Publications

For a complete list of Bing Ren's publications, click here.

This year

  • Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
    Sebastian Preissl, Rongxin Fang, Hui Huang, Yuan Zhao, Ramya Raviram, David U. Gorkin, Yanxiao Zhang, Brandon C. Sos, Veena Afzal, Diane E. Dickel, Samantha Kuan, Axel Visel, Len A. Pennacchio, Kun Zhang, Bing Ren
    Nature Neuroscience, 2018 March 01;21(3): 432--439. doi:10.1038/s41593-018-0079-3

  • Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers
    Jian Yan, Shi-An A. Chen, Andrea Local, Tristin Liu, Yunjiang Qiu, Kristel M. Dorighi, Sebastian Preissl, Chloe M. Rivera, Chaochen Wang, Zhen Ye, Kai Ge, Ming Hu, Joanna Wysocka, Bing Ren
    Cell Research, 2018 February 01;28(2): 204--220. doi:10.1038/cr.2018.1

  • Identification of H3K4me1-associated proteins at mammalian enhancers
    Andrea Local, Hui Huang, Claudio P. Albuquerque, Namit Singh, Ah Young Lee, Wei Wang, Chaochen Wang, Judy E. Hsia, Andrew K. Shiau, Kai Ge, Kevin D. Corbett, Dong Wang, Huilin Zhou, Bing Ren
    Nature Genetics, 2018 January 01;50(1): 73--82. doi:10.1038/s41588-017-0015-6

  • 2017

    • The Three-Dimensional Organization of Mammalian Genomes
      Miao Yu, Bing Ren
      Annual Review of Cell and Developmental Biology, 2017 October 06;33(): 265--289. doi:10.1146/annurev-cellbio-100616-060531

    • A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
      Yarui Diao, Rongxin Fang, Bin Li, Zhipeng Meng, Juntao Yu, Yunjiang Qiu, Kimberly C. Lin, Hui Huang, Tristin Liu, Ryan J. Marina, Inkyung Jung, Yin Shen, Kun-Liang Guan, Bing Ren
      Nature Methods, 2017 June 01;14(6): 629--635. doi:10.1038/nmeth.4264

    • A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis.
      Xiong Xiong, Yanxiao Zhang, Jian Yan, Surbhi Jain, Sora Chee, Bing Ren, Huimin Zhao
      ACS synthetic biology, 2017 March 07;(): . doi:10.1021/acssynbio.6b00358

    • Human centromeric CENP-A chromatin is a homotypic octameric nucleosome at all cell cycle points.
      Yael Nechemia-Arbely, Daniele Fachinetti, Karen H. Miga, Nikolina Sekulic, Gautam V. Soni, Dong Hyun Kim, Adeline K. Wong, Ah Young Lee, Kristen Nguyen, Cees Dekker, Bing Ren, Ben E. Black, Don W. Cleveland
      The Journal of cell biology, 2017 March 06;216(3): 607--621. doi:10.1083/jcb.201608083

    • Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity.
      Kristen M. Turner, Viraj Deshpande, Doruk Beyter, Tomoyuki Koga, Jessica Rusert, Catherine Lee, Bin Li, Karen Arden, Bing Ren, David A. Nathanson, Harley I. Kornblum, Michael D. Taylor, Sharmeela Kaushal, Webster K. Cavenee, Robert Wechsler-Reya, Frank B. Furnari, Scott R. Vandenberg, P. Nagesh Rao, Geoffrey M. Wahl, Vineet Bafna, Paul S. Mischel
      Nature, 2017 March 02;543(7643): 122--125. doi:10.1038/nature21356

    • Improved regulatory element prediction based on tissue-specific local epigenomic signatures.
      Yupeng He, David U. Gorkin, Diane E. Dickel, Joseph R. Nery, Rosa G. Castanon, Ah Young Lee, Yin Shen, Axel Visel, Len A. Pennacchio, Bing Ren, Joseph R. Ecker
      Proceedings of the National Academy of Sciences of the United States of America, 2017 February 28;114(9): E1633--E1640. doi:10.1073/pnas.1618353114

    • Neoadjuvant Therapy in Microsatellite Stable Colorectal Carcinoma Induces Concomitant Loss of MSH6 and Ki67 Expression.
      Shih-Fan Kuan, Bing Ren, Randall Brand, Beth Dudley, Reetesh K. Pai
      Human pathology, 2017 February 20;(): . doi:10.1016/j.humpath.2017.02.003

    2016

    • Diagnosing colorectal medullary carcinoma: interobserver variability and clinicopathological implications.
      Lik Hang Lee, Rhonda K. Yantiss, Eran Sadot, Bing Ren, Marcela Santos Calvacanti, Jaclyn F. Hechtman, Sinisa Ivelja, Be Huynh, Yue Xue, Tatiana Shitilbans, Hamza Guend, Zsofia K. Stadler, Martin R. Weiser, Efsevia Vakiani, Mithat Gonen, David S. Klimstra, Jinru Shia
      Human pathology, 2016 December 26;(): . doi:10.1016/j.humpath.2016.12.013

    • Genome-wide mapping and analysis of chromosome architecture.
      Anthony D. Schmitt, Ming Hu, Bing Ren
      Nature reviews. Molecular cell biology, 2016 December 01;17(12): 743--755. doi:10.1038/nrm.2016.104

    • Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq.
      Rongxin Fang, Miao Yu, Guoqiang Li, Sora Chee, Tristin Liu, Anthony D. Schmitt, Bing Ren
      Cell research, 2016 December 01;26(12): 1345--1348. doi:10.1038/cr.2016.137

    • A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.
      Anthony D. Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine L. Tan, Yun Li, Shin Lin, Yiing Lin, Cathy L. Barr, Bing Ren
      Cell reports, 2016 November 15;17(8): 2042--2059. doi:10.1016/j.celrep.2016.10.061

    • Programmed Death-Ligand 1 Expression Is Common in Gastric Cancer Associated With Epstein-Barr Virus or Microsatellite Instability.
      Changqing Ma, Krishna Patel, Aatur D. Singhi, Bing Ren, Benjamin Zhu, Fyza Shaikh, Weijing Sun
      The American journal of surgical pathology, 2016 November 01;40(11): 1496--1506. doi:10.1097/PAS.0000000000000698

    • Genome-wide compendium and functional assessment of in vivo heart enhancers.
      Diane E. Dickel, Iros Barozzi, Yiwen Zhu, Yoko Fukuda-Yuzawa, Marco Osterwalder, Brandon J. Mannion, Dalit May, Cailyn H. Spurrell, Ingrid Plajzer-Frick, Catherine S. Pickle, Elizabeth Lee, Tyler H. Garvin, Momoe Kato, Jennifer A. Akiyama, Veena Afzal, Ah Young Lee, David U. Gorkin, Bing Ren, Edward M. Rubin, Axel Visel, Len A. Pennacchio
      Nature communications, 2016 October 05;7(): 12923. doi:10.1038/ncomms12923

    • Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition.
      John Arne Dahl, Inkyung Jung, Havard Aanes, Gareth D. Greggains, Adeel Manaf, Mads Lerdrup, Guoqiang Li, Samantha Kuan, Bin Li, Ah Young Lee, Sebastian Preissl, Ingunn Jermstad, Mads Haugland Haugen, Rajikala Suganthan, Magnar Bjoras, Klaus Hansen, Knut Tomas Dalen, Peter Fedorcsak, Bing Ren, Arne Klungland
      Nature, 2016 September 22;537(7621): 548--552. doi:10.1038/nature19360

    • Chromatin Domains: The Unit of Chromosome Organization.
      Jesse R. Dixon, David U. Gorkin, Bing Ren
      Molecular cell, 2016 June 02;62(5): 668--680. doi:10.1016/j.molcel.2016.05.018

    • A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening.
      Yarui Diao, Bin Li, Zhipeng Meng, Inkyung Jung, Ah Young Lee, Jesse Dixon, Lenka Maliskova, Kun-Liang Guan, Yin Shen, Bing Ren
      Genome research, 2016 March 01;26(3): 397--405. doi:10.1101/gr.197152.115

    • Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation.
      Matthew D. Schultz, Yupeng He, John W. Whitaker, Manoj Hariharan, Eran A. Mukamel, Danny Leung, Nisha Rajagopal, Joseph R. Nery, Mark A. Urich, Huaming Chen, Shin Lin, Yiing Lin, Inkyung Jung, Anthony D. Schmitt, Siddarth Selvaraj, Bing Ren, Terrence J. Sejnowski, Wei Wang, Joseph R. Ecker
      Nature, 2016 February 11;530(7589): 242. doi:10.1038/nature16179

    2015

    • Identification of global regulators of T-helper cell lineage specification.
      Kartiek Kanduri, Subhash Tripathi, Antti Larjo, Henrik Mannerstrom, Ubaid Ullah, Riikka Lund, R. David Hawkins, Bing Ren, Harri Lahdesmaki, Riitta Lahesmaa
      Genome medicine, 2015 November 20;7(): 122. doi:10.1186/s13073-015-0237-0

    • Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.
      Siddarth Selvaraj, Anthony D. Schmitt, Jesse R. Dixon, Bing Ren
      BMC genomics, 2015 November 05;16(): 900. doi:10.1186/s12864-015-1949-7

    • EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling.
      Feng Liu, Gary C. Hon, Genaro R. Villa, Kristen M. Turner, Shiro Ikegami, Huijun Yang, Zhen Ye, Bin Li, Samantha Kuan, Ah Young Lee, Ciro Zanca, Bowen Wei, Greg Lucey, David Jenkins, Wei Zhang, Cathy L. Barr, Frank B. Furnari, Timothy F. Cloughesy, William H. Yong, Timothy C. Gahman, Andrew K. Shiau, Webster K. Cavenee, Bing Ren, Paul S. Mischel
      Molecular cell, 2015 October 15;60(2): 307--318. doi:10.1016/j.molcel.2015.09.002

    • Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions.
      Elena M. Pugacheva, Samuel Rivero-Hinojosa, Celso A. Espinoza, Claudia Fabiola Mendez-Catala, Sungyun Kang, Teruhiko Suzuki, Natsuki Kosaka-Suzuki, Susan Robinson, Vijayaraj Nagarajan, Zhen Ye, Abdelhalim Boukaba, John E. J. Rasko, Alexander V. Strunnikov, Dmitri Loukinov, Bing Ren, Victor V. Lobanenkov
      Genome biology, 2015 August 14;16(): 161. doi:10.1186/s13059-015-0736-8

    • CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.
      Ya Guo, Quan Xu, Daniele Canzio, Jia Shou, Jinhuan Li, David U. Gorkin, Inkyung Jung, Haiyang Wu, Yanan Zhai, Yuanxiao Tang, Yichao Lu, Yonghu Wu, Zhilian Jia, Wei Li, Michael Q. Zhang, Bing Ren, Adrian R. Krainer, Tom Maniatis, Qiang Wu
      Cell, 2015 August 13;162(4): 900--910. doi:10.1016/j.cell.2015.07.038

    • Human body epigenome maps reveal noncanonical DNA methylation variation.
      Matthew D. Schultz, Yupeng He, John W. Whitaker, Manoj Hariharan, Eran A. Mukamel, Danny Leung, Nisha Rajagopal, Joseph R. Nery, Mark A. Urich, Huaming Chen, Shin Lin, Yiing Lin, Inkyung Jung, Anthony D. Schmitt, Siddarth Selvaraj, Bing Ren, Terrence J. Sejnowski, Wei Wang, Joseph R. Ecker
      Nature, 2015 July 09;523(7559): 212--216. doi:10.1038/nature14465

    • MPE-seq a new method for the genome-wide analysis of chromatin structure.
      Haruhiko Ishii, James T. Kadonaga, Bing Ren
      Proceedings of the National Academy of Sciences of the United States of America, 2015 July 07;112(27): E3457--3465. doi:10.1073/pnas.1424804112

    • An alternative pluripotent state confers interspecies chimaeric competency.
      Jun Wu, Daiji Okamura, Mo Li, Keiichiro Suzuki, Chongyuan Luo, Li Ma, Yupeng He, Zhongwei Li, Chris Benner, Isao Tamura, Marie N. Krause, Joseph R. Nery, Tingting Du, Zhuzhu Zhang, Tomoaki Hishida, Yuta Takahashi, Emi Aizawa, Na Young Kim, Jeronimo Lajara, Pedro Guillen, Josep M. Campistol, Concepcion Rodriguez Esteban, Pablo J. Ross, Alan Saghatelian, Bing Ren, Joseph R. Ecker, Juan Carlos Izpisua Belmonte
      Nature, 2015 May 21;521(7552): 316--321. doi:10.1038/nature14413

    • A CRISPR Connection between Chromatin Topology and Genetic Disorders.
      Bing Ren, Jesse R. Dixon
      Cell, 2015 May 21;161(5): 955--957. doi:10.1016/j.cell.2015.04.047

    • Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates.
      Allen Wang, Feng Yue, Yan Li, Ruiyu Xie, Thomas Harper, Nisha A. Patel, Kayla Muth, Jeffrey Palmer, Yunjiang Qiu, Jinzhao Wang, Dieter K. Lam, Jeffrey C. Raum, Doris A. Stoffers, Bing Ren, Maike Sander
      Cell stem cell, 2015 April 02;16(4): 386--399. doi:10.1016/j.stem.2015.02.013

    • Integrative analysis of haplotype-resolved epigenomes across human tissues.
      Danny Leung, Inkyung Jung, Nisha Rajagopal, Anthony Schmitt, Siddarth Selvaraj, Ah Young Lee, Chia-An Yen, Shin Lin, Yiing Lin, Yunjiang Qiu, Wei Xie, Feng Yue, Manoj Hariharan, Pradipta Ray, Samantha Kuan, Lee Edsall, Hongbo Yang, Neil C. Chi, Michael Q. Zhang, Joseph R. Ecker, Bing Ren
      Nature, 2015 February 19;518(7539): 350--354. doi:10.1038/nature14217

    • Integrative analysis of 111 reference human epigenomes.
      Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis
      Nature, 2015 February 19;518(7539): 317--330. doi:10.1038/nature14248

    • Chromatin architecture reorganization during stem cell differentiation.
      Jesse R. Dixon, Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E. Antosiewicz-Bourget, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Wei Xie, Yarui Diao, Jing Liang, Huimin Zhao, Victor V. Lobanenkov, Joseph R. Ecker, James A. Thomson, Bing Ren
      Nature, 2015 February 19;518(7539): 331--336. doi:10.1038/nature14222

    • Transcriptional Enhancers: Bridging the Genome and Phenome.
      Bing Ren, Feng Yue
      Cold Spring Harbor symposia on quantitative biology, 2015 January 01;80(): 17--26. doi:10.1101/sqb.2015.80.027219

    • DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.
      Yongheng Chen, Chunxia Chen, Zhe Zhang, Chun-Chi Liu, Matthew E. Johnson, Celso A. Espinoza, Lee E. Edsall, Bing Ren, Xianghong Jasmine Zhou, Struan F. A. Grant, Andrew D. Wells, Lin Chen
      Nucleic acids research, 2015 January 01;43(2): 1268--1282. doi:10.1093/nar/gku1373

    2014

    • A comparative encyclopedia of DNA elements in the mouse genome.
      Feng Yue, Yong Cheng, Alessandra Breschi, Jeff Vierstra, Weisheng Wu, Tyrone Ryba, Richard Sandstrom, Zhihai Ma, Carrie Davis, Benjamin D. Pope, Yin Shen, Dmitri D. Pervouchine, Sarah Djebali, Robert E. Thurman, Rajinder Kaul, Eric Rynes, Anthony Kirilusha, Georgi K. Marinov, Brian A. Williams, Diane Trout, Henry Amrhein, Katherine Fisher-Aylor, Igor Antoshechkin, Gilberto DeSalvo, Lei-Hoon See, Meagan Fastuca, Jorg Drenkow, Chris Zaleski, Alex Dobin, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer, Olgert Denas, Kanwei Li, M. A. Bender, Miaohua Zhang, Rachel Byron, Mark T. Groudine, David McCleary, Long Pham, Zhen Ye, Samantha Kuan, Lee Edsall, Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis, Cheryl A. Keller, Christapher S. Morrissey, Tejaswini Mishra, Deepti Jain, Nergiz Dogan, Robert S. Harris, Philip Cayting, Trupti Kawli, Alan P. Boyle, Ghia Euskirchen, Anshul Kundaje, Shin Lin, Yiing Lin, Camden Jansen, Venkat S. Malladi, Melissa S. Cline, Drew T. Erickson, Vanessa M. Kirkup, Katrina Learned, Cricket A. Sloan, Kate R. Rosenbloom, Beatriz Lacerda de Sousa, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian, Tamer Kahveci, Dongwon Lee, W. James Kent, Miguel Ramalho Santos, Javier Herrero, Cedric Notredame, Audra Johnson, Shinny Vong, Kristen Lee, Daniel Bates, Fidencio Neri, Morgan Diegel, Theresa Canfield, Peter J. Sabo, Matthew S. Wilken, Thomas A. Reh, Erika Giste, Anthony Shafer, Tanya Kutyavin, Eric Haugen, Douglas Dunn, Alex P. Reynolds, Shane Neph, Richard Humbert, R. Scott Hansen, Marella De Bruijn, Licia Selleri, Alexander Rudensky, Steven Josefowicz, Robert Samstein, Evan E. Eichler, Stuart H. Orkin, Dana Levasseur, Thalia Papayannopoulou, Kai-Hsin Chang, Arthur Skoultchi, Srikanta Gosh, Christine Disteche, Piper Treuting, Yanli Wang, Mitchell J. Weiss, Gerd A. Blobel, Xiaoyi Cao, Sheng Zhong, Ting Wang, Peter J. Good, Rebecca F. Lowdon, Leslie B. Adams, Xiao-Qiao Zhou, Michael J. Pazin, Elise A. Feingold, Barbara Wold, James Taylor, Ali Mortazavi, Sherman M. Weissman, John A. Stamatoyannopoulos, Michael P. Snyder, Roderic Guigo, Thomas R. Gingeras, David M. Gilbert, Ross C. Hardison, Michael A. Beer, Bing Ren
      Nature, 2014 November 20;515(7527): 355--364. doi:10.1038/nature13992

    • Topologically associating domains are stable units of replication-timing regulation.
      Benjamin D. Pope, Tyrone Ryba, Vishnu Dileep, Feng Yue, Weisheng Wu, Olgert Denas, Daniel L. Vera, Yanli Wang, R. Scott Hansen, Theresa K. Canfield, Robert E. Thurman, Yong Cheng, Gunhan Gulsoy, Jonathan H. Dennis, Michael P. Snyder, John A. Stamatoyannopoulos, James Taylor, Ross C. Hardison, Tamer Kahveci, Bing Ren, David M. Gilbert
      Nature, 2014 November 20;515(7527): 402--405. doi:10.1038/nature13986

    • 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation.
      Gary C. Hon, Chun-Xiao Song, Tingting Du, Fulai Jin, Siddarth Selvaraj, Ah Young Lee, Chia-An Yen, Zhen Ye, Shi-Qing Mao, Bang-An Wang, Samantha Kuan, Lee E. Edsall, Boxuan Simen Zhao, Guo-Liang Xu, Chuan He, Bing Ren
      Molecular cell, 2014 October 23;56(2): 286--297. doi:10.1016/j.molcel.2014.08.026

    • The highly-cited Electrocardiogram-related articles in science citation index expanded: characteristics and hotspots.
      Xianglin Yang, Jiaojiao Gu, Hong Yan, Zhi Xu, Bing Ren, Yaming Yang, Xiaodong Yang, Qi Chen, Shaohua Tan
      Journal of electrocardiology, 2014 October 01;47(5): 738--744. doi:10.1016/j.jelectrocard.2014.03.005

    • [Grain filling dynamics and germination characteristics of Bupleurum chinense seeds].
      Xin Jin, Bing Ren, Ai-Nong Cao, Xiao-Jun Jin
      Zhongguo Zhong yao za zhi , 2014 October 01;39(19): 3731--3735. doi:

    • Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.
      Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Ewan Birney, Gregory E. Crawford, Job Dekker, Ian Dunham, Laura L. Elnitski, Peggy J. Farnham, Elise A. Feingold, Mark Gerstein, Morgan C. Giddings, David M. Gilbert, Thomas R. Gingeras, Eric D. Green, Roderic Guigo, Tim Hubbard, Jim Kent, Jason D. Lieb, Richard M. Myers, Michael J. Pazin, Bing Ren, John Stamatoyannopoulos, Zhiping Weng, Kevin P. White, Ross C. Hardison
      Proceedings of the National Academy of Sciences of the United States of America, 2014 August 19;111(33): E3366. doi:

    • Distinct and predictive histone lysine acetylation patterns at promoters enhancers and gene bodies.
      Nisha Rajagopal, Jason Ernst, Pradipta Ray, Jie Wu, Michael Zhang, Manolis Kellis, Bing Ren
      G3 (Bethesda Md.), 2014 August 12;4(11): 2051--2063. doi:10.1534/g3.114.013565

    • The 3D genome in transcriptional regulation and pluripotency.
      David U. Gorkin, Danny Leung, Bing Ren
      Cell stem cell, 2014 June 05;14(6): 762--775. doi:10.1016/j.stem.2014.05.017

    • Clinical observation on removal of small foreign bodies touching the optic nerve in the deep orbital region: a case series.
      Yan-Ming Tian, Xiao-Wei Gao, Bing Ren, Yan Ju, Peng Li, Lei Qiao, Xi-Dong Yan
      Orbit (Amsterdam Netherlands), 2014 June 01;33(3): 210--213. doi:10.3109/01676830.2014.881397

    • Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis.
      Catia Attanasio, Alex S. Nord, Yiwen Zhu, Matthew J. Blow, Simon C. Biddie, Eric M. Mendenhall, Jesse Dixon, Crystal Wright, Roya Hosseini, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Veena Afzal, Bing Ren, Bradley E. Bernstein, Edward M. Rubin, Axel Visel, Len A. Pennacchio
      Genome research, 2014 June 01;24(6): 920--929. doi:10.1101/gr.168930.113

    • Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1.
      Danny Leung, Tingting Du, Ulrich Wagner, Wei Xie, Ah Young Lee, Preeti Goyal, Yujing Li, Keith E. Szulwach, Peng Jin, Matthew C. Lorincz, Bing Ren
      Proceedings of the National Academy of Sciences of the United States of America, 2014 May 06;111(18): 6690--6695. doi:10.1073/pnas.1322273111

    • [Clinical observation on removal of small foreign bodies touching the optic nerve in the deep orbital region].
      Yanming Tian, Junling Wang, Sheng Yang, Lei Qiao, Peng Li, Xiaowei Gao, Yan Ju, Xidong Yan, Bing Ren, Yujie Yang
      [Zhonghua yan ke za zhi] Chinese journal of ophthalmology, 2014 May 01;50(5): 360--363. doi:

    • Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark.
      Lunzhi Dai, Chao Peng, Emilie Montellier, Zhike Lu, Yue Chen, Haruhiko Ishii, Alexandra Debernardi, Thierry Buchou, Sophie Rousseaux, Fulai Jin, Benjamin R. Sabari, Zhiyou Deng, C. David Allis, Bing Ren, Saadi Khochbin, Yingming Zhao
      Nature chemical biology, 2014 May 01;10(5): 365--370. doi:10.1038/nchembio.1497

    • Defining functional DNA elements in the human genome.
      Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Ewan Birney, Gregory E. Crawford, Job Dekker, Ian Dunham, Laura L. Elnitski, Peggy J. Farnham, Elise A. Feingold, Mark Gerstein, Morgan C. Giddings, David M. Gilbert, Thomas R. Gingeras, Eric D. Green, Roderic Guigo, Tim Hubbard, Jim Kent, Jason D. Lieb, Richard M. Myers, Michael J. Pazin, Bing Ren, John A. Stamatoyannopoulos, Zhiping Weng, Kevin P. White, Ross C. Hardison
      Proceedings of the National Academy of Sciences of the United States of America, 2014 April 29;111(17): 6131--6138. doi:10.1073/pnas.1318948111

    • Genetics: Closing the distance on obesity culprits.
      David U. Gorkin, Bing Ren
      Nature, 2014 March 20;507(7492): 309--310. doi:10.1038/nature13212

    • Neuromuscular and vascular hamartoma: is it a true hamartoma?
      Bing Ren, Wenqing Cao
      Journal of clinical pathology, 2014 March 01;67(3): 284--287. doi:10.1136/jclinpath-2013-201913

    • Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells.
      Timothy J. Looney, Li Zhang, Chih-Hsin Chen, Jae Hyun Lee, Sheila Chari, Frank Fuxiang Mao, Mattia Pelizzola, Lu Zhang, Ryan Lister, Samuel W. Baker, Croydon J. Fernandes, Jedidiah Gaetz, Kara M. Foshay, Kayla L. Clift, Zhenyu Zhang, Wei-Qiang Li, Eric J. Vallender, Ulrich Wagner, Jane Yuxia Qin, Katelyn J. Michelini, Branimir Bugarija, Donghyun Park, Emmanuel Aryee, Thomas Stricker, Jie Zhou, Kevin P. White, Bing Ren, Gary P. Schroth, Joseph R. Ecker, Andy Peng Xiang, Bruce T. Lahn
      Genome research, 2014 February 01;24(2): 267--280. doi:10.1101/gr.143891.112

    • Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells.
      Jessica Zuin, Jesse R. Dixon, Michael I. J. A. van der Reijden, Zhen Ye, Petros Kolovos, Rutger W. W. Brouwer, Mariette P. C. van de Corput, Harmen J. G. van de Werken, Tobias A. Knoch, Wilfred F. J. van IJcken, Frank G. Grosveld, Bing Ren, Kerstin S. Wendt
      Proceedings of the National Academy of Sciences of the United States of America, 2014 January 21;111(3): 996--1001. doi:10.1073/pnas.1317788111

    • N6-methyladenosine-dependent regulation of messenger RNA stability.
      Xiao Wang, Zhike Lu, Adrian Gomez, Gary C. Hon, Yanan Yue, Dali Han, Ye Fu, Marc Parisien, Qing Dai, Guifang Jia, Bing Ren, Tao Pan, Chuan He
      Nature, 2014 January 02;505(7481): 117--120. doi:10.1038/nature12730

    • Inhibition of retinopathy of prematurity in rat by intravitreal injection of sorafenib.
      Li-Li Tian, Bing Ren, Xiao-Wei Gao, Ying Luo, Yan Cai, Kun Zhou, An-Jie Du, Yong Zhao
      International journal of ophthalmology, 2014 January 01;7(2): 198--204. doi:10.3980/j.issn.2222-3959.2014.02.03

    • CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.
      Yan Li, Chloe M. Rivera, Haruhiko Ishii, Fulai Jin, Siddarth Selvaraj, Ah Young Lee, Jesse R. Dixon, Bing Ren
      PloS one, 2014 January 01;9(12): e114485. doi:10.1371/journal.pone.0114485

    2013

    • STAR: an integrated solution to management and visualization of sequencing data.
      Tao Wang, Jie Liu, Li Shen, Julian Tonti-Filippini, Yun Zhu, Haiyang Jia, Ryan Lister, John W. Whitaker, Joseph R. Ecker, A. Harvey Millar, Bing Ren, Wei Wang
      Bioinformatics (Oxford England), 2013 December 15;29(24): 3204--3210. doi:10.1093/bioinformatics/btt558

    • Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.
      Siddarth Selvaraj, Jesse R Dixon, Vikas Bansal, Bing Ren
      Nature biotechnology, 2013 December 01;31(12): 1111--1118. doi:10.1038/nbt.2728

    • A high-resolution map of the three-dimensional chromatin interactome in human cells.
      Fulai Jin, Yan Li, Jesse R. Dixon, Siddarth Selvaraj, Zhen Ye, Ah Young Lee, Chia-An Yen, Anthony D. Schmitt, Celso A. Espinoza, Bing Ren
      Nature, 2013 November 14;503(7475): 290--294. doi:10.1038/nature12644

    • MACC1 is related to colorectal cancer initiation and early-stage invasive growth.
      Bing Ren, Vladislav Zakharov, Qi Yang, Loralee McMahon, JiangZhou Yu, Wenqing Cao
      American journal of clinical pathology, 2013 November 01;140(5): 701--707. doi:10.1309/AJCPRH1H5RWWSXRB

    • Fine tuning of craniofacial morphology by distant-acting enhancers.
      Catia Attanasio, Alex S. Nord, Yiwen Zhu, Matthew J. Blow, Zirong Li, Denise K. Liberton, Harris Morrison, Ingrid Plajzer-Frick, Amy Holt, Roya Hosseini, Sengthavy Phouanenavong, Jennifer A. Akiyama, Malak Shoukry, Veena Afzal, Edward M. Rubin, David R. FitzPatrick, Bing Ren, Benedikt Hallgrimsson, Len A. Pennacchio, Axel Visel
      Science (New York N.Y.), 2013 October 25;342(6157): 1241006. doi:10.1126/science.1241006

    • Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues.
      Gary C. Hon, Nisha Rajagopal, Yin Shen, David F. McCleary, Feng Yue, My D. Dang, Bing Ren
      Nature genetics, 2013 October 01;45(10): 1198--1206. doi:10.1038/ng.2746

    • Mapping human epigenomes.
      Chloe M. Rivera, Bing Ren
      Cell, 2013 September 26;155(1): 39--55. doi:10.1016/j.cell.2013.09.011

    • Developmental biology. Enhancing pluripotency and lineage specification.
      Wei Xie, Bing Ren
      Science (New York N.Y.), 2013 July 19;341(6143): 245--247. doi:10.1126/science.1236254

    • Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.
      R. David Hawkins, Antti Larjo, Subhash K. Tripathi, Ulrich Wagner, Ying Luu, Tapio Lonnberg, Sunil K. Raghav, Leonard K. Lee, Riikka Lund, Bing Ren, Harri Lahdesmaki, Riitta Lahesmaa
      Immunity, 2013 June 27;38(6): 1271--1284. doi:10.1016/j.immuni.2013.05.011

    • Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis.
      Katherine Noelani Chang, Shan Zhong, Matthew T. Weirauch, Gary Hon, Mattia Pelizzola, Hai Li, Shao-Shan Carol Huang, Robert J. Schmitz, Mark A. Urich, Dwight Kuo, Joseph R. Nery, Hong Qiao, Ally Yang, Abdullah Jamali, Huaming Chen, Trey Ideker, Bing Ren, Ziv Bar-Joseph, Timothy R. Hughes, Joseph R. Ecker
      eLife, 2013 June 11;2(): e00675. doi:10.7554/eLife.00675

    • Genome organization and long-range regulation of gene expression by enhancers.
      Andrea Smallwood, Bing Ren
      Current opinion in cell biology, 2013 June 01;25(3): 387--394. doi:10.1016/j.ceb.2013.02.005

    • Epigenomic analysis of multilineage differentiation of human embryonic stem cells.
      Wei Xie, Matthew D. Schultz, Ryan Lister, Zhonggang Hou, Nisha Rajagopal, Pradipta Ray, John W. Whitaker, Shulan Tian, R. David Hawkins, Danny Leung, Hongbo Yang, Tao Wang, Ah Young Lee, Scott A. Swanson, Jiuchun Zhang, Yun Zhu, Audrey Kim, Joseph R. Nery, Mark A. Urich, Samantha Kuan, Chia-an Yen, Sarit Klugman, Pengzhi Yu, Kran Suknuntha, Nicholas E. Propson, Huaming Chen, Lee E. Edsall, Ulrich Wagner, Yan Li, Zhen Ye, Ashwinikumar Kulkarni, Zhenyu Xuan, Wen-Yu Chung, Neil C. Chi, Jessica E. Antosiewicz-Bourget, Igor Slukvin, Ron Stewart, Michael Q. Zhang, Wei Wang, James A. Thomson, Joseph R. Ecker, Bing Ren
      Cell, 2013 May 23;153(5): 1134--1148. doi:10.1016/j.cell.2013.04.022

    • Histone acetyltransferase cofactor Trrap maintains self-renewal and restricts differentiation of embryonic stem cells.
      Carla Sawan, Hector Hernandez-Vargas, Rabih Murr, Fabrice Lopez, Thomas Vaissiere, Akram Y. Ghantous, Cyrille Cuenin, Jean Imbert, Zhao-Qi Wang, Bing Ren, Zdenko Herceg
      Stem cells (Dayton Ohio), 2013 May 01;31(5): 979--991. doi:10.1002/stem.1341

    • Diagnostic value of HMGAs p53 and beta-catenin in discriminating adenocarcinoma from adenoma or reactive atypia in ampulla and common bile duct biopsies.
      Vladislav Zakharov, Bing Ren, Charlotte Ryan, Wenqing Cao
      Histopathology, 2013 April 01;62(5): 778--787. doi:10.1111/his.12084

    • Comparative annotation of functional regions in the human genome using epigenomic data.
      Kyoung-Jae Won, Xian Zhang, Tao Wang, Bo Ding, Debasish Raha, Michael Snyder, Bing Ren, Wei Wang
      Nucleic acids research, 2013 April 01;41(8): 4423--4432. doi:10.1093/nar/gkt143

    • Comparative study of modified and conventional secondary hydroxyapatite orbital implantations.
      Yong Zhao, Mao-Nian Zhang, Yun-Xian Gao, Xiao-Wei Gao, Bing Ren
      International journal of ophthalmology, 2013 January 01;6(5): 646--649. doi:10.3980/j.issn.2222-3959.2013.05.17

    • Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing.
      Liang Zhang, Keith E. Szulwach, Gary C. Hon, Chun-Xiao Song, Beomseok Park, Miao Yu, Xingyu Lu, Qing Dai, Xiao Wang, Craig R. Street, Huiping Tan, Jung-Hyun Min, Bing Ren, Peng Jin, Chuan He
      Nature communications, 2013 January 01;4(): 1517. doi:10.1038/ncomms2527

    • RFECS: a random-forest based algorithm for enhancer identification from chromatin state.
      Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren
      PLoS computational biology, 2013 January 01;9(3): e1002968. doi:10.1371/journal.pcbi.1002968

    • Posterior chamber phakic intraocular lens implantation for high myopia.
      Yan Ju, Xiao-Wei Gao, Bing Ren
      International journal of ophthalmology, 2013 January 01;6(6): 831--835. doi:10.3980/j.issn.2222-3959.2013.06.16

    • Bayesian inference of spatial organizations of chromosomes.
      Ming Hu, Ke Deng, Zhaohui Qin, Jesse Dixon, Siddarth Selvaraj, Jennifer Fang, Bing Ren, Jun S. Liu
      PLoS computational biology, 2013 January 01;9(1): e1002893. doi:10.1371/journal.pcbi.1002893

    • Effects of aminoguanidine on retinal apoptosis in mice with oxygen-induced retinopathy.
      An-Jie Du, Bing Ren, Xiao-Wei Gao, Lei Yang, Yan Fu, Xu-Dong Zhao
      International journal of ophthalmology, 2013 January 01;6(4): 436--441. doi:10.3980/j.issn.2222-3959.2013.04.05

    2012

    • Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine.
      Miao Yu, Gary C. Hon, Keith E. Szulwach, Chun-Xiao Song, Peng Jin, Bing Ren, Chuan He
      Nature protocols, 2012 December 01;7(12): 2159--2170. doi:10.1038/nprot.2012.137

    • HiCNorm: removing biases in Hi-C data via Poisson regression.
      Ming Hu, Ke Deng, Siddarth Selvaraj, Zhaohui Qin, Bing Ren, Jun S. Liu
      Bioinformatics (Oxford England), 2012 December 01;28(23): 3131--3133. doi:10.1093/bioinformatics/bts570

    • Progressive degeneration of human neural stem cells caused by pathogenic LRRK2.
      Guang-Hui Liu, Jing Qu, Keiichiro Suzuki, Emmanuel Nivet, Mo Li, Nuria Montserrat, Fei Yi, Xiuling Xu, Sergio Ruiz, Weiqi Zhang, Ulrich Wagner, Audrey Kim, Bing Ren, Ying Li, April Goebl, Jessica Kim, Rupa Devi Soligalla, Ilir Dubova, James Thompson, John 3rd Yates, Concepcion Rodriguez Esteban, Ignacio Sancho-Martinez, Juan Carlos Izpisua Belmonte
      Nature, 2012 November 22;491(7425): 603--607. doi:10.1038/nature11557

    • The absence of PspA or presence of antibody to PspA facilitates the complement-dependent phagocytosis of pneumococci in vitro.
      Bing Ren, Jie Li, Kristopher Genschmer, Susan K. Hollingshead, David E. Briles
      Clinical and vaccine immunology : CVI, 2012 October 01;19(10): 1574--1582. doi:10.1128/CVI.00393-12

    • Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells.
      Kyoung-Jae Won, Zheng Xu, Xian Zhang, John W. Whitaker, Robert Shoemaker, Bing Ren, Yang Xu, Wei Wang
      Nucleic acids research, 2012 September 01;40(17): 8199--8209. doi:10.1093/nar/gks584

    • Combined gene expression and DNA occupancy profiling identifies potential therapeutic targets of t(8;21) AML.
      Miao-Chia Lo, Luke F. Peterson, Ming Yan, Xiuli Cong, Fulai Jin, Wei-Jong Shia, Shinobu Matsuura, Eun-Young Ahn, Yukiko Komeno, Minh Ly, Hans B. Ommen, I.-Ming Chen, Peter Hokland, Cheryl L. Willman, Bing Ren, Dong-Er Zhang
      Blood, 2012 August 16;120(7): 1473--1484. doi:10.1182/blood-2011-12-395335

    • An encyclopedia of mouse DNA elements (Mouse ENCODE).
      John A. Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M. Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J. Sabo, Richard Sandstrom, A. Sandra Stehling, Robert E. Thurman, Sherman M. Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G. Landt, Zhihai Ma, Barbara J. Wold, Job Dekker, Gregory E. Crawford, Cheryl A. Keller, Weisheng Wu, Christopher Morrissey, Swathi A. Kumar, Tejaswini Mishra, Deepti Jain, Marta Byrska-Bishop, Daniel Blankenberg, Bryan R. Lajoie, Gaurav Jain, Amartya Sanyal, Kaun-Bei Chen, Olgert Denas, James Taylor, Gerd A. Blobel, Mitchell J. Weiss, Max Pimkin, Wulan Deng, Georgi K. Marinov, Brian A. Williams, Katherine I. Fisher-Aylor, Gilberto Desalvo, Anthony Kiralusha, Diane Trout, Henry Amrhein, Ali Mortazavi, Lee Edsall, David McCleary, Samantha Kuan, Yin Shen, Feng Yue, Zhen Ye, Carrie A. Davis, Chris Zaleski, Sonali Jha, Chenghai Xue, Alex Dobin, Wei Lin, Meagan Fastuca, Huaien Wang, Roderic Guigo, Sarah Djebali, Julien Lagarde, Tyrone Ryba, Takayo Sasaki, Venkat S. Malladi, Melissa S. Cline, Vanessa M. Kirkup, Katrina Learned, Kate R. Rosenbloom, W. James Kent, Elise A. Feingold, Peter J. Good, Michael Pazin, Rebecca F. Lowdon, Leslie B. Adams
      Genome biology, 2012 August 13;13(8): 418. doi:10.1186/gb-2012-13-8-418

    • A map of the cis-regulatory sequences in the mouse genome.
      Yin Shen, Feng Yue, David F. McCleary, Zhen Ye, Lee Edsall, Samantha Kuan, Ulrich Wagner, Jesse Dixon, Leonard Lee, Victor V. Lobanenkov, Bing Ren
      Nature, 2012 August 02;488(7409): 116--120. doi:10.1038/nature11243

    • CBX3 regulates efficient RNA processing genome-wide.
      Andrea Smallwood, Gary C. Hon, Fulai Jin, Ryan E. Henry, Joaquin M. Espinosa, Bing Ren
      Genome research, 2012 August 01;22(8): 1426--1436. doi:10.1101/gr.124818.111

    • Magnetic resonance tumor targeting imaging using gadolinium labeled human telomerase reverse transcriptase antisense probes.
      Bing Xiu Ren, Fan Yang, Gao Hong Zhu, Zi Xing Huang, Hua Ai, Rui Xia, Xi Jiao Liu, Man Lu, Bin Song
      Cancer science, 2012 August 01;103(8): 1434--1439. doi:10.1111/j.1349-7006.2012.02316.x

    • [Near-infrared spectroscopy analysis of adenosine and water in fermentation cordyceps powder and wavelength assignment].
      Ning Xu, Xuan Wei, Bing Ren, Yong He, Lei Feng
      Guang pu xue yu guang pu fen xi , 2012 July 01;32(7): 1762--1765. doi:

    • Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
      Miao Yu, Gary C. Hon, Keith E. Szulwach, Chun-Xiao Song, Liang Zhang, Audrey Kim, Xuekun Li, Qing Dai, Yin Shen, Beomseok Park, Jung-Hyun Min, Peng Jin, Bing Ren, Chuan He
      Cell, 2012 June 08;149(6): 1368--1380. doi:10.1016/j.cell.2012.04.027

    • Topological domains in mammalian genomes identified by analysis of chromatin interactions.
      Jesse R. Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S. Liu, Bing Ren
      Nature, 2012 April 11;485(7398): 376--380. doi:10.1038/nature11082

    • Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome.
      Wei Xie, Cathy L. Barr, Audrey Kim, Feng Yue, Ah Young Lee, James Eubanks, Emma L. Dempster, Bing Ren
      Cell, 2012 February 17;148(4): 816--831. doi:10.1016/j.cell.2011.12.035

    • Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.
      Gary C. Hon, R. David Hawkins, Otavia L. Caballero, Christine Lo, Ryan Lister, Mattia Pelizzola, Armand Valsesia, Zhen Ye, Samantha Kuan, Lee E. Edsall, Anamaria Aranha Camargo, Brian J. Stevenson, Joseph R. Ecker, Vineet Bafna, Robert L. Strausberg, Andrew J. Simpson, Bing Ren
      Genome research, 2012 February 01;22(2): 246--258. doi:10.1101/gr.125872.111

    • Transcriptional regulation by Pol II(G) involving mediator and competitive interactions of Gdown1 and TFIIF with Pol II.
      Miki Jishage, Sohail Malik, Ulrich Wagner, Beatrix Uberheide, Yasushi Ishihama, Xiaopeng Hu, Brian T. Chait, Averell Gnatt, Bing Ren, Robert G. Roeder
      Molecular cell, 2012 January 13;45(1): 51--63. doi:10.1016/j.molcel.2011.12.014

    • Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
      Julie Hunkapiller, Yin Shen, Aaron Diaz, Gerard Cagney, David McCleary, Miguel Ramalho-Santos, Nevan Krogan, Bing Ren, Jun S. Song, Jeremy F. Reiter
      PLoS genetics, 2012 January 01;8(3): e1002576. doi:10.1371/journal.pgen.1002576

    2011

    • Enhancers: multi-dimensional signal integrators.
      Fulai Jin, Yan Li, Bing Ren, Rama Natarajan
      Transcription, 2011 October 01;2(5): 226--230. doi:10.4161/trns.2.5.17712

    • Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.
      R. David Hawkins, Gary C. Hon, Chuhu Yang, Jessica E. Antosiewicz-Bourget, Leonard K. Lee, Que-Minh Ngo, Sarit Klugman, Keith A. Ching, Lee E. Edsall, Zhen Ye, Samantha Kuan, Pengzhi Yu, Hui Liu, Xinmin Zhang, Roland D. Green, Victor V. Lobanenkov, Ron Stewart, James A. Thomson, Bing Ren
      Cell research, 2011 October 01;21(10): 1393--1409. doi:10.1038/cr.2011.146

    • Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.
      Minjia Tan, Hao Luo, Sangkyu Lee, Fulai Jin, Jeong Soo Yang, Emilie Montellier, Thierry Buchou, Zhongyi Cheng, Sophie Rousseaux, Nisha Rajagopal, Zhike Lu, Zhen Ye, Qin Zhu, Joanna Wysocka, Yang Ye, Saadi Khochbin, Bing Ren, Yingming Zhao
      Cell, 2011 September 16;146(6): 1016--1028. doi:10.1016/j.cell.2011.08.008

    • Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual.
      Pedro A. F. Galante, Raphael B. Parmigiani, Qi Zhao, Otavia L. Caballero, Jorge E. de Souza, Fabio C. P. Navarro, Alexandra L. Gerber, Marisa F. Nicolas, Anna Christina M. Salim, Ana Paula M. Silva, Lee Edsall, Sylvie Devalle, Luiz G. Almeida, Zhen Ye, Samantha Kuan, Daniel G. Pinheiro, Israel Tojal, Renato G. Pedigoni, Rodrigo G. M. A. de Sousa, Thiago Y. K. Oliveira, Marcelo G. de Paula, Lucila Ohno-Machado, Ewen F. Kirkness, Samuel Levy, Wilson A. Jr da Silva, Ana Tereza R. Vasconcelos, Bing Ren, Marco Antonio Zago, Robert L. Strausberg, Andrew J. G. Simpson, Sandro J. de Souza, Anamaria A. Camargo
      Nucleic acids research, 2011 August 01;39(14): 6056--6068. doi:10.1093/nar/gkr221

    • SERPINB13 is a novel RUNX1 target gene.
      Anita Boyapati, Bing Ren, Dong-Er Zhang
      Biochemical and biophysical research communications, 2011 July 22;411(1): 115--120. doi:10.1016/j.bbrc.2011.06.107

    • Mapping higher order structure of chromatin domains.
      Celso A. Espinoza, Bing Ren
      Nature genetics, 2011 June 28;43(7): 615--616. doi:10.1038/ng.869

    • Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells.
      Keith E. Szulwach, Xuekun Li, Yujing Li, Chun-Xiao Song, Ji Woong Han, SangSung Kim, Sandeep Namburi, Karen Hermetz, Julie J. Kim, M. Katharine Rudd, Young-Sup Yoon, Bing Ren, Chuan He, Peng Jin
      PLoS genetics, 2011 June 01;7(6): e1002154. doi:10.1371/journal.pgen.1002154

    • Insulin-like growth factor binding protein-3 interacts with the thyroid hormone receptor alpha1 and modulates transcription of thyroid hormone responsive gene.
      Qiu Jia, Ma Xiao-li, Wang Xin, Chen Hong, Huang Bing-ren
      Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae, 2011 April 01;33(2): 156--161. doi:10.3881/j.issn.1000-503X.2011.02.012

    • PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers.
      Fulai Jin, Yan Li, Bing Ren, Rama Natarajan
      Proceedings of the National Academy of Sciences of the United States of America, 2011 March 29;108(13): 5290--5295. doi:10.1073/pnas.1017214108

    • A cis-regulatory map of the Drosophila genome.
      Nicolas Negre, Christopher D. Brown, Lijia Ma, Christopher Aaron Bristow, Steven W. Miller, Ulrich Wagner, Pouya Kheradpour, Matthew L. Eaton, Paul Loriaux, Rachel Sealfon, Zirong Li, Haruhiko Ishii, Rebecca F. Spokony, Jia Chen, Lindsay Hwang, Chao Cheng, Richard P. Auburn, Melissa B. Davis, Marc Domanus, Parantu K. Shah, Carolyn A. Morrison, Jennifer Zieba, Sarah Suchy, Lionel Senderowicz, Alec Victorsen, Nicholas A. Bild, A. Jason Grundstad, David Hanley, David M. MacAlpine, Mattias Mannervik, Koen Venken, Hugo Bellen, Robert White, Mark Gerstein, Steven Russell, Robert L. Grossman, Bing Ren, James W. Posakony, Manolis Kellis, Kevin P. White
      Nature, 2011 March 24;471(7339): 527--531. doi:10.1038/nature09990

    • Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A.
      Todd S. Macfarlan, Wesley D. Gifford, Saurabh Agarwal, Shawn Driscoll, Karen Lettieri, Jianxun Wang, Shane E. Andrews, Laura Franco, Michael G. Rosenfeld, Bing Ren, Samuel L. Pfaff
      Genes & development, 2011 March 15;25(6): 594--607. doi:10.1101/gad.2008511

    • Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.
      Ryan Lister, Mattia Pelizzola, Yasuyuki S. Kida, R. David Hawkins, Joseph R. Nery, Gary Hon, Jessica Antosiewicz-Bourget, Ronan O'Malley, Rosa Castanon, Sarit Klugman, Michael Downes, Ruth Yu, Ron Stewart, Bing Ren, James A. Thomson, Ronald M. Evans, Joseph R. Ecker
      Nature, 2011 March 03;471(7336): 68--73. doi:10.1038/nature09798

    • 9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response.
      Olivier Harismendy, Dimple Notani, Xiaoyuan Song, Nazli G. Rahim, Bogdan Tanasa, Nathaniel Heintzman, Bing Ren, Xiang-Dong Fu, Eric J. Topol, Michael G. Rosenfeld, Kelly A. Frazer
      Nature, 2011 February 10;470(7333): 264--268. doi:10.1038/nature09753

    • Effects of minocycline on expression of bcl-2 bax in early retinal neuropathy of diabetes in rats.
      Hai-Dong Lian, Bing Ren, Xiao-Wei Gao
      International journal of ophthalmology, 2011 January 01;4(2): 162--164. doi:10.3980/j.issn.2222-3959.2011.02.10

    • An assessment of histone-modification antibody quality.
      Thea A. Egelhofer, Aki Minoda, Sarit Klugman, Kyungjoon Lee, Paulina Kolasinska-Zwierz, Artyom A. Alekseyenko, Ming-Sin Cheung, Daniel S. Day, Sarah Gadel, Andrey A. Gorchakov, Tingting Gu, Peter V. Kharchenko, Samantha Kuan, Isabel Latorre, Daniela Linder-Basso, Ying Luu, Queminh Ngo, Marc Perry, Andreas Rechtsteiner, Nicole C. Riddle, Yuri B. Schwartz, Gregory A. Shanower, Anne Vielle, Julie Ahringer, Sarah C. R. Elgin, Mitzi I. Kuroda, Vincenzo Pirrotta, Bing Ren, Susan Strome, Peter J. Park, Gary H. Karpen, R. David Hawkins, Jason D. Lieb
      Nature structural & molecular biology, 2011 January 01;18(1): 91--93. doi:10.1038/nsmb.1972

    2010

    • Identification of functional elements and regulatory circuits by Drosophila modENCODE.
      Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L. Eaton, Jane M. Landolin, Christopher A. Bristow, Lijia Ma, Michael F. Lin, Stefan Washietl, Bradley I. Arshinoff, Ferhat Ay, Patrick E. Meyer, Nicolas Robine, Nicole L. Washington, Luisa Di Stefano, Eugene Berezikov, Christopher D. Brown, Rogerio Candeias, Joseph W. Carlson, Adrian Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael Y. Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo Artieri, Benjamin W. Booth, Angela N. Brooks, Qi Dai, Carrie A. Davis, Michael O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara K. Powell, Nicole C. Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca Spokony, David Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu, Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael R. Brent, Lucy Cherbas, Sarah C. R. Elgin, Thomas R. Gingeras, Robert Grossman, Roger A. Hoskins, Thomas C. Kaufman, William Kent, Mitzi I. Kuroda, Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James W. Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park, Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln D. Stein, Kevin P. White, Manolis Kellis
      Science (New York N.Y.), 2010 December 24;330(6012): 1787--1797. doi:10.1126/science.1198374

    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
      R. Alan Harris, Ting Wang, Cristian Coarfa, Raman P. Nagarajan, Chibo Hong, Sara L. Downey, Brett E. Johnson, Shaun D. Fouse, Allen Delaney, Yongjun Zhao, Adam Olshen, Tracy Ballinger, Xin Zhou, Kevin J. Forsberg, Junchen Gu, Lorigail Echipare, Henriette O'Geen, Ryan Lister, Mattia Pelizzola, Yuanxin Xi, Charles B. Epstein, Bradley E. Bernstein, R. David Hawkins, Bing Ren, Wen-Yu Chung, Hongcang Gu, Christoph Bock, Andreas Gnirke, Michael Q. Zhang, David Haussler, Joseph R. Ecker, Wei Li, Peggy J. Farnham, Robert A. Waterland, Alexander Meissner, Marco A. Marra, Martin Hirst, Aleksandar Milosavljevic, Joseph F. Costello
      Nature biotechnology, 2010 October 01;28(10): 1097--1105. doi:10.1038/nbt.1682

    • The NIH Roadmap Epigenomics Mapping Consortium.
      Bradley E. Bernstein, John A. Stamatoyannopoulos, Joseph F. Costello, Bing Ren, Aleksandar Milosavljevic, Alexander Meissner, Manolis Kellis, Marco A. Marra, Arthur L. Beaudet, Joseph R. Ecker, Peggy J. Farnham, Martin Hirst, Eric S. Lander, Tarjei S. Mikkelsen, James A. Thomson
      Nature biotechnology, 2010 October 01;28(10): 1045--1048. doi:10.1038/nbt1010-1045

    • p16(INK4a) -mediated suppression of telomerase in normal and malignant human breast cells.
      Alexey V. Bazarov, Marjolein Van Sluis, William C. Hines, Ekaterina Bassett, Alain Beliveau, Eric Campeau, Rituparna Mukhopadhyay, Won Jae Lee, Sonya Melodyev, Yuri Zaslavsky, Leonard Lee, Francis Rodier, Agustin Chicas, Scott W. Lowe, Jean Benhattar, Bing Ren, Judith Campisi, Paul Yaswen
      Aging cell, 2010 October 01;9(5): 736--746. doi:10.1111/j.1474-9726.2010.00599.x

    • ChIP-Seq identification of weakly conserved heart enhancers.
      Matthew J. Blow, David J. McCulley, Zirong Li, Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, James Bristow, Bing Ren, Brian L. Black, Edward M. Rubin, Axel Visel, Len A. Pennacchio
      Nature genetics, 2010 September 01;42(9): 806--810. doi:10.1038/ng.650

    • Next-generation genomics: an integrative approach.
      R. David Hawkins, Gary C. Hon, Bing Ren
      Nature reviews. Genetics, 2010 July 01;11(7): 476--486. doi:10.1038/nrg2795

    • Transcription: Enhancers make non-coding RNA.
      Bing Ren
      Nature, 2010 May 13;465(7295): 173--174. doi:10.1038/465173a

    • Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.
      R. David Hawkins, Gary C. Hon, Leonard K. Lee, Queminh Ngo, Ryan Lister, Mattia Pelizzola, Lee E. Edsall, Samantha Kuan, Ying Luu, Sarit Klugman, Jessica Antosiewicz-Bourget, Zhen Ye, Celso Espinoza, Saurabh Agarwahl, Li Shen, Victor Ruotti, Wei Wang, Ron Stewart, James A. Thomson, Joseph R. Ecker, Bing Ren
      Cell stem cell, 2010 May 07;6(5): 479--491. doi:10.1016/j.stem.2010.03.018

    • Genome-wide prediction of transcription factor binding sites using an integrated model.
      Kyoung-Jae Won, Bing Ren, Wei Wang
      Genome biology, 2010 January 22;11(1): R7. doi:10.1186/gb-2010-11-1-r7

    • Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing.
      Qi Zhao, Ewen F. Kirkness, Otavia L. Caballero, Pedro A. Galante, Raphael B. Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R. Vasconcelos, Bing Ren, Sandro J. de Souza, Anamaria A. Camargo, Andrew J. G. Simpson, Robert L. Strausberg
      Genome biology, 2010 January 01;11(11): R114. doi:10.1186/gb-2010-11-11-r114

    2009

    • Finding distal regulatory elements in the human genome.
      Nathaniel D. Heintzman, Bing Ren
      Current opinion in genetics & development, 2009 December 01;19(6): 541--549. doi:10.1016/j.gde.2009.09.006

    • Human DNA methylomes at base resolution show widespread epigenomic differences.
      Ryan Lister, Mattia Pelizzola, Robert H. Dowen, R. David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R. Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo, Lee Edsall, Jessica Antosiewicz-Bourget, Ron Stewart, Victor Ruotti, A. Harvey Millar, James A. Thomson, Bing Ren, Joseph R. Ecker
      Nature, 2009 November 19;462(7271): 315--322. doi:10.1038/nature08514

    • Discovery and annotation of functional chromatin signatures in the human genome.
      Gary Hon, Wei Wang, Bing Ren
      PLoS computational biology, 2009 November 01;5(11): e1000566. doi:10.1371/journal.pcbi.1000566

    • Predictive chromatin signatures in the mammalian genome.
      Gary C. Hon, R. David Hawkins, Bing Ren
      Human molecular genetics, 2009 October 15;18(): R195--201. doi:10.1093/hmg/ddp409

    • Histone modifications at human enhancers reflect global cell-type-specific gene expression.
      Nathaniel D. Heintzman, Gary C. Hon, R. David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, Leonard K. Lee, Rhona K. Stuart, Christina W. Ching, Keith A. Ching, Jessica E. Antosiewicz-Bourget, Hui Liu, Xinmin Zhang, Roland D. Green, Victor V. Lobanenkov, Ron Stewart, James A. Thomson, Gregory E. Crawford, Manolis Kellis, Bing Ren
      Nature, 2009 May 07;459(7243): 108--112. doi:10.1038/nature07829

    • ChIP-seq accurately predicts tissue-specific activity of enhancers.
      Axel Visel, Matthew J. Blow, Zirong Li, Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin, Len A. Pennacchio
      Nature, 2009 February 12;457(7231): 854--858. doi:10.1038/nature07730

    • An integrated approach to identifying cis-regulatory modules in the human genome.
      Kyoung-Jae Won, Saurabh Agarwal, Li Shen, Robert Shoemaker, Bing Ren, Wei Wang
      PloS one, 2009 January 01;4(5): e5501. doi:10.1371/journal.pone.0005501

    2008

    • Prediction of regulatory elements in mammalian genomes using chromatin signatures.
      Kyoung-Jae Won, Iouri Chepelev, Bing Ren, Wei Wang
      BMC bioinformatics, 2008 December 18;9(): 547. doi:10.1186/1471-2105-9-547

    • HPLC method for the determination of bezafibrate in human plasma and application to a pharmacokinetic study of bezafibrate dispersible tablet.
      Zhang Wei, Xiang Bing-ren, Zhan Ying, Yu Liyan, Wang Teng, Wang Cai-yun
      Journal of chromatographic science, 2008 December 01;46(10): 844--847. doi:

    • ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.
      Gary Hon, Bing Ren, Wei Wang
      PLoS computational biology, 2008 October 01;4(10): e1000201. doi:10.1371/journal.pcbi.1000201

    • Role of the histone H3 lysine 4 methyltransferase SET7/9 in the regulation of
      Yan Li, Marpadga A. Reddy, Feng Miao, Narkunaraja Shanmugam, Jiing-Kuan Yee, David Hawkins, Bing Ren, Rama Natarajan
      The Journal of biological chemistry, 2008 September 26;283(39): 26771--26781. doi:10.1074/jbc.M802800200

    • Genome-wide mapping of allele-specific protein-DNA interactions in human cells.
      Nathaniel D. Maynard, Jing Chen, Rhona K. Stuart, Jian-Bing Fan, Bing Ren
      Nature methods, 2008 April 01;5(4): 307--309. doi:10.1038/nmeth.1194

    • Vaccine-induced human antibodies to PspA augment complement C3 deposition on Streptococcus pneumoniae.
      Martina M. Ochs, William Bartlett, David E. Briles, Bryony Hicks, Audra Jurkuvenas, Peggy Lau, Bing Ren, Amanda Millar
      Microbial pathogenesis, 2008 March 01;44(3): 204--214. doi:10.1016/j.micpath.2007.09.007

    • Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
      David S. Johnson, Wei Li, D. Benjamin Gordon, Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S. Carroll, Myles Brown, Paul Flicek, Christoph M. Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J. Farnham, Philipp Kapranov, David A. Nix, Thomas R. Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland D. Green, Jun S. Song, Scott A. McCuine, Elizabeth Anton, Loan Nguyen, Nathan D. Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C. Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P. Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M. Myers, Jason D. Lieb, X. Shirley Liu
      Genome research, 2008 March 01;18(3): 393--403. doi:10.1101/gr.7080508

    • Unraveling epigenetic regulation in embryonic stem cells.
      Marina Bibikova, Louise C. Laurent, Bing Ren, Jeanne F. Loring, Jian-Bing Fan
      Cell stem cell, 2008 February 07;2(2): 123--134. doi:10.1016/j.stem.2008.01.005

    • Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs.
      Leah O. Barrera, Zirong Li, Andrew D. Smith, Karen C. Arden, Webster K. Cavenee, Michael Q. Zhang, Roland D. Green, Bing Ren
      Genome research, 2008 January 01;18(1): 46--59. doi:10.1101/gr.6654808

    2007

    • Identification of the transcriptional targets of FOXP2 a gene linked to speech and language in developing human brain.
      Elizabeth Spiteri, Genevieve Konopka, Giovanni Coppola, Jamee Bomar, Michael Oldham, Jing Ou, Sonja C. Vernes, Simon E. Fisher, Bing Ren, Daniel H. Geschwind
      American journal of human genetics, 2007 December 01;81(6): 1144--1157. doi:10.1086/522237

    • ChIP-chip: data model and analysis.
      Ming Zheng, Leah O. Barrera, Bing Ren, Ying Nian Wu
      Biometrics, 2007 September 01;63(3): 787--796. doi:10.1111/j.1541-0420.2007.00768.x

    • Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.
      Hualin Xi, Hennady P. Shulha, Jane M. Lin, Teresa R. Vales, Yutao Fu, David M. Bodine, Ronald D. G. McKay, Josh G. Chenoweth, Paul J. Tesar, Terrence S. Furey, Bing Ren, Zhiping Weng, Gregory E. Crawford
      PLoS genetics, 2007 August 01;3(8): e136. doi:10.1371/journal.pgen.0030136

    • ChIP-chip for genome-wide analysis of protein binding in mammalian cells.
      Tae Hoon Kim, Leah O. Barrera, Bing Ren
      Current protocols in molecular biology, 2007 July 01;Chapter 21(): Unit 21.13. doi:10.1002/0471142727.mb2113s79

    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
      Ewan Birney, John A. Stamatoyannopoulos, Anindya Dutta, Roderic Guigo, Thomas R. Gingeras, Elliott H. Margulies, Zhiping Weng, Michael Snyder, Emmanouil T. Dermitzakis, Robert E. Thurman, Michael S. Kuehn, Christopher M. Taylor, Shane Neph, Christoph M. Koch, Saurabh Asthana, Ankit Malhotra, Ivan Adzhubei, Jason A. Greenbaum, Robert M. Andrews, Paul Flicek, Patrick J. Boyle, Hua Cao, Nigel P. Carter, Gayle K. Clelland, Sean Davis, Nathan Day, Pawandeep Dhami, Shane C. Dillon, Michael O. Dorschner, Heike Fiegler, Paul G. Giresi, Jeff Goldy, Michael Hawrylycz, Andrew Haydock, Richard Humbert, Keith D. James, Brett E. Johnson, Ericka M. Johnson, Tristan T. Frum, Elizabeth R. Rosenzweig, Neerja Karnani, Kirsten Lee, Gregory C. Lefebvre, Patrick A. Navas, Fidencio Neri, Stephen C. J. Parker, Peter J. Sabo, Richard Sandstrom, Anthony Shafer, David Vetrie, Molly Weaver, Sarah Wilcox, Man Yu, Francis S. Collins, Job Dekker, Jason D. Lieb, Thomas D. Tullius, Gregory E. Crawford, Shamil Sunyaev, William S. Noble, Ian Dunham, France Denoeud, Alexandre Reymond, Philipp Kapranov, Joel Rozowsky, Deyou Zheng, Robert Castelo, Adam Frankish, Jennifer Harrow, Srinka Ghosh, Albin Sandelin, Ivo L. Hofacker, Robert Baertsch, Damian Keefe, Sujit Dike, Jill Cheng, Heather A. Hirsch, Edward A. Sekinger, Julien Lagarde, Josep F. Abril, Atif Shahab, Christoph Flamm, Claudia Fried, Jorg Hackermuller, Jana Hertel, Manja Lindemeyer, Kristin Missal, Andrea Tanzer, Stefan Washietl, Jan Korbel, Olof Emanuelsson, Jakob S. Pedersen, Nancy Holroyd, Ruth Taylor, David Swarbreck, Nicholas Matthews, Mark C. Dickson, Daryl J. Thomas, Matthew T. Weirauch, James Gilbert, Jorg Drenkow, Ian Bell, XiaoDong Zhao, K. G. Srinivasan, Wing-Kin Sung, Hong Sain Ooi, Kuo Ping Chiu, Sylvain Foissac, Tyler Alioto, Michael Brent, Lior Pachter, Michael L. Tress, Alfonso Valencia, Siew Woh Choo, Chiou Yu Choo, Catherine Ucla, Caroline Manzano, Carine Wyss, Evelyn Cheung, Taane G. Clark, James B. Brown, Madhavan Ganesh, Sandeep Patel, Hari Tammana, Jacqueline Chrast, Charlotte N. Henrichsen, Chikatoshi Kai, Jun Kawai, Ugrappa Nagalakshmi, Jiaqian Wu, Zheng Lian, Jin Lian, Peter Newburger, Xueqing Zhang, Peter Bickel, John S. Mattick, Piero Carninci, Yoshihide Hayashizaki, Sherman Weissman, Tim Hubbard, Richard M. Myers, Jane Rogers, Peter F. Stadler, Todd M. Lowe, Chia-Lin Wei, Yijun Ruan, Kevin Struhl, Mark Gerstein, Stylianos E. Antonarakis, Yutao Fu, Eric D. Green, Ulas Karaoz, Adam Siepel, James Taylor, Laura A. Liefer, Kris A. Wetterstrand, Peter J. Good, Elise A. Feingold, Mark S. Guyer, Gregory M. Cooper, George Asimenos, Colin N. Dewey, Minmei Hou, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Loytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, Haiyan Huang, Nancy R. Zhang, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Michael Seringhaus, Deanna Church, Kate Rosenbloom, W. James Kent, Eric A. Stone, Serafim Batzoglou, Nick Goldman, Ross C. Hardison, David Haussler, Webb Miller, Arend Sidow, Nathan D. Trinklein, Zhengdong D. Zhang, Leah Barrera, Rhona Stuart, David C. King, Adam Ameur, Stefan Enroth, Mark C. Bieda, Jonghwan Kim, Akshay A. Bhinge, Nan Jiang, Jun Liu, Fei Yao, Vinsensius B. Vega, Charlie W. H. Lee, Patrick Ng, Atif Shahab, Annie Yang, Zarmik Moqtaderi, Zhou Zhu, Xiaoqin Xu, Sharon Squazzo, Matthew J. Oberley, David Inman, Michael A. Singer, Todd A. Richmond, Kyle J. Munn, Alvaro Rada-Iglesias, Ola Wallerman, Jan Komorowski, Joanna C. Fowler, Phillippe Couttet, Alexander W. Bruce, Oliver M. Dovey, Peter D. Ellis, Cordelia F. Langford, David A. Nix, Ghia Euskirchen, Stephen Hartman, Alexander E. Urban, Peter Kraus, Sara Van Calcar, Nate Heintzman, Tae Hoon Kim, Kun Wang, Chunxu Qu, Gary Hon, Rosa Luna, Christopher K. Glass, M. Geoff Rosenfeld, Shelley Force Aldred, Sara J. Cooper, Anason Halees, Jane M. Lin, Hennady P. Shulha, Xiaoling Zhang, Mousheng Xu, Jaafar N. S. Haidar, Yong Yu, Yijun Ruan, Vishwanath R. Iyer, Roland D. Green, Claes Wadelius, Peggy J. Farnham, Bing Ren, Rachel A. Harte, Angie S. Hinrichs, Heather Trumbower, Hiram Clawson, Jennifer Hillman-Jackson, Ann S. Zweig, Kayla Smith, Archana Thakkapallayil, Galt Barber, Robert M. Kuhn, Donna Karolchik, Lluis Armengol, Christine P. Bird, Paul I. W. de Bakker, Andrew D. Kern, Nuria Lopez-Bigas, Joel D. Martin, Barbara E. Stranger, Abigail Woodroffe, Eugene Davydov, Antigone Dimas, Eduardo Eyras, Ingileif B. Hallgrimsdottir, Julian Huppert, Michael C. Zody, Goncalo R. Abecasis, Xavier Estivill, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V. B. Maduro, Baishali Maskeri, Jennifer C. McDowell, Morgan Park, Pamela J. Thomas, Alice C. Young, Robert W. Blakesley, Donna M. Muzny, Erica Sodergren, David A. Wheeler, Kim C. Worley, Huaiyang Jiang, George M. Weinstock, Richard A. Gibbs, Tina Graves, Robert Fulton, Elaine R. Mardis, Richard K. Wilson, Michele Clamp, James Cuff, Sante Gnerre, David B. Jaffe, Jean L. Chang, Kerstin Lindblad-Toh, Eric S. Lander, Maxim Koriabine, Mikhail Nefedov, Kazutoyo Osoegawa, Yuko Yoshinaga, Baoli Zhu, Pieter J. de Jong
      Nature, 2007 June 14;447(7146): 799--816. doi:10.1038/nature05874

    • Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.
      Tae Hoon Kim, Ziedulla K. Abdullaev, Andrew D. Smith, Keith A. Ching, Dmitri I. Loukinov, Roland D. Green, Michael Q. Zhang, Victor V. Lobanenkov, Bing Ren
      Cell, 2007 March 23;128(6): 1231--1245. doi:10.1016/j.cell.2006.12.048

    • Liquid chromatography-mass spectrometry method for the determination of venlafaxine in human plasma and application to a pharmacokinetic study.
      Zhang Wei, Xiang Bing-Ren, Wang Cai-Yun
      Biomedical chromatography : BMC, 2007 March 01;21(3): 266--272. doi:10.1002/bmc.748

    • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
      Nathaniel D. Heintzman, Rhona K. Stuart, Gary Hon, Yutao Fu, Christina W. Ching, R. David Hawkins, Leah O. Barrera, Sara Van Calcar, Chunxu Qu, Keith A. Ching, Wei Wang, Zhiping Weng, Roland D. Green, Gregory E. Crawford, Bing Ren
      Nature genetics, 2007 March 01;39(3): 311--318. doi:10.1038/ng1966

    2006

    • A new single-well potential stochastic resonance algorithm to detect the weak signal.
      Zhang Wei, Xiang Bing-Ren
      Talanta, 2006 September 15;70(2): 267--271. doi:10.1016/j.talanta.2006.02.039

    • Mnt-deficient mammary glands exhibit impaired involution and tumors with characteristics of myc overexpression.
      Kazuhito Toyo-oka, Timothy J. Bowen, Shinji Hirotsune, Zirong Li, Sonia Jain, Sara Ota, Laure Escoubet-Lozach, Ivan Garcia-Bassets, Jean Lozach, Michael G. Rosenfeld, Christopher K. Glass, Robert Eisenman, Bing Ren, Peter Hurlin, Anthony Wynshaw-Boris
      Cancer research, 2006 June 01;66(11): 5565--5573. doi:10.1158/0008-5472.CAN-05-2683

    • The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding.
      Leah O. Barrera, Bing Ren
      Current opinion in cell biology, 2006 June 01;18(3): 291--298. doi:10.1016/j.ceb.2006.04.002

    • Genome-wide location analysis: insights on transcriptional regulation.
      R. David Hawkins, Bing Ren
      Human molecular genetics, 2006 April 15;15 Spec No 1(): R1--7. doi:10.1093/hmg/ddl043

    • Positive inter-regulation between beta-catenin/T cell factor-4 signaling and endothelin-1 signaling potentiates proliferation and survival of prostate cancer cells.
      Ping Sun, Hui Xiong, Tae Hoon Kim, Bing Ren, Zhuohua Zhang
      Molecular pharmacology, 2006 February 01;69(2): 520--531. doi:10.1124/mol.105.019620

    • Genome-wide analysis of protein-DNA interactions.
      Tae Hoon Kim, Bing Ren
      Annual review of genomics and human genetics, 2006 January 01;7(): 81--102. doi:10.1146/annurev.genom.7.080505.115634

    • An all-round view of eukaryotic transcription.
      Tae Hoon Kim, Bing Ren
      Genome biology, 2006 January 01;7(7): 323. doi:10.1186/gb-2006-7-7-323

    2005

    • A high-resolution map of active promoters in the human genome.
      Tae Hoon Kim, Leah O. Barrera, Ming Zheng, Chunxu Qu, Michael A. Singer, Todd A. Richmond, Yingnian Wu, Roland D. Green, Bing Ren
      Nature, 2005 August 11;436(7052): 876--880. doi:10.1038/nature03877

    • Direct isolation and identification of promoters in the human genome.
      Tae Hoon Kim, Leah O. Barrera, Chunxu Qu, Sara Van Calcar, Nathan D. Trinklein, Sara J. Cooper, Rosa M. Luna, Christopher K. Glass, Michael G. Rosenfeld, Richard M. Myers, Bing Ren
      Genome research, 2005 June 01;15(6): 830--839. doi:10.1101/gr.3430605

    • beta-Catenin activates the growth factor endothelin-1 in colon cancer cells.
      Tae Hoon Kim, Hui Xiong, Zhuohua Zhang, Bing Ren
      Oncogene, 2005 January 20;24(4): 597--604. doi:10.1038/sj.onc.1208237

    2004

    • The virulence function of Streptococcus pneumoniae surface protein A involves inhibition of complement activation and impairment of complement receptor-mediated protection.
      Bing Ren, Mark A. McCrory, Christina Pass, Daniel C. Bullard, Christie M. Ballantyne, Yuanyuan Xu, David E. Briles, Alexander J. Szalai
      Journal of immunology (Baltimore Md. : 1950), 2004 December 15;173(12): 7506--7512. doi:

    • [Effects of aspirin on lowering plasma level of lysophosphatidic acid in cerebral ischemic patients].
      Cun-shan Yao, Qi-zhuan Wu, Chao-shu Tang, Xiao-luo Meng, Bing Ren, Zhen-guang Li, Shi-chang Huang, Yun-heng Sun, He-qiu Bao
      Zhonghua yi xue za zhi, 2004 November 17;84(22): 1926--1928. doi:

    • [The change of renin endothelin and prostaglandin in blood during long time left ventricular assist].
      Lian-wei Tong, Bing Ren, Xiao-dong Zhu
      Zhonghua wai ke za zhi [Chinese journal of surgery], 2004 March 22;42(6): 355--357. doi:

    • Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors.
      Bing Ren, Brian D. Dynlacht
      Methods in enzymology, 2004 January 01;376(): 304--315. doi:10.1016/S0076-6879(03)76020-0

    • Effects of PspA and antibodies to PspA on activation and deposition of complement on the pneumococcal surface.
      Bing Ren, Alexander J. Szalai, Susan K. Hollingshead, David E. Briles
      Infection and immunity, 2004 January 01;72(1): 114--122. doi:

    2003

    • [Continuous veno-venous hemofiltration in treatment of acute severe hyponatremia: a report of 6 cases].
      Da-xi Ji, De-hua Gong, Bin Xu, Jing Tao, Bing Ren, Yi-dan Zhang, Yun Liu, Wei-xin Hu, Lei-shi Li
      Zhonghua nei ke za zhi, 2003 November 01;42(11): 781--784. doi:

    • Relative roles of genetic background and variation in PspA in the ability of antibodies to PspA to protect against capsular type 3 and 4 strains of Streptococcus pneumoniae.
      Hazeline Roche, Bing Ren, Larry S. McDaniel, Anders Hakansson, David E. Briles
      Infection and immunity, 2003 August 01;71(8): 4498--4505. doi:

    • A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells.
      Zirong Li, Sara Van Calcar, Chunxu Qu, Webster K. Cavenee, Michael Q. Zhang, Bing Ren
      Proceedings of the National Academy of Sciences of the United States of America, 2003 July 08;100(14): 8164--8169. doi:10.1073/pnas.1332764100

    • [In vivo and in vitro evaluation of inflow cannula of left ventricular assist].
      Lian-wei Tong, Bing Ren, Xiao-dong Zhu
      Zhonghua wai ke za zhi [Chinese journal of surgery], 2003 January 01;41(1): 64--66. doi:

    • Both family 1 and family 2 PspA proteins can inhibit complement deposition and confer virulence to a capsular serotype 3 strain of Streptococcus pneumoniae.
      Bing Ren, Alexander J. Szalai, Orlanda Thomas, Susan K. Hollingshead, David E. Briles
      Infection and immunity, 2003 January 01;71(1): 75--85. doi:

    2002

    • Transcriptional regulatory networks in Saccharomyces cerevisiae.
      Tong Ihn Lee, Nicola J. Rinaldi, Francois Robert, Duncan T. Odom, Ziv Bar-Joseph, Georg K. Gerber, Nancy M. Hannett, Christopher T. Harbison, Craig M. Thompson, Itamar Simon, Julia Zeitlinger, Ezra G. Jennings, Heather L. Murray, D. Benjamin Gordon, Bing Ren, John J. Wyrick, Jean-Bosco Tagne, Thomas L. Volkert, Ernest Fraenkel, David K. Gifford, Richard A. Young
      Science (New York N.Y.), 2002 October 25;298(5594): 799--804. doi:10.1126/science.1075090

    • Preliminary in vivo study of an intra-aortic impeller pump driven by an extracorporeal whirling magnet.
      Guorong Li, Hong Zhao, Xiaodong Zhu, Bing Ren
      Artificial organs, 2002 October 01;26(10): 890--893. doi:

    • E2F integrates cell cycle progression with DNA repair replication and G(2)/M checkpoints.
      Bing Ren, Hieu Cam, Yasuhiko Takahashi, Thomas Volkert, Jolyon Terragni, Richard A. Young, Brian David Dynlacht
      Genes & development, 2002 January 15;16(2): 245--256. doi:10.1101/gad.949802