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

Removing unwanted variation between samples in Hi-C experiments.

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

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

Subject Terms: Locus (Genetics), Sampling (Process)

Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines

Authors: Benaglio, Paola, Zhu, Han, Okino, Mei-Lin, Yan, Jian, Elgamal, Ruth, Nariai, Naoki, Beebe, Elisha, Korgaonkar, Katha, Qiu, Yunjiang, Donovan, Margaret K.R., Chiou, Joshua, Wang, Gaowei, Newsome, Jacklyn, Kaur, Jaspreet, Miller, Michael, Preissl, Sebastian, Corban, Sierra, Aylward, Anthony, Taipale, Jussi, Ren, Bing, Frazer, Kelly A., Sander, Maike, Gaulton, Kyle J.

Source: In Cell Genomics 14 December 2022 2(12)

A single-cell atlas of chromatin accessibility in the human genome

Authors: Zhang, Kai, Hocker, James D., Miller, Michael, Hou, Xiaomeng, Chiou, Joshua, Poirion, Olivier B., Qiu, Yunjiang, Li, Yang E., Gaulton, Kyle J., Wang, Allen, Preissl, Sebastian, Ren, Bing

Source: In Cell 24 November 2021 184(24):5985-6001

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

FIREcaller: Detecting frequently interacting regions from Hi-C data

Authors: Crowley, Cheynna, Yang, Yuchen, Qiu, Yunjiang, Hu, Benxia, Abnousi, Armen, Lipiński, Jakub, Plewczyński, Dariusz, Wu, Di, Won, Hyejung, Ren, Bing, Hu, Ming, Li, Yun

Source: Computational and Structural Biotechnology Journal. 19:355-362

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100186876709.0x000001&indx=1&recIds=ETOCvdc_100186876709.0x000001

The Hippo pathway effector proteins YAP and TAZ have both distinct and overlapping functions in the cell

Alternate Title: YAP and TAZ have both distinct and overlapping functions (English)

Authors: Plouffe, Steven W., Lin, Kimberly C., Moore, Jerrell L., 3rd, Tan, Frederick E., Ma, Shenghong, Ye, Zhen, Qiu, Yunjiang, Ren, Bing, Guan, Kun-Liang

Source: In Journal of Biological Chemistry 13 July 2018 293(28):11230-11240

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

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

Source: Genome biology. 20(1):1-25

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190650750.0x000001&indx=1&recIds=ETOCvdc_100190650750.0x000001

Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk

Authors: Greenwald, William, Chiou, Joshua, Yan, Jian, Qiu, Yunjiang, Dai, Ning, Wang, Allen, Nariai, Naoki, Aylward, Anthony, Han, Jee, Kadakia, Nikita, Regue, Laura, Okino, Mei-Lin, Drees, Frauke, Kramer, Dana, Vinckier, Nicholas, Minichiello, Liliana, Gorkin, David, Avruch, Joseph, Frazer, Kelly, Sander, Maike, Ren, Bing, Gaulton, Kyle

Source: Nature communications. 10(1):1-12

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100138177701.0x000001&indx=1&recIds=ETOCvdc_100138177701.0x000001

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

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

Source: Nature communications. 10(1):1-16

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100132429870.0x000001&indx=1&recIds=ETOCvdc_100132429870.0x000001

Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates

Authors: Wang, Allen, Yue, Feng, Li, Yan, Xie, Ruiyu, Harper, Thomas, Patel, Nisha A., Muth, Kayla, Palmer, Jeffrey, Qiu, Yunjiang, Wang, Jinzhao, Lam, Dieter K., Raum, Jeffrey C., Stoffers, Doris A., Ren, Bing, Sander, Maike

Source: In Cell Stem Cell 2 April 2015 16(4):386-399

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.

Authors: Miko, Henriette^1,2 (AUTHOR), Qiu, Yunjiang^3,4 (AUTHOR), Gaertner, Bjoern^5,6 (AUTHOR), Sander, Maike^5,6 (AUTHOR), Ohler, Uwe^1,2,7 (AUTHOR) uwe.ohler@mdc-berlin.de

Source: BMC Genomics. 1/28/2021, Vol. 22 Issue 1, p1-19. 19p.

Subject Terms: *BASE pairs, *TIME series analysis, *GENETIC regulation, *EXPECTATION-maximization algorithms, *DATABASES, *GENE expression

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

Authors: Schmitt, Anthony D., Hu, Ming, Jung, Inkyung, Xu, Zheng, Qiu, Yunjiang, Tan, Catherine L., Li, Yun, Lin, Shin, Lin, Yiing, Barr, Cathy L., Ren, Bing

Source: Cell reports. 17(8):2042-2059

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100050073307.0x000001&indx=1&recIds=ETOCvdc_100050073307.0x000001

A deep population reference panel of tandem repeat variation.

Authors: Ziaei Jam, Helyaneh, Li, Yang, DeVito, Ross, Mousavi, Nima, Ma, Nichole, Lujumba, Ibra, Adam, Yagoub, Maksimov, Mikhail, Huang, Bonnie, Dolzhenko, Egor, Qiu, Yunjiang, Kakembo, Fredrick Elishama, Joseph, Habi, Onyido, Blessing, Adeyemi, Jumoke, Bakhtiari, Mehrdad, Park, Jonghun, Javadzadeh, Sara, Jjingo, Daudi, Adebiyi, Ezekiel

Source: Nature Communications; 10/23/2023, Vol. 14 Issue 1, p1-15, 15p

Subject Terms: TANDEM repeats, HUMAN genetic variation, SINGLE nucleotide polymorphisms, SHORT tandem repeat analysis, HUMAN genome, WHOLE genome sequencing, HETEROZYGOSITY

REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats.

Authors: Dolzhenko, Egor, Weisburd, Ben, Ibañez, Kristina, Rajan-Babu, Indhu-Shree, Anyansi, Christine, Bennett, Mark F., Billingsley, Kimberley, Carroll, Ashley, Clamons, Samuel, Danzi, Matt C., Deshpande, Viraj, Ding, Jinhui, Fazal, Sarah, Halman, Andreas, Jadhav, Bharati, Qiu, Yunjiang, Richmond, Phillip A., Saunders, Christopher T., Scheffler, Konrad, van Vugt, Joke J. F. A.

Source: Genome Medicine; 8/10/2022, Vol. 14 Issue 1, p1-10, 10p

Subject Terms: TANDEM repeats, SHORT tandem repeat analysis, MICROSATELLITE repeats, AMYOTROPHIC lateral sclerosis, WHOLE genome sequencing, HUNTINGTON disease

Efficient and Specific Multi-Locus Editing of Allogeneic CAR T Cells for Hypoimmunity during Large Scale Manufacture Using Cas12b

Authors: Chaivorapol, Christina ^*, Beauchesne, Pascal ^*, De Jesus, Rowena ^*, Dowdle, William E ^*, Chen, Xiaoyu ^*, Bayley, Alison ^*, Qiu, Yunjiang ^*, Birnberg, Andrew ^*, Zheng, Yu ^*, Montalbano, Antonino ^*, Liu, Angela ^*, Zafar, Misbah ^*, Manner, Karl ^*, Ankala, Ramya ^*, Tham, Eleonore ^*, Shah, Heer ^*, Lam, Ben ^*, Lock, Jaclyn ^*, Weng, Lindong ^*, Watts, Kate ^*, Valdiosera, Amanda ^*, Davis, Kimberly ^*, Wang, Lei ^*, Kangeyan, PhD, Divy ^*, Devos, Nicolas ^*, Wong, Athena ^*, Lih, Jason ^*, Rebar, Edward J ^*

Source: In Blood 15 November 2022 140 Supplement 1:1606-1607

Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors.

Authors: Geusz, Ryan J., Wang, Allen, Lam, Dieter K., Vinckier, Nicholas K., Alysandratos, Konstantinos-Dionysios, Roberts, David A., Wang, Jinzhao, Kefalopoulou, Samy, Ramirez, Araceli, Qiu, Yunjiang, Chiou, Joshua, Gaulton, Kyle J., Ren, Bing, Kotton, Darrell N., Sander, Maike

Source: Nature Communications; 11/17/2021, Vol. 12 Issue 1, p1-19, 19p

Subject Terms: HUMAN stem cells, MORPHOGENESIS, LUNG development, CHROMATIN, TRANSCRIPTION factors, PANCREAS

An atlas of gene regulatory elements in adult mouse cerebrum

Authors: Li, Yang Eric, Preissl, Sebastian, Hou, Xiaomeng, Zhang, Ziyang, Zhang, Kai, Qiu, Yunjiang, Poirion, Olivier B., Li, Bin, Chiou, Joshua, Liu, Hanqing, Pinto-Duarte, Antonio, Kubo, Naoki, Yang, Xiaoyu, Fang, Rongxin, Wang, Xinxin, Han, Jee Yun, Lucero, Jacinta, Yan, Yiming, Miller, Michael, Kuan, Samantha, Gorkin, David, Gaulton, Kyle J., Shen, Yin, Nunn, Michael, Mukamel, Eran A., Behrens, M. Margarita, Ecker, Joseph R., Ren, Bing

Source: Nature; October 2021, Vol. 598 Issue: 7879 p129-136, 8p

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

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