The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Authors: Rozowsky, Joel, Gao, Jiahao, Borsari, Beatrice, Yang, Yucheng T., Galeev, Timur, Gürsoy, Gamze, Epstein, Charles B., Xiong, Kun, Xu, Jinrui, Li, Tianxiao, Liu, Jason, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Sun, Maxwell S., Wright, James, Chang, Justin, Cameron, Christopher J.F., Shoresh, Noam, Gaskell, Elizabeth, Drenkow, Jorg, Adrian, Jessika, Aganezov, Sergey, Aguet, François, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo Barreto, Chee, Sora, Chhetri, Surya B., Cortez Martins, Gabriel Conte, Danyko, Cassidy, Davis, Carrie A., Farid, Daniel, Farrell, Nina P., Gabdank, Idan, Gofin, Yoel, Gorkin, David U., Gu, Mengting, Hecht, Vivian, Hitz, Benjamin C., Issner, Robbyn, Jiang, Yunzhe, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita R., Li, Shantao, Li, Bian, Li, Xiqi, Lin, Khine Zin, Luo, Ruibang, Mackiewicz, Mark, Meng, Ran, Moore, Jill E., Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry E., Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob M., Sedlazeck, Fritz J., See, Lei Hoon, Sherman, Rachel M., Shi, Xu, Shi, Minyi, Sloan, Cricket Alicia, Strattan, J Seth, Tan, Zhen, Tanaka, Forrest Y., Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Ardlie, Kristin, Cherry, J Michael, Mendenhall, Eric M., Noble, William S., Weng, Zhiping, Levine, Morgan E., Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard M., Snyder, Michael P., Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael C., Bernstein, Bradley E., Guigó, Roderic, Gingeras, Thomas R., Gerstein, Mark

Source: In Cell 30 March 2023 186(7):1493-1511

Rapid changes in chromatin structure during dedifferentiation of primary hepatocytes in vitro

Authors: Seirup, Morten, Sengupta, Srikumar, Swanson, Scott, McIntosh, Brian E., Collins, Mike, Chu, Li-Fang, Cheng, Zhang, Gorkin, David U., Duffin, Bret, Bolin, Jennifer M., Argus, Cara, Stewart, Ron, Thomson, James A.

Source: In Genomics May 2022 114(3)

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

Authors: Yu, Miao, Zemke, Nathan R., Chen, Ziyin, Juric, Ivan, Hu, Rong, Raviram, Ramya, Abnousi, Armen, Fang, Rongxin, Zhang, Yanxiao, Gorkin, David U., Li, Yang E., Zhao, Yuan, Lee, Lindsay, Mishra, Shreya, Schmitt, Anthony D., Qiu, Yunjiang, Dickel, Diane E., Visel, Axel, Pennacchio, Len A., Hu, Ming, Ren, Bing

Source: Nature Structural and Molecular Biology; March 2025, Vol. 32 Issue: 3 p479-490, 12p

N6-methyladenine DNA Modification in Glioblastoma

Authors: Xie, Qi, Wu, Tao P., Gimple, Ryan C., Li, Zheng, Prager, Briana C., Wu, Qiulian, Yu, Yang, Wang, Pengcheng, Wang, Yinsheng, Gorkin, David U., Zhang, Cheng, Dowiak, Alexis V., Lin, Kaixuan, Zeng, Chun, Sui, Yinghui, Kim, Leo J.Y., Miller, Tyler E., Jiang, Li, Lee-Poturalski, Christine, Huang, Zhi, Fang, Xiaoguang, Zhai, Kui, Mack, Stephen C., Sander, Maike, Bao, Shideng, Kerstetter-Fogle, Amber E., Sloan, Andrew E., Xiao, Andrew Z., Rich, Jeremy N.

Source: In Cell 15 November 2018 175(5):1228-1243

Removing unwanted variation between samples in Hi-C experiments.

Authors: Fletez-Brant, Kipper^1,2, cafletezbrant@gmail.com, Qiu, Yunjiang^3,4, Gorkin, David U^4,5,6, Hu, Ming⁷, Hansen, Kasper D^1,2

Source: Briefings in Bioinformatics; May2024, Vol. 25 Issue 3, p1-12, 12p

Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex immune trait variants using single nucleus ATAC-seq in peripheral blood.

Authors: Benaglio, Paola¹, Newsome, Jacklyn², Han, Jee Yun³, Chiou, Joshua⁴, Aylward, Anthony², Corban, Sierra¹, Miller, Michael³, Okino, Mei-Lin¹, Kaur, Jaspreet¹, Preissl, Sebastian³, Gorkin, David U.³, Gaulton, Kyle J.¹, kgaulton@ucsd.edu

Source: PLoS Genetics; 6/8/2023, Vol. 19 Issue 6, p1-28, 28p

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

Authors: He, Yupeng, Gorkin, David U., Dickel, Diane E., Nery, Joseph R., Castanon, Rosa G., Lee, Ah Young, Shen, Yin, Visel, Axel, Pennacchio, Len A., Ren, Bing, Ecker, Joseph R.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2017 Feb . 114(9), E1633-E1640.

Access URL: https://www.jstor.org/stable/26479515

Chromatin Domains: The Unit of Chromosome Organization

Authors: Dixon, Jesse R., Gorkin, David U., Ren, Bing

Source: In Molecular Cell 2 June 2016 62(5):668-680

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

Authors: Guo, Ya, Xu, Quan, Canzio, Daniele, Shou, Jia, Li, Jinhuan, Gorkin, David U., Jung, Inkyung, Wu, Haiyang, Zhai, Yanan, Tang, Yuanxiao, Lu, Yichao, Wu, Yonghu, Jia, Zhilian, Li, Wei, Zhang, Michael Q., Ren, Bing, Krainer, Adrian R., Maniatis, Tom, Wu, Qiang

Source: In Cell 13 August 2015 162(4):900-910

The 3D Genome in Transcriptional Regulation and Pluripotency

Authors: Gorkin, David U., Leung, Danny, Ren, Bing

Source: In Cell Stem Cell 5 June 2014 14(6):762-775

A Polymorphism in IRF4 Affects Human Pigmentation through a Tyrosinase-Dependent MITF/TFAP2A Pathway

Authors: Praetorius, Christian, Grill, Christine, Stacey, Simon N., Metcalf, Alexander M., Gorkin, David U., Robinson, Kathleen C., Van Otterloo, Eric, Kim, Reuben S.Q., Bergsteinsdottir, Kristin, Ogmundsdottir, Margret H., Magnusdottir, Erna, Mishra, Pravin J., Davis, Sean R., Guo, Theresa, Zaidi, M. Raza, Helgason, Agnar S., Sigurdsson, Martin I., Meltzer, Paul S., Merlino, Glenn, Petit, Valerie, Larue, Lionel, Loftus, Stacie K., Adams, David R., Sobhiafshar, Ulduz, Emre, N.C. Tolga, Pavan, William J., Cornell, Robert, Smith, Aaron G., McCallion, Andrew S., Fisher, David E., Stefansson, Kari, Sturm, Richard A., Steingrimsson, Eirikur

Source: In Cell 21 November 2013 155(5):1022-1033

Common DNA sequence variation influences 3-dimensional conformation of the human genome

Authors: Gorkin, David U., Qiu, Yunjiang, Hu, Ming, Fletez-Brant, Kipper, Liu, Tristin, Schmitt, Anthony D., Noor, Amina, Chiou, Joshua, Gaulton, Kyle J., Sebat, Jonathan, Li, Yun, Hansen, Kasper D., Ren, Bing

Source: Genome biology. 20(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100130835114.0x000001&indx=1&recIds=ETOCvdc_100130835114.0x000001

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Authors: Chaisson, Mark J. P., Sanders, Ashley D., Zhao, Xuefang, Malhotra, Ankit, Porubsky, David, Rausch, Tobias, Gardner, Eugene J., Rodriguez, Oscar L., Guo, Li, Collins, Ryan L., Fan, Xian, Wen, Jia, Handsaker, Robert E., Fairley, Susan, Kronenberg, Zev N., Kong, Xiangmeng, Hormozdiari, Fereydoun, Lee, Dillon, Wenger, Aaron M., Hastie, Alex R., Antaki, Danny, Anantharaman, Thomas, Audano, Peter A., Brand, Harrison, Cantsilieris, Stuart, Cao, Han, Cerveira, Eliza, Chen, Chong, Chen, Xintong, Chin, Chen-Shan, Chong, Zechen, Chuang, Nelson T., Lambert, Christine C., Church, Deanna M., Clarke, Laura, Farrell, Andrew, Flores, Joey, Galeev, Timur, Gorkin, David U., Gujral, Madhusudan, Guryev, Victor, Heaton, William Haynes, Korlach, Jonas, Kumar, Sushant, Kwon, Jee Young, Lam, Ernest T., Lee, Jong Eun, Lee, Joyce, Lee, Wan-Ping, Lee, Sau Peng, Li, Shantao, Marks, Patrick, Viaud-Martinez, Karine, Meiers, Sascha, Munson, Katherine M., Navarro, Fabio C. P., Nelson, Bradley J., Nodzak, Conor, Noor, Amina, Kyriazopoulou-Panagiotopoulou, Sofia, Pang, Andy W. C., Qiu, Yunjiang, Rosanio, Gabriel, Ryan, Mallory, Stütz, Adrian, Spierings, Diana C. J., Ward, Alistair, Welch, AnneMarie E., Xiao, Ming, Xu, Wei, Zhang, Chengsheng, Zhu, Qihui, Zheng-Bradley, Xiangqun, Lowy, Ernesto, Yakneen, Sergei, McCarroll, Steven, Jun, Goo, Ding, Li, Koh, Chong Lek, Ren, Bing, Flicek, Paul, Chen, Ken, Gerstein, Mark B., Kwok, Pui-Yan, Lansdorp, Peter M., Marth, Gabor T., Sebat, Jonathan, Shi, Xinghua, Bashir, Ali, Ye, Kai, Devine, Scott E., Talkowski, Michael E., Mills, Ryan E., Marschall, Tobias, Korbel, Jan O., Eichler, Evan E., Lee, Charles

Source: Nature communications. 10(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131089632.0x000001&indx=1&recIds=ETOCvdc_100131089632.0x000001

A method to predict the impact of regulatory variants from DNA sequence.

Authors: Lee, Dongwon¹, Gorkin, David U¹, Baker, Maggie¹, McCallion, Andrew S¹, Strober, Benjamin J², Asoni, Alessandro L², Beer, Michael A³

Source: Nature Genetics. Aug2015, Vol. 47 Issue 8, p955-961. 7p. 1 Diagram, 2 Charts, 5 Graphs.

Subject Terms: *DNA, *GENOMICS, *MUTAGENESIS, *AUTOIMMUNE disease diagnosis, *CHROMATIN

Spatiotemporal DNA methylome dynamics of the developing mouse fetus.

Authors: He, Yupeng, Hariharan, Manoj, Gorkin, David U., Dickel, Diane E., Luo, Chongyuan, Castanon, Rosa G., Nery, Joseph R., Lee, Ah Young, Zhao, Yuan, Huang, Hui, Williams, Brian A., Trout, Diane, Amrhein, Henry, Fang, Rongxin, Chen, Huaming, Li, Bin, Visel, Axel, Pennacchio, Len A., Ren, Bing, Ecker, Joseph R.

Source: Nature; 7/30/2020, Vol. 583 Issue 7818, p752-759, 8p, 15 Graphs

An atlas of dynamic chromatin landscapes in mouse fetal development.

Authors: Gorkin, David U., Barozzi, Iros, Zhao, Yuan, Zhang, Yanxiao, Huang, Hui, Lee, Ah Young, Li, Bin, Chiou, Joshua, Wildberg, Andre, Ding, Bo, Zhang, Bo, Wang, Mengchi, Strattan, J. Seth, Davidson, Jean M., Qiu, Yunjiang, Afzal, Veena, Akiyama, Jennifer A., Plajzer-Frick, Ingrid, Novak, Catherine S., Kato, Momoe

Source: Nature; 7/30/2020, Vol. 583 Issue 7818, p744-751, 8p, 23 Graphs

Interpreting type 1 diabetes risk with genetics and single-cell epigenomics

Authors: Chiou, Joshua, Geusz, Ryan J., Okino, Mei-Lin, Han, Jee Yun, Miller, Michael, Melton, Rebecca, Beebe, Elisha, Benaglio, Paola, Huang, Serina, Korgaonkar, Katha, Heller, Sandra, Kleger, Alexander, Preissl, Sebastian, Gorkin, David U., Sander, Maike, Gaulton, Kyle J.

Source: Nature; June 2021, Vol. 594 Issue: 7863 p398-402, 5p

Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk

Authors: Chiou, Joshua, Zeng, Chun, Cheng, Zhang, Han, Jee Yun, Schlichting, Michael, Miller, Michael, Mendez, Robert, Huang, Serina, Wang, Jinzhao, Sui, Yinghui, Deogaygay, Allison, Okino, Mei-Lin, Qiu, Yunjiang, Sun, Ying, Kudtarkar, Parul, Fang, Rongxin, Preissl, Sebastian, Sander, Maike, Gorkin, David U., Gaulton, Kyle J.

Source: Nature Genetics; April 2021, Vol. 53 Issue: 4 p455-466, 12p

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Authors: Moore, Jill E., Purcaro, Michael J., Pratt, Henry E., Epstein, Charles B., Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A., Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L., Freese, Peter, Gorkin, David U., Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A., Mortazavi, Ali, Keller, Cheryl A., Zhang, Xiao-Ou, Elhajjajy, Shaimae I., Huey, Jack, Dickel, Diane E., Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B., Zhang, Jialing, Victorsen, Alec, White, Kevin P., Visel, Axel, Yeo, Gene W., Burge, Christopher B., Lécuyer, Eric, Gilbert, David M., Dekker, Job, Rinn, John, Mendenhall, Eric M., Ecker, Joseph R., Kellis, Manolis, Klein, Robert J., Noble, William S., Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J., Cherry, J. Michael, Myers, Richard M., Ren, Bing, Graveley, Brenton R., Gerstein, Mark B., Pennacchio, Len A., Snyder, Michael P., Bernstein, Bradley E., Wold, Barbara, Hardison, Ross C., Gingeras, Thomas R., Stamatoyannopoulos, John A., Weng, Zhiping

Source: Nature; July 2020, Vol. 583 Issue: 7818 p699-710, 12p

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