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dc.contributor.authorRozowsky, Joel
dc.contributor.authorGao, Jiahao
dc.contributor.authorBorsari, Beatrice
dc.contributor.authorYang, Yucheng T
dc.contributor.authorGaleev, Timur
dc.contributor.authorGürsoy, Gamze
dc.contributor.authorEpstein, Charles B
dc.contributor.authorXiong, Kun
dc.contributor.authorXu, Jinrui
dc.contributor.authorLi, Tianxiao
dc.contributor.authorLiu, Jason
dc.contributor.authorYu, Keyang
dc.contributor.authorBerthel, Ana
dc.contributor.authorChen, Zhanlin
dc.contributor.authorNavarro, Fabio
dc.contributor.authorSun, Maxwell S
dc.contributor.authorWright, James
dc.contributor.authorChang, Justin
dc.contributor.authorCameron, Christopher J F
dc.contributor.authorShoresh, Noam
dc.contributor.authorGaskell, Elizabeth
dc.contributor.authorDrenkow, Jorg
dc.contributor.authorAdrian, Jessika
dc.contributor.authorAganezov, Sergey
dc.contributor.authorAguet, François
dc.contributor.authorBalderrama-Gutierrez, Gabriela
dc.contributor.authorBanskota, Samridhi
dc.contributor.authorCorona, Guillermo Barreto
dc.contributor.authorChee, Sora
dc.contributor.authorChhetri, Surya B
dc.contributor.authorCortez Martins, Gabriel Conte
dc.contributor.authorDanyko, Cassidy
dc.contributor.authorDavis, Carrie A
dc.contributor.authorFarid, Daniel
dc.contributor.authorFarrell, Nina P
dc.contributor.authorGabdank, Idan
dc.contributor.authorGofin, Yoel
dc.contributor.authorGorkin, David U
dc.contributor.authorGu, Mengting
dc.contributor.authorHecht, Vivian
dc.contributor.authorHitz, Benjamin C
dc.contributor.authorIssner, Robbyn
dc.contributor.authorJiang, Yunzhe
dc.contributor.authorKirsche, Melanie
dc.contributor.authorKong, Xiangmeng
dc.contributor.authorLam, Bonita R
dc.contributor.authorLi, Shantao
dc.contributor.authorLi, Bian
dc.contributor.authorLi, Xiqi
dc.contributor.authorLin, Khine Zin
dc.contributor.authorLuo, Ruibang
dc.contributor.authorMackiewicz, Mark
dc.contributor.authorMeng, Ran
dc.contributor.authorMoore, Jill E
dc.contributor.authorMudge, Jonathan
dc.contributor.authorNelson, Nicholas
dc.contributor.authorNusbaum, Chad
dc.contributor.authorPopov, Ioann
dc.contributor.authorPratt, Henry E
dc.contributor.authorQiu, Yunjiang
dc.contributor.authorRamakrishnan, Srividya
dc.contributor.authorRaymond, Joe
dc.contributor.authorSalichos, Leonidas
dc.contributor.authorScavelli, Alexandra
dc.contributor.authorSchreiber, Jacob M
dc.contributor.authorSedlazeck, Fritz J
dc.contributor.authorSee, Lei Hoon
dc.contributor.authorSherman, Rachel M
dc.contributor.authorShi, Xu
dc.contributor.authorShi, Minyi
dc.contributor.authorSloan, Cricket Alicia
dc.contributor.authorStrattan, J Seth
dc.contributor.authorTan, Zhen
dc.contributor.authorTanaka, Forrest Y
dc.contributor.authorVlasova, Anna
dc.contributor.authorWang, Jun
dc.contributor.authorWerner, Jonathan
dc.contributor.authorWilliams, Brian
dc.contributor.authorXu, Min
dc.contributor.authorYan, Chengfei
dc.contributor.authorYu, Lu
dc.contributor.authorZaleski, Christopher
dc.contributor.authorZhang, Jing
dc.contributor.authorArdlie, Kristin
dc.contributor.authorCherry, J Michael
dc.contributor.authorMendenhall, Eric M
dc.contributor.authorNoble, William S
dc.contributor.authorWeng, Zhiping
dc.contributor.authorLevine, Morgan E
dc.contributor.authorDobin, Alexander
dc.contributor.authorWold, Barbara
dc.contributor.authorMortazavi, Ali
dc.contributor.authorRen, Bing
dc.contributor.authorGillis, Jesse
dc.contributor.authorMyers, Richard M
dc.contributor.authorSnyder, Michael P
dc.contributor.authorChoudhary, Jyoti
dc.contributor.authorMilosavljevic, Aleksandar
dc.contributor.authorSchatz, Michael C
dc.contributor.authorBernstein, Bradley E
dc.contributor.authorGuigó, Roderic
dc.contributor.authorGingeras, Thomas R
dc.contributor.authorGerstein, Mark
dc.date.accessioned2023-04-14T18:09:21Z
dc.date.available2023-04-14T18:09:21Z
dc.date.issued2023-03-30
dc.identifier.citationRozowsky 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. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 2023 Mar 30;186(7):1493-1511.e40. doi: 10.1016/j.cell.2023.02.018. PMID: 37001506; PMCID: PMC10074325.en_US
dc.identifier.eissn1097-4172
dc.identifier.doi10.1016/j.cell.2023.02.018en_US
dc.identifier.pmid37001506
dc.identifier.urihttp://hdl.handle.net/20.500.14038/51962
dc.description.abstractUnderstanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.en_US
dc.language.isoenen_US
dc.relation.ispartofCellen_US
dc.relation.urlhttps://doi.org/10.1016/j.cell.2023.02.018en_US
dc.rightsCopyright 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).en_US
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectENCODEen_US
dc.subjectGTExen_US
dc.subjectallele-specific activityen_US
dc.subjecteQTLsen_US
dc.subjectfunctional epigenomesen_US
dc.subjectfunctional genomicsen_US
dc.subjectgenome annotationsen_US
dc.subjectpersonal genomeen_US
dc.subjectpredictive modelsen_US
dc.subjectstructural variantsen_US
dc.subjecttissue specificityen_US
dc.subjecttransformer modelen_US
dc.titleThe EN-TEx resource of multi-tissue personal epigenomes & variant-impact modelsen_US
dc.typeJournal Articleen_US
dc.source.journaltitleCell
dc.source.volume186
dc.source.issue7
dc.source.beginpage1493
dc.source.endpage1511.e40
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryUnited States
dc.identifier.journalCell
refterms.dateFOA2023-04-14T18:09:22Z
dc.contributor.departmentMorningside Graduate School of Biomedical Sciencesen_US
dc.contributor.departmentProgram in Bioinformatics and Integrative Biologyen_US
dc.contributor.studentHenry Pratt


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Copyright 2023 The Authors. Published by Elsevier Inc.
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Except where otherwise noted, this item's license is described as Copyright 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).