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Bing Ren, Ph.D. - Publications

Affiliations: 
Ludwig Institute for Cancer Research, San Diego, CA, United States 
Area:
Genomics
Website:
http://www.ludwigcancerresearch.org/location/san-diego-branch/bing-ren-lab

221 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 D'Aurizio R, Catona O, Pitasi M, Li YE, Ren B, Nicolis SK. Bridging between Mouse and Human Enhancer-Promoter Long-Range Interactions in Neural Stem Cells, to Understand Enhancer Function in Neurodevelopmental Disease. International Journal of Molecular Sciences. 23. PMID 35887306 DOI: 10.3390/ijms23147964  0.466
2022 Preissl S, Gaulton KJ, Ren B. Characterizing cis-regulatory elements using single-cell epigenomics. Nature Reviews. Genetics. PMID 35840754 DOI: 10.1038/s41576-022-00509-1  0.433
2022 Meng Z, Li FL, Fang C, Yeoman B, Qiu Y, Wang Y, Cai X, Lin KC, Yang D, Luo M, Fu V, Ma X, Diao Y, Giancotti FG, Ren B, et al. The Hippo pathway mediates Semaphorin signaling. Science Advances. 8: eabl9806. PMID 35613278 DOI: 10.1126/sciadv.abl9806  0.698
2022 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, et al. Author Correction: Perspectives on ENCODE. Nature. PMID 35474002 DOI: 10.1038/s41586-021-04213-8  0.67
2022 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, ... ... Ren B, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3  0.808
2022 Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, ... ... Ren B, et al. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genomics. 2. PMID 35419551 DOI: 10.1016/j.xgen.2022.100107  0.707
2022 Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, ... ... Ren B, et al. Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. PMID 35319013 DOI: 10.1038/s41586-022-04562-y  0.604
2021 Zhang K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A, Preissl S, Ren B. A single-cell atlas of chromatin accessibility in the human genome. Cell. PMID 34774128 DOI: 10.1016/j.cell.2021.10.024  0.524
2021 Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, ... ... Ren B, et al. An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 598: 129-136. PMID 34616068 DOI: 10.1038/s41586-021-03604-1  0.674
2021 Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, ... ... Ren B, et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 598: 103-110. PMID 34616066 DOI: 10.1038/s41586-021-03500-8  0.665
2021 Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, ... ... Ren B, et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 598: 111-119. PMID 34616062 DOI: 10.1038/s41586-021-03465-8  0.689
2021 Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, ... ... Ren B, et al. DNA methylation atlas of the mouse brain at single-cell resolution. Nature. 598: 120-128. PMID 34616061 DOI: 10.1038/s41586-020-03182-8  0.734
2021 Ren X, Wang M, Li B, Jamieson K, Zheng L, Jones IR, Li B, Takagi MA, Lee J, Maliskova L, Tam TW, Yu M, Hu R, Lee L, Abnousi A, ... ... Ren B, et al. Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Science Advances. 7: eabi4360. PMID 34524848 DOI: 10.1126/sciadv.abi4360  0.562
2021 Yu M, Abnousi A, Zhang Y, Li G, Lee L, Chen Z, Fang R, Lagler TM, Yang Y, Wen J, Sun Q, Li Y, Ren B, Hu M. SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. Nature Methods. PMID 34446921 DOI: 10.1038/s41592-021-01231-2  0.309
2021 Yu M, Juric I, Abnousi A, Hu M, Ren B. Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq). Methods in Molecular Biology (Clifton, N.J.). 2351: 181-199. PMID 34382190 DOI: 10.1007/978-1-0716-1597-3_10  0.391
2021 Hocker JD, Poirion OB, Zhu F, Buchanan J, Zhang K, Chiou J, Wang TM, Zhang Q, Hou X, Li YE, Zhang Y, Farah EN, Wang A, McCulloch AD, Gaulton KJ, ... Ren B, et al. Cardiac cell type-specific gene regulatory programs and disease risk association. Science Advances. 7. PMID 33990324 DOI: 10.1126/sciadv.abf1444  0.425
2021 Fang R, Preissl S, Li Y, Hou X, Lucero J, Wang X, Motamedi A, Shiau AK, Zhou X, Xie F, Mukamel EA, Zhang K, Zhang Y, Behrens MM, Ecker JR, ... Ren B, et al. Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nature Communications. 12: 1337. PMID 33637727 DOI: 10.1038/s41467-021-21583-9  0.479
2021 Zhu C, Zhang Y, Li YE, Lucero J, Behrens MM, Ren B. Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Nature Methods. PMID 33589836 DOI: 10.1038/s41592-021-01060-3  0.461
2021 Geusz RJ, Wang A, Chiou J, Lancman JJ, Wetton N, Kefalopoulou S, Wang J, Qui Y, Yan J, Aylward A, Ren B, Dong PDS, Gaulton KJ, Sander M. Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development. Elife. 10. PMID 33544077 DOI: 10.7554/eLife.59067  0.53
2021 Yan J, Qiu Y, Ribeiro Dos Santos AM, Yin Y, Li YE, Vinckier N, Nariai N, Benaglio P, Raman A, Li X, Fan S, Chiou J, Chen F, Frazer KA, Gaulton KJ, ... ... Ren B, et al. Systematic analysis of binding of transcription factors to noncoding variants. Nature. PMID 33505025 DOI: 10.1038/s41586-021-03211-0  0.605
2021 Agarwal S, Bonefas KM, Garay PM, Brookes E, Murata-Nakamura Y, Porter RS, Macfarlan TS, Ren B, Iwase S. KDM1A maintains genome-wide homeostasis of transcriptional enhancers. Genome Research. PMID 33414108 DOI: 10.1101/gr.234559.118  0.382
2021 Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker JD, Conte M, Gorkin D, Yu M, Li B, Dixon JR, Hu M, Nicodemi M, Zhao H, ... Ren B, et al. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nature Structural & Molecular Biology. PMID 33398174 DOI: 10.1038/s41594-020-00539-5  0.733
2021 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, ... ... Ren B, et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. PMID 33398137 DOI: 10.1038/s41586-020-03089-4  0.549
2021 Zhou Q, Yu M, Tirado-Magallanes R, Li B, Kong L, Guo M, Tan ZH, Lee S, Chai L, Numata A, Benoukraf T, Fullwood MJ, Osato M, Ren B, Tenen DG. ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine hematopoietic stem and progenitor cell function. Nature Communications. 12: 43. PMID 33397967 DOI: 10.1038/s41467-020-20282-1  0.383
2020 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, ... ... Ren B, et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. PMID 33037424 DOI: 10.1038/s41586-020-2841-4  0.538
2020 You Q, Cheng AY, Gu X, Harada BT, Yu M, Wu T, Ren B, Ouyang Z, He C. Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution. Nature Biotechnology. PMID 32839564 DOI: 10.1038/S41587-020-0643-8  0.41
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Ren B, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.841
2020 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/S41586-020-2449-8  0.805
2020 He P, Williams BA, Trout D, Marinov GK, Amrhein H, Berghella L, Goh ST, Plajzer-Frick I, Afzal V, Pennacchio LA, Dickel DE, Visel A, Ren B, Hardison RC, Zhang Y, et al. The changing mouse embryo transcriptome at whole tissue and single-cell resolution. Nature. 583: 760-767. PMID 32728245 DOI: 10.1038/S41586-020-2536-X  0.634
2020 He Y, Hariharan M, Gorkin DU, Dickel DE, Luo C, Castanon RG, Nery JR, Lee AY, Zhao Y, Huang H, Williams BA, Trout D, Amrhein H, Fang R, Chen H, ... ... Ren B, et al. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature. 583: 752-759. PMID 32728242 DOI: 10.1038/S41586-020-2119-X  0.503
2020 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, ... ... Ren B, et al. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 583: 744-751. PMID 32728240 DOI: 10.1038/S41586-020-2093-3  0.703
2020 Arvanitis M, Tampakakis E, Zhang Y, Wang W, Auton A, Dutta D, Glavaris S, Keramati A, Chatterjee N, Chi NC, Ren B, Post WS, Battle A. Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure. Nature Communications. 11: 1122. PMID 32111823 DOI: 10.1038/S41467-020-14843-7  0.363
2020 Pugacheva EM, Kubo N, Loukinov D, Tajmul M, Kang S, Kovalchuk AL, Strunnikov AV, Zentner GE, Ren B, Lobanenkov VV. CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention. Proceedings of the National Academy of Sciences of the United States of America. PMID 31937660 DOI: 10.1073/Pnas.1911708117  0.384
2020 Zhu C, Preissl S, Ren B. Single-cell multimodal omics: the power of many. Nature Methods. 17: 11-14. PMID 31907462 DOI: 10.1038/S41592-019-0691-5  0.39
2020 Wahl G, Ma Z, Chung C, Dravis C, Spike B, Giraddi R, Balcioglu O, Fan C, Hagos B, Heinz R, Herrera-Valdez J, Hou X, Hwang J, Lasken R, Luna G, ... ... Ren B, et al. Abstract ES10-2: Understanding breast cancer using a developmental perspective Cancer Research. 80. DOI: 10.1158/1538-7445.Sabcs19-Es10-2  0.391
2020 Raviram R, Raman A, Preissl S, Ning J, Wu S, Deynze K, Chen C, Ren B. EPCO-19. INTEGRATED ANALYSIS OF INTRA-TUMORAL HETEROGENEITY IN GLIOBLASTOMAS THROUGH SINGLE NUCLEI ATAC-SEQ AND RNA-SEQ Neuro-Oncology. 22: ii73-ii73. DOI: 10.1093/neuonc/noaa215.298  0.762
2019 Gorkin DU, Qiu Y, Hu M, Fletez-Brant K, Liu T, Schmitt AD, Noor A, Chiou J, Gaulton KJ, Sebat J, Li Y, Hansen KD, Ren B. Common DNA sequence variation influences 3-dimensional conformation of the human genome. Genome Biology. 20: 255. PMID 31779666 DOI: 10.1186/S13059-019-1855-4  0.46
2019 Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, ... ... Ren B, et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. PMID 31748743 DOI: 10.1038/S41586-019-1763-5  0.837
2019 Wells A, Heckerman D, Torkamani A, Yin L, Sebat J, Ren B, Telenti A, di Iulio J. Ranking of non-coding pathogenic variants and putative essential regions of the human genome. Nature Communications. 10: 5241. PMID 31748530 DOI: 10.1038/S41467-019-13212-3  0.437
2019 Nott A, Holtman IR, Coufal NG, Schlachetzki JCM, Yu M, Hu R, Han CZ, Pena M, Xiao J, Wu Y, Keulen Z, Pasillas MP, O'Connor C, Nickl CK, Schafer ST, ... ... Ren B, et al. Brain cell type-specific enhancer-promoter interactome maps and disease risk association. Science (New York, N.Y.). PMID 31727856 DOI: 10.1126/Science.Aay0793  0.365
2019 Zhu C, Yu M, Huang H, Juric I, Abnousi A, Hu R, Lucero J, Behrens MM, Hu M, Ren B. An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nature Structural & Molecular Biology. PMID 31695190 DOI: 10.1038/S41594-019-0323-X  0.43
2019 Zhang D, Tang Z, Huang H, Zhou G, Cui C, Weng Y, Liu W, Kim S, Lee S, Perez-Neut M, Ding J, Czyz D, Hu R, Ye Z, He M, ... ... Ren B, et al. Metabolic regulation of gene expression by histone lactylation. Nature. 574: 575-580. PMID 31645732 DOI: 10.1038/S41586-019-1678-1  0.431
2019 Chung CY, Ma Z, Dravis C, Preissl S, Poirion O, Luna G, Hou X, Giraddi RR, Ren B, Wahl GM. Single-Cell Chromatin Analysis of Mammary Gland Development Reveals Cell-State Transcriptional Regulators and Lineage Relationships. Cell Reports. 29: 495-510.e6. PMID 31597106 DOI: 10.1016/J.Celrep.2019.08.089  0.473
2019 Ishii H, Kadonaga JT, Ren B. Correction for Ishii et al., MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proceedings of the National Academy of Sciences of the United States of America. 116: 21331. PMID 31591251 DOI: 10.1073/Pnas.1916397116  0.341
2019 Dall'Agnese A, Caputo L, Nicoletti C, di Iulio J, Schmitt A, Gatto S, Diao Y, Ye Z, Forcato M, Perera R, Bicciato S, Telenti A, Ren B, Puri PL. Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation. Molecular Cell. PMID 31519520 DOI: 10.1016/J.Molcel.2019.07.036  0.8
2019 Jung I, Schmitt A, Diao Y, Lee AJ, Liu T, Yang D, Tan C, Eom J, Chan M, Chee S, Chiang Z, Kim C, Masliah E, Barr CL, Li B, ... ... Ren B, et al. A compendium of promoter-centered long-range chromatin interactions in the human genome. Nature Genetics. PMID 31501517 DOI: 10.1038/S41588-019-0494-8  0.812
2019 Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, ... ... Ren B, et al. Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nature Genetics. PMID 31427791 DOI: 10.1038/S41588-019-0479-7  0.4
2019 Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, Ren B. Joint profiling of DNA methylation and chromatin architecture in single cells. Nature Methods. PMID 31384045 DOI: 10.1038/S41592-019-0502-Z  0.619
2019 Yang Y, Zhang Y, Ren B, Dixon JR, Ma J. Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Cell Systems. PMID 31229558 DOI: 10.1016/J.Cels.2019.05.011  0.718
2019 Nechemia-Arbely Y, Miga KH, Shoshani O, Aslanian A, McMahon MA, Lee AY, Fachinetti D, Yates JR, Ren B, Cleveland DW. DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres. Nature Cell Biology. 21: 743-754. PMID 31160708 DOI: 10.1038/S41556-019-0331-4  0.425
2019 Greenwald WW, Chiou J, Yan J, Qiu Y, Dai N, Wang A, Nariai N, Aylward A, Han JY, Kadakia N, Regue L, Okino ML, Drees F, Kramer D, Vinckier N, ... ... Ren B, et al. Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. Nature Communications. 10: 2078. PMID 31064983 DOI: 10.1038/S41467-019-09975-4  0.569
2019 Chowdhry S, Zanca C, Rajkumar U, Koga T, Diao Y, Raviram R, Liu F, Turner K, Yang H, Brunk E, Bi J, Furnari F, Bafna V, Ren B, Mischel PS. NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling. Nature. PMID 31019297 DOI: 10.1038/S41586-019-1150-2  0.776
2019 Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, ... ... Ren B, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10: 1784. PMID 30992455 DOI: 10.1038/S41467-018-08148-Z  0.432
2019 Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, Ren B, Hu M. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. Plos Computational Biology. 15: e1006982. PMID 30986246 DOI: 10.1371/Journal.Pcbi.1006982  0.769
2019 Patel L, Kang R, Rosenberg SC, Qiu Y, Raviram R, Chee S, Hu R, Ren B, Cole F, Corbett KD. Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase. Nature Structural & Molecular Biology. PMID 30778236 DOI: 10.1038/S41594-019-0187-0  0.75
2019 Jiang Q, Isquith J, Zipeto MA, Diep RH, Pham J, Delos Santos N, Reynoso E, Chau J, Leu H, Lazzari E, Melese E, Ma W, Fang R, Minden M, Morris S, ... Ren B, et al. Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation. Cancer Cell. 35: 81-94.e7. PMID 30612940 DOI: 10.1016/J.Ccell.2018.11.017  0.347
2019 Larsson AJM, Johnsson P, Hagemann-Jensen M, Hartmanis L, Faridani OR, Reinius B, Segerstolpe Å, Rivera CM, Ren B, Sandberg R. Genomic encoding of transcriptional burst kinetics. Nature. 565: 251-254. PMID 30602787 DOI: 10.1038/S41586-018-0836-1  0.437
2018 Peng Q, Lu S, Shi Y, Pan Y, Limsakul P, Chernov AV, Qiu J, Chai X, Shi Y, Wang P, Ji Y, Li YJ, Strongin AY, Verkhusha VV, Izpisua Belmonte JC, ... Ren B, et al. Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors. Proceedings of the National Academy of Sciences of the United States of America. PMID 30478057 DOI: 10.1073/Pnas.1811818115  0.393
2018 Meng Z, Qiu Y, Lin KC, Kumar A, Placone JK, Fang C, Wang KC, Lu S, Pan M, Hong AW, Moroishi T, Luo M, Plouffe SW, Diao Y, Ye Z, ... ... Ren B, et al. RAP2 mediates mechanoresponses of the Hippo pathway. Nature. PMID 30135582 DOI: 10.1038/S41586-018-0444-0  0.723
2018 Plouffe SW, Lin KC, Moore JL, Tan FE, Ma S, Ye Z, Qiu Y, Ren B, Guan KL. The Hippo pathway effector proteins YAP and TAZ have both distinct and overlapping functions in the cell. The Journal of Biological Chemistry. PMID 29802201 DOI: 10.1074/Jbc.Ra118.002715  0.407
2018 Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, ... ... Ren B, et al. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell. PMID 29779944 DOI: 10.1016/J.Cell.2018.04.018  0.409
2018 Fei J, Ishii H, Hoeksema MA, Meitinger F, Kassavetis GA, Glass CK, Ren B, Kadonaga JT. NDF, a nucleosome destabilizing factor that facilitates transcription through nucleosomes. Genes & Development. PMID 29759984 DOI: 10.1101/Gad.313973.118  0.443
2018 Koga T, Li B, Figueroa JM, Ren B, Chen CC, Carter BS, Furnari FB. Mapping of genomic EGFRvIII deletions in glioblastoma: insight into rearrangement mechanisms and biomarker development. Neuro-Oncology. PMID 29660021 DOI: 10.1093/Neuonc/Noy058  0.332
2018 Yan J, Chen SA, Local A, Liu T, Qiu Y, Dorighi KM, Preissl S, Rivera CM, Wang C, Ye Z, Ge K, Hu M, Wysocka J, Ren B. Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Cell Research. 28: 387. PMID 29497152 DOI: 10.1038/Cr.2018.18  0.529
2018 Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. Author Correction: Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nature Neuroscience. PMID 29497140 DOI: 10.1038/S41593-018-0114-4  0.729
2018 di Iulio J, Bartha I, Wong EHM, Yu HC, Lavrenko V, Yang D, Jung I, Hicks MA, Shah N, Kirkness EF, Fabani MM, Biggs WH, Ren B, Venter JC, Telenti A. The human noncoding genome defined by genetic diversity. Nature Genetics. PMID 29483654 DOI: 10.1038/S41588-018-0062-7  0.479
2018 Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nature Neuroscience. PMID 29434377 DOI: 10.1038/S41593-018-0079-3  0.784
2018 O'Brien LL, Guo Q, Bahrami-Samani E, Park JS, Hasso SM, Lee YJ, Fang A, Kim AD, Guo J, Hong TM, Peterson KA, Lozanoff S, Raviram R, Ren B, Fogelgren B, et al. Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies. Plos Genetics. 14: e1007181. PMID 29377931 DOI: 10.1371/Journal.Pgen.1007181  0.775
2018 Yan J, Chen SA, Local A, Liu T, Qiu Y, Dorighi KM, Preissl S, Rivera CM, Wang C, Ye Z, Ge K, Hu M, Wysocka J, Ren B. Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Cell Research. PMID 29313530 DOI: 10.1038/cr.2018.1  0.578
2018 Deshpande A, Chen B, Ramezani-Rad P, Pastore A, Zhao L, Weigert O, Armstrong SA, Rickert RC, Ren B, Deshpande AJ. Targeting MYC-Driven B-Cell Lymphoma By Inhibition of the Histone Methyltransferase DOT1L Blood. 132: 2839-2839. DOI: 10.1182/Blood-2018-99-115475  0.376
2017 Local A, Huang H, Albuquerque CP, Singh N, Lee AY, Wang W, Wang C, Hsia JE, Shiau AK, Ge K, Corbett KD, Wang D, Zhou H, Ren B. Identification of H3K4me1-associated proteins at mammalian enhancers. Nature Genetics. PMID 29255264 DOI: 10.1038/S41588-017-0015-6  0.424
2017 Local A, Huang H, Albuquerque CP, Singh N, Lee AY, Wang W, Wang C, Hsia JE, Shiau AK, Ge K, Corbett KD, Wang D, Zhou H, Ren B. Identification of H3K4me1-associated proteins at mammalian enhancers. Nature Genetics. PMID 29255264 DOI: 10.1038/S41588-017-0015-6  0.424
2017 Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature. 549: 219-226. PMID 28905911 DOI: 10.1038/Nature23884  0.432
2017 Rosa-Garrido M, Chapski DJ, Schmitt AD, Kimball TH, Karbassi E, Monte E, Balderas E, Pellegrini M, Shih TT, Soehalim E, Liem DA, Ping P, Galjart NJ, Ren S, Wang Y, ... Ren B, et al. High Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure. Circulation. PMID 28802249 DOI: 10.1161/Circulationaha.117.029430  0.363
2017 Yu M, Ren B. The Three-Dimensional Organization of Mammalian Genomes. Annual Review of Cell and Developmental Biology. PMID 28783961 DOI: 10.1146/Annurev-Cellbio-100616-060531  0.481
2017 Wang HX, Gao XW, Ren B, Cai Y, Li WJ, Yang YL, Li YJ. Comparative analysis of different feeder layers with 3T3 fibroblasts for culturing rabbits limbal stem cells. International Journal of Ophthalmology. 10: 1021-1027. PMID 28730101 DOI: 10.18240/Ijo.2017.07.01  0.31
2017 Martin JS, Xu Z, Reiner AP, Mohlke KL, Sullivan P, Ren B, Hu M, Li Y. HUGIn: Hi-C Unifying Genomic Interrogator. Bioinformatics (Oxford, England). PMID 28582503 DOI: 10.1093/Bioinformatics/Btx359  0.406
2017 Diao Y, Fang R, Li B, Meng Z, Yu J, Qiu Y, Lin KC, Huang H, Liu T, Marina RJ, Jung I, Shen Y, Guan KL, Ren B. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nature Methods. PMID 28417999 DOI: 10.1038/Nmeth.4264  0.825
2017 DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, et al. Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. Cell Stem Cell. 20: 533-546.e7. PMID 28388430 DOI: 10.1016/J.Stem.2017.03.009  0.442
2017 Nechemia-Arbely Y, Fachinetti D, Miga KH, Sekulic N, Soni GV, Kim DH, Wong AK, Lee AY, Nguyen K, Dekker C, Ren B, Black BE, Cleveland DW. Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points. The Journal of Cell Biology. PMID 28235947 DOI: 10.1083/Jcb.201608083  0.413
2017 Xiong X, Zhang Y, Yan J, Jain S, Chee S, Ren B, Zhao H. A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. Acs Synthetic Biology. PMID 28215080 DOI: 10.1021/Acssynbio.6B00358  0.665
2017 He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR. Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28193886 DOI: 10.1073/Pnas.1618353114  0.681
2017 Turner KM, Deshpande V, Beyter D, Koga T, Rusert J, Lee C, Li B, Arden K, Ren B, Nathanson DA, Kornblum HI, Taylor MD, Kaushal S, Cavenee WK, Wechsler-Reya R, et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature. PMID 28178237 DOI: 10.1038/Nature21356  0.395
2016 Fang R, Yu M, Li G, Chee S, Liu T, Schmitt AD, Ren B. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Research. PMID 27886167 DOI: 10.1038/Cr.2016.137  0.325
2016 Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL, Ren B. A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Reports. 17: 2042-2059. PMID 27851967 DOI: 10.1016/J.Celrep.2016.10.061  0.547
2016 Dickel DE, Barozzi I, Zhu Y, Fukuda-Yuzawa Y, Osterwalder M, Mannion BJ, May D, Spurrell CH, Plajzer-Frick I, Pickle CS, Lee E, Garvin TH, Kato M, Akiyama JA, Afzal V, ... ... Ren B, et al. Genome-wide compendium and functional assessment of in vivo heart enhancers. Nature Communications. 7: 12923. PMID 27703156 DOI: 10.1038/Ncomms12923  0.403
2016 Dahl JA, Jung I, Aanes H, Greggains GD, Manaf A, Lerdrup M, Li G, Kuan S, Li B, Lee AY, Preissl S, Jermstad I, Haugen MH, Suganthan R, Bjørås M, ... ... Ren B, et al. Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature. PMID 27626377 DOI: 10.1038/Nature19360  0.509
2016 Schmitt AD, Hu M, Ren B. Genome-wide mapping and analysis of chromosome architecture. Nature Reviews. Molecular Cell Biology. PMID 27580841 DOI: 10.1038/Nrm.2016.104  0.445
2016 Dixon JR, Gorkin DU, Ren B. Chromatin Domains: The Unit of Chromosome Organization. Molecular Cell. 62: 668-80. PMID 27259200 DOI: 10.1016/J.Molcel.2016.05.018  0.715
2016 Diao Y, Li B, Meng Z, Jung I, Lee A, Dixon J, Maliskova L, Guan KL, Shen Y, Ren B. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9 mediated genetic screening. Genome Research. PMID 26813977 DOI: 10.1101/Gr.197152.115  0.857
2016 Ren B. Organization and Regulation of the Human Genome Blood. 128: SCI-16-SCI-16. DOI: 10.1182/blood.v128.22.sci-16.sci-16  0.428
2015 Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, ... Ren B, et al. Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. PMID 26605523 DOI: 10.1038/Nature16179  0.407
2015 Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R. Identification of global regulators of T-helper cell lineage specification. Genome Medicine. 7: 122. PMID 26589177 DOI: 10.1186/S13073-015-0237-0  0.616
2015 Ren B, Yue F. Transcriptional Enhancers: Bridging the Genome and Phenome. Cold Spring Harbor Symposia On Quantitative Biology. PMID 26582789 DOI: 10.1101/Sqb.2015.80.027219  0.707
2015 Selvaraj S, Schmitt AD, Dixon JR, Ren B. Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. Bmc Genomics. 16: 900. PMID 26541200 DOI: 10.1186/S12864-015-1949-7  0.672
2015 Liu F, Hon GC, Villa GR, Turner KM, Ikegami S, Yang H, Ye Z, Li B, Kuan S, Lee AY, Zanca C, Wei B, Lucey G, Jenkins D, Zhang W, ... ... Ren B, et al. EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling. Molecular Cell. PMID 26455392 DOI: 10.1016/J.Molcel.2015.09.002  0.689
2015 Kiat Lim K, Rui Ong TY, Rong Tan Y, Guorong Yang E, Ren B, Shan Seah K, Yang Z, Soo Tan T, Dymock BW, Sin Chen E. Mutation of histone H3 serine 86 disrupts GATA factor Ams2 expression and precise chromosome segregation in fission yeast. Scientific Reports. 5: 14064. PMID 26369364 DOI: 10.1038/srep14064  0.304
2015 Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, ... Ren B, et al. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell. 162: 900-10. PMID 26276636 DOI: 10.1016/J.Cell.2015.07.038  0.814
2015 Pugacheva EM, Rivero-Hinojosa S, Espinoza CA, Méndez-Catalá CF, Kang S, Suzuki T, Kosaka-Suzuki N, Robinson S, Nagarajan V, Ye Z, Boukaba A, Rasko JE, Strunnikov AV, Loukinov D, Ren B, et al. Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions. Genome Biology. 16: 161. PMID 26268681 DOI: 10.1186/S13059-015-0736-8  0.405
2015 Ishii H, Kadonaga JT, Ren B. MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proceedings of the National Academy of Sciences of the United States of America. 112: E3457-65. PMID 26080409 DOI: 10.1073/Pnas.1424804112  0.477
2015 Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, ... Ren B, et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 523: 212-6. PMID 26030523 DOI: 10.1038/Nature14465  0.498
2015 Ren B, Dixon JR. A CRISPR Connection between Chromatin Topology and Genetic Disorders. Cell. 161: 955-7. PMID 26000472 DOI: 10.1016/J.Cell.2015.04.047  0.718
2015 Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, ... ... Ren B, et al. An alternative pluripotent state confers interspecies chimaeric competency. Nature. 521: 316-21. PMID 25945737 DOI: 10.1038/Nature14413  0.363
2015 Wang A, Yue F, Li Y, Xie R, Harper T, Patel NA, Muth K, Palmer J, Qiu Y, Wang J, Lam DK, Raum JC, Stoffers DA, Ren B, Sander M. Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates. Cell Stem Cell. 16: 386-99. PMID 25842977 DOI: 10.1016/J.Stem.2015.02.013  0.654
2015 Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, ... ... Ren B, et al. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 518: 350-4. PMID 25693566 DOI: 10.1038/Nature14217  0.695
2015 Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, ... ... Ren B, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 518: 331-6. PMID 25693564 DOI: 10.1038/Nature14222  0.848
2015 Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Ren B, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248  0.83
2015 Chen Y, Chen C, Zhang Z, Liu CC, Johnson ME, Espinoza CA, Edsall LE, Ren B, Zhou XJ, Grant SF, Wells AD, Chen L. DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions. Nucleic Acids Research. 43: 1268-82. PMID 25567984 DOI: 10.1093/Nar/Gku1373  0.495
2015 Yue F, Shen Y, Ye Z, Ren B. Abstract 2211: A comparative analysis of the cis-regulatory landscape between human and mouse Cancer Research. 75: 2211-2211. DOI: 10.1158/1538-7445.Am2015-2211  0.735
2014 Li Y, Rivera CM, Ishii H, Jin F, Selvaraj S, Lee AY, Dixon JR, Ren B. CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. Plos One. 9: e114485. PMID 25486255 DOI: 10.1371/Journal.Pone.0114485  0.841
2014 Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, ... ... Ren B, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 515: 402-5. PMID 25409831 DOI: 10.1038/Nature13986  0.687
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... ... Ren B, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.83
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, ... ... Ren B, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/Pnas.1410434111  0.673
2014 Hon GC, Song CX, Du T, Jin F, Selvaraj S, Lee AY, Yen CA, Ye Z, Mao SQ, Wang BA, Kuan S, Edsall LE, Zhao BS, Xu GL, He C, ... Ren B, et al. 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Molecular Cell. 56: 286-97. PMID 25263596 DOI: 10.1016/J.Molcel.2014.08.026  0.821
2014 Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, Ren B. Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3 (Bethesda, Md.). 4: 2051-63. PMID 25122670 DOI: 10.1534/G3.114.013565  0.456
2014 Gorkin DU, Leung D, Ren B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell. 14: 762-75. PMID 24905166 DOI: 10.1016/J.Stem.2014.05.017  0.456
2014 Leung D, Du T, Wagner U, Xie W, Lee AY, Goyal P, Li Y, Szulwach KE, Jin P, Lorincz MC, Ren B. Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1. Proceedings of the National Academy of Sciences of the United States of America. 111: 6690-5. PMID 24757056 DOI: 10.1073/Pnas.1322273111  0.538
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, ... ... Ren B, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/Pnas.1318948111  0.752
2014 Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, et al. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Research. 24: 920-9. PMID 24752179 DOI: 10.1101/Gr.168930.113  0.746
2014 Dai L, Peng C, Montellier E, Lu Z, Chen Y, Ishii H, Debernardi A, Buchou T, Rousseaux S, Jin F, Sabari BR, Deng Z, Allis CD, Ren B, Khochbin S, et al. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nature Chemical Biology. 10: 365-70. PMID 24681537 DOI: 10.1038/Nchembio.1497  0.782
2014 Zuin J, Dixon JR, van der Reijden MI, Ye Z, Kolovos P, Brouwer RW, van de Corput MP, van de Werken HJ, Knoch TA, van IJcken WF, Grosveld FG, Ren B, Wendt KS. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proceedings of the National Academy of Sciences of the United States of America. 111: 996-1001. PMID 24335803 DOI: 10.1073/Pnas.1317788111  0.759
2014 Looney TJ, Zhang L, Chen CH, Lee JH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker SW, Fernandes CJ, Gaetz J, Foshay KM, Clift KL, Zhang Z, ... ... Ren B, et al. Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. Genome Research. 24: 267-80. PMID 24310002 DOI: 10.1101/Gr.143891.112  0.491
2014 Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 505: 117-20. PMID 24284625 DOI: 10.1038/Nature12730  0.657
2014 Hon G, Song C, Jin F, Selvaraj S, Lee AY, Yen C, Ye Z, Mao S, Wang B, Kuan S, Edsall L, Zhao BS, Xu G, He C, Ren B. Abstract 460: Base resolution epigenomic analysis reveals a role for Tet2 in modulating enhancer activity Molecular and Cellular Biology. 74: 460-460. DOI: 10.1158/1538-7445.Am2014-460  0.839
2014 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells Nature. 514: 126. DOI: 10.1038/Nature13843  0.763
2013 Selvaraj S, R Dixon J, Bansal V, Ren B. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nature Biotechnology. 31: 1111-8. PMID 24185094 DOI: 10.1038/Nbt.2728  0.41
2013 Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, Shoukry M, Afzal V, Rubin EM, ... ... Ren B, et al. Fine tuning of craniofacial morphology by distant-acting enhancers. Science (New York, N.Y.). 342: 1241006. PMID 24159046 DOI: 10.1126/Science.1241006  0.451
2013 Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 503: 290-4. PMID 24141950 DOI: 10.1038/Nature12644  0.849
2013 Rivera CM, Ren B. Mapping human epigenomes. Cell. 155: 39-55. PMID 24074860 DOI: 10.1016/J.Cell.2013.09.011  0.402
2013 Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genetics. 45: 1198-206. PMID 23995138 DOI: 10.1038/Ng.2746  0.821
2013 Xie W, Ren B. Developmental biology. Enhancing pluripotency and lineage specification. Science (New York, N.Y.). 341: 245-7. PMID 23869010 DOI: 10.1126/Science.1236254  0.513
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, ... ... Ren B, et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2: e00675. PMID 23795294 DOI: 10.7554/Elife.00675  0.705
2013 Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R. Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity. 38: 1271-84. PMID 23791644 DOI: 10.1016/J.Immuni.2013.05.011  0.676
2013 Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, ... ... Ren B, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 153: 1134-48. PMID 23664764 DOI: 10.1016/J.Cell.2013.04.022  0.757
2013 Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. Plos Computational Biology. 9: e1002968. PMID 23526891 DOI: 10.1371/Journal.Pcbi.1002968  0.635
2013 Won KJ, Zhang X, Wang T, Ding B, Raha D, Snyder M, Ren B, Wang W. Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Research. 41: 4423-32. PMID 23482391 DOI: 10.1093/Nar/Gkt143  0.509
2013 Smallwood A, Ren B. Genome organization and long-range regulation of gene expression by enhancers. Current Opinion in Cell Biology. 25: 387-94. PMID 23465541 DOI: 10.1016/J.Ceb.2013.02.005  0.513
2013 Zhang L, Szulwach KE, Hon GC, Song CX, Park B, Yu M, Lu X, Dai Q, Wang X, Street CR, Tan H, Min JH, Ren B, Jin P, He C. Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nature Communications. 4: 1517. PMID 23443545 DOI: 10.1038/Ncomms2527  0.729
2013 Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. Bayesian inference of spatial organizations of chromosomes. Plos Computational Biology. 9: e1002893. PMID 23382666 DOI: 10.1371/Journal.Pcbi.1002893  0.725
2013 Sawan C, Hernandez-Vargas H, Murr R, Lopez F, Vaissière T, Ghantous AY, Cuenin C, Imbert J, Wang ZQ, Ren B, Herceg Z. Histone acetyltransferase cofactor Trrap maintains self-renewal and restricts differentiation of embryonic stem cells. Stem Cells (Dayton, Ohio). 31: 979-91. PMID 23362228 DOI: 10.1002/Stem.1341  0.46
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SC, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, ... ... Ren B, et al. Author response: Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis Elife. DOI: 10.7554/Elife.00675.022  0.659
2013 Hon GC, Shen Y, McCleary DF, Edsall L, Kuan S, Ren B. Abstract 1111: Whole genome bisulfite sequencing reveals tissue-specific DNA methylation in a normal mouse. Cancer Research. 73: 1111-1111. DOI: 10.1158/1538-7445.Am2013-1111  0.807
2012 Yu M, Hon GC, Szulwach KE, Song CX, Jin P, Ren B, He C. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nature Protocols. 7: 2159-70. PMID 23196972 DOI: 10.1038/Nprot.2012.137  0.727
2012 Liu GH, Qu J, Suzuki K, Nivet E, Li M, Montserrat N, Yi F, Xu X, Ruiz S, Zhang W, Wagner U, Kim A, Ren B, Li Y, Goebl A, et al. Progressive degeneration of human neural stem cells caused by pathogenic LRRK2. Nature. 491: 603-7. PMID 23075850 DOI: 10.1038/Nature11557  0.306
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.789
2012 Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. A map of the cis-regulatory sequences in the mouse genome. Nature. 488: 116-20. PMID 22763441 DOI: 10.1038/Nature11243  0.841
2012 Lo MC, Peterson LF, Yan M, Cong X, Jin F, Shia WJ, Matsuura S, Ahn EY, Komeno Y, Ly M, Ommen HB, Chen IM, Hokland P, Willman CL, Ren B, et al. Combined gene expression and DNA occupancy profiling identifies potential therapeutic targets of t(8;21) AML. Blood. 120: 1473-84. PMID 22740448 DOI: 10.1182/Blood-2011-12-395335  0.734
2012 Won KJ, Xu Z, Zhang X, Whitaker JW, Shoemaker R, Ren B, Xu Y, Wang W. Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells Nucleic Acids Research. 40: 8199-8209. PMID 22730289 DOI: 10.1093/Nar/Gks584  0.509
2012 Smallwood A, Hon GC, Jin F, Henry RE, Espinosa JM, Ren B. CBX3 regulates efficient RNA processing genome-wide. Genome Research. 22: 1426-36. PMID 22684280 DOI: 10.1101/Gr.124818.111  0.831
2012 Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell. 149: 1368-80. PMID 22608086 DOI: 10.1016/J.Cell.2012.04.027  0.795
2012 Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 485: 376-80. PMID 22495300 DOI: 10.1038/Nature11082  0.83
2012 Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. Plos Genetics. 8: e1002576. PMID 22438827 DOI: 10.1371/Journal.Pgen.1002576  0.658
2012 Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, Dempster EL, Ren B. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell. 148: 816-31. PMID 22341451 DOI: 10.1016/J.Cell.2011.12.035  0.703
2012 Jishage M, Malik S, Wagner U, Uberheide B, Ishihama Y, Hu X, Chait BT, Gnatt A, Ren B, Roeder RG. Transcriptional regulation by Pol II(G) involving mediator and competitive interactions of Gdown1 and TFIIF with Pol II. Molecular Cell. 45: 51-63. PMID 22244332 DOI: 10.1016/J.Molcel.2011.12.014  0.31
2012 Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, ... ... Ren B, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research. 22: 246-58. PMID 22156296 DOI: 10.1101/Gr.125872.111  0.794
2011 Jin F, Li Y, Ren B, Natarajan R. Enhancers: multi-dimensional signal integrators. Transcription. 2: 226-30. PMID 22231119 DOI: 10.4161/trns.2.5.17712  0.774
2011 Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, ... ... Ren B, et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell. 146: 1016-28. PMID 21925322 DOI: 10.1016/J.Cell.2011.08.008  0.774
2011 Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, ... ... Ren B, et al. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Research. 21: 1393-409. PMID 21876557 DOI: 10.1038/Cr.2011.146  0.826
2011 Szulwach KE, Li X, Li Y, Song CX, Han JW, Kim S, Namburi S, Hermetz K, Kim JJ, Rudd MK, Yoon YS, Ren B, He C, Jin P. Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. Plos Genetics. 7: e1002154. PMID 21731508 DOI: 10.1371/Journal.Pgen.1002154  0.551
2011 Boyapati A, Ren B, Zhang DE. SERPINB13 is a novel RUNX1 target gene. Biochemical and Biophysical Research Communications. 411: 115-20. PMID 21723253 DOI: 10.1016/J.Bbrc.2011.06.107  0.453
2011 Espinoza CA, Ren B. Mapping higher order structure of chromatin domains. Nature Genetics. 43: 615-6. PMID 21709679 DOI: 10.1038/Ng.869  0.393
2011 Galante PA, Parmigiani RB, Zhao Q, Caballero OL, de Souza JE, Navarro FC, Gerber AL, Nicolás MF, Salim AC, Silva AP, Edsall L, Devalle S, Almeida LG, Ye Z, Kuan S, ... ... Ren B, et al. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Research. 39: 6056-68. PMID 21493686 DOI: 10.1093/Nar/Gkr221  0.397
2011 Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, ... ... Ren B, et al. A cis-regulatory map of the Drosophila genome. Nature. 471: 527-31. PMID 21430782 DOI: 10.1038/Nature09990  0.744
2011 Jin F, Li Y, Ren B, Natarajan R. PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers. Proceedings of the National Academy of Sciences of the United States of America. 108: 5290-5. PMID 21402921 DOI: 10.1073/Pnas.1017214108  0.76
2011 Macfarlan TS, Gifford WD, Agarwal S, Driscoll S, Lettieri K, Wang J, Andrews SE, Franco L, Rosenfeld MG, Ren B, Pfaff SL. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes & Development. 25: 594-607. PMID 21357675 DOI: 10.1101/Gad.2008511  0.544
2011 Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA. 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature. 470: 264-8. PMID 21307941 DOI: 10.1038/Nature09753  0.584
2011 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. PMID 21289626 DOI: 10.1038/Nature09798  0.805
2011 Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, ... ... Ren B, et al. An assessment of histone-modification antibody quality. Nature Structural & Molecular Biology. 18: 91-3. PMID 21131980 DOI: 10.1038/Nsmb.1972  0.606
2010 Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Ren B, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374  0.81
2010 Zhao Q, Kirkness EF, Caballero OL, Galante PA, Parmigiani RB, Edsall L, Kuan S, Ye Z, Levy S, Vasconcelos AT, Ren B, de Souza SJ, Camargo AA, Simpson AJ, Strausberg RL. Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing. Genome Biology. 11: R114. PMID 21108794 DOI: 10.1186/Gb-2010-11-11-R114  0.399
2010 Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nature Biotechnology. 28: 1045-8. PMID 20944595 DOI: 10.1038/Nbt1010-1045  0.308
2010 Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, ... ... Ren B, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/Nbt.1682  0.692
2010 Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Bristow J, Ren B, Black BL, Rubin EM, et al. ChIP-Seq identification of weakly conserved heart enhancers. Nature Genetics. 42: 806-10. PMID 20729851 DOI: 10.1038/Ng.650  0.353
2010 Bazarov AV, Van Sluis M, Hines WC, Bassett E, Beliveau A, Campeau E, Mukhopadhyay R, Lee WJ, Melodyev S, Zaslavsky Y, Lee L, Rodier F, Chicas A, Lowe SW, Benhattar J, ... Ren B, et al. p16(INK4a) -mediated suppression of telomerase in normal and malignant human breast cells. Aging Cell. 9: 736-46. PMID 20569236 DOI: 10.1111/J.1474-9726.2010.00599.X  0.366
2010 Hawkins RD, Hon GC, Ren B. Next-generation genomics: An integrative approach Nature Reviews Genetics. 11: 476-486. PMID 20531367 DOI: 10.1038/Nrg2795  0.797
2010 Ren B. Transcription: Enhancers make non-coding RNA. Nature. 465: 173-4. PMID 20463730 DOI: 10.1038/465173A  0.399
2010 Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, ... ... Ren B, et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 6: 479-91. PMID 20452322 DOI: 10.1016/J.Stem.2010.03.018  0.829
2010 Won KJ, Ren B, Wang W. Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biology. 11: R7. PMID 20096096 DOI: 10.1186/Gb-2010-11-1-R7  0.46
2010 Harismendy O, Bhatia G, Rahim NG, Bansal V, Nakano M, Scott M, Wang X, Dib C, Turlotte E, Heintzman N, Murray SS, Deleuze J, Sipe JC, Ren B, Bafna V, et al. Deciphering the genetic basis of common diseases by integrated functional annotation of common and rare variants Genome Biology. 11. DOI: 10.1186/Gb-2010-11-S1-I8  0.426
2009 Hon G, Wang W, Ren B. Discovery and annotation of functional chromatin signatures in the human genome. Plos Computational Biology. 5: e1000566. PMID 19918365 DOI: 10.1371/Journal.Pcbi.1000566  0.801
2009 Heintzman ND, Ren B. Finding distal regulatory elements in the human genome Current Opinion in Genetics and Development. 19: 541-549. PMID 19854636 DOI: 10.1016/J.Gde.2009.09.006  0.485
2009 Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, ... ... Ren B, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462: 315-22. PMID 19829295 DOI: 10.1038/Nature08514  0.828
2009 Hon GC, Hawkins RD, Ren B. Predictive chromatin signatures in the mammalian genome Human Molecular Genetics. 18: R195-R201. PMID 19808796 DOI: 10.1093/Hmg/Ddp409  0.818
2009 Won KJ, Agarwal S, Shen L, Shoemaker R, Ren B, Wang W. An integrated approach to identifying cis-regulatory modules in the human genome Plos One. 4. PMID 19434238 DOI: 10.1371/Journal.Pone.0005501  0.466
2009 Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, ... ... Ren B, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 459: 108-12. PMID 19295514 DOI: 10.1038/Nature07829  0.832
2009 Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 457: 854-8. PMID 19212405 DOI: 10.1038/Nature07730  0.459
2009 Li S, Matsuguchi T, Stohr BA, Xu L, Perry K, Ren B, Blackburn EH. Abstract IA-22: Cellular responses to telomerase perturbations Cancer Research. 69. DOI: 10.1158/0008-5472.Fbcr09-Ia-22  0.383
2008 Won KJ, Chepelev I, Ren B, Wang W. Prediction of regulatory elements in mammalian genomes using chromatin signatures Bmc Bioinformatics. 9. PMID 19094206 DOI: 10.1186/1471-2105-9-547  0.548
2008 Hon G, Ren B, Wang W. ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome Plos Computational Biology. 4. PMID 18927605 DOI: 10.1371/Journal.Pcbi.1000201  0.79
2008 Li Y, Reddy MA, Miao F, Shanmugam N, Yee JK, Hawkins D, Ren B, Natarajan R. Role of the histone H3 lysine 4 methyltransferase, SET7/9, in the regulation of NF-kappaB-dependent inflammatory genes. Relevance to diabetes and inflammation. The Journal of Biological Chemistry. 283: 26771-81. PMID 18650421 DOI: 10.1074/Jbc.M802800200  0.379
2008 Bibikova M, Laurent LC, Ren B, Loring JF, Fan JB. Unraveling Epigenetic Regulation in Embryonic Stem Cells Cell Stem Cell. 2: 123-134. PMID 18371433 DOI: 10.1016/J.Stem.2008.01.005  0.443
2008 Maynard ND, Chen J, Stuart RK, Fan JB, Ren B. Genome-wide mapping of allele-specific protein-DNA interactions in human cells. Nature Methods. 5: 307-9. PMID 18345007 DOI: 10.1038/Nmeth.1194  0.443
2008 Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, ... ... Ren B, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/Gr.7080508  0.55
2008 Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B. Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Research. 18: 46-59. PMID 18042645 DOI: 10.1101/Gr.6654808  0.509
2007 Kim TH, Barrera LO, Ren B. ChIP-chip for genome-wide analysis of protein binding in mammalian cells. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.13. PMID 18265397 DOI: 10.1002/0471142727.Mb2113S79  0.642
2007 Spiteri E, Konopka G, Coppola G, Bomar J, Oldham M, Ou J, Vernes SC, Fisher SE, Ren B, Geschwind DH. Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain. American Journal of Human Genetics. 81: 1144-57. PMID 17999357 DOI: 10.1086/522237  0.382
2007 Zheng M, Barrera LO, Ren B, Wu YN. ChIP-chip: data, model, and analysis. Biometrics. 63: 787-96. PMID 17825010 DOI: 10.1111/J.1541-0420.2007.00768.X  0.353
2007 Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RD, Chenoweth JG, Tesar PJ, Furey TS, Ren B, Weng Z, Crawford GE. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. Plos Genetics. 3: e136. PMID 17708682 DOI: 10.1371/Journal.Pgen.0030136  0.48
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Ren B, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.831
2007 Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell. 128: 1231-45. PMID 17382889 DOI: 10.1016/J.Cell.2006.12.048  0.653
2007 Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nature Genetics. 39: 311-318. PMID 17277777 DOI: 10.1038/Ng1966  0.836
2007 Heintzman ND, Ren B. The gateway to transcription: Identifying, characterizing and understanding promoters in the eukaryotic genome Cellular and Molecular Life Sciences. 64: 386-400. PMID 17171231 DOI: 10.1007/S00018-006-6295-0  0.508
2006 Kim TH, Ren B. An all-round view of eukaryotic transcription. Genome Biology. 7: 323. PMID 16879733 DOI: 10.1186/Gb-2006-7-7-323  0.583
2006 Toyo-oka K, Bowen TJ, Hirotsune S, Li Z, Jain S, Ota S, Escoubet-Lozach L, Lozach LE, Garcia-Bassets I, Bassett IG, Lozach J, Rosenfeld MG, Glass CK, Eisenman R, Ren B, et al. Mnt-deficient mammary glands exhibit impaired involution and tumors with characteristics of myc overexpression. Cancer Research. 66: 5565-73. PMID 16740691 DOI: 10.1158/0008-5472.Can-05-2683  0.365
2006 Kim TH, Ren B. Genome-wide analysis of protein-DNA interactions. Annual Review of Genomics and Human Genetics. 7: 81-102. PMID 16722805 DOI: 10.1146/Annurev.Genom.7.080505.115634  0.676
2006 Hawkins RD, Ren B. Genome-wide location analysis: insights on transcriptional regulation. Human Molecular Genetics. 15: R1-7. PMID 16651365 DOI: 10.1093/Hmg/Ddl043  0.74
2006 Barrera LO, Ren B. The transcriptional regulatory code of eukaryotic cells - insights from genome-wide analysis of chromatin organization and transcription factor binding Current Opinion in Cell Biology. 18: 291-298. PMID 16647254 DOI: 10.1016/J.Ceb.2006.04.002  0.536
2006 Sun P, Xiong H, Kim TH, Ren B, Zhang Z. Positive inter-regulation between beta-catenin/T cell factor-4 signaling and endothelin-1 signaling potentiates proliferation and survival of prostate cancer cells. Molecular Pharmacology. 69: 520-31. PMID 16291872 DOI: 10.1124/Mol.105.019620  0.51
2005 Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. A high-resolution map of active promoters in the human genome. Nature. 436: 876-80. PMID 15988478 DOI: 10.1038/Nature03877  0.689
2005 Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B. Direct isolation and identification of promoters in the human genome. Genome Research. 15: 830-9. PMID 15899964 DOI: 10.1101/Gr.3430605  0.845
2005 Kim TH, Xiong H, Zhang Z, Ren B. beta-Catenin activates the growth factor endothelin-1 in colon cancer cells. Oncogene. 24: 597-604. PMID 15558022 DOI: 10.1038/Sj.Onc.1208237  0.524
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Ren B, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/Science.1105136  0.591
2004 Ren B, Dynlacht BD. Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods in Enzymology. 376: 304-15. PMID 14975314 DOI: 10.1016/S0076-6879(03)76020-0  0.535
2003 Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren B. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proceedings of the National Academy of Sciences of the United States of America. 100: 8164-9. PMID 12808131 DOI: 10.1073/Pnas.1332764100  0.808
2002 Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (New York, N.Y.). 298: 799-804. PMID 12399584 DOI: 10.1126/Science.1075090  0.711
2002 Ren B, Cam H, Takahashi Y, Volkert T, Terragni J, Young RA, Dynlacht BD. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes & Development. 16: 245-56. PMID 11799067 DOI: 10.1101/Gad.949802  0.595
2001 Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA. Remodeling of yeast genome expression in response to environmental changes. Molecular Biology of the Cell. 12: 323-37. PMID 11179418 DOI: 10.1091/Mbc.12.2.323  0.534
2000 Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA. Genome-wide location and function of DNA binding proteins. Science (New York, N.Y.). 290: 2306-9. PMID 11125145 DOI: 10.1126/science.290.5500.2306  0.561
1999 Ren B, Chee KJ, Kim TH, Maniatis T. PRDI-BF1/Blimp-1 repression is mediated by corepressors of the Groucho family of proteins. Genes & Development. 13: 125-37. PMID 9887105 DOI: 10.1101/Gad.13.1.125  0.725
1999 Ren B, Young P, Young RA. A yeast genome expression monitoring database Nature Genetics. 23: 70-70. DOI: 10.1038/14389  0.536
1998 Ren B, Maniatis T. Regulation of Drosophila Adh promoter switching by an initiator-targeted repression mechanism. The Embo Journal. 17: 1076-86. PMID 9463385 DOI: 10.1093/Emboj/17.4.1076  0.669
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