Benjamin P. Berman - Publications

Affiliations: 
2019- Faculty of Medicine Hebrew University, Jerusalem, Jerusalem, Israel 
Area:
Regulation of gene expression, DNA methylation
Website:
http://methylgrammar.org

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

Year Citation  Score
2019 Reyes ALP, Silva TC, Coetzee SG, Plummer JT, Davis BD, Chen S, Hazelett DJ, Lawrenson K, Berman BP, Gayther SA, Jones MR. GENAVi: a shiny web application for gene expression normalization, analysis and visualization. Bmc Genomics. 20: 745. PMID 31619158 DOI: 10.1186/s12864-019-6073-7  0.52
2019 Gao GF, Parker JS, Reynolds SM, Silva TC, Wang LB, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, et al. Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data. Cell Systems. 9: 24-34.e10. PMID 31344359 DOI: 10.1016/j.cels.2019.06.006  0.72
2018 Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, Spitsyna VN, Guo Y, Berman BP, Evgrafov OV, Knowles JA, Farnham PJ. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Science Advances. 4: eaav8550. PMID 30555922 DOI: 10.1126/sciadv.aav8550  0.68
2018 Lin L, Huang M, Shi X, Mayakonda A, Hu K, Jiang YY, Guo X, Chen L, Pang B, Doan N, Said JW, Xie J, Gery S, Cheng X, Lin Z, ... ... Berman BP, et al. Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1. Nucleic Acids Research. PMID 30496486 DOI: 10.1093/nar/gky1207  0.48
2018 Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin DC, Berman BP. ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics (Oxford, England). PMID 30364927 DOI: 10.1093/bioinformatics/bty902  0.6
2018 Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, ... ... Berman BP, et al. The chromatin accessibility landscape of primary human cancers. Science (New York, N.Y.). 362. PMID 30361341 DOI: 10.1126/science.aav1898  0.72
2018 Jiang Y, Jiang YY, Xie JJ, Mayakonda A, Hazawa M, Chen L, Xiao JF, Li CQ, Huang ML, Ding LW, Sun QY, Xu L, Kanojia D, Jeitany M, Deng JW, ... ... Berman BP, et al. Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression. Nature Communications. 9: 3619. PMID 30190462 DOI: 10.1038/s41467-018-06081-9  0.48
2018 Xu L, Chen Y, Mayakonda A, Koh L, Chong YK, Buckley DL, Sandanaraj E, Lim SW, Lin RY, Ke XY, Huang ML, Chen J, Sun W, Wang LZ, Goh BC, ... ... Berman BP, et al. Targetable BET proteins- and E2F1-dependent transcriptional program maintains the malignancy of glioblastoma. Proceedings of the National Academy of Sciences of the United States of America. PMID 29764999 DOI: 10.1073/pnas.1712363115  0.48
2018 Shahid M, Gull N, Yeon A, Cho E, Bae J, Yoon HS, You S, Yoon H, Kim M, Berman BP, Kim J. Author Correction: Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A. Scientific Reports. 8: 6294. PMID 29662153 DOI: 10.1038/s41598-018-24827-9  0.48
2018 Zhou W, Dinh HQ, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H, Laird PW, Berman BP. DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nature Genetics. PMID 29610480 DOI: 10.1038/s41588-018-0073-4  0.8
2018 Shahid M, Gull N, Yeon A, Cho E, Bae J, Yoon HS, You S, Yoon H, Kim M, Berman BP, Kim J. Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A. Scientific Reports. 8: 4505. PMID 29540744 DOI: 10.1038/s41598-018-22771-2  0.48
2017 Yáñez A, Coetzee SG, Olsson A, Muench DE, Berman BP, Hazelett DJ, Salomonis N, Grimes HL, Goodridge HS. Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes. Immunity. 47: 890-902.e4. PMID 29166589 DOI: 10.1016/j.immuni.2017.10.021  0.52
2017 Lin DC, Dinh HQ, Xie JJ, Mayakonda A, Silva TC, Jiang YY, Ding LW, He JZ, Xu XE, Hao JJ, Wang MR, Li C, Xu LY, Li EM, Berman BP, et al. Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas. Gut. PMID 28860350 DOI: 10.1136/gutjnl-2017-314607  0.48
2017 Lin DC, Mayakonda A, Dinh HQ, Huang P, Lin L, Liu X, Ding LW, Wang J, Berman B, Song E, Yin D, Koeffler HP. Genomic and epigenomic heterogeneity of hepatocellular carcinoma. Cancer Research. PMID 28302680 DOI: 10.1158/0008-5472.CAN-16-2822  0.48
2016 Hao JJ, Lin DC, Dinh HQ, Mayakonda A, Jiang YY, Chang C, Jiang Y, Lu CC, Shi ZZ, Xu X, Zhang Y, Cai Y, Wang JW, Zhan QM, Wei WQ, ... Berman BP, et al. Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma. Nature Genetics. PMID 27749841 DOI: 10.1038/ng.3683  0.44
2015 Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, ... ... Berman BP, et al. The PsychENCODE project. Nature Neuroscience. 18: 1707-1712. PMID 26605881 DOI: 10.1038/nn.4156  0.84
2015 Han B, Qu Y, Jin Y, Yu Y, Deng N, Wawrowsky K, Zhang X, Li N, Bose S, Wang Q, Sakkiah S, Abrol R, Jensen TW, Berman BP, Tanaka H, et al. FOXC1 Activates Smoothened-Independent Hedgehog Signaling in Basal-like Breast Cancer. Cell Reports. 13: 1046-1058. PMID 26565916 DOI: 10.1016/j.celrep.2015.09.063  0.84
2015 Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Critical Reviews in Biochemistry and Molecular Biology. 1-24. PMID 26446758 DOI: 10.3109/10409238.2015.1087961  0.84
2015 Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biology. 16: 105. PMID 25994056 DOI: 10.1186/s13059-015-0668-3  0.84
2015 Reizel Y, Spiro A, Sabag O, Skversky Y, Hecht M, Keshet I, Berman BP, Cedar H. Gender-specific postnatal demethylation and establishment of epigenetic memory. Genes & Development. 29: 923-33. PMID 25934504 DOI: 10.1101/gad.259309.115  0.84
2015 Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Research. 25: 467-77. PMID 25747664 DOI: 10.1101/gr.183368.114  0.84
2014 Yao L, Tak YG, Berman BP, Farnham PJ. Functional annotation of colon cancer risk SNPs. Nature Communications. 5: 5114. PMID 25268989 DOI: 10.1038/ncomms6114  0.84
2014 Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, Farnham PJ. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biology. 15: 469. PMID 25239471 DOI: 10.1186/s13059-014-0469-0  0.84
2014 Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I. Multiscale representation of genomic signals. Nature Methods. 11: 689-94. PMID 24727652 DOI: 10.1038/nmeth.2924  0.84
2014 Shi J, Marconett CN, Duan J, Hyland PL, Li P, Wang Z, Wheeler W, Zhou B, Campan M, Lee DS, Huang J, Zhou W, Triche T, Amundadottir L, Warner A, ... ... Berman BP, et al. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nature Communications. 5: 3365. PMID 24572595 DOI: 10.1038/ncomms4365  0.84
2014 Biancolella M, Fortini BK, Tring S, Plummer SJ, Mendoza-Fandino GA, Hartiala J, Hitchler MJ, Yan C, Schumacher FR, Conti DV, Edlund CK, Noushmehr H, Coetzee SG, Bresalier RS, Ahnen DJ, ... ... Berman BP, et al. Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1. Human Molecular Genetics. 23: 2198-209. PMID 24256810 DOI: 10.1093/hmg/ddt584  0.84
2013 Marconett CN, Zhou B, Rieger ME, Selamat SA, Dubourd M, Fang X, Lynch SK, Stueve TR, Siegmund KD, Berman BP, Borok Z, Laird-Offringa IA. Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation. Plos Genetics. 9: e1003513. PMID 23818859 DOI: 10.1371/journal.pgen.1003513  0.84
2012 Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Research. 22: 2497-506. PMID 22960375 DOI: 10.1101/gr.143008.112  0.84
2012 Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biology. 13: R61. PMID 22784381 DOI: 10.1186/gb-2012-13-7-r61  0.84
2012 Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H. FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. Nucleic Acids Research. 40: e139. PMID 22684628 DOI: 10.1093/nar/gks542  0.84
2012 Little GH, Noushmehr H, Baniwal SK, Berman BP, Coetzee GA, Frenkel B. Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion. Nucleic Acids Research. 40: 3538-47. PMID 22187159 DOI: 10.1093/nar/gkr1219  0.84
2012 Chimge NO, Baniwal SK, Luo J, Coetzee S, Khalid O, Berman BP, Tripathy D, Ellis MJ, Frenkel B. Opposing effects of Runx2 and estradiol on breast cancer cell proliferation: in vitro identification of reciprocally regulated gene signature related to clinical letrozole responsiveness. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 18: 901-11. PMID 22147940 DOI: 10.1158/1078-0432.CCR-11-1530  0.84
2012 Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA, Van Den Berg D, Laird PW. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nature Genetics. 44: 40-6. PMID 22120008 DOI: 10.1038/ng.969  0.84
2012 Juve G, Deelman E, Berriman GB, Berman BP, Maechling P. An Evaluation of the Cost and Performance of Scientific Workflows on Amazon EC2 Journal of Grid Computing. 10: 5-21. DOI: 10.1007/s10723-012-9207-6  0.84
2011 Andreu-Vieyra C, Lai J, Berman BP, Frenkel B, Jia L, Jones PA, Coetzee GA. Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells. Molecular and Cellular Biology. 31: 4648-62. PMID 21969603 DOI: 10.1128/MCB.05934-11  0.84
2010 Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, Jones PA. H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Molecular Cell. 39: 901-11. PMID 20864037 DOI: 10.1016/j.molcel.2010.08.026  0.84
2010 Chung TL, Brena RM, Kolle G, Grimmond SM, Berman BP, Laird PW, Pera MF, Wolvetang EJ. Vitamin C promotes widespread yet specific DNA demethylation of the epigenome in human embryonic stem cells. Stem Cells (Dayton, Ohio). 28: 1848-55. PMID 20687155 DOI: 10.1002/stem.493  0.84
2010 Berman BP, Frenkel B, Coetzee GA, Jia L. Androgen receptor responsive enhancers are flanked by consistently-positioned H3-acetylated nucleosomes. Cell Cycle (Georgetown, Tex.). 9: 2249-50. PMID 20495358 DOI: 10.4161/cc.9.11.11621  0.84
2010 Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, Pan F, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM, Schmidt HK, et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 17: 510-22. PMID 20399149 DOI: 10.1016/j.ccr.2010.03.017  0.84
2010 Juve G, Deelman E, Vahi K, Mehta G, Berriman B, Berman BP, Maechling P. Data sharing options for scientific workflows on Amazon EC2 2010 Acm/Ieee International Conference For High Performance Computing, Networking, Storage and Analysis, Sc 2010. DOI: 10.1109/SC.2010.17  0.84
2009 Jia L, Landan G, Pomerantz M, Jaschek R, Herman P, Reich D, Yan C, Khalid O, Kantoff P, Oh W, Manak JR, Berman BP, Henderson BE, Frenkel B, Haiman CA, et al. Functional enhancers at the gene-poor 8q24 cancer-linked locus. Plos Genetics. 5: e1000597. PMID 19680443 DOI: 10.1371/journal.pgen.1000597  0.84
2009 Berman BP, Weisenberger DJ, Laird PW. Locking in on the human methylome. Nature Biotechnology. 27: 341-2. PMID 19352369 DOI: 10.1038/nbt0409-341  0.84
2009 Berman BP, Frenkel B, Coetzee GA. Location, location, (ChIP-)location! Mapping chromatin landscapes one immunoprecipitation at a time. Journal of Cellular Biochemistry. 107: 1-5. PMID 19308935 DOI: 10.1002/jcb.22133  0.84
2009 Juve G, Deelman E, Vahi K, Mehta G, Berman BP, Berriman B, Maechling P. Scientific workflow applications on amazon EC2 E-Science 2009 - Proceedings of the 2009 5th Ieee International Conference On E-Science Workshops. 59-66. DOI: 10.1109/ESCIW.2009.5408002  0.84
2008 Jia L, Berman BP, Jariwala U, Yan X, Cogan JP, Walters A, Chen T, Buchanan G, Frenkel B, Coetzee GA. Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity. Plos One. 3: e3645. PMID 18997859 DOI: 10.1371/journal.pone.0003645  0.84
2007 Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker SE, Rubin GM. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biology. 8: R145. PMID 17645804 DOI: 10.1186/gb-2007-8-7-r145  0.84
2004 Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biology. 5: R61. PMID 15345045 DOI: 10.1186/gb-2004-5-9-r61  0.84
2003 Gelbart WM, Bayraktaroglu L, Bettencourt B, Campbell K, Crosby M, Emmert D, Hradecky P, Huang Y, Letovsky S, Matthews B, Russo S, Schroeder A, Smutniak F, Zhou P, Zytkovics M, ... ... Berman B, et al. The FlyBase database of the Drosophila genome projects and community literature Nucleic Acids Research. 31: 172-175. PMID 12519974 DOI: 10.1093/nar/gkg094  0.84
2002 Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, et al. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biology. 3: RESEARCH0083. PMID 12537572  0.84
2002 Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, et al. An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biology. 3: RESEARCH0081. PMID 12537570  0.84
2002 Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proceedings of the National Academy of Sciences of the United States of America. 99: 757-62. PMID 11805330 DOI: 10.1073/pnas.231608898  0.84
2000 Hoskins RA, Nelson CR, Berman BP, Laverty TR, George RA, Ciesiolka L, Naeemuddin M, Arenson AD, Durbin J, David RG, Tabor PE, Bailey MR, DeShazo DR, Catanese J, Mammoser A, et al. A BAC-based physical map of the major autosomes of Drosophila melanogaster. Science (New York, N.Y.). 287: 2271-4. PMID 10731150 DOI: 10.1126/science.287.5461.2271  0.84
2000 Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, ... ... Berman BP, et al. The genome sequence of Drosophila melanogaster. Science (New York, N.Y.). 287: 2185-95. PMID 10731132 DOI: 10.1126/science.287.5461.2185  0.84
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