L, Broadaway KA, Wang D, Jackson AU, Welch R, Currin KW, Tomlinson M, Vadlamudi S, Stringham HM, Roberts AL, Lakka TA, Oravilahti A, Silva LF, Narisu N, Erdos MR, Yan T, Bonnycastle LL, Raulerson CK, Raza Y, Yan X, Parker SCJ, Kuusisto J, Pajukanta P, Tuomilehto J, Collins FS, Boehnke M, Love MI, Koistinen HA, Laakso M, Mohlke KL, Small KS, Scott LJ | bioRxiv : the preprint server for biology | 37961277 | bioRxiv | 2023 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/37961277 |
| Transferability of Single- and Cross-Tissue Transcriptome Imputation Models Across Ancestry Groups. | Pagnuco I, Eyre S, Rattray M, Morris AP | Genetic epidemiology | 39812501 | Genet Epidemiol | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39812501 |
| Cross-population joint analysis of eQTLs: fine mapping and functional annotation. | Wen X, Luca F, Pique-Regi R | PLoS genetics | 25906321 | PLoS Genet | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25906321 |
| New basal cell carcinoma susceptibility loci. | Stacey SN, Helgason H, Gudjonsson SA, Thorleifsson G, Zink F, Sigurdsson A, Kehr B, Gudmundsson J, Sulem P, Sigurgeirsson B, Benediktsdottir KR, Thorisdottir K, Ragnarsson R, Fuentelsaz V, Corredera C, Gilaberte Y, Grasa M, Planelles D, Sanmartin O, Rudnai P, Gurzau E, Koppova K, Nexø BA, Tjønneland A, Overvad K, Jonasson JG, Tryggvadottir L, Johannsdottir H, Kristinsdottir AM, Stefansson H, Masson G, Magnusson OT, Halldorsson BV, Kong A, Rafnar T, Thorsteinsdottir U, Vogel U, Kumar R, Nagore E, Mayordomo JI, Gudbjartsson DF, Olafsson JH, Stefansson K | Nature communications | 25855136 | Nat Commun | 2015 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/25855136 |
| WASP: allele-specific software for robust molecular quantitative trait locus discovery. | van de Geijn B, McVicker G, Gilad Y, Pritchard JK | Nature methods | 26366987 | Nat Methods | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26366987 |
| False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors. | Saha A, Battle A | F1000Research | 30613398 | F1000Res | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30613398 |
| Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder. | Hou L, Bergen SE, Akula N, Song J, Hultman CM, Landén M, Adli M, Alda M, Ardau R, Arias B, Aubry JM, Backlund L, Badner JA, Barrett TB, Bauer M, Baune BT, Bellivier F, Benabarre A, Bengesser S, Berrettini WH, Bhattacharjee AK, Biernacka JM, Birner A, Bloss CS, Brichant-Petitjean C, Bui ET, Byerley W, Cervantes P, Chillotti C, Cichon S, Colom F, Coryell W, Craig DW, Cruceanu C, Czerski PM, Davis T, Dayer A, Degenhardt F, Del Zompo M, DePaulo JR, Edenberg HJ, Étain B, Falkai P, Foroud T, Forstner AJ, Frisén L, Frye MA, Fullerton JM, Gard S, Garnham JS, Gershon ES, Goes FS, Greenwood TA, Grigoroiu-Serbanescu M, Hauser J, Heilbronner U, Heilmann-Heimbach S, Herms S, Hipolito M, Hitturlingappa S, Hoffmann P, Hofmann A, Jamain S, Jiménez E, Kahn JP, Kassem L, Kelsoe JR, Kittel-Schneider S, Kliwicki S, Koller DL, König B, Lackner N, Laje G, Lang M, Lavebratt C, Lawson WB, Leboyer M, Leckband SG, Liu C, Maaser A, Mahon PB, Maier W, Maj M, Manchia M, Martinsson L, McCarthy MJ, McElroy SL, McInnis MG, McKinney R, Mitchell PB, Mitjans M, Mondimore FM, Monteleone P, Mühleisen TW, Nievergelt CM, Nöthen MM, Novák T, Nurnberger JI Jr, Nwulia EA, Ösby U, Pfennig A, Potash JB, Propping P, Reif A, Reininghaus E, Rice J, Rietschel M, Rouleau GA, Rybakowski JK, Schalling M, Scheftner WA, Schofield PR, Schork NJ, Schulze TG, Schumacher J, Schweizer BW, Severino G, Shekhtman T, Shilling PD, Simhandl C, Slaney CM, Smith EN, Squassina A, Stamm T, Stopkova P, Streit F, Strohmaier J, Szelinger S, Tighe SK, Tortorella A, Turecki G, Vieta E, Volkert J, Witt SH, Wright A, Zandi PP, Zhang P, Zollner S, McMahon FJ | Human molecular genetics | 27329760 | Hum Mol Genet | 2016 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/27329760 |
| Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. | Lan X, Pritchard JK | Science (New York, N.Y.) | 27199432 | Science | 2016 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/27199432 |
| Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve. | Yang B, Zhou W, Jiao J, Nielsen JB, Mathis MR, Heydarpour M, Lettre G, Folkersen L, Prakash S, Schurmann C, Fritsche L, Farnum GA, Lin M, Othman M, Hornsby W, Driscoll A, Levasseur A, Thomas M, Farhat L, Dubé MP, Isselbacher EM, Franco-Cereceda A, Guo DC, Bottinger EP, Deeb GM, Booher A, Kheterpal S, Chen YE, Kang HM, Kitzman J, Cordell HJ, Keavney BD, Goodship JA, Ganesh SK, Abecasis G, Eagle KA, Boyle AP, Loos RJF, Eriksson P, Tardif JC, Brummett CM, Milewicz DM, Body SC, Willer CJ | Nature communications | 28541271 | Nat Commun | 2017 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/28541271 |
| A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk. | Manning A, Highland HM, Gasser J, Sim X, Tukiainen T, Fontanillas P, Grarup N, Rivas MA, Mahajan A, Locke AE, Cingolani P, Pers TH, Viñuela A, Brown AA, Wu Y, Flannick J, Fuchsberger C, Gamazon ER, Gaulton KJ, Im HK, Teslovich TM, Blackwell TW, Bork-Jensen J, Burtt NP, Chen Y, Green T, Hartl C, Kang HM, Kumar A, Ladenvall C, Ma C, Moutsianas L, Pearson RD, Perry JRB, Rayner NW, Robertson NR, Scott LJ, van de Bunt M, Eriksson JG, Jula A, Koskinen S, Lehtimäki T, Palotie A, Raitakari OT, Jacobs SBR, Wessel J, Chu AY, Scott RA, Goodarzi MO, Blancher C, Buck G, Buck D, Chines PS, Gabriel S, Gjesing AP, Groves CJ, Hollensted M, Huyghe JR, Jackson AU, Jun G, Justesen JM, Mangino M, Murphy J, Neville M, Onofrio R, Small KS, Stringham HM, Trakalo J, Banks E, Carey J, Carneiro MO, DePristo M, Farjoun Y, Fennell T, Goldstein JI, Grant G, Hrabé de Angelis M, Maguire J, Neale BM, Poplin R, Purcell S, Schwarzmayr T, Shakir K, Smith JD, Strom TM, Wieland T, Lindstrom J, Brandslund I, Christensen C, Surdulescu GL, Lakka TA, Doney ASF, Nilsson P, Wareham NJ, Langenberg C, Varga TV, Franks PW, Rolandsson O, Rosengren AH, Farook VS, Thameem F, Puppala S, Kumar S, Lehman DM, Jenkinson CP, Curran JE, Hale DE, Fowler SP, Arya R, DeFronzo RA, Abboud HE, Syvänen AC, Hicks PJ, Palmer ND, Ng MCY, Bowden DW, Freedman BI, Esko T, Mägi R, Milani L, Mihailov E, Metspalu A, Narisu N, Kinnunen L, Bonnycastle LL, Swift A, Pasko D, Wood AR, Fadista J, Pollin TI, Barzilai N, Atzmon G, Glaser B, Thorand B, Strauch K, Peters A, Roden M, Müller-Nurasyid M, Liang L, Kriebel J, Illig T, Grallert H, Gieger C, Meisinger C, Lannfelt L, Musani SK, Griswold M, Taylor HA Jr, Wilson G Sr, Correa A, Oksa H, Scott WR, Afzal U, Tan ST, Loh M, Chambers JC, Sehmi J, Kooner JS, Lehne B, Cho YS, Lee JY, Han BG, Käräjämäki A, Qi Q, Qi L, Huang J, Hu FB, Melander O, Orho-Melander M, Below JE, Aguilar D, Wong TY, Liu J, Khor CC, Chia KS, Lim WY, Cheng CY, Chan E, Tai ES, Aung T, Linneberg A, Isomaa B, Meitinger T, Tuomi T, Hakaste L, Kravic J, Jørgensen ME, Lauritzen T, Deloukas P, Stirrups KE, Owen KR, Farmer AJ, Frayling TM, O'Rahilly SP, Walker M, Levy JC, Hodgkiss D, Hattersley AT, Kuulasmaa T, Stančáková A, Barroso I, Bharadwaj D, Chan J, Chandak GR, Daly MJ, Donnelly PJ, Ebrahim SB, Elliott P, Fingerlin T, Froguel P, Hu C, Jia W, Ma RCW, McVean G, Park T, Prabhakaran D, Sandhu M, Scott J, Sladek R, Tandon N, Teo YY, Zeggini E, Watanabe RM, Koistinen HA, Kesaniemi YA, Uusitupa M, Spector TD, Salomaa V, Rauramaa R, Palmer CNA, Prokopenko I, Morris AD, Bergman RN, Collins FS, Lind L, Ingelsson E, Tuomilehto J, Karpe F, Groop L, Jørgensen T, Hansen T, Pedersen O, Kuusisto J, Abecasis G, Bell GI, Blangero J, Cox NJ, Duggirala R, Seielstad M, Wilson JG, Dupuis J, Ripatti S, Hanis CL, Florez JC, Mohlke KL, Meigs JB, Laakso M, Morris AP, Boehnke M, Altshuler D, McCarthy MI, Gloyn AL, Lindgren CM | Diabetes | 28341696 | Diabetes | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28341696 |
| The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites. | She J, Du M, Xu Z, Jin Y, Li Y, Zhang D, Tao C, Chen J, Wang J, Yang E | Genome biology | 36329469 | Genome Biol | 2022 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/36329469 |
| Retrotransposon insertions associated with risk of neurologic and psychiatric diseases. | Ahn HW, Worman ZF, Lechsinska A, Payer LM, Wang T, Malik N, Li W, Burns KH, Nath A, Levin HL | EMBO reports | 36367221 | EMBO Rep | 2023 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/36367221 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35274098 |
| Pleiotropic Locus 15q24.1 Reveals a Gender-Specific Association with Neovascular but Not Atrophic Age-Related Macular Degeneration (AMD). | Kiel C, Strunz T, International Amd Genomics Consortium Project Manager Susan Blanton Iamdgc, Grassmann F, Weber BHF | Cells | 33050031 | Cells | 2020 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/33050031 |
| Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data. | Deutelmoser H, Scherer D, Brenner H, Waldenberger M, INTERVAL study, Suhre K, Kastenmüller G, Lorenzo Bermejo J | Briefings in bioinformatics | 33063116 | Brief Bioinform | 2021 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/33063116 |
| Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease. | Fairbrother-Browne A, Ali AT, Reynolds RH, Garcia-Ruiz S, Zhang D, Chen Z, Ryten M, Hodgkinson A | Communications biology | 34737414 | Commun Biol | 2021 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/34737414 |
| Mapping the miRNA-mRNA Interactome in Human Hepatocytes and Identification of Functional mirSNPs in Pharmacogenes. | Powell NR, Zhao H, Ipe J, Liu Y, Skaar TC | Clinical pharmacology and therapeutics | 34314509 | Clin Pharmacol Ther | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34314509 |
| Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues. | Wheeler HE, Shah KP, Brenner J, Garcia T, Aquino-Michaels K, GTEx Consortium, Cox NJ, Nicolae DL, Im HK | PLoS genetics | 27835642 | PLoS Genet | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27835642 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27738015 |
| Integrating GWAS and Co-expression Network Data Identifies Bone Mineral Density Genes SPTBN1 and MARK3 and an Osteoblast Functional Module. | Calabrese GM, Mesner LD, Stains JP, Tommasini SM, Horowitz MC, Rosen CJ, Farber CR | Cell systems | 27866947 | Cell Syst | 2017 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/27866947 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28112683 |
| Novel Common Genetic Susceptibility Loci for Colorectal Cancer. | Schmit SL, Edlund CK, Schumacher FR, Gong J, Harrison TA, Huyghe JR, Qu C, Melas M, Van Den Berg DJ, Wang H, Tring S, Plummer SJ, Albanes D, Alonso MH, Amos CI, Anton K, Aragaki AK, Arndt V, Barry EL, Berndt SI, Bezieau S, Bien S, Bloomer A, Boehm J, Boutron-Ruault MC, Brenner H, Brezina S, Buchanan DD, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castelao JE, Chan AT, Chang-Claude J, Chanock SJ, Cheng I, Cheng YW, Chin LS, Church JM, Church T, Coetzee GA, Cotterchio M, Cruz Correa M, Curtis KR, Duggan D, Easton DF, English D, Feskens EJM, Fischer R, FitzGerald LM, Fortini BK, Fritsche LG, Fuchs CS, Gago-Dominguez M, Gala M, Gallinger SJ, Gauderman WJ, Giles GG, Giovannucci EL, Gogarten SM, Gonzalez-Villalpando C, Gonzalez-Villalpando EM, Grady WM, Greenson JK, Gsur A, Gunter M, Haiman CA, Hampe J, Harlid S, Harju JF, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Huang SC, Huerta JM, Hudson TJ, Hunter DJ, Idos GE, Iwasaki M, Jackson RD, Jacobs EJ, Jee SH, Jenkins MA, Jia WH, Jiao S, Joshi AD, Kolonel LN, Kono S, Kooperberg C, Krogh V, Kuehn T, Küry S, LaCroix A, Laurie CA, Lejbkowicz F, Lemire M, Lenz HJ, Levine D, Li CI, Li L, Lieb W, Lin Y, Lindor NM, Liu YR, Loupakis F, Lu Y, Luh F, Ma J, Mancao C, Manion FJ, Markowitz SD, Martin V, Matsuda K, Matsuo K, McDonnell KJ, McNeil CE, Milne R, Molina AJ, Mukherjee B, Murphy N, Newcomb PA, Offit K, Omichessan H, Palli D, Cotoré JPP, Pérez-Mayoral J, Pharoah PD, Potter JD, Qu C, Raskin L, Rennert G, Rennert HS, Riggs BM, Schafmayer C, Schoen RE, Sellers TA, Seminara D, Severi G, Shi W, Shibata D, Shu XO, Siegel EM, Slattery ML, Southey M, Stadler ZK, Stern MC, Stintzing S, Taverna D, Thibodeau SN, Thomas DC, Trichopoulou A, Tsugane S, Ulrich CM, van Duijnhoven FJB, van Guelpan B, Vijai J, Virtamo J, Weinstein SJ, White E, Win AK, Wolk A, Woods M, Wu AH, Wu K, Xiang YB, Yen Y, Zanke BW, Zeng YX, Zhang B, Zubair N, Kweon SS, Figueiredo JC, Zheng W, Marchand LL, Lindblom A, Moreno V, Peters U, Casey G, Hsu L, Conti DV, Gruber SB | Journal of the National Cancer Institute | 29917119 | J Natl Cancer Inst | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/29917119 |
| Impact of regulatory variation across human iPSCs and differentiated cells. | Banovich NE, Li YI, Raj A, Ward MC, Greenside P, Calderon D, Tung PY, Burnett JE, Myrthil M, Thomas SM, Burrows CK, Romero IG, Pavlovic BJ, Kundaje A, Pritchard JK, Gilad Y | Genome research | 29208628 | Genome Res | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29208628 |
| Identification of human mitochondrial RNA cleavage sites and candidate RNA processing factors. | Carbajosa G, Ali AT, Hodgkinson A | BMC biology | 35869520 | BMC Biol | 2022 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/35869520 |
| Comparison of confound adjustment methods in the construction of gene co-expression networks. | Cote AC, Young HE, Huckins LM | Genome biology | 35115012 | Genome Biol | 2022 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/35115012 |
| PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs. | Vochteloo M, Deelen P, Vink B, BIOS Consortium, Tsai EA, Runz H, Andreu-Sánchez S, Fu J, Zhernakova A, Westra HJ, Franke L | Genome biology | 38254182 | Genome Biol | 2024 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/38254182 |
| IL1RL1 asthma risk variants regulate airway type 2 inflammation. | Gordon ED, Palandra J, Wesolowska-Andersen A, Ringel L, Rios CL, Lachowicz-Scroggins ME, Sharp LZ, Everman JL, MacLeod HJ, Lee JW, Mason RJ, Matthay MA, Sheldon RT, Peters MC, Nocka KH, Fahy JV, Seibold MA | JCI insight | 27699235 | JCI Insight | 2016 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/27699235 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28195142 |
| Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. | Urbut SM, Wang G, Carbonetto P, Stephens M | Nature genetics | 30478440 | Nat Genet | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30478440 |
| Feasibility of predicting allele specific expression from DNA sequencing using machine learning. | Zhang Z, van Dijk F, de Klein N, van Gijn ME, Franke LH, Sinke RJ, Swertz MA, van der Velde KJ | Scientific reports | 34012022 | Sci Rep | 2021 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/34012022 |
| Bipolar disorder with binge eating behavior: a genome-wide association study implicates PRR5-ARHGAP8. | McElroy SL, Winham SJ, Cuellar-Barboza AB, Colby CL, Ho AM, Sicotte H, Larrabee BR, Crow S, Frye MA, Biernacka JM | Translational psychiatry | 29391396 | Transl Psychiatry | 2018 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/29391396 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27315375 |
| Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. | Mohammadi P, Castel SE, Brown AA, Lappalainen T | Genome research | 29021289 | Genome Res | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/29021289 |
| Genome-wide association study identifies a novel locus for cannabis dependence. | Agrawal A, Chou YL, Carey CE, Baranger DAA, Zhang B, Sherva R, Wetherill L, Kapoor M, Wang JC, Bertelsen S, Anokhin AP, Hesselbrock V, Kramer J, Lynskey MT, Meyers JL, Nurnberger JI, Rice JP, Tischfield J, Bierut LJ, Degenhardt L, Farrer LA, Gelernter J, Hariri AR, Heath AC, Kranzler HR, Madden PAF, Martin NG, Montgomery GW, Porjesz B, Wang T, Whitfield JB, Edenberg HJ, Foroud T, Goate AM, Bogdan R, Nelson EC | Molecular psychiatry | 29112194 | Mol Psychiatry | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29112194 |
| Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues. | Zhang M, Lykke-Andersen S, Zhu B, Xiao W, Hoskins JW, Zhang X, Rost LM, Collins I, Bunt MV, Jia J, Parikh H, Zhang T, Song L, Jermusyk A, Chung CC, Zhu B, Zhou W, Matters GL, Kurtz RC, Yeager M, Jensen TH, Brown KM, Ongen H, Bamlet WR, Murray BA, McCarthy MI, Chanock SJ, Chatterjee N, Wolpin BM, Smith JP, Olson SH, Petersen GM, Shi J, Amundadottir L | Gut | 28634199 | Gut | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28634199 |
| The impact of structural variation on human gene expression. | Chiang C, Scott AJ, Davis JR, Tsang EK, Li X, Kim Y, Hadzic T, Damani FN, Ganel L, GTEx Consortium, Montgomery SB, Battle A, Conrad DF, Hall IM | Nature genetics | 28369037 | Nat Genet | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28369037 |
| Multi-tissue transcriptome analyses identify genetic mechanisms underlying neuropsychiatric traits. | Gamazon ER, Zwinderman AH, Cox NJ, Denys D, Derks EM | Nature genetics | 31086352 | Nat Genet | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31086352 |
| Genome-wide association study identifies novel single nucleotide polymorphisms having age-specific effect on prostate-specific antigen levels. | Li W, Bicak M, Sjoberg DD, Vertosick E, Dahlin A, Melander O, Ulmert D, Lilja H, Klein RJ | The Prostate | 32914890 | Prostate | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32914890 |
| Alpha-2 macroglobulin in Alzheimer's disease: a marker of neuronal injury through the RCAN1 pathway. | Varma VR, Varma S, An Y, Hohman TJ, Seddighi S, Casanova R, Beri A, Dammer EB, Seyfried NT, Pletnikova O, Moghekar A, Wilson MR, Lah JJ, O'Brien RJ, Levey AI, Troncoso JC, Albert MS, Thambisetty M | Molecular psychiatry | 27872486 | Mol Psychiatry | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27872486 |
| Reproducible RNA-seq analysis using recount2. | Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT | Nature biotechnology | 28398307 | Nat Biotechnol | 2017 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/28398307 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35082309 |
| A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank. | Manigbas CA, Jadhav B, Garg P, Shadrina M, Lee W, Altman G, Martin-Trujillo A, Sharp AJ | Nature communications | 39627187 | Nat Commun | 2024 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/39627187 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28388432 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32641134 |
| Loss of Function of GALNT2 Lowers High-Density Lipoproteins in Humans, Nonhuman Primates, and Rodents. | Khetarpal SA, Schjoldager KT, Christoffersen C, Raghavan A, Edmondson AC, Reutter HM, Ahmed B, Ouazzani R, Peloso GM, Vitali C, Zhao W, Somasundara AV, Millar JS, Park Y, Fernando G, Livanov V, Choi S, Noé E, Patel P, Ho SP, Myocardial Infarction Exome Sequencing Study, Kirchgessner TG, Wandall HH, Hansen L, Bennett EP, Vakhrushev SY, Saleheen D, Kathiresan S, Brown CD, Abou Jamra R, LeGuern E, Clausen H, Rader DJ | Cell metabolism | 27508872 | Cell Metab | 2016 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/27508872 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33864768 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27467526 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29056226 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27956632 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30097539 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28855262 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25648650 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27864351 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29982387 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27618447 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26071445 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28135054 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25439722 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25307299 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30668570 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24711425 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27548312 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28185111 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28651527 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24493630 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25818895 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25221879 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26496228 |
| Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results. | Khramtsova EA, Stranger BE | Bioinformatics (Oxford, England) | 28172529 | Bioinformatics | 2017 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/28172529 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28530654 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26868379 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29296818 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31104770 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24799323 |
| GWAS to Sequencing: Divergence in Study Design and Analysis. | King CR, Nicolae DL | Genes | 24879455 | Genes (Basel) | 2014 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/24879455 |
| The impact of human copy number variation on gene expression. | Gamazon ER, Stranger BE | Briefings in functional genomics | 25922366 | Brief Funct Genomics | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25922366 |
| A gene-based association method for mapping traits using reference transcriptome data. | Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC, GTEx Consortium, Nicolae DL, Cox NJ, Im HK | Nature genetics | 26258848 | Nat Genet | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26258848 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32492425 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29739930 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26888256 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24204291 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35615339 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28039263 |
| Opportunities and challenges for transcriptome-wide association studies. | Wainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira AN, Knowles DA, Golan D, Ermel R, Ruusalepp A, Quertermous T, Hao K, Björkegren JLM, Im HK, Pasaniuc B, Rivas MA, Kundaje A | Nature genetics | 30926968 | Nat Genet | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30926968 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30281024 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27398621 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23824859 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24646999 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24185610 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27743375 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29335598 |
| Fine-mapping additive and dominant SNP effects using group-LASSO and fractional resample model averaging. | Sabourin J, Nobel AB, Valdar W | Genetic epidemiology | 25417853 | Genet Epidemiol | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25417853 |
| A TESTING BASED APPROACH TO THE DISCOVERY OF DIFFERENTIALLY CORRELATED VARIABLE SETS. | Bodwin BK, Zhang K, Nobel A | The annals of applied statistics | 31871518 | Ann Appl Stat | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31871518 |
| Significance-based community detection in weighted networks. | Palowitch J, Bhamidi S, Nobel AB | Journal of machine learning research : JMLR | 30853860 | J Mach Learn Res | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30853860 |
| Convergence of Sample Eigenvalues, Eigenvectors, and Principal Component Scores for Ultra-High Dimensional Data. | Lee S, Zou F, Wright FA | Biometrika | 25143634 | Biometrika | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25143634 |
| IsoDOT Detects Differential RNA-isoform Expression/Usage with respect to a Categorical or Continuous Covariate with High Sensitivity and Specificity. | Sun W, Liu Y, Crowley JJ, Chen TH, Zhou H, Chu H, Huang S, Kuan PF, Li Y, Miller DR, Shaw GD, Wu Y, Zhabotynsky V, McMillan L, Zou F, Sullivan PF, de Villena FP | Journal of the American Statistical Association | 26617424 | J Am Stat Assoc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26617424 |
| HT-eQTL: integrative expression quantitative trait loci analysis in a large number of human tissues. | Li G, Jima D, Wright FA, Nobel AB | BMC bioinformatics | 29523079 | BMC Bioinformatics | 2018 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/29523079 |
| Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation. | Ha MJ, Sun W | Biometrics | 24845967 | Biometrics | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24845967 |
| Space Time Clustering and the Permutation Moments of Quadratic Form. | Zhou YH, Mayhew G, Sun Z, Xu X, Zou F, Wright FA | Stat | 25210205 | Stat | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/25210205 |
| Estimation of cis-eQTL effect sizes using a log of linear model. | Palowitch J, Shabalin A, Zhou YH, Nobel AB, Wright FA | Biometrics | 29073327 | Biometrics | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29073327 |
| Community Extraction in Multilayer Networks with Heterogeneous Community Structure. | Wilson JD, Palowitch J, Bhamidi S, Nobel AB | Journal of machine learning research : JMLR | 31871433 | J Mach Learn Res | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/31871433 |
| A permutation approach for selecting the penalty parameter in penalized model selection. | Sabourin JA, Valdar W, Nobel AB | Biometrics | 26243050 | Biometrics | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26243050 |
| The projack: a resampling approach to correct for ranking bias in high-throughput studies. | Zhou YH, Wright FA | Biostatistics (Oxford, England) | 26040912 | Biostatistics | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26040912 |
| Human genomics. The human transcriptome across tissues and individuals. | Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ, Johnson R, Segrè AV, Djebali S, Niarchou A, GTEx Consortium, Wright FA, Lappalainen T, Calvo M, Getz G, Dermitzakis ET, Ardlie KG, Guigó R | Science (New York, N.Y.) | 25954002 | Science | 2015 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/25954002 |
| Hypothesis testing at the extremes: fast and robust association for high-throughput data. | Zhou YH, Wright FA | Biostatistics (Oxford, England) | 25792622 | Biostatistics | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25792622 |
| Heritability and genomics of gene expression in peripheral blood. | Wright FA, Sullivan PF, Brooks AI, Zou F, Sun W, Xia K, Madar V, Jansen R, Chung W, Zhou YH, Abdellaoui A, Batista S, Butler C, Chen G, Chen TH, D'Ambrosio D, Gallins P, Ha MJ, Hottenga JJ, Huang S, Kattenberg M, Kochar J, Middeldorp CM, Qu A, Shabalin A, Tischfield J, Todd L, Tzeng JY, van Grootheest G, Vink JM, Wang Q, Wang W, Wang W, Willemsen G, Smit JH, de Geus EJ, Yin Z, Penninx BW, Boomsma DI | Nature genetics | 24728292 | Nat Genet | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24728292 |
| Eigenvalue significance testing for genetic association. | Zhou YH, Marron JS, Wright FA | Biometrics | 28853138 | Biometrics | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28853138 |
| The Genotype-Tissue Expression (GTEx) project. | GTEx Consortium | Nature genetics | 23715323 | Nat Genet | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23715323 |
| DCAF1 regulates Treg senescence via the ROS axis during immunological aging. | Guo Z, Wang G, Wu B, Chou WC, Cheng L, Zhou C, Lou J, Wu D, Su L, Zheng J, Ting JP, Wan YY | The Journal of clinical investigation | 32730228 | J Clin Invest | 2020 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/32730228 |
| Gene expression in transformed lymphocytes reveals variation in endomembrane and HLA pathways modifying cystic fibrosis pulmonary phenotypes. | O'Neal WK, Gallins P, Pace RG, Dang H, Wolf WE, Jones LC, Guo X, Zhou YH, Madar V, Huang J, Liang L, Moffatt MF, Cutting GR, Drumm ML, Rommens JM, Strug LJ, Sun W, Stonebraker JR, Wright FA, Knowles MR | American journal of human genetics | 25640674 | Am J Hum Genet | 2015 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/25640674 |
| Genomic Characterization of Metformin Hepatic Response. | Luizon MR, Eckalbar WL, Wang Y, Jones SL, Smith RP, Laurance M, Lin L, Gallins PJ, Etheridge AS, Wright F, Zhou Y, Molony C, Innocenti F, Yee SW, Giacomini KM, Ahituv N | PLoS genetics | 27902686 | PLoS Genet | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27902686 |
| PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4. | Salsman J, Stathakis A, Parker E, Chung D, Anthes LE, Koskowich KL, Lahsaee S, Gaston D, Kukurba KR, Smith KS, Chute IC, Léger D, Frost LD, Montgomery SB, Lewis SM, Eskiw C, Dellaire G | Scientific reports | 28332630 | Sci Rep | 2017 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/28332630 |
| Towards a complete map of the human long non-coding RNA transcriptome. | Uszczynska-Ratajczak B, Lagarde J, Frankish A, Guigó R, Johnson R | Nature reviews. Genetics | 29795125 | Nat Rev Genet | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29795125 |
| Determining causality and consequence of expression quantitative trait loci. | Battle A, Montgomery SB | Human genetics | 24770875 | Hum Genet | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24770875 |
| Impact of the X Chromosome and sex on regulatory variation. | Kukurba KR, Parsana P, Balliu B, Smith KS, Zappala Z, Knowles DA, Favé MJ, Davis JR, Li X, Zhu X, Potash JB, Weissman MM, Shi J, Kundaje A, Levinson DF, Awadalla P, Mostafavi S, Battle A, Montgomery SB | Genome research | 27197214 | Genome Res | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27197214 |
| Tools and best practices for data processing in allelic expression analysis. | Castel SE, Levy-Moonshine A, Mohammadi P, Banks E, Lappalainen T | Genome biology | 26381377 | Genome Biol | 2015 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/26381377 |
| DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs. | Aparicio-Prat E, Arnan C, Sala I, Bosch N, Guigó R, Johnson R | BMC genomics | 26493208 | BMC Genomics | 2015 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/26493208 |
| Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. | Viñuela A, Varshney A, van de Bunt M, Prasad RB, Asplund O, Bennett A, Boehnke M, Brown AA, Erdos MR, Fadista J, Hansson O, Hatem G, Howald C, Iyengar AK, Johnson P, Krus U, MacDonald PE, Mahajan A, Manning Fox JE, Narisu N, Nylander V, Orchard P, Oskolkov N, Panousis NI, Payne A, Stitzel ML, Vadlamudi S, Welch R, Collins FS, Mohlke KL, Gloyn AL, Scott LJ, Dermitzakis ET, Groop L, Parker SCJ, McCarthy MI | Nature communications | 32999275 | Nat Commun | 2020 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/32999275 |
| Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. | Garrido-Martín D, Borsari B, Calvo M, Reverter F, Guigó R | Nature communications | 33526779 | Nat Commun | 2021 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/33526779 |
| Day-night and seasonal variation of human gene expression across tissues. | Wucher V, Sodaei R, Amador R, Irimia M, Guigó R | bioRxiv : the preprint server for biology | 33688644 | bioRxiv | 2022 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/33688644 |
| Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. | McAllister K, Mechanic LE, Amos C, Aschard H, Blair IA, Chatterjee N, Conti D, Gauderman WJ, Hsu L, Hutter CM, Jankowska MM, Kerr J, Kraft P, Montgomery SB, Mukherjee B, Papanicolaou GJ, Patel CJ, Ritchie MD, Ritz BR, Thomas DC, Wei P, Witte JS | American journal of epidemiology | 28978193 | Am J Epidemiol | 2017 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/28978193 |
| Identification of genetic variants associated with alternative splicing using sQTLseekeR. | Monlong J, Calvo M, Ferreira PG, Guigó R | Nature communications | 25140736 | Nat Commun | 2014 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/25140736 |
| veqtl-mapper: variance association mapping for molecular phenotypes. | Brown AA | Bioinformatics (Oxford, England) | 28449110 | Bioinformatics | 2017 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/28449110 |
| Abundant associations with gene expression complicate GWAS follow-up. | Liu B, Gloudemans MJ, Rao AS, Ingelsson E, Montgomery SB | Nature genetics | 31043754 | Nat Genet | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31043754 |
| Functional genomics bridges the gap between quantitative genetics and molecular biology. | Lappalainen T | Genome research | 26430152 | Genome Res | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26430152 |
| Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data. | Fernández-Tajes J, Gaulton KJ, van de Bunt M, Torres J, Thurner M, Mahajan A, Gloyn AL, Lage K, McCarthy MI | Genome medicine | 30914061 | Genome Med | 2019 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/30914061 |
| Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms. | Liu B, Calton MA, Abell NS, Benchorin G, Gloudemans MJ, Chen M, Hu J, Li X, Balliu B, Bok D, Montgomery SB, Vollrath D | Communications biology | 31123710 | Commun Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31123710 |
| The effects of death and post-mortem cold ischemia on human tissue transcriptomes. | Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R | Nature communications | 29440659 | Nat Commun | 2018 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/29440659 |
| A limited set of transcriptional programs define major cell types. | Breschi A, Muñoz-Aguirre M, Wucher V, Davis CA, Garrido-Martín D, Djebali S, Gillis J, Pervouchine DD, Vlasova A, Dobin A, Zaleski C, Drenkow J, Danyko C, Scavelli A, Reverter F, Snyder MP, Gingeras TR, Guigó R | Genome research | 32759341 | Genome Res | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32759341 |
| A vast resource of allelic expression data spanning human tissues. | Castel SE, Aguet F, Mohammadi P, GTEx Consortium, Ardlie KG, Lappalainen T | Genome biology | 32912332 | Genome Biol | 2020 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/32912332 |
| Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability. | Lagou V, Mägi R, Hottenga JJ, Grallert H, Perry JRB, Bouatia-Naji N, Marullo L, Rybin D, Jansen R, Min JL, Dimas AS, Ulrich A, Zudina L, Gådin JR, Jiang L, Faggian A, Bonnefond A, Fadista J, Stathopoulou MG, Isaacs A, Willems SM, Navarro P, Tanaka T, Jackson AU, Montasser ME, O'Connell JR, Bielak LF, Webster RJ, Saxena R, Stafford JM, Pourcain BS, Timpson NJ, Salo P, Shin SY, Amin N, Smith AV, Li G, Verweij N, Goel A, Ford I, Johnson PCD, Johnson T, Kapur K, Thorleifsson G, Strawbridge RJ, Rasmussen-Torvik LJ, Esko T, Mihailov E, Fall T, Fraser RM, Mahajan A, Kanoni S, Giedraitis V, Kleber ME, Silbernagel G, Meyer J, Müller-Nurasyid M, Ganna A, Sarin AP, Yengo L, Shungin D, Luan J, Horikoshi M, An P, Sanna S, Boettcher Y, Rayner NW, Nolte IM, Zemunik T, Iperen EV, Kovacs P, Hastie ND, Wild SH, McLachlan S, Campbell S, Polasek O, Carlson O, Egan J, Kiess W, Willemsen G, Kuusisto J, Laakso M, Dimitriou M, Hicks AA, Rauramaa R, Bandinelli S, Thorand B, Liu Y, Miljkovic I, Lind L, Doney A, Perola M, Hingorani A, Kivimaki M, Kumari M, Bennett AJ, Groves CJ, Herder C, Koistinen HA, Kinnunen L, Faire U, Bakker SJL, Uusitupa M, Palmer CNA, Jukema JW, Sattar N, Pouta A, Snieder H, Boerwinkle E, Pankow JS, Magnusson PK, Krus U, Scapoli C, de Geus EJCN, Blüher M, Wolffenbuttel BHR, Province MA, Abecasis GR, Meigs JB, Hovingh GK, Lindström J, Wilson JF, Wright AF, Dedoussis GV, Bornstein SR, Schwarz PEH, Tönjes A, Winkelmann BR, Boehm BO, März W, Metspalu A, Price JF, Deloukas P, Körner A, Lakka TA, Keinanen-Kiukaanniemi SM, Saaristo TE, Bergman RN, Tuomilehto J, Wareham NJ, Langenberg C, Männistö S, Franks PW, Hayward C, Vitart V, Kaprio J, Visvikis-Siest S, Balkau B, Altshuler D, Rudan I, Stumvoll M, Campbell H, van Duijn CM, Gieger C, Illig T, Ferrucci L, Pedersen NL, Pramstaller PP, Boehnke M, Frayling TM, Shuldiner AR, Peyser PA, Kardia SLR, Palmer LJ, Penninx BW, Meneton P, Harris TB, Navis G, Harst PV, Smith GD, Forouhi NG, Loos RJF, Salomaa V, Soranzo N, Boomsma DI, Groop L, Tuomi T, Hofman A, Munroe PB, Gudnason V, Siscovick DS, Watkins H, Lecoeur C, Vollenweider P, Franco-Cereceda A, Eriksson P, Jarvelin MR, Stefansson K, Hamsten A, Nicholson G, Karpe F, Dermitzakis ET, Lindgren CM, McCarthy MI, Froguel P, Kaakinen MA, Lyssenko V, Watanabe RM, Ingelsson E, Florez JC, Dupuis J, Barroso I, Morris AP, Prokopenko I, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) | Nature communications | 33402679 | Nat Commun | 2021 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/33402679 |
| Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice. | Carrat GR, Hu M, Nguyen-Tu MS, Chabosseau P, Gaulton KJ, van de Bunt M, Siddiq A, Falchi M, Thurner M, Canouil M, Pattou F, Leclerc I, Pullen TJ, Cane MC, Prabhala P, Greenwald W, Schulte A, Marchetti P, Ibberson M, MacDonald PE, Manning Fox JE, Gloyn AL, Froguel P, Solimena M, McCarthy MI, Rutter GA | American journal of human genetics | 28132686 | Am J Hum Genet | 2017 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/28132686 |
| Whole-transcriptome sequencing in blood provides a diagnosis of spinal muscular atrophy with progressive myoclonic epilepsy. | Kernohan KD, Frésard L, Zappala Z, Hartley T, Smith KS, Wagner J, Xu H, McBride A, Bourque PR, Consortium CRC, Bennett SAL, Dyment DA, Boycott KM, Montgomery SB, Warman Chardon J | Human mutation | 28251733 | Hum Mutat | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28251733 |
| Non-Coding Loss-of-Function Variation in Human Genomes. | Zappala Z, Montgomery SB | Human heredity | 28076858 | Hum Hered | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28076858 |
| The landscape of genomic imprinting across diverse adult human tissues. | Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C, GTEx Consortium, Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA, Lappalainen T | Genome research | 25953952 | Genome Res | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25953952 |
| Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci. | Liu B, Pjanic M, Wang T, Nguyen T, Gloudemans M, Rao A, Castano VG, Nurnberg S, Rader DJ, Elwyn S, Ingelsson E, Montgomery SB, Miller CL, Quertermous T | American journal of human genetics | 30146127 | Am J Hum Genet | 2018 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/30146127 |
| Day-night and seasonal variation of human gene expression across tissues. | Wucher V, Sodaei R, Amador R, Irimia M, Guigó R | PLoS biology | 36745672 | PLoS Biol | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36745672 |
| ORegAnno 3.0: a community-driven resource for curated regulatory annotation. | Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL, Open Regulatory Annotation Consortium | Nucleic acids research | 26578589 | Nucleic Acids Res | 2016 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/26578589 |
| Population- and individual-specific regulatory variation in Sardinia. | Pala M, Zappala Z, Marongiu M, Li X, Davis JR, Cusano R, Crobu F, Kukurba KR, Gloudemans MJ, Reinier F, Berutti R, Piras MG, Mulas A, Zoledziewska M, Marongiu M, Sorokin EP, Hess GT, Smith KS, Busonero F, Maschio A, Steri M, Sidore C, Sanna S, Fiorillo E, Bassik MC, Sawcer SJ, Battle A, Novembre J, Jones C, Angius A, Abecasis GR, Schlessinger D, Cucca F, Montgomery SB | Nature genetics | 28394350 | Nat Genet | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28394350 |
| Assessing allele-specific expression across multiple tissues from RNA-seq read data. | Pirinen M, Lappalainen T, Zaitlen NA, GTEx Consortium, Dermitzakis ET, Donnelly P, McCarthy MI, Rivas MA | Bioinformatics (Oxford, England) | 25819081 | Bioinformatics | 2015 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/25819081 |
| Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. | Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso T, Palumbo E, Ponomarenko J, Guigo R, Johnson R | PLoS computational biology | 28253259 | PLoS Comput Biol | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28253259 |
| MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets. | Fort A, Panousis NI, Garieri M, Antonarakis SE, Lappalainen T, Dermitzakis ET, Delaneau O | Bioinformatics (Oxford, England) | 28186259 | Bioinformatics | 2017 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/28186259 |
| Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. | Castel SE, Cervera A, Mohammadi P, Aguet F, Reverter F, Wolman A, Guigo R, Iossifov I, Vasileva A, Lappalainen T | Nature genetics | 30127527 | Nat Genet | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30127527 |
| Identifying causal variants and genes using functional genomics in specialized cell types and contexts. | Liu B, Montgomery SB | Human genetics | 31317254 | Hum Genet | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31317254 |
| Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. | Võsa U, Claringbould A, Westra HJ, Bonder MJ, Deelen P, Zeng B, Kirsten H, Saha A, Kreuzhuber R, Yazar S, Brugge H, Oelen R, de Vries DH, van der Wijst MGP, Kasela S, Pervjakova N, Alves I, Favé MJ, Agbessi M, Christiansen MW, Jansen R, Seppälä I, Tong L, Teumer A, Schramm K, Hemani G, Verlouw J, Yaghootkar H, Sönmez Flitman R, Brown A, Kukushkina V, Kalnapenkis A, Rüeger S, Porcu E, Kronberg J, Kettunen J, Lee B, Zhang F, Qi T, Hernandez JA, Arindrarto W, Beutner F, BIOS Consortium, i2QTL Consortium, Dmitrieva J, Elansary M, Fairfax BP, Georges M, Heijmans BT, Hewitt AW, Kähönen M, Kim Y, Knight JC, Kovacs P, Krohn K, Li S, Loeffler M, Marigorta UM, Mei H, Momozawa Y, Müller-Nurasyid M, Nauck M, Nivard MG, Penninx BWJH, Pritchard JK, Raitakari OT, Rotzschke O, Slagboom EP, Stehouwer CDA, Stumvoll M, Sullivan P, 't Hoen PAC, Thiery J, Tönjes A, van Dongen J, van Iterson M, Veldink JH, Völker U, Warmerdam R, Wijmenga C, Swertz M, Andiappan A, Montgomery GW, Ripatti S, Perola M, Kutalik Z, Dermitzakis E, Bergmann S, Frayling T, van Meurs J, Prokisch H, Ahsan H, Pierce BL, Lehtimäki T, Boomsma DI, Psaty BM, Gharib SA, Awadalla P, Milani L, Ouwehand WH, Downes K, Stegle O, Battle A, Visscher PM, Yang J, Scholz M, Powell J, Gibson G, Esko T, Franke L | Nature genetics | 34475573 | Nat Genet | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34475573 |
| A Genome-Wide Association Study of Diabetic Kidney Disease in Subjects With Type 2 Diabetes. | van Zuydam NR, Ahlqvist E, Sandholm N, Deshmukh H, Rayner NW, Abdalla M, Ladenvall C, Ziemek D, Fauman E, Robertson NR, McKeigue PM, Valo E, Forsblom C, Harjutsalo V, Finnish Diabetic Nephropathy Study (FinnDiane), Perna A, Rurali E, Marcovecchio ML, Igo RP Jr, Salem RM, Perico N, Lajer M, Käräjämäki A, Imamura M, Kubo M, Takahashi A, Sim X, Liu J, van Dam RM, Jiang G, Tam CHT, Luk AOY, Lee HM, Lim CKP, Szeto CC, So WY, Chan JCN, Hong Kong Diabetes Registry Theme-based Research Scheme Project Group, Ang SF, Dorajoo R, Wang L, Clara TSH, McKnight AJ, Duffy S, Warren 3 and Genetics of Kidneys in Diabetes (GoKinD) Study Group, Pezzolesi MG, GENIE (GEnetics of Nephropathy an International Effort) Consortium, Marre M, Gyorgy B, Hadjadj S, Hiraki LT, Diabetes Control and Complications Trial (DCCT)/Epidemiology of Diabetes Interventions and Complications (EDIC) Research Group, Ahluwalia TS, Almgren P, Schulz CA, Orho-Melander M, Linneberg A, Christensen C, Witte DR, Grarup N, Brandslund I, Melander O, Paterson AD, Tregouet D, Maxwell AP, Lim SC, Ma RCW, Tai ES, Maeda S, Lyssenko V, Tuomi T, Krolewski AS, Rich SS, Hirschhorn JN, Florez JC, Dunger D, Pedersen O, Hansen T, Rossing P, Remuzzi G, SUrrogate markers for Micro- and Macrovascular hard endpoints for Innovative diabetes Tools (SUMMIT) Consortium, Brosnan MJ, Palmer CNA, Groop PH, Colhoun HM, Groop LC, McCarthy MI | Diabetes | 29703844 | Diabetes | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29703844 |
| Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. | Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET | Cell | 26300124 | Cell | 2015 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/26300124 |
| An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants. | Davis JR, Fresard L, Knowles DA, Pala M, Bustamante CD, Battle A, Montgomery SB | American journal of human genetics | 26749306 | Am J Hum Genet | 2016 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/26749306 |
| Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). | Lagarde J, Uszczynska-Ratajczak B, Santoyo-Lopez J, Gonzalez JM, Tapanari E, Mudge JM, Steward CA, Wilming L, Tanzer A, Howald C, Chrast J, Vela-Boza A, Rueda A, Lopez-Domingo FJ, Dopazo J, Reymond A, Guigó R, Harrow J | Nature communications | 27531712 | Nat Commun | 2016 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/27531712 |
| Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions. | Ritchie MD, Davis JR, Aschard H, Battle A, Conti D, Du M, Eskin E, Fallin MD, Hsu L, Kraft P, Moore JH, Pierce BL, Bien SA, Thomas DC, Wei P, Montgomery SB | American journal of epidemiology | 28978191 | Am J Epidemiol | 2017 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/28978191 |
| 10 Years of GWAS Discovery: Biology, Function, and Translation. | Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, Yang J | American journal of human genetics | 28686856 | Am J Hum Genet | 2017 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/28686856 |
| Cohort-specific imputation of gene expression improves prediction of warfarin dose for African Americans. | Gottlieb A, Daneshjou R, DeGorter M, Bourgeois S, Svensson PJ, Wadelius M, Deloukas P, Montgomery SB, Altman RB | Genome medicine | 29178968 | Genome Med | 2017 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/29178968 |
| The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. | Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M | Cell | 37001506 | Cell | 2023 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/37001506 |
| Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides. | Nikolskiy I, Conrad DF, Chun S, Fay JC, Cheverud JM, Lawson HA | BMC genomics | 26016481 | BMC Genomics | 2015 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/26016481 |
| Multiplex shRNA Screening of Germ Cell Development by in Vivo Transfection of Mouse Testis. | Ho NR, Usmani AR, Yin Y, Ma L, Conrad DF | G3 (Bethesda, Md.) | 27856695 | G3 (Bethesda) | 2017 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/27856695 |
| Identification of genetic variants in CFAP221 as a cause of primary ciliary dyskinesia. | Bustamante-Marin XM, Shapiro A, Sears PR, Charng WL, Conrad DF, Leigh MW, Knowles MR, Ostrowski LE, Zariwala MA | Journal of human genetics | 31636325 | J Hum Genet | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31636325 |
| Multispecies Purification of Testicular Germ Cells. | Lima AC, Jung M, Rusch J, Usmani A, Lopes A, Conrad DF | Biology of reproduction | 27557646 | Biol Reprod | 2016 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/27557646 |
| How to Map the Genetic Basis for Conditions that are Comorbid with Male Infertility. | Nagirnaja L, Vigh-Conrad K, Conrad DF | Seminars in reproductive medicine | 28658705 | Semin Reprod Med | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28658705 |
| Guidelines for investigating causality of sequence variants in human disease. | MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C | Nature | 24759409 | Nature | 2014 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/24759409 |
| The genetic architecture of sporadic and multiple consecutive miscarriage. | Laisk T, Soares ALG, Ferreira T, Painter JN, Censin JC, Laber S, Bacelis J, Chen CY, Lepamets M, Lin K, Liu S, Millwood IY, Ramu A, Southcombe J, Andersen MS, Yang L, Becker CM, Børglum AD, Gordon SD, Bybjerg-Grauholm J, Helgeland Ø, Hougaard DM, Jin X, Johansson S, Juodakis J, Kartsonaki C, Kukushkina V, Lind PA, Metspalu A, Montgomery GW, Morris AP, Mors O, Mortensen PB, Njølstad PR, Nordentoft M, Nyholt DR, Lippincott M, Seminara S, Salumets A, Snieder H, Zondervan K, Werge T, Chen Z, Conrad DF, Jacobsson B, Li L, Martin NG, Neale BM, Nielsen R, Walters RG, Granne I, Medland SE, Mägi R, Lawlor DA, Lindgren CM | Nature communications | 33239672 | Nat Commun | 2020 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/33239672 |
| 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 XM, Horani A, Stoyanova M, Charng WL, Bottier M, Sears PR, Yin WN, Daniels LA, Bowen H, Conrad DF, Knowles MR, Ostrowski LE, Zariwala MA, Dutcher SK | PLoS genetics | 32764743 | PLoS Genet | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32764743 |
| A de novo paradigm for male infertility. | Oud MS, Smits RM, Smith HE, Mastrorosa FK, Holt GS, Houston BJ, de Vries PF, Alobaidi BKS, Batty LE, Ismail H, Greenwood J, Sheth H, Mikulasova A, Astuti GDN, Gilissen C, McEleny K, Turner H, Coxhead J, Cockell S, Braat DDM, Fleischer K, D'Hauwers KWM, Schaafsma E, Genetics of Male Infertility Initiative (GEMINI) consortium, Nagirnaja L, Conrad DF, Friedrich C, Kliesch S, Aston KI, Riera-Escamilla A, Krausz C, Gonzaga-Jauregui C, Santibanez-Koref M, Elliott DJ, Vissers LELM, Tüttelmann F, O'Bryan MK, Ramos L, Xavier MJ, van der Heijden GW, Veltman JA | Nature communications | 35013161 | Nat Commun | 2022 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/35013161 |
| Validating single-cell genomics for the study of renal development. | Jain S, Noordam MJ, Hoshi M, Vallania FL, Conrad DF | Kidney international | 24759149 | Kidney Int | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24759149 |
| Reduced burden of very large and rare CNVs in bipolar affective disorder. | Grozeva D, Kirov G, Conrad DF, Barnes CP, Hurles M, Owen MJ, O'Donovan MC, Craddock N | Bipolar disorders | 24127788 | Bipolar Disord | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24127788 |
| A Standardized Approach for Multispecies Purification of Mammalian Male Germ Cells by Mechanical Tissue Dissociation and Flow Cytometry. | Lima AC, Jung M, Rusch J, Usmani A, Lopes AM, Conrad DF | Journal of visualized experiments : JoVE | 28745623 | J Vis Exp | 2017 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/28745623 |
| Unified single-cell analysis of testis gene regulation and pathology in five mouse strains. | Jung M, Wells D, Rusch J, Ahmad S, Marchini J, Myers SR, Conrad DF | eLife | 31237565 | Elife | 2019 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/31237565 |
| Bi-allelic Recessive Loss-of-Function Variants in FANCM Cause Non-obstructive Azoospermia. | Kasak L, Punab M, Nagirnaja L, Grigorova M, Minajeva A, Lopes AM, Punab AM, Aston KI, Carvalho F, Laasik E, Smith LB, GEMINI Consortium, Conrad DF, Laan M | American journal of human genetics | 30075111 | Am J Hum Genet | 2018 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/30075111 |
| Rare mutations in the complement regulatory gene CSMD1 are associated with male and female infertility. | Lee AS, Rusch J, Lima AC, Usmani A, Huang N, Lepamets M, Vigh-Conrad KA, Worthington RE, Mägi R, Wu X, Aston KI, Atkinson JP, Carrell DT, Hess RA, O'Bryan MK, Conrad DF | Nature communications | 31604923 | Nat Commun | 2019 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/31604923 |
| Genome-wide significance testing of variation from single case exomes. | Wilfert AB, Chao KR, Kaushal M, Jain S, Zöllner S, Adams DR, Conrad DF | Nature genetics | 27776118 | Nat Genet | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27776118 |
| Defining the Phenotype and Assessing Severity in Phosphoglucomutase-1 Deficiency. | Wong SY, Beamer LJ, Gadomski T, Honzik T, Mohamed M, Wortmann SB, Brocke Holmefjord KS, Mork M, Bowling F, Sykut-Cegielska J, Koch D, Ackermann A, Stanley CA, Rymen D, Zeharia A, Al-Sayed M, Marquardt T, Jaeken J, Lefeber D, Conrad DF, Kozicz T, Morava E | The Journal of pediatrics | 27206562 | J Pediatr | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27206562 |
| Rare double sex and mab-3-related transcription factor 1 regulatory variants in severe spermatogenic failure. | Lima AC, Carvalho F, Gonçalves J, Fernandes S, Marques PI, Sousa M, Barros A, Seixas S, Amorim A, Conrad DF, Lopes AM | Andrology | 26139570 | Andrology | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26139570 |
| Female Genomics: Infertility and Overall Health. | Joshi N, Chan JL | Seminars in reproductive medicine | 28658704 | Semin Reprod Med | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28658704 |
| The origins and functional effects of postzygotic mutations throughout the human life span. | Rockweiler NB, Ramu A, Nagirnaja L, Wong WH, Noordam MJ, Drubin CW, Huang N, Miller B, Todres EZ, Vigh-Conrad KA, Zito A, Small KS, Ardlie KG, Cohen BA, Conrad DF | Science (New York, N.Y.) | 37053313 | Science | 2023 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/37053313 |
| Hypotheses on a tree: new error rates and testing strategies. | Bogomolov M, Peterson CB, Benjamini Y, Sabatti C | Biometrika | 36825068 | Biometrika | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36825068 |
| Controlling the Rate of GWAS False Discoveries. | Brzyski D, Peterson CB, Sobczyk P, Candès EJ, Bogdan M, Sabatti C | Genetics | 27784720 | Genetics | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27784720 |
| Gene-Gene Interactions Detection Using a Two-stage Model. | Wang Z, Sul JH, Snir S, Lozano JA, Eskin E | Journal of computational biology : a journal of computational molecular cell biology | 25871811 | J Comput Biol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25871811 |
| Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data. | Kang EY, Martin LJ, Mangul S, Isvilanonda W, Zou J, Ben-David E, Han B, Lusis AJ, Shifman S, Eskin E | Genetics | 27765809 | Genetics | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27765809 |
| Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia. | Olde Loohuis LM, Mangul S, Ori APS, Jospin G, Koslicki D, Yang HT, Wu T, Boks MP, Lomen-Hoerth C, Wiedau-Pazos M, Cantor RM, de Vos WM, Kahn RS, Eskin E, Ophoff RA | Translational psychiatry | 29743478 | Transl Psychiatry | 2018 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/29743478 |
| ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. | Mangul S, Yang HT, Strauli N, Gruhl F, Porath HT, Hsieh K, Chen L, Daley T, Christenson S, Wesolowska-Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Levanon EY, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N | Genome biology | 29548336 | Genome Biol | 2018 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/29548336 |
| Population structure in genetic studies: Confounding factors and mixed models. | Sul JH, Martin LS, Eskin E | PLoS genetics | 30589851 | PLoS Genet | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30589851 |
| Efficiently identifying significant associations in genome-wide association studies. | Kostem E, Eskin E | Journal of computational biology : a journal of computational molecular cell biology | 24033261 | J Comput Biol | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24033261 |
| BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference. | Rahmani E, Schweiger R, Shenhav L, Wingert T, Hofer I, Gabel E, Eskin E, Halperin E | Genome biology | 30241486 | Genome Biol | 2018 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/30241486 |
| Selection-adjusted inference: an application to confidence intervals for cis-eQTL effect sizes. | Panigrahi S, Zhu J, Sabatti C | Biostatistics (Oxford, England) | 31301173 | Biostatistics | 2021 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/31301173 |
| Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for Bipolar Disorder. | Peterson CB, Service SK, Jasinska AJ, Gao F, Zelaya I, Teshiba TM, Bearden CE, Cantor RM, Reus VI, Macaya G, López-Jaramillo C, Bogomolov M, Benjamini Y, Eskin E, Coppola G, Freimer NB, Sabatti C | PLoS genetics | 27176483 | PLoS Genet | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27176483 |
| Finding associated variants in genome-wide association studies on multiple traits. | Gai L, Eskin E | Bioinformatics (Oxford, England) | 29949991 | Bioinformatics | 2018 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/29949991 |
| Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate. | Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi OW, DeYoung J, Eskin E, Fairbanks LA, Fears S, Furterer AE, Huang YS, Ramensky V, Schmitt CA, Svardal H, Jorgensen MJ, Kaplan JR, Villar D, Aken BL, Flicek P, Nag R, Wong ES, Blangero J, Dyer TD, Bogomolov M, Benjamini Y, Weinstock GM, Dewar K, Sabatti C, Wilson RK, Jentsch JD, Warren W, Coppola G, Woods RP, Freimer NB | Nature genetics | 29083405 | Nat Genet | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29083405 |
| Joint Bayesian variable and graph selection for regression models with network-structured predictors. | Peterson CB, Stingo FC, Vannucci M | Statistics in medicine | 26514925 | Stat Med | 2016 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/26514925 |
| Many Phenotypes Without Many False Discoveries: Error Controlling Strategies for Multitrait Association Studies. | Peterson CB, Bogomolov M, Benjamini Y, Sabatti C | Genetic epidemiology | 26626037 | Genet Epidemiol | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26626037 |
| Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions. | Duong D, Ahmad WU, Eskin E, Chang KW, Li JJ | Journal of computational biology : a journal of computational molecular cell biology | 30383443 | J Comput Biol | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30383443 |
| Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure. | Joo JW, Kang EY, Org E, Furlotte N, Parks B, Hormozdiari F, Lusis AJ, Eskin E | Genetics | 27770036 | Genetics | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27770036 |
| Efficient multiple-trait association and estimation of genetic correlation using the matrix-variate linear mixed model. | Furlotte NA, Eskin E | Genetics | 25724382 | Genetics | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25724382 |
| Improving the usability and archival stability of bioinformatics software. | Mangul S, Martin LS, Eskin E, Blekhman R | Genome biology | 30813962 | Genome Biol | 2019 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/30813962 |
| Leveraging allelic imbalance to refine fine-mapping for eQTL studies. | Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E | PLoS genetics | 31834882 | PLoS Genet | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31834882 |
| Identifying causal variants by fine mapping across multiple studies. | LaPierre N, Taraszka K, Huang H, He R, Hormozdiari F, Eskin E | PLoS genetics | 34543273 | PLoS Genet | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34543273 |
| Identification of causal genes for complex traits. | Hormozdiari F, Kichaev G, Yang WY, Pasaniuc B, Eskin E | Bioinformatics (Oxford, England) | 26072484 | Bioinformatics | 2015 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/26072484 |
| ForestPMPlot: A Flexible Tool for Visualizing Heterogeneity Between Studies in Meta-analysis. | Kang EY, Park Y, Li X, Segrè AV, Han B, Eskin E | G3 (Bethesda, Md.) | 27194809 | G3 (Bethesda) | 2016 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/27194809 |
| Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation. | Rahmani E, Zaitlen N, Baran Y, Eng C, Hu D, Galanter J, Oh S, Burchard EG, Eskin E, Zou J, Halperin E | Nature methods | 28245214 | Nat Methods | 2017 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/28245214 |
| A Comprehensive Map of Genetic Variation in the World's Largest Ethnic Group-Han Chinese. | Chiang CWK, Mangul S, Robles C, Sankararaman S | Molecular biology and evolution | 30169787 | Mol Biol Evol | 2018 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/30169787 |
| Leveraging pleiotropy for joint analysis of genome-wide association studies with per trait interpretations. | Taraszka K, Zaitlen N, Eskin E | PLoS genetics | 36342933 | PLoS Genet | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36342933 |
| DETECTING MULTIPLE REPLICATING SIGNALS USING ADAPTIVE FILTERING PROCEDURES. | Wang J, Gui L, Su WJ, Sabatti C, Owen AB | Annals of statistics | 39421244 | Ann Stat | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/39421244 |
| Accurate viral population assembly from ultra-deep sequencing data. | Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E | Bioinformatics (Oxford, England) | 24932001 | Bioinformatics | 2014 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/24932001 |
| Chromosome conformation elucidates regulatory relationships in developing human brain. | Won H, de la Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, Gandal MJ, Sutton GJ, Hormozdiari F, Lu D, Lee C, Eskin E, Voineagu I, Ernst J, Geschwind DH | Nature | 27760116 | Nature | 2016 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/27760116 |
| Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies. | Rahmani E, Zaitlen N, Baran Y, Eng C, Hu D, Galanter J, Oh S, Burchard EG, Eskin E, Zou J, Halperin E | Nature methods | 27018579 | Nat Methods | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27018579 |
| Using genomic annotations increases statistical power to detect eGenes. | Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E | Bioinformatics (Oxford, England) | 27307612 | Bioinformatics | 2016 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/27307612 |
| An Association Mapping Framework To Account for Potential Sex Difference in Genetic Architectures. | Kang EY, Lee CH, Furlotte NA, Joo JWJ, Kostem E, Zaitlen N, Eskin E, Han B | Genetics | 29752291 | Genetics | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29752291 |
| Challenges and recommendations to improve the installability and archival stability of omics computational tools. | Mangul S, Mosqueiro T, Abdill RJ, Duong D, Mitchell K, Sarwal V, Hill B, Brito J, Littman RJ, Statz B, Lam AK, Dayama G, Grieneisen L, Martin LS, Flint J, Eskin E, Blekhman R | PLoS biology | 31220077 | PLoS Biol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31220077 |
| A spatial haplotype copying model with applications to genotype imputation. | Yang WY, Hormozdiari F, Eskin E, Pasaniuc B | Journal of computational biology : a journal of computational molecular cell biology | 25526526 | J Comput Biol | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25526526 |
| Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes. | Duong D, Gai L, Snir S, Kang EY, Han B, Sul JH, Eskin E | Bioinformatics (Oxford, England) | 28881962 | Bioinformatics | 2017 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/28881962 |
| Widespread Allelic Heterogeneity in Complex Traits. | Hormozdiari F, Zhu A, Kichaev G, Ju CJ, Segrè AV, Joo JWJ, Won H, Sankararaman S, Pasaniuc B, Shifman S, Eskin E | American journal of human genetics | 28475861 | Am J Hum Genet | 2017 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/28475861 |
| Multiple testing correction in linear mixed models. | Joo JW, Hormozdiari F, Han B, Eskin E | Genome biology | 27039378 | Genome Biol | 2016 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/27039378 |
| MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples. | LaPierre N, Mangul S, Alser M, Mandric I, Wu NC, Koslicki D, Eskin E | BMC genomics | 31167634 | BMC Genomics | 2019 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/31167634 |
| Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies. | Joo JW, Sul JH, Han B, Ye C, Eskin E | Genome biology | 24708878 | Genome Biol | 2014 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/24708878 |
| Transcriptome assembly and quantification from Ion Torrent RNA-Seq data. | Mangul S, Caciula A, Al Seesi S, Brinza D, Mӑndoiu I, Zelikovsky A | BMC genomics | 25082147 | BMC Genomics | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25082147 |
| Identifying causal variants at loci with multiple signals of association. | Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E | Genetics | 25104515 | Genetics | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25104515 |
| Allele-specific expression and eQTL analysis in mouse adipose tissue. | Hasin-Brumshtein Y, Hormozdiari F, Martin L, van Nas A, Eskin E, Lusis AJ, Drake TA | BMC genomics | 24927774 | BMC Genomics | 2014 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/24927774 |
| Meta-analysis identifies gene-by-environment interactions as demonstrated in a study of 4,965 mice. | Kang EY, Han B, Furlotte N, Joo JW, Shih D, Davis RC, Lusis AJ, Eskin E | PLoS genetics | 24415945 | PLoS Genet | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24415945 |
| Memory efficient assembly of human genome. | Hormozdiari F, Eskin E | Journal of bioinformatics and computational biology | 25603998 | J Bioinform Comput Biol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25603998 |
| Colocalization of GWAS and eQTL Signals Detects Target Genes. | Hormozdiari F, van de Bunt M, Segrè AV, Li X, Joo JWJ, Bilow M, Sul JH, Sankararaman S, Pasaniuc B, Eskin E | American journal of human genetics | 27866706 | Am J Hum Genet | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/27866706 |
| Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits. | Hormozdiari F, Gazal S, van de Geijn B, Finucane HK, Ju CJ, Loh PR, Schoech A, Reshef Y, Liu X, O'Connor L, Gusev A, Eskin E, Price AL | Nature genetics | 29942083 | Nat Genet | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29942083 |
| Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies. | Wu Y, Hormozdiari F, Joo JWJ, Eskin E | Journal of computational biology : a journal of computational molecular cell biology | 30272994 | J Comput Biol | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30272994 |
| Erratum: Genetic effects on gene expression across human tissues. | GTEx Consortium | Nature | 29258290 | Nature | 2018 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/29258290 |
| Metalign: efficient alignment-based metagenomic profiling via containment min hash. | LaPierre N, Alser M, Eskin E, Koslicki D, Mangul S | Genome biology | 32912225 | Genome Biol | 2020 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/32912225 |
| Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models. | Sul JH, Bilow M, Yang WY, Kostem E, Furlotte N, He D, Eskin E | PLoS genetics | 26943367 | PLoS Genet | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26943367 |
| TreeQTL: hierarchical error control for eQTL findings. | Peterson CB, Bogomolov M, Benjamini Y, Sabatti C | Bioinformatics (Oxford, England) | 27153635 | Bioinformatics | 2016 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/27153635 |
| Imputing Phenotypes for Genome-wide Association Studies. | Hormozdiari F, Kang EY, Bilow M, Ben-David E, Vulpe C, McLachlan S, Lusis AJ, Han B, Eskin E | American journal of human genetics | 27292110 | Am J Hum Genet | 2016 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/27292110 |
| Fast and Accurate Construction of Confidence Intervals for Heritability. | Schweiger R, Kaufman S, Laaksonen R, Kleber ME, März W, Eskin E, Rosset S, Halperin E | American journal of human genetics | 27259052 | Am J Hum Genet | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27259052 |
| Simultaneous Modeling of Disease Status and Clinical Phenotypes To Increase Power in Genome-Wide Association Studies. | Bilow M, Crespo F, Pan Z, Eskin E, Eyheramendy S | Genetics | 28132020 | Genetics | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28132020 |
| Controls of nucleosome positioning in the human genome. | Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK | PLoS genetics | 23166509 | PLoS Genet | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23166509 |
| DNase I sensitivity QTLs are a major determinant of human expression variation. | Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK | Nature | 22307276 | Nature | 2012 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/22307276 |
| BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS. | Wen X, Stephens M | The annals of applied statistics | 26413181 | Ann Appl Stat | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/26413181 |
| Comparison of the transcriptional landscapes between human and mouse tissues. | Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP | Proceedings of the National Academy of Sciences of the United States of America | 25413365 | Proc Natl Acad Sci U S A | 2014 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/25413365 |
| The Genotype-Tissue Expression (GTEx) Project: Linking Clinical Data with Molecular Analysis to Advance Personalized Medicine. | Keen JC, Moore HM | Journal of personalized medicine | 25809799 | J Pers Med | 2015 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/25809799 |
| Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk. | Lin WY, Camp NJ, Ghoussaini M, Beesley J, Michailidou K, Hopper JL, Apicella C, Southey MC, Stone J, Schmidt MK, Broeks A, Van't Veer LJ, Th Rutgers EJ, Muir K, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Fasching PA, Haeberle L, Ekici AB, Beckmann MW, Peto J, Dos-Santos-Silva I, Fletcher O, Johnson N, Bolla MK, Wang Q, Dennis J, Sawyer EJ, Cheng T, Tomlinson I, Kerin MJ, Miller N, Marmé F, Surowy HM, Burwinkel B, Guénel P, Truong T, Menegaux F, Mulot C, Bojesen SE, Nordestgaard BG, Nielsen SF, Flyger H, Benitez J, Zamora MP, Arias Perez JI, Menéndez P, González-Neira A, Pita G, Alonso MR, Alvarez N, Herrero D, Anton-Culver H, Brenner H, Dieffenbach AK, Arndt V, Stegmaier C, Meindl A, Lichtner P, Schmutzler RK, Müller-Myhsok B, Brauch H, Brüning T, Ko YD, GENICA Network, Tessier DC, Vincent D, Bacot F, Nevanlinna H, Aittomäki K, Blomqvist C, Khan S, Matsuo K, Ito H, Iwata H, Horio A, Bogdanova NV, Antonenkova NN, Dörk T, Lindblom A, Margolin S, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, kConFab Investigators, Australian Ovarian Cancer Study Group, Wu AH, Tseng CC, Van Den Berg D, Stram DO, Neven P, Wauters E, Wildiers H, Lambrechts D, Chang-Claude J, Rudolph A, Seibold P, Flesch-Janys D, Radice P, Peterlongo P, Manoukian S, Bonanni B, Couch FJ, Wang X, Vachon C, Purrington K, Giles GG, Milne RL, Mclean C, Haiman CA, Henderson BE, Schumacher F, Le Marchand L, Simard J, Goldberg MS, Labrèche F, Dumont M, Teo SH, Yip CH, Hassan N, Vithana EN, Kristensen V, Zheng W, Deming-Halverson S, Shrubsole MJ, Long J, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Kauppila S, Andrulis IL, Knight JA, Glendon G, Tchatchou S, Devilee P, Tollenaar RA, Seynaeve C, Van Asperen CJ, García-Closas M, Figueroa J, Lissowska J, Brinton L, Czene K, Darabi H, Eriksson M, Brand JS, Hooning MJ, Hollestelle A, Van Den Ouweland AM, Jager A, Li J, Liu J, Humphreys K, Shu XO, Lu W, Gao YT, Cai H, Cross SS, Reed MW, Blot W, Signorello LB, Cai Q, Pharoah PD, Perkins B, Shah M, Blows FM, Kang D, Yoo KY, Noh DY, Hartman M, Miao H, Chia KS, Putti TC, Hamann U, Luccarini C, Baynes C, Ahmed S, Maranian M, Healey CS, Jakubowska A, Lubinski J, Jaworska-Bieniek K, Durda K, Sangrajrang S, Gaborieau V, Brennan P, Mckay J, Slager S, Toland AE, Yannoukakos D, Shen CY, Hsiung CN, Wu PE, Ding SL, Ashworth A, Jones M, Orr N, Swerdlow AJ, Tsimiklis H, Makalic E, Schmidt DF, Bui QM, Chanock SJ, Hunter DJ, Hein R, Dahmen N, Beckmann L, Aaltonen K, Muranen TA, Heikkinen T, Irwanto A, Rahman N, Turnbull CA, Breast and Ovarian Cancer Susceptibility (BOCS) Study, Waisfisz Q, Meijers-Heijboer HE, Adank MA, Van Der Luijt RB, Hall P, Chenevix-Trench G, Dunning A, Easton DF, Cox A | Human molecular genetics | 25168388 | Hum Mol Genet | 2015 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/25168388 |
| Bicc1 is a genetic determinant of osteoblastogenesis and bone mineral density. | Mesner LD, Ray B, Hsu YH, Manichaikul A, Lum E, Bryda EC, Rich SS, Rosen CJ, Criqui MH, Allison M, Budoff MJ, Clemens TL, Farber CR | The Journal of clinical investigation | 24789909 | J Clin Invest | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24789909 |
| Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. | Simmons S, Peng J, Bienkowska J, Berger B | Journal of computational biology : a journal of computational molecular cell biology | 26098139 | J Comput Biol | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26098139 |
| Fine mapping and functional studies of risk variants for type 1 diabetes at chromosome 16p13.13. | Tomlinson MJ 4th, Pitsillides A, Pickin R, Mika M, Keene KL, Hou X, Mychaleckyj J, Chen WM, Concannon P, Onengut-Gumuscu S | Diabetes | 25008175 | Diabetes | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25008175 |
| RNA-Seq optimization with eQTL gold standards. | Ellis SE, Gupta S, Ashar FN, Bader JS, West AB, Arking DE | BMC genomics | 24341889 | BMC Genomics | 2013 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/24341889 |
| Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. | Zhang X, Gierman HJ, Levy D, Plump A, Dobrin R, Goring HH, Curran JE, Johnson MP, Blangero J, Kim SK, O'Donnell CJ, Emilsson V, Johnson AD | BMC genomics | 24973796 | BMC Genomics | 2014 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/24973796 |
| Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. | Veyrieras JB, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, Pritchard JK | PloS one | 22359548 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22359548 |
| Dissecting the regulatory architecture of gene expression QTLs. | Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK | Genome biology | 22293038 | Genome Biol | 2012 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/22293038 |
| REDIportal: a comprehensive database of A-to-I RNA editing events in humans. | Picardi E, D'Erchia AM, Lo Giudice C, Pesole G | Nucleic acids research | 27587585 | Nucleic Acids Res | 2017 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/27587585 |
| Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies. | Panousis NI, Gutierrez-Arcelus M, Dermitzakis ET, Lappalainen T | Genome biology | 25239376 | Genome Biol | 2014 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/25239376 |
| A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits. | Zhu J, Chen C, Yang B, Guo Y, Ai H, Ren J, Peng Z, Tu Z, Yang X, Meng Q, Friend S, Huang L | BMC genomics | 25765547 | BMC Genomics | 2015 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/25765547 |
| A robust blood gene expression-based prognostic model for castration-resistant prostate cancer. | Wang L, Gong Y, Chippada-Venkata U, Heck MM, Retz M, Nawroth R, Galsky M, Tsao CK, Schadt E, de Bono J, Olmos D, Zhu J, Oh WK | BMC medicine | 26297150 | BMC Med | 2015 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/26297150 |
| Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains. | Huynh JL, Garg P, Thin TH, Yoo S, Dutta R, Trapp BD, Haroutunian V, Zhu J, Donovan MJ, Sharp AJ, Casaccia P | Nature neuroscience | 24270187 | Nat Neurosci | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24270187 |
| Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets. | Tu Z, Keller MP, Zhang C, Rabaglia ME, Greenawalt DM, Yang X, Wang IM, Dai H, Bruss MD, Lum PY, Zhou YP, Kemp DM, Kendziorski C, Yandell BS, Attie AD, Schadt EE, Zhu J | PLoS genetics | 23236292 | PLoS Genet | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23236292 |
| Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases. | Narayanan M, Huynh JL, Wang K, Yang X, Yoo S, McElwee J, Zhang B, Zhang C, Lamb JR, Xie T, Suver C, Molony C, Melquist S, Johnson AD, Fan G, Stone DJ, Schadt EE, Casaccia P, Emilsson V, Zhu J | Molecular systems biology | 25080494 | Mol Syst Biol | 2014 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/25080494 |
| Modeling causality for pairs of phenotypes in system genetics. | Neto EC, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS | Genetics | 23288936 | Genetics | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23288936 |
| Functional Characterization of DNA Methylation in the Oligodendrocyte Lineage. | Moyon S, Huynh JL, Dutta D, Zhang F, Ma D, Yoo S, Lawrence R, Wegner M, John GR, Emery B, Lubetzki C, Franklin RJM, Fan G, Zhu J, Dupree JL, Casaccia P | Cell reports | 27149841 | Cell Rep | 2016 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/27149841 |
| Quantile-based permutation thresholds for quantitative trait loci hotspots. | Neto EC, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS | Genetics | 22661325 | Genetics | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22661325 |
| Phosphorylation of Spo0A by the histidine kinase KinD requires the lipoprotein med in Bacillus subtilis. | Banse AV, Hobbs EC, Losick R | Journal of bacteriology | 21622736 | J Bacteriol | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21622736 |
| Bayesian Partition Models for Identifying Expression Quantitative Trait Loci. | Jiang B, Liu JS | Journal of the American Statistical Association | 29056798 | J Am Stat Assoc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/29056798 |
| 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 E, Gennarelli M, Sacco C, Filippini A, Mingardi J, Magri C, Barbon A | BMC genomics | 30587120 | BMC Genomics | 2018 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/30587120 |
| Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. | Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D | Genome research | 24092820 | Genome Res | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24092820 |
| Mapping cis- and trans-regulatory effects across multiple tissues in twins. | Grundberg E, Small KS, Hedman ÅK, Nica AC, Buil A, Keildson S, Bell JT, Yang TP, Meduri E, Barrett A, Nisbett J, Sekowska M, Wilk A, Shin SY, Glass D, Travers M, Min JL, Ring S, Ho K, Thorleifsson G, Kong A, Thorsteindottir U, Ainali C, Dimas AS, Hassanali N, Ingle C, Knowles D, Krestyaninova M, Lowe CE, Di Meglio P, Montgomery SB, Parts L, Potter S, Surdulescu G, Tsaprouni L, Tsoka S, Bataille V, Durbin R, Nestle FO, O'Rahilly S, Soranzo N, Lindgren CM, Zondervan KT, Ahmadi KR, Schadt EE, Stefansson K, Smith GD, McCarthy MI, Deloukas P, Dermitzakis ET, Spector TD, Multiple Tissue Human Expression Resource (MuTHER) Consortium | Nature genetics | 22941192 | Nat Genet | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22941192 |
| 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 M, Manning Fox JE, Dai X, Barrett A, Grey C, Li L, Bennett AJ, Johnson PR, Rajotte RV, Gaulton KJ, Dermitzakis ET, MacDonald PE, McCarthy MI, Gloyn AL | PLoS genetics | 26624892 | PLoS Genet | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26624892 |
| 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 | 26624926 | Transl Psychiatry | 2015 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/26624926 |
| Rare and common regulatory variation in population-scale sequenced human genomes. | Montgomery SB, Lappalainen T, Gutierrez-Arcelus M, Dermitzakis ET | PLoS genetics | 21811411 | PLoS Genet | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21811411 |
| Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing. | Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, Gameroff MJ, Gindes H, Adams P, Goes FS, Mondimore FM, MacKinnon DF, Notes L, Schweizer B, Furman D, Montgomery SB, Urban AE, Koller D, Levinson DF | Molecular psychiatry | 24296977 | Mol Psychiatry | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24296977 |
| Transcriptome and genome sequencing uncovers functional variation in humans. | Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET | Nature | 24037378 | Nature | 2013 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/24037378 |
| Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci. | Thurner M, van de Bunt M, Torres JM, Mahajan A, Nylander V, Bennett AJ, Gaulton KJ, Barrett A, Burrows C, Bell CG, Lowe R, Beck S, Rakyan VK, Gloyn AL, McCarthy MI | eLife | 29412141 | Elife | 2018 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/29412141 |
| Sex-biased genetic effects on gene regulation in humans. | Dimas AS, Nica AC, Montgomery SB, Stranger BE, Raj T, Buil A, Giger T, Lappalainen T, Gutierrez-Arcelus M, MuTHER Consortium, McCarthy MI, Dermitzakis ET | Genome research | 22960374 | Genome Res | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22960374 |
| Putative cis-regulatory drivers in colorectal cancer. | Ongen H, Andersen CL, Bramsen JB, Oster B, Rasmussen MH, Ferreira PG, Sandoval J, Vidal E, Whiffin N, Planchon A, Padioleau I, Bielser D, Romano L, Tomlinson I, Houlston RS, Esteller M, Orntoft TF, Dermitzakis ET | Nature | 25079323 | Nature | 2014 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/25079323 |
| Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. | Small KS, Hedman AK, Grundberg E, Nica AC, Thorleifsson G, Kong A, Thorsteindottir U, Shin SY, Richards HB, GIANT Consortium, MAGIC Investigators, DIAGRAM Consortium, Soranzo N, Ahmadi KR, Lindgren CM, Stefansson K, Dermitzakis ET, Deloukas P, Spector TD, McCarthy MI, MuTHER Consortium | Nature genetics | 21572415 | Nat Genet | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21572415 |
| Estimation of alternative splicing variability in human populations. | Gonzàlez-Porta M, Calvo M, Sammeth M, Guigó R | Genome research | 22113879 | Genome Res | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22113879 |
| Gene expression changes with age in skin, adipose tissue, blood and brain. | Glass D, Viñuela A, Davies MN, Ramasamy A, Parts L, Knowles D, Brown AA, Hedman AK, Small KS, Buil A, Grundberg E, Nica AC, Di Meglio P, Nestle FO, Ryten M, UK Brain Expression consortium, MuTHER consortium, Durbin R, McCarthy MI, Deloukas P, Dermitzakis ET, Weale ME, Bataille V, Spector TD | Genome biology | 23889843 | Genome Biol | 2013 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/23889843 |
| Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. | 't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M, GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T | Nature biotechnology | 24037425 | Nat Biotechnol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24037425 |
| Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. | Ferreira PG, Patalano S, Chauhan R, Ffrench-Constant R, Gabaldón T, Guigó R, Sumner S | Genome biology | 23442883 | Genome Biol | 2013 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/23442883 |
| IRBIS: a systematic search for conserved complementarity. | Pervouchine DD | RNA (New York, N.Y.) | 25142064 | RNA | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25142064 |
| Analysis of mitochondrial m1A/G RNA modification reveals links to nuclear genetic variants and associated disease processes. | Ali AT, Idaghdour Y, Hodgkinson A | Communications biology | 32221480 | Commun Biol | 2020 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/32221480 |
| The GEM mapper: fast, accurate and versatile alignment by filtration. | Marco-Sola S, Sammeth M, Guigó R, Ribeca P | Nature methods | 23103880 | Nat Methods | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23103880 |
| Alterations observed in the interferon α and β signaling pathway in MDD patients are marginally influenced by cis-acting alleles. | Magri C, Giacopuzzi E, Sacco C, Bocchio-Chiavetto L, Minelli A, Gennarelli M | Scientific reports | 33436853 | Sci Rep | 2021 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/33436853 |
| Genetic risk factors for type 2 diabetes: a trans-regulatory genetic architecture? | Elbein SC, Gamazon ER, Das SK, Rasouli N, Kern PA, Cox NJ | American journal of human genetics | 22958899 | Am J Hum Genet | 2012 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/22958899 |
| Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants. | Gamazon ER, Badner JA, Cheng L, Zhang C, Zhang D, Cox NJ, Gershon ES, Kelsoe JR, Greenwood TA, Nievergelt CM, Chen C, McKinney R, Shilling PD, Schork NJ, Smith EN, Bloss CS, Nurnberger JI, Edenberg HJ, Foroud T, Koller DL, Scheftner WA, Coryell W, Rice J, Lawson WB, Nwulia EA, Hipolito M, Byerley W, McMahon FJ, Schulze TG, Berrettini WH, Potash JB, Zandi PP, Mahon PB, McInnis MG, Zöllner S, Zhang P, Craig DW, Szelinger S, Barrett TB, Liu C | Molecular psychiatry | 22212596 | Mol Psychiatry | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22212596 |
| A genome-wide integrative study of microRNAs in human liver. | Gamazon ER, Innocenti F, Wei R, Wang L, Zhang M, Mirkov S, Ramírez J, Huang RS, Cox NJ, Ratain MJ, Liu W | BMC genomics | 23758991 | BMC Genomics | 2013 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/23758991 |
| An exponential combination procedure for set-based association tests in sequencing studies. | Chen LS, Hsu L, Gamazon ER, Cox NJ, Nicolae DL | American journal of human genetics | 23159251 | Am J Hum Genet | 2012 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/23159251 |
| Trans-population analysis of genetic mechanisms of ethnic disparities in neuroblastoma survival. | Gamazon ER, Pinto N, Konkashbaev A, Im HK, Diskin SJ, London WB, Maris JM, Dolan ME, Cox NJ, Cohn SL | Journal of the National Cancer Institute | 23243203 | J Natl Cancer Inst | 2013 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/23243203 |
| Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. | Lee Y, Li H, Li J, Rebman E, Achour I, Regan KE, Gamazon ER, Chen JL, Yang XH, Cox NJ, Lussier YA | Journal of the American Medical Informatics Association : JAMIA | 23355459 | J Am Med Inform Assoc | 2013 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/23355459 |
| Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. | Gamazon ER, Huang RS, Dolan ME, Cox NJ, Im HK | Frontiers in genetics | 23755062 | Front Genet | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23755062 |
| On sharing quantitative trait GWAS results in an era of multiple-omics data and the limits of genomic privacy. | Im HK, Gamazon ER, Nicolae DL, Cox NJ | American journal of human genetics | 22463877 | Am J Hum Genet | 2012 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/22463877 |
| Marbled inflation from population structure in gene-based association studies with rare variants. | Liu Q, Nicolae DL, Chen LS | Genetic epidemiology | 23468125 | Genet Epidemiol | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23468125 |
| Validation of Monte Carlo estimates of three-class ideal observer operating points for normal data. | Edwards DC | Academic radiology | 23747155 | Acad Radiol | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23747155 |
| Variants affecting exon skipping contribute to complex traits. | Lee Y, Gamazon ER, Rebman E, Lee Y, Lee S, Dolan ME, Cox NJ, Lussier YA | PLoS genetics | 23133393 | PLoS Genet | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23133393 |
| A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. | Gamazon ER, Nicolae DL, Cox NJ | PLoS genetics | 21304891 | PLoS Genet | 2011 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/21304891 |
| Copy number polymorphisms and anticancer pharmacogenomics. | Gamazon ER, Huang RS, Dolan ME, Cox NJ | Genome biology | 21609475 | Genome Biol | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21609475 |
| Cross-disorder genome-wide analyses suggest a complex genetic relationship between Tourette's syndrome and OCD. | Yu D, Mathews CA, Scharf JM, Neale BM, Davis LK, Gamazon ER, Derks EM, Evans P, Edlund CK, Crane J, Fagerness JA, Osiecki L, Gallagher P, Gerber G, Haddad S, Illmann C, McGrath LM, Mayerfeld C, Arepalli S, Barlassina C, Barr CL, Bellodi L, Benarroch F, Berrió GB, Bienvenu OJ, Black DW, Bloch MH, Brentani H, Bruun RD, Budman CL, Camarena B, Campbell DD, Cappi C, Silgado JC, Cavallini MC, Chavira DA, Chouinard S, Cook EH, Cookson MR, Coric V, Cullen B, Cusi D, Delorme R, Denys D, Dion Y, Eapen V, Egberts K, Falkai P, Fernandez T, Fournier E, Garrido H, Geller D, Gilbert DL, Girard SL, Grabe HJ, Grados MA, Greenberg BD, Gross-Tsur V, Grünblatt E, Hardy J, Heiman GA, Hemmings SM, Herrera LD, Hezel DM, Hoekstra PJ, Jankovic J, Kennedy JL, King RA, Konkashbaev AI, Kremeyer B, Kurlan R, Lanzagorta N, Leboyer M, Leckman JF, Lennertz L, Liu C, Lochner C, Lowe TL, Lupoli S, Macciardi F, Maier W, Manunta P, Marconi M, McCracken JT, Mesa Restrepo SC, Moessner R, Moorjani P, Morgan J, Muller H, Murphy DL, Naarden AL, Nurmi E, Ochoa WC, Ophoff RA, Pakstis AJ, Pato MT, Pato CN, Piacentini J, Pittenger C, Pollak Y, Rauch SL, Renner T, Reus VI, Richter MA, Riddle MA, Robertson MM, Romero R, Rosário MC, Rosenberg D, Ruhrmann S, Sabatti C, Salvi E, Sampaio AS, Samuels J, Sandor P, Service SK, Sheppard B, Singer HS, Smit JH, Stein DJ, Strengman E, Tischfield JA, Turiel M, Valencia Duarte AV, Vallada H, Veenstra-VanderWeele J, Walitza S, Wang Y, Weale M, Weiss R, Wendland JR, Westenberg HG, Shugart YY, Hounie AG, Miguel EC, Nicolini H, Wagner M, Ruiz-Linares A, Cath DC, McMahon W, Posthuma D, Oostra BA, Nestadt G, Rouleau GA, Purcell S, Jenike MA, Heutink P, Hanna GL, Conti DV, Arnold PD, Freimer NB, Stewart SE, Knowles JA, Cox NJ, Pauls DL | The American journal of psychiatry | 25158072 | Am J Psychiatry | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25158072 |
| Matrix eQTL: ultra fast eQTL analysis via large matrix operations. | Shabalin AA | Bioinformatics (Oxford, England) | 22492648 | Bioinformatics | 2012 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/22492648 |
| Reprioritizing genetic associations in hit regions using LASSO-based resample model averaging. | Valdar W, Sabourin J, Nobel A, Holmes CC | Genetic epidemiology | 22549815 | Genet Epidemiol | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22549815 |
| eQTL Mapping Using RNA-seq Data. | Sun W, Hu Y | Statistics in biosciences | 23667399 | Stat Biosci | 2013 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/23667399 |
| Toxicogenetics: population-based testing of drug and chemical safety in mouse models. | Rusyn I, Gatti DM, Wiltshire T, Kleeberger SR, Threadgill DW | Pharmacogenomics | 20704464 | Pharmacogenomics | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20704464 |
| An empirical Bayes approach for multiple tissue eQTL analysis. | Li G, Shabalin AA, Rusyn I, Wright FA, Nobel AB | Biostatistics (Oxford, England) | 29029013 | Biostatistics | 2018 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/29029013 |
| JOINT AND INDIVIDUAL VARIATION EXPLAINED (JIVE) FOR INTEGRATED ANALYSIS OF MULTIPLE DATA TYPES. | Lock EF, Hoadley KA, Marron JS, Nobel AB | The annals of applied statistics | 23745156 | Ann Appl Stat | 2013 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/23745156 |
| Computational tools for discovery and interpretation of expression quantitative trait loci. | Wright FA, Shabalin AA, Rusyn I | Pharmacogenomics | 22304583 | Pharmacogenomics | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22304583 |
| Heading down the wrong pathway: on the influence of correlation within gene sets. | Gatti DM, Barry WT, Nobel AB, Rusyn I, Wright FA | BMC genomics | 20955544 | BMC Genomics | 2010 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/20955544 |
| Quantification of population structure using correlated SNPs by shrinkage principal components. | Zou F, Lee S, Knowles MR, Wright FA | Human heredity | 20413978 | Hum Hered | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20413978 |
| seeQTL: a searchable database for human eQTLs. | Xia K, Shabalin AA, Huang S, Madar V, Zhou YH, Wang W, Zou F, Sun W, Sullivan PF, Wright FA | Bioinformatics (Oxford, England) | 22171328 | Bioinformatics | 2012 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/22171328 |
| A tiered, Bayesian approach to estimating of population variability for regulatory decision-making. | Chiu WA, Wright FA, Rusyn I | ALTEX | 27960008 | ALTEX | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/27960008 |
| DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors. | Walter V, Nobel AB, Wright FA | Bioinformatics (Oxford, England) | 21183584 | Bioinformatics | 2011 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21183584 |
