Bing Ren

Title(s)Professor, Cellular and Molecular Medicine
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Overview 
    Collapse Overview
    Our laboratory is interested in understanding how the complex gene regulatory networks in mammalian cells control cellular proliferation and differentiation. The research is divided into two general areas: 1) the development of genomics and bioinformatics tools that allow genome wide identification of regulatory targets for transcription factors; and, 2) the application of these tools to the study of transcription factors that play critical roles in cancer.

    Research Focus Areas:

  • Genetics and Genomics

  • Gene Expression and Regulation

  • Signal Transduction


    • Collapse Research 
    Collapse Research Activities and Funding
    High-throughput Single Cell Co-assay of Histone Modifications and Transcriptome
    NIH R41GM146330Sep 15, 2021 - Aug 31, 2022
    Role: Principal Investigator
    Ultra-high Throughout Single Cell Multi-omic Analysis of Histone Modifications and Transcriptome in Mouse and Human Brains
    NIH RF1MH128838Sep 13, 2021 - Sep 12, 2024
    Role: Principal Investigator
    The impact of genomic variation on environment-induced changes in pancreatic beta cell states
    NIH U01HG012059Sep 7, 2021 - May 31, 2026
    Role: Co-Principal Investigator
    Comparative Single-Cell Epigenomic Analysis of AD-like Pathogenesis in Unconventional Animal Models
    NIH R24AG073198Sep 1, 2021 - May 31, 2025
    Role: Co-Principal Investigator
    Unraveling the molecular pathology of retinal degeneration through single cell genomics
    NIH R01EY031663Jun 1, 2021 - May 31, 2026
    Role: Co-Principal Investigator
    Single-Cell Analysis of Aging-Associated 4D Nucleome in the Human Hippocampus
    NIH U01DA052769Sep 30, 2020 - Aug 31, 2025
    Role: Co-Principal Investigator
    Center for Integrated Multi-modal and Multi-scale Nucleome Research
    NIH UM1HG011585Sep 24, 2020 - Jun 30, 2025
    Role: Principal Investigator
    Large scale discovery and validation of brain cell type enhancers for viral targeting and circuit manipulation
    NIH RF1MH124612Sep 23, 2020 - Sep 22, 2023
    Role: Co-Principal Investigator
    Multi-omic Brain Cell Atlas of Alzheimer's Disease Progression
    NIH R56AG069107Sep 17, 2020 - Aug 31, 2022
    Role: Principal Investigator
    Epigenomic analysis of neural circuits in Alzheimer's disease mouse models
    NIH R01AG067153Apr 15, 2020 - Mar 31, 2025
    Role: Co-Principal Investigator
    Epigenome-based Cell Census and Regulatory Element Discovery in the Aging Mouse Brain
    NIH R01AG066018Sep 30, 2019 - Jun 30, 2024
    Role: Co-Principal Investigator
    High throughput CRISPR-mediated functional validation of regulatory elements
    NIH UM1HG009402Feb 1, 2017 - Jan 31, 2022
    Role: Principal Investigator
    San Diego Center for 4D Nucleome Research
    NIH U54DK107977Sep 30, 2015 - Jul 31, 2021
    Role: Principal Investigator
    The second phase of NIH Common Fund 4D Nucleome Network Organizational Hub
    NIH U01CA200147Sep 1, 2015 - Aug 31, 2025
    Role: Principal Investigator
    Non-coding Variants Predisposing to Age-related Macular Degeneration
    NIH R01HG008135Aug 24, 2015 - Jun 30, 2019
    Role: Principal Investigator
    Functional Analysis of T2D Associated Non-coding SNPs
    NIH U01DK105541May 1, 2015 - Apr 30, 2020
    Role: Principal Investigator
    Integrative Analysis of Haplotype-Resolved Human Epigenome Maps
    NIH R01ES024984Sep 8, 2014 - Aug 31, 2017
    Role: Principal Investigator
    Center for Mammalian Regulatory Genomics
    NIH U54HG006997Sep 21, 2012 - Jul 31, 2018
    Role: Principal Investigator
    The San Diego Epigenome Center
    NIH U01ES017166Sep 29, 2008 - Jun 30, 2014
    Role: Principal Investigator
    Genome-wide map of active promoters in the mouse cells
    NIH R01HG003991Sep 18, 2008 - Jul 31, 2012
    Role: Principal Investigator
    TRANSCRIPTION FACTOR TARGET MAPPING IN MAMMALIAN GENOME
    NIH R33CA105829Aug 16, 2004 - Oct 31, 2008
    Role: Principal Investigator
    TRANSCRIPTION FACTOR TARGET MAPPING IN MAMMALIAN GENOME
    NIH R21CA105829Aug 16, 2004 - Jul 31, 2005
    Role: Principal Investigator
    Mapping transcriptional regulatory elements in human DNA
    NIH U01HG003151Sep 30, 2003 - Sep 30, 2008
    Role: Principal Investigator
    Graduate Training Program in Bioinformatics
    NIH T32GM008806Jul 1, 2001 - Jun 30, 2021
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Author Correction: A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nat Biotechnol. 2023 Jan 16. Jia BB, Jussila A, Kern C, Zhu Q, Ren B. PMID: 36646934.
      View in: PubMed   Mentions:    Fields:    
    2. A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nat Biotechnol. 2023 Jan 02. Jia BB, Jussila A, Kern C, Zhu Q, Ren B. PMID: 36593410.
      View in: PubMed   Mentions:    Fields:    
    3. Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines. Cell Genom. 2022 Dec 14; 2(12):100214. Benaglio P, Zhu H, Okino ML, Yan J, Elgamal R, Nariai N, Beebe E, Korgaonkar K, Qiu Y, Donovan MKR, Chiou J, Wang G, Newsome J, Kaur J, Miller M, Preissl S, Corban S, Aylward A, Taipale J, Ren B, Frazer KA, Sander M, Gaulton KJ. PMID: 36778047; PMCID: PMC9903835.
      View in: PubMed   Mentions:
    4. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. Cell Rep. 2022 11 08; 41(6):111630. Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M, Wang W, McVicker G, Mischel PS, Ren B. PMID: 36351387; PMCID: PMC9687083.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    5. Human-gained heart enhancers are associated with species-specific cardiac attributes. Nat Cardiovasc Res. 2022 Sep; 1(9):830-843. Destici E, Zhu F, Tran S, Preissl S, Farah EN, Zhang Y, Hou X, Poirion OB, Lee AY, Grinstein JD, Bloomekatz J, Kim HS, Hu R, Evans SM, Ren B, Benner C, Chi NC. PMID: 36817700; PMCID: PMC9937543.
      View in: PubMed   Mentions:
    6. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet. 2023 01; 24(1):21-43. Preissl S, Gaulton KJ, Ren B. PMID: 35840754; PMCID: PMC9771884.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    7. The Hippo pathway mediates Semaphorin signaling. Sci Adv. 2022 May 27; 8(21):eabl9806. 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, Engler AJ, Guan KL. PMID: 35613278; PMCID: PMC9132450.
      View in: PubMed   Mentions:    Fields:    
    8. Improved epicardial cardiac fibroblast generation from iPSCs. J Mol Cell Cardiol. 2022 03; 164:58-68. Whitehead AJ, Hocker JD, Ren B, Engler AJ. PMID: 34826415; PMCID: PMC9048147.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    9. Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. Nat Commun. 2021 11 17; 12(1):6636. Geusz RJ, Wang A, Lam DK, Vinckier NK, Alysandratos KD, Roberts DA, Wang J, Kefalopoulou S, Ramirez A, Qiu Y, Chiou J, Gaulton KJ, Ren B, Kotton DN, Sander M. PMID: 34789735; PMCID: PMC8599738.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    10. A single-cell atlas of chromatin accessibility in the human genome. Cell. 2021 11 24; 184(24):5985-6001.e19. Zhang K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A, Preissl S, Ren B. PMID: 34774128; PMCID: PMC8664161.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    11. Cardiac cell type-specific gene regulatory programs and disease risk association. Sci Adv. 2021 05; 7(20). 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, Chi NC, Preissl S. PMID: 33990324; PMCID: PMC8121433.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    12. Publisher Correction: Chromothripsis drives the evolution of gene amplification in cancer. Nature. 2021 Mar; 591(7850):E19. Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JSZ, Sun Y, Ellisman MH, Ren B, Campbell PJ, Cleveland DW. PMID: 33649505.
      View in: PubMed   Mentions: 2     Fields:    
    13. Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development. Elife. 2021 02 05; 10. Geusz RJ, Wang A, Chiou J, Lancman JJ, Wetton N, Kefalopoulou S, Wang J, Qiu Y, Yan J, Aylward A, Ren B, Dong PDS, Gaulton KJ, Sander M. PMID: 33544077; PMCID: PMC7864636.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    14. KDM1A maintains genome-wide homeostasis of transcriptional enhancers. Genome Res. 2021 Jan 07. Agarwal S, Bonefas KM, Garay PM, Brookes E, Murata-Nakamura Y, Porter RS, Macfarlan TS, Ren B, Iwase S. PMID: 33414108; PMCID: PMC7849409.
      View in: PubMed   Mentions: 6     Fields:    
    15. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nat Struct Mol Biol. 2021 02; 28(2):152-161. 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. PMID: 33398174; PMCID: PMC7913465.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    16. Chromothripsis drives the evolution of gene amplification in cancer. Nature. 2021 03; 591(7848):137-141. Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JSZ, Sun Y, Ellisman MH, Ren B, Campbell PJ, Cleveland DW. PMID: 33361815; PMCID: PMC7933129.
      View in: PubMed   Mentions: 91     Fields:    Translation:HumansCells
    17. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 2019 11; 575(7784):699-703. 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, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. PMID: 31748743; PMCID: PMC7094777.
      View in: PubMed   Mentions: 136     Fields:    Translation:HumansCells
    18. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science. 2019 11 29; 366(6469):1134-1139. 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, Shen Z, Rissman RA, Brewer JB, Gosselin D, Gonda DD, Levy ML, Rosenfeld MG, McVicker G, Gage FH, Ren B, Glass CK. PMID: 31727856; PMCID: PMC7028213.
      View in: PubMed   Mentions: 202     Fields:    Translation:HumansCells
    19. DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres. Nat Cell Biol. 2019 06; 21(6):743-754. Nechemia-Arbely Y, Miga KH, Shoshani O, Aslanian A, McMahon MA, Lee AY, Fachinetti D, Yates JR, Ren B, Cleveland DW. PMID: 31160708; PMCID: PMC7015266.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    20. NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling. Nature. 2019 05; 569(7757):570-575. 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. PMID: 31019297; PMCID: PMC7138021.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansAnimalsCells
    21. Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase. Nat Struct Mol Biol. 2019 03; 26(3):164-174. Patel L, Kang R, Rosenberg SC, Qiu Y, Raviram R, Chee S, Hu R, Ren B, Cole F, Corbett KD. PMID: 30778236; PMCID: PMC6403010.
      View in: PubMed   Mentions: 56     Fields:    Translation:AnimalsCells
    22. Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation. Cancer Cell. 2019 01 14; 35(1):81-94.e7. 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, Pineda G, Holm F, Jamieson C. PMID: 30612940; PMCID: PMC6333511.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCells
    23. Mapping of genomic EGFRvIII deletions in glioblastoma: insight into rearrangement mechanisms and biomarker development. Neuro Oncol. 2018 09 03; 20(10):1310-1320. Koga T, Li B, Figueroa JM, Ren B, Chen CC, Carter BS, Furnari FB. PMID: 29660021; PMCID: PMC6120357.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    24. RAP2 mediates mechanoresponses of the Hippo pathway. Nature. 2018 08; 560(7720):655-660. 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, Park HW, Wang X, Yu FX, Chien S, Wang CY, Ren B, Engler AJ, Guan KL. PMID: 30135582; PMCID: PMC6128698.
      View in: PubMed   Mentions: 120     Fields:    Translation:HumansAnimalsCells
    25. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell. 2018 06 14; 173(7):1796-1809.e17. 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, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. PMID: 29779944; PMCID: PMC6003872.
      View in: PubMed   Mentions: 77     Fields:    Translation:AnimalsCells
    26. NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes. Genes Dev. 2018 05 01; 32(9-10):682-694. Fei J, Ishii H, Hoeksema MA, Meitinger F, Kassavetis GA, Glass CK, Ren B, Kadonaga JT. PMID: 29759984; PMCID: PMC6004073.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    27. Preventive Inhibition of Liver Tumorigenesis by Systemic Activation of Innate Immune Functions. Cell Rep. 2017 Nov 14; 21(7):1870-1882. Lee J, Liao R, Wang G, Yang BH, Luo X, Varki NM, Qiu SJ, Ren B, Fu W, Feng GS. PMID: 29141219; PMCID: PMC5737819.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    28. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure. Circulation. 2017 Oct 24; 136(17):1613-1625. Rosa-Garrido M, Chapski DJ, Schmitt AD, Kimball TH, Karbassi E, Monte E, Balderas E, Pellegrini M, Shih TT, Soehalim E, Liem D, Ping P, Galjart NJ, Ren S, Wang Y, Ren B, Vondriska TM. PMID: 28802249; PMCID: PMC5648689.
      View in: PubMed   Mentions: 73     Fields:    Translation:AnimalsCells
    29. The Three-Dimensional Organization of Mammalian Genomes. Annu Rev Cell Dev Biol. 2017 10 06; 33:265-289. Yu M, Ren B. PMID: 28783961; PMCID: PMC5837811.
      View in: PubMed   Mentions: 143     Fields:    Translation:HumansAnimals
    30. Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. Cell Stem Cell. 2017 04 06; 20(4):533-546.e7. 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, Smith EN, D'Antonio-Chronowska A, Farley EK, Frazer KA. PMID: 28388430; PMCID: PMC5444918.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCells
    31. Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points. J Cell Biol. 2017 03 06; 216(3):607-621. 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. PMID: 28235947; PMCID: PMC5350519.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    32. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature. 2017 03 02; 543(7643):122-125. 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, Furnari FB, Vandenberg SR, Rao PN, Wahl GM, Bafna V, Mischel PS. PMID: 28178237; PMCID: PMC5334176.
      View in: PubMed   Mentions: 240     Fields:    Translation:HumansCells
    33. A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Rep. 2016 11 15; 17(8):2042-2059. Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL, Ren B. PMID: 27851967; PMCID: PMC5478386.
      View in: PubMed   Mentions: 346     Fields:    Translation:HumansAnimalsCells
    34. Genome-wide mapping and analysis of chromosome architecture. Nat Rev Mol Cell Biol. 2016 12; 17(12):743-755. Schmitt AD, Hu M, Ren B. PMID: 27580841; PMCID: PMC5763923.
      View in: PubMed   Mentions: 156     Fields:    Translation:HumansAnimalsCells
    35. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. Genome Res. 2016 Mar; 26(3):397-405. Diao Y, Li B, Meng Z, Jung I, Lee AY, Dixon J, Maliskova L, Guan KL, Shen Y, Ren B. PMID: 26813977; PMCID: PMC4772021.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    36. Transcriptional Enhancers: Bridging the Genome and Phenome. Cold Spring Harb Symp Quant Biol. 2015; 80:17-26. Ren B, Yue F. PMID: 26582789.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    37. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2015 Jul 09; 523(7559):212-6. 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, Sejnowski TJ, Wang W, Ecker JR. PMID: 26030523; PMCID: PMC4499021.
      View in: PubMed   Mentions: 316     Fields:    Translation:HumansCells
    38. A CRISPR Connection between Chromatin Topology and Genetic Disorders. Cell. 2015 May 21; 161(5):955-957. Ren B, Dixon JR. PMID: 26000472; PMCID: PMC4478077.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    39. Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates. Cell Stem Cell. 2015 Apr 02; 16(4):386-99. 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. PMID: 25842977; PMCID: PMC4478079.
      View in: PubMed   Mentions: 114     Fields:    Translation:HumansCells
    40. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015 Feb 19; 518(7539):331-6. 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, Thomson JA, Ren B. PMID: 25693564; PMCID: PMC4515363.
      View in: PubMed   Mentions: 699     Fields:    Translation:HumansCells
    41. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20; 515(7527):355-64. 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, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium. PMID: 25409824; PMCID: PMC4266106.
      View in: PubMed   Mentions: 797     Fields:    Translation:HumansAnimalsCells
    42. Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3 (Bethesda). 2014 Aug 12; 4(11):2051-63. Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, Ren B. PMID: 25122670; PMCID: PMC4232531.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    43. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell. 2014 Jun 05; 14(6):762-75. Gorkin DU, Leung D, Ren B. PMID: 24905166; PMCID: PMC4107214.
      View in: PubMed   Mentions: 185     Fields:    Translation:HumansAnimalsCells
    44. Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1. Proc Natl Acad Sci U S A. 2014 May 06; 111(18):6690-5. Leung D, Du T, Wagner U, Xie W, Lee AY, Goyal P, Li Y, Szulwach KE, Jin P, Lorincz MC, Ren B. PMID: 24757056; PMCID: PMC4020067.
      View in: PubMed   Mentions: 57     Fields:    Translation:AnimalsCells
    45. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol. 2013 Dec; 31(12):1111-8. Selvaraj S, R Dixon J, Bansal V, Ren B. PMID: 24185094; PMCID: PMC4180835.
      View in: PubMed   Mentions: 141     Fields:    Translation:HumansCells
    46. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics. 2013 Dec 15; 29(24):3204-10. Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W. PMID: 24078702; PMCID: PMC3842760.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    47. Mapping human epigenomes. Cell. 2013 Sep 26; 155(1):39-55. Rivera CM, Ren B. PMID: 24074860; PMCID: PMC3838898.
      View in: PubMed   Mentions: 242     Fields:    Translation:HumansAnimalsCells
    48. Developmental biology. Enhancing pluripotency and lineage specification. Science. 2013 Jul 19; 341(6143):245-7. Xie W, Ren B. PMID: 23869010.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    49. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput Biol. 2013; 9(3):e1002968. Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B. PMID: 23526891; PMCID: PMC3597546.
      View in: PubMed   Mentions: 106     Fields:    Translation:HumansCells
    50. Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Res. 2013 Apr; 41(8):4423-32. Won KJ, Zhang X, Wang T, Ding B, Raha D, Snyder M, Ren B, Wang W. PMID: 23482391; PMCID: PMC3632130.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    51. Combined gene expression and DNA occupancy profiling identifies potential therapeutic targets of t(8;21) AML. Blood. 2012 Aug 16; 120(7):1473-84. 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, Zhang DE. PMID: 22740448; PMCID: PMC3423785.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    52. Enhancers: multi-dimensional signal integrators. Transcription. 2011 Sep-Oct; 2(5):226-30. Jin F, Li Y, Ren B, Natarajan R. PMID: 22231119; PMCID: PMC3265780.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    53. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Res. 2011 Oct; 21(10):1393-409. 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, Lobanenkov VV, Stewart R, Thomson JA, Ren B. PMID: 21876557; PMCID: PMC3193447.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansCells
    54. PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers. Proc Natl Acad Sci U S A. 2011 Mar 29; 108(13):5290-5. Jin F, Li Y, Ren B, Natarajan R. PMID: 21402921; PMCID: PMC3069155.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimalsCells
    55. 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature. 2011 Feb 10; 470(7333):264-8. Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA. PMID: 21307941; PMCID: PMC3079517.
      View in: PubMed   Mentions: 295     Fields:    Translation:HumansCells
    56. Next-generation genomics: an integrative approach. Nat Rev Genet. 2010 Jul; 11(7):476-86. Hawkins RD, Hon GC, Ren B. PMID: 20531367; PMCID: PMC3321268.
      View in: PubMed   Mentions: 267     Fields:    
    57. Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biol. 2010 Jan 22; 11(1):R7. Won KJ, Ren B, Wang W. PMID: 20096096; PMCID: PMC2847719.
      View in: PubMed   Mentions: 68     Fields:    Translation:AnimalsCells
    58. Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol. 2009 Nov; 5(11):e1000566. Hon G, Wang W, Ren B. PMID: 19918365; PMCID: PMC2775352.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansCells
    59. Finding distal regulatory elements in the human genome. Curr Opin Genet Dev. 2009 Dec; 19(6):541-9. Heintzman ND, Ren B. PMID: 19854636; PMCID: PMC3321269.
      View in: PubMed   Mentions: 122     Fields:    Translation:HumansCells
    60. Predictive chromatin signatures in the mammalian genome. Hum Mol Genet. 2009 Oct 15; 18(R2):R195-201. Hon GC, Hawkins RD, Ren B. PMID: 19808796; PMCID: PMC2912651.
      View in: PubMed   Mentions: 129     Fields:    Translation:HumansAnimalsCells
    61. An integrated approach to identifying cis-regulatory modules in the human genome. PLoS One. 2009; 4(5):e5501. Won KJ, Agarwal S, Shen L, Shoemaker R, Ren B, Wang W. PMID: 19434238; PMCID: PMC2677454.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    62. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009 May 07; 459(7243):108-12. 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, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B. PMID: 19295514; PMCID: PMC2910248.
      View in: PubMed   Mentions: 1412     Fields:    Translation:HumansCells
    63. Prediction of regulatory elements in mammalian genomes using chromatin signatures. BMC Bioinformatics. 2008 Dec 18; 9:547. Won KJ, Chepelev I, Ren B, Wang W. PMID: 19094206; PMCID: PMC2657164.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansAnimalsCells
    64. ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol. 2008 Oct; 4(10):e1000201. Hon G, Ren B, Wang W. PMID: 18927605; PMCID: PMC2556089.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansCells
    65. Genome-wide mapping of allele-specific protein-DNA interactions in human cells. Nat Methods. 2008 Apr; 5(4):307-9. Maynard ND, Chen J, Stuart RK, Fan JB, Ren B. PMID: 18345007.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    66. Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res. 2008 Jan; 18(1):46-59. Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B. PMID: 18042645; PMCID: PMC2134779.
      View in: PubMed   Mentions: 66     Fields:    Translation:AnimalsCells
    67. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell. 2007 Mar 23; 128(6):1231-45. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. PMID: 17382889; PMCID: PMC2572726.
      View in: PubMed   Mentions: 593     Fields:    Translation:HumansAnimalsCells
    68. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007 Mar; 39(3):311-8. 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. PMID: 17277777.
      View in: PubMed   Mentions: 1802     Fields:    Translation:HumansCells
    69. Mnt-deficient mammary glands exhibit impaired involution and tumors with characteristics of myc overexpression. Cancer Res. 2006 Jun 01; 66(11):5565-73. 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, Hurlin P, Wynshaw-Boris A. PMID: 16740691.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    70. The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr Opin Cell Biol. 2006 Jun; 18(3):291-8. Barrera LO, Ren B. PMID: 16647254.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansAnimalsCells
    71. Genome-wide location analysis: insights on transcriptional regulation. Hum Mol Genet. 2006 Apr 15; 15 Spec No 1:R1-7. Hawkins RD, Ren B. PMID: 16651365.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    72. Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet. 2006; 7:81-102. Kim TH, Ren B. PMID: 16722805.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansCells
    73. An all-round view of eukaryotic transcription. Genome Biol. 2006; 7(7):323. Kim TH, Ren B. PMID: 16879733; PMCID: PMC1779551.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    74. A high-resolution map of active promoters in the human genome. Nature. 2005 Aug 11; 436(7052):876-80. Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. PMID: 15988478; PMCID: PMC1895599.
      View in: PubMed   Mentions: 502     Fields:    Translation:HumansCells
    75. Direct isolation and identification of promoters in the human genome. Genome Res. 2005 Jun; 15(6):830-9. Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B. PMID: 15899964; PMCID: PMC1142473.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    76. beta-Catenin activates the growth factor endothelin-1 in colon cancer cells. Oncogene. 2005 Jan 20; 24(4):597-604. Kim TH, Xiong H, Zhang Z, Ren B. PMID: 15558022.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    77. Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol. 2004; 376:304-15. Ren B, Dynlacht BD. PMID: 14975314.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    78. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A. 2003 Jul 08; 100(14):8164-9. Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren B. PMID: 12808131; PMCID: PMC166200.
      View in: PubMed   Mentions: 250     Fields:    Translation:HumansCells
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