| Year |
Citation |
Score |
| 2024 |
Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, ... ... Ren B, et al. Dynamic enhancer landscapes in human craniofacial development. Nature Communications. 15: 2030. PMID 38448444 DOI: 10.1038/s41467-024-46396-4 |
0.362 |
|
| 2024 |
Wang Z, Ren B. Role of H3K4 monomethylation in gene regulation. Current Opinion in Genetics & Development. 84: 102153. PMID 38278054 DOI: 10.1016/j.gde.2024.102153 |
0.389 |
|
| 2024 |
Zhang K, Zemke NR, Armand EJ, Ren B. A fast, scalable and versatile tool for analysis of single-cell omics data. Nature Methods. PMID 38191932 DOI: 10.1038/s41592-023-02139-9 |
0.345 |
|
| 2023 |
Liu S, Zheng P, Wang CY, Jia BB, Zemke NR, Ren B, Zhuang X. Cell-type-specific 3D-genome organization and transcription regulation in the brain. Biorxiv : the Preprint Server For Biology. PMID 38105994 DOI: 10.1101/2023.12.04.570024 |
0.419 |
|
| 2023 |
Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, ... ... Ren B, et al. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature. 624: 390-402. PMID 38092918 DOI: 10.1038/s41586-023-06819-6 |
0.454 |
|
| 2023 |
Zu S, Li YE, Wang K, Armand EJ, Mamde S, Amaral ML, Wang Y, Chu A, Xie Y, Miller M, Xu J, Wang Z, Zhang K, Jia B, Hou X, ... ... Ren B, et al. Single-cell analysis of chromatin accessibility in the adult mouse brain. Nature. 624: 378-389. PMID 38092917 DOI: 10.1038/s41586-023-06824-9 |
0.691 |
|
| 2023 |
Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, ... ... Ren B, et al. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature. 624: 366-377. PMID 38092913 DOI: 10.1038/s41586-023-06805-y |
0.806 |
|
| 2023 |
Calandrelli R, Wen X, Charles Richard JL, Luo Z, Nguyen TC, Chen CJ, Qi Z, Xue S, Chen W, Yan Z, Wu W, Zaleta-Rivera K, Hu R, Yu M, Wang Y, ... ... Ren B, et al. Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Nature Communications. 14: 6519. PMID 37845234 DOI: 10.1038/s41467-023-42274-7 |
0.367 |
|
| 2023 |
Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, ... ... Ren B, et al. Single-cell DNA methylation and 3D genome architecture in the human brain. Science (New York, N.Y.). 382: eadf5357. PMID 37824674 DOI: 10.1126/science.adf5357 |
0.404 |
|
| 2023 |
Li YE, Preissl S, Miller M, Johnson ND, Wang Z, Jiao H, Zhu C, Wang Z, Xie Y, Poirion O, Kern C, Pinto-Duarte A, Tian W, Siletti K, Emerson N, ... ... Ren B, et al. A comparative atlas of single-cell chromatin accessibility in the human brain. Science (New York, N.Y.). 382: eadf7044. PMID 37824643 DOI: 10.1126/science.adf7044 |
0.369 |
|
| 2023 |
Zhang K, Zemke NR, Armand EJ, Ren B. SnapATAC2: a fast, scalable and versatile tool for analysis of single-cell omics data. Biorxiv : the Preprint Server For Biology. PMID 37745443 DOI: 10.1101/2023.09.11.557221 |
0.328 |
|
| 2023 |
Xie Y, Zhu C, Wang Z, Tastemel M, Chang L, Li YE, Ren B. Droplet-based single-cell joint profiling of histone modifications and transcriptomes. Nature Structural & Molecular Biology. PMID 37563440 DOI: 10.1038/s41594-023-01060-1 |
0.397 |
|
| 2023 |
Xie F, Armand EJ, Yao Z, Liu H, Bartlett A, Behrens MM, Li YE, Lucero JD, Luo C, Nery JR, Pinto-Duarte A, Poirion OB, Preissl S, Rivkin AC, Tasic B, ... ... Ren B, et al. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. Cell Genomics. 3: 100342. PMID 37492103 DOI: 10.1016/j.xgen.2023.100342 |
0.705 |
|
| 2023 |
Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, ... ... Ren B, et al. Cell Type- and Tissue-specific Enhancers in Craniofacial Development. Biorxiv : the Preprint Server For Biology. PMID 37425964 DOI: 10.1101/2023.06.26.546603 |
0.356 |
|
| 2023 |
Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, ... ... Ren B, et al. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. PMID 37419111 DOI: 10.1016/j.molcel.2023.06.018 |
0.605 |
|
| 2023 |
Fixsen BR, Han CZ, Zhou Y, Spann NJ, Saisan P, Shen Z, Balak C, Sakai M, Cobo I, Holtman IR, Warden AS, Ramirez G, Collier JG, Pasillas MP, Yu M, ... ... Ren B, et al. SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity. Nature Immunology. PMID 37322178 DOI: 10.1038/s41590-023-01528-8 |
0.303 |
|
| 2023 |
Gaulton KJ, Preissl S, Ren B. Interpreting non-coding disease-associated human variants using single-cell epigenomics. Nature Reviews. Genetics. PMID 37161089 DOI: 10.1038/s41576-023-00598-6 |
0.371 |
|
| 2023 |
Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, Zhang K, Brennan CW, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel AK, ... ... Ren B, et al. Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proceedings of the National Academy of Sciences of the United States of America. 120: e2210991120. PMID 37155843 DOI: 10.1073/pnas.2210991120 |
0.771 |
|
| 2023 |
Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, ... ... Ren B, et al. Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. Biorxiv : the Preprint Server For Biology. PMID 37131654 DOI: 10.1101/2023.04.16.536509 |
0.804 |
|
| 2023 |
Zhou P, VanDusen NJ, Zhang Y, Cao Y, Sethi I, Hu R, Zhang S, Wang G, Ye L, Mazumdar N, Chen J, Zhang X, Guo Y, Li B, Ma Q, ... ... Ren B, et al. Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation. Developmental Cell. PMID 37071996 DOI: 10.1016/j.devcel.2023.03.020 |
0.322 |
|
| 2023 |
Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, ... ... Ren B, et al. Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex. Biorxiv : the Preprint Server For Biology. PMID 37066152 DOI: 10.1101/2023.04.08.536119 |
0.465 |
|
| 2023 |
Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, ... ... Ren B, et al. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 186: 1493-1511.e40. PMID 37001506 DOI: 10.1016/j.cell.2023.02.018 |
0.537 |
|
| 2023 |
Zhu C, Wang Z, Ren B. Single-Cell Joint Profiling of Open Chromatin and Transcriptome by Paired-Seq. Methods in Molecular Biology (Clifton, N.J.). 2611: 155-185. PMID 36807069 DOI: 10.1007/978-1-0716-2899-7_10 |
0.364 |
|
| 2023 |
Qiu H, Makarov V, Bolzenius JK, Halstead A, Parker Y, Wang A, Iyer GV, Wise H, Kim D, Thayaparan V, Lindner DJ, Haber GP, Ting AH, Ren B, Chan TA, et al. KDM6A loss triggers an epigenetic switch that disrupts urothelial differentiation and drives cell proliferation in bladder cancer. Cancer Research. PMID 36638328 DOI: 10.1158/0008-5472.CAN-22-1444 |
0.353 |
|
| 2023 |
Jia BB, Jussila A, Kern C, Zhu Q, Ren B. A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nature Biotechnology. PMID 36593410 DOI: 10.1038/s41587-022-01568-9 |
0.305 |
|
| 2022 |
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, ... ... Ren B, et al. Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines. Cell Genomics. 2: 100214. PMID 36778047 DOI: 10.1016/j.xgen.2022.100214 |
0.528 |
|
| 2022 |
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. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. Cell Reports. 41: 111630. PMID 36351387 DOI: 10.1016/j.celrep.2022.111630 |
0.504 |
|
| 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 |
0.459 |
|
| 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 |
0.43 |
|
| 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 |
0.664 |
|
| 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 |
0.667 |
|
| 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 |
0.802 |
|
| 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 |
0.691 |
|
| 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 |
0.572 |
|
| 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 |
0.511 |
|
| 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 |
0.669 |
|
| 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 |
0.642 |
|
| 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 |
0.667 |
|
| 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 |
0.722 |
|
| 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 |
0.554 |
|
| 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 |
0.308 |
|
| 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 |
0.385 |
|
| 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 |
0.414 |
|
| 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 |
0.473 |
|
| 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 |
0.459 |
|
| 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 |
0.525 |
|
| 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 |
0.596 |
|
| 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 |
0.38 |
|
| 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 |
0.721 |
|
| 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 |
0.534 |
|
| 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 |
0.524 |
|
| 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 |
0.407 |
|
| 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 |
0.837 |
|
| 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 |
0.804 |
|
| 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 |
0.635 |
|
| 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 |
0.498 |
|
| 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 |
0.693 |
|
| 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 |
0.357 |
|
| 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 |
0.382 |
|
| 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 |
0.393 |
|
| 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 |
0.39 |
|
| 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 |
0.758 |
|
| 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 |
0.452 |
|
| 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 |
0.839 |
|
| 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 |
0.435 |
|
| 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 |
0.371 |
|
| 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 |
0.436 |
|
| 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 |
0.432 |
|
| 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 |
0.477 |
|
| 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 |
0.338 |
|
| 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 |
0.781 |
|
| 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 |
0.793 |
|
| 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 |
0.399 |
|
| 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 |
0.584 |
|
| 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 |
0.703 |
|
| 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 |
0.42 |
|
| 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 |
0.568 |
|
| 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 |
0.778 |
|
| 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 |
0.425 |
|
| 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 |
0.764 |
|
| 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 |
0.744 |
|
| 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 |
0.44 |
|
| 2019 |
Han CZ, Duttke SH, Ouyang Z, Preissl S, Schlachetzki JCM, Nott A, Fitzpatrick C, O'Connor C, Coufal NG, Gupta M, Gonda DD, Levy ML, Sharona B, David B, Ciacci JD, ... ... Ren B, et al. Abstract A078: Dissecting the myeloid lineage in human gliomas Cancer Immunology Research. 7. DOI: 10.1158/2326-6074.Cricimteatiaacr18-A078 |
0.303 |
|
| 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 |
0.391 |
|
| 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 |
0.696 |
|
| 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 |
0.412 |
|
| 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 |
0.412 |
|
| 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 |
0.448 |
|
| 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 |
0.33 |
|
| 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 |
0.522 |
|
| 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 |
0.725 |
|
| 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 |
0.474 |
|
| 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 |
0.781 |
|
| 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 |
0.772 |
|
| 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 |
0.57 |
|
| 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 |
0.377 |
|
| 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 |
0.42 |
|
| 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 |
0.42 |
|
| 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 |
0.434 |
|
| 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 |
0.36 |
|
| 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 |
0.477 |
|
| 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 |
0.302 |
|
| 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 |
0.401 |
|
| 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 |
0.81 |
|
| 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 |
0.444 |
|
| 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 |
0.408 |
|
| 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 |
0.661 |
|
| 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 |
0.672 |
|
| 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 |
0.39 |
|
| 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 |
0.324 |
|
| 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 |
0.537 |
|
| 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 |
0.398 |
|
| 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 |
0.503 |
|
| 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 |
0.442 |
|
| 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 |
0.699 |
|
| 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 |
0.858 |
|
| 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 |
0.429 |
|
| 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 |
0.395 |
|
| 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 |
0.491 |
|
| 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 |
0.699 |
|
| 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 |
0.655 |
|
| 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 |
0.679 |
|
| 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 |
0.811 |
|
| 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 |
0.403 |
|
| 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 |
0.474 |
|
| 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 |
0.484 |
|
| 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 |
0.704 |
|
| 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 |
0.355 |
|
| 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 |
0.641 |
|
| 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 |
0.682 |
|
| 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 |
0.849 |
|
| 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 |
0.831 |
|
| 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 |
0.726 |
|
| 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 |
0.843 |
|
| 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 |
0.678 |
|
| 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 |
0.824 |
|
| 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 |
0.666 |
|
| 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 |
0.82 |
|
| 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 |
0.454 |
|
| 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 |
0.455 |
|
| 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 |
0.525 |
|
| 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 |
0.747 |
|
| 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 |
0.732 |
|
| 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 |
0.832 |
|
| 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 |
0.747 |
|
| 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 |
0.496 |
|
| 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 |
0.643 |
|
| 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 |
0.838 |
|
| 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 |
0.71 |
|
| 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 |
0.403 |
|
| 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 |
0.448 |
|
| 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 |
0.4 |
|
| 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 |
0.812 |
|
| 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 |
0.502 |
|
| 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 |
0.696 |
|
| 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 |
0.568 |
|
| 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 |
0.687 |
|
| 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 |
0.623 |
|
| 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 |
0.504 |
|
| 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 |
0.516 |
|
| 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 |
0.715 |
|
| 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 |
0.711 |
|
| 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 |
0.455 |
|
| 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 |
0.647 |
|
| 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 |
0.795 |
|
| 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 |
0.713 |
|
| 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 |
0.303 |
|
| 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 |
0.78 |
|
| 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 |
0.832 |
|
| 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 |
0.727 |
|
| 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 |
0.508 |
|
| 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 |
0.833 |
|
| 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 |
0.785 |
|
| 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 |
0.822 |
|
| 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 |
0.648 |
|
| 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 |
0.689 |
|
| 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 |
0.314 |
|
| 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 |
0.751 |
|
| 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 |
0.767 |
|
| 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 |
0.765 |
|
| 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 |
0.791 |
|
| 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 |
0.545 |
|
| 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 |
0.455 |
|
| 2011 |
Espinoza CA, Ren B. Mapping higher order structure of chromatin domains. Nature Genetics. 43: 615-6. PMID 21709679 DOI: 10.1038/Ng.869 |
0.392 |
|
| 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 |
0.394 |
|
| 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 |
0.746 |
|
| 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 |
0.753 |
|
| 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 |
0.542 |
|
| 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 |
0.583 |
|
| 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 |
0.761 |
|
| 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 |
0.473 |
|
| 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 |
0.811 |
|
| 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 |
0.402 |
|
| 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 |
0.304 |
|
| 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 |
0.584 |
|
| 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 |
0.35 |
|
| 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 |
0.367 |
|
| 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 |
0.754 |
|
| 2010 |
Ren B. Transcription: Enhancers make non-coding RNA. Nature. 465: 173-4. PMID 20463730 DOI: 10.1038/465173A |
0.4 |
|
| 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 |
0.791 |
|
| 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 |
0.459 |
|
| 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 |
0.425 |
|
| 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 |
0.791 |
|
| 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 |
0.484 |
|
| 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 |
0.791 |
|
| 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 |
0.779 |
|
| 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 |
0.464 |
|
| 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 |
0.799 |
|
| 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 |
0.454 |
|
| 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 |
0.377 |
|
| 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 |
0.541 |
|
| 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 |
0.78 |
|
| 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 |
0.378 |
|
| 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 |
0.438 |
|
| 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 |
0.439 |
|
| 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 |
0.543 |
|
| 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 |
0.506 |
|
| 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 |
0.635 |
|
| 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 |
0.387 |
|
| 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 |
0.35 |
|
| 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 |
0.479 |
|
| 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 |
0.648 |
|
| 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 |
0.838 |
|
| 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 |
0.514 |
|
| 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 |
0.581 |
|
| 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 |
0.363 |
|
| 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 |
0.672 |
|
| 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 |
0.661 |
|
| 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 |
0.541 |
|
| 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 |
0.504 |
|
| 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 |
0.686 |
|
| 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 |
0.517 |
|
| 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 |
0.735 |
|
| 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 |
0.534 |
|
| 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 |
0.81 |
|
| 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 |
0.784 |
|
| 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 |
0.598 |
|
| 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 |
0.535 |
|
| 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 |
0.749 |
|
| 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 |
0.722 |
|
| 1999 |
Ren B, Young P, Young RA. A yeast genome expression monitoring database Nature Genetics. 23: 70-70. DOI: 10.1038/14389 |
0.533 |
|
| 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 |
|
| Show low-probability matches. |
