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The Faculty of Medicine - Developmental Biology and Cancer Research: Berman Benjamin


Last updated December 2021 - Developmental Biology and Cancer Research

List of Publications

(1) Zheng Y, Huang G, Silva TC, Yang Q, Jiang Y-, Koeffler HP, et al. Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes (Nature Communications, (2021), 12, 1, (2485), 10.1038/s41467-021-22720-0). Nat Commun 2021;12(1).

(2) Zheng Y, Huang G, Silva TC, Yang Q, Jiang Y-, Koeffler HP, et al. A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes. Nat Commun 2021;12(1).

(3) Walravens A-, Smolgovsky S, Li L, Kelly L, Antes T, Peck K, et al. Mechanistic and therapeutic distinctions between cardiosphere-derived cell and mesenchymal stem cell extracellular vesicle non-coding RNA. Sci Rep 2021;11(1).

(4) Huang Y, Yang Q, Zheng Y, Lin L, Xu X, Xu X-, et al. Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma. Nucleic Acids Res 2021;49(16):9246-9263.

(5) Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, et al. Erratum: Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway (Cell Reports (2021) 34(5), (S2211124721000206), (10.1016/j.celrep.2021.108707)). Cell Rep 2021;34(8).

(6) Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, et al. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell Rep 2021;34(5).

(7) Unterman I, Bloch I, Cazacu S, Kazimirsky G, Ben-Zeev B, Berman BP, et al. Expanding the mecp2 network using comparative genomics reveals potential therapeutic targets for rett syndrome. eLife 2021;10.

(8) Bailey MH, Meyerson WU, Dursi LJ, Wang L-, Dong G, Liang W-, et al. Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (Nature Communications, (2020), 11, 1, (4748), 10.1038/s41467-020-18151-y). Nat Commun 2020;11(1).

(9) Corona RI, Seo J-, Lin X, Hazelett DJ, Reddy J, Fonseca MAS, et al. Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer. Nat Commun 2020;11(1).

(10) Bailey MH, Meyerson WU, Dursi LJ, Wang L-, Dong G, Liang W-, et al. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun 2020;11(1).

(11) Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, Al-Shahrour F, et al. Sex differences in oncogenic mutational processes. Nat Commun 2020;11(1).

(12) Jones MR, Peng P-, Coetzee SG, Tyrer J, Reyes ALP, Corona RI, et al. Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites. Am J Hum Genet 2020;107(4):622-635.

(13) Pan J, Silva TC, Gull N, Yang Q, Plummer JT, Chen S, et al. Lineage-specific epigenomic and genomic activation of oncogene HNF4A promotes gastrointestinal adenocarcinomas. Cancer Res 2020;80(13):2722-2736.

(14) Chen L, Huang M, Plummer J, Pan J, Jiang YY, Yang Q, et al. Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma. Gut 2020;69(4):630-640.

(15) Campbell PJ, Getz G, Korbel JO, Stuart JM, Jennings JL, Stein LD, et al. Pan-cancer analysis of whole genomes. Nature 2020;578(7793):82-93.

(16) Loh X-, Sun Q-, Ding L-, Mayakonda A, Venkatachalam N, Yeo M-, et al. RNA-binding protein ZFP36L1 suppresses hypoxia and cell-cycle signaling. Cancer Res 2020;80(2):219-233.

(17) Reyes ALP, Silva TC, Coetzee SG, Plummer JT, Davis BD, Chen S, et al. GENAVi: A shiny web application for gene expression normalization, analysis and visualization. BMC Genomics 2019;20(1).

(18) Gao GF, Parker JS, Reynolds SM, Silva TC, Wang L-, Zhou W, et al. Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data. Cell Syst 2019;9(1):24-34.e10.

(19) Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, et al. ELmer v.2: An r/bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics 2019;35(11):1974-1977.

(20) Fert-Bober J, Venkatraman V, Hunter CL, Liu R, Crowgey EL, Pandey R, et al. Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library. J Proteome Res 2019;18(5):2270-2278.

(21) Lin L, Huang M, Shi X, Mayakonda A, Hu K, Jiang Y-, et al. Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1. Nucleic Acids Res 2019;47(3):1255-12567.

(22) Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, et al. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Sci Adv 2018;4(12).

(23) Jiang Y, Jiang Y-, Xie J-, Mayakonda A, Hazawa M, Chen L, et al. Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression. Nat Commun 2018;9(1).

(24) Shahid M, Gull N, Yeon A, Cho E, Bae J, Yoon HS, et al. Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A. Sci Rep 2018;8(1).

(25) Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, et al. The chromatin accessibility landscape of primary human cancers. Sci 2018;362(6413).

(26) Xu L, Chen Y, Mayakonda A, Koh L, Chong YK, Buckley DL, et al. Targetable BET proteins- and E2F1-dependent transcriptional program maintains the malignancy of glioblastoma. Proc Natl Acad Sci U S A 2018;115(22):E5086-E5095.

(27) Shahid M, Gull N, Yeon A, Cho E, Bae J, Yoon HS, et al. Erratum: Author Correction: Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A (Scientific reports (2018) 8 1 (4505)). Sci Rep 2018;8(1):6294.

(28) Zhou W, Dinh HQ, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H, et al. DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nat Genet 2018;50(4):591-602.

(29) Silva TC, Colaprico A, Olsen C, Malta TM, Bontempi G, Ceccarelli M, et al. TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data [version 1; peer review: 1 approved, 1 approved with reservations]. F1000 Res 2018;7.

(30) Coetzee SG, Ramjan Z, Dinh HQ, Berman BP, Hazelett DJ. Statehub-statepaintr: Rapid and reproducible chromatin state evaluation for custom genome annotation [version 1; peer review: 3 approved with reservations]. F1000 Res 2018;7.

(31) Lin D-, Dinh HQ, Xie J-, Mayakonda A, Silva TC, Jiang Y-, et al. Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas. Gut 2018;67(10):1769-1779.

(32) Yáñez A, Coetzee SG, Olsson A, Muench DE, Berman BP, Hazelett DJ, et al. Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes. Immunity 2017;47(5):890-902.e4.

(33) De Couto G, Gallet R, Cambier L, Jaghatspanyan E, Makkar N, Dawkins JF, et al. Exosomal MicroRNA Transfer into Macrophages Mediates Cellular Postconditioning. Circulation 2017;136(2):200-214.

(34) Lin D-, Mayakonda A, Dinh HQ, Huang P, Lin L, Liu X, et al. Genomic and epigenomic heterogeneity of hepatocellular carcinoma. Cancer Res 2017;77(9):2255-2265.

(35) Hao J-, Lin D-, Dinh HQ, Mayakonda A, Jiang Y-, Chang C, et al. Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma. Nat Genet 2016;48(12):1500-1507.

(36) Huang F, Ma Z, Pollan S, Yuan X, Swartwood S, Gertych A, et al. Quantitative imaging for development of companion diagnostics to drugs targeting HGF/MET. J Pathol Clin Res 2016;2(4):210-222.

(37) Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, et al. The PsychENCODE project. Nat Neurosci 2015;18(12):1707-1712.

(38) Han B, Qu Y, Jin Y, Yu Y, Deng N, Wawrowsky K, et al. FOXC1 Activates Smoothened-Independent Hedgehog Signaling in Basal-like Breast Cancer. Cell Rep 2015;13(5):1046-1058.

(39) Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: Linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 2015;50(6):550-573.

(40) Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol 2015;16(1).

(41) Reizel Y, Spiro A, Sabag O, Skversky Y, Hecht M, Keshet I, et al. Gender-specific postnatal demethylation and establishment of epigenetic memory. Genes Dev 2015;29(9):923-933.

(42) Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, et al. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res 2015;25(4):467-477.

(43) Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 2014;158(4):929-944.

(44) Biancolella M, Fortini BK, Tring S, Plummer SJ, Mendoza-Fandino GA, Hartiala J, et al. Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1. Hum Mol Genet 2014;23(8):2198-2209.

(45) Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, et al. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol 2014;15(9):469.

(46) Yao L, Tak YG, Berman BP, Farnham PJ. Functional annotation of colon cancer risk SNPs. Nat Commun 2014;5.

(47) Shi J, Marconett CN, Duan J, Hyland PL, Li P, Wang Z, et al. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nat Commun 2014;5:3365.

(48) Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AFA, Wessels LFA, et al. Multiscale representation of genomic signals. Nat Methods 2014;11(6):689-694.

(49) Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, et al. The cancer genome atlas pan-cancer analysis project. Nat Genet 2013;45(10):1113-1120.

(50) Creighton CJ, Morgan M, Gunaratne PH, Wheeler DA, Gibbs RA, Robertson G, et al. Comprehensivemolecular characterization of clear cell renal cell carcinoma. Nature 2013;499(7456):43-49.

(51) Marconett CN, Zhou B, Rieger ME, Selamat SA, Dubourd M, Fang X, et al. Integrated Transcriptomic and Epigenomic Analysis of Primary Human Lung Epithelial Cell Differentiation. PLoS Genet 2013;9(6).

(52) 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 Res 2012;22(12):2497-2506.

(53) Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, et al. Comprehensive molecular portraits of human breast tumours. Nature 2012;490(7418):61-70.

(54) 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 Res 2012;40(18).

(55) Muzny DM, Bainbridge MN, Chang K, Dinh HH, Drummond JA, Fowler G, et al. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487(7407):330-337.

(56) Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol 2012;13(7).

(57) 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 Res 2012;40(8):3538-3547.

(58) Juve G, Deelman E, Berriman GB, Berman BP, Maechling P. An Evaluation of the Cost and Performance of Scientific Workflows on Amazon EC2. J Grid Comput 2012;10(1):5-21.

(59) Chimge N-, Baniwal SK, Luo J, Coetzee S, Khalid O, Berman BP, et al. Opposing effects of Runx2 and estradiol on breast cancer cell proliferation: In vitro identification of reciprocally regulated gene signature related to clinical letrozole responsiveness. Clin Cancer Res 2012;18(3):901-911.

(60) Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear laminag-associated domains. Nat Genet 2012;44(1):40-46.

(61) Claudia A-, Lai J, Berman BP, Frenkel B, Jia L, Jones PA, et al. Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells. Mol Cell Biol 2011;31(23):4648-4662.

(62) Bell D, Berchuck A, Birrer M, Chien J, Cramer DW, Dao F, et al. Integrated genomic analyses of ovarian carcinoma. Nature 2011;474(7353):609-615.

(63) Data sharing options for scientific workflows on Amazon EC2. 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2010; 2010.

(64) Chung T-, Brena RM, Kolle G, Grimmond SM, Berman BP, Laird PW, et al. Vitamin C promotes widespread yet specific DNA demethylation of the epigenome in human embryonic stem cells. Stem Cells 2010;28(10):1848-1855.

(65) Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, et al. H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell 2010;39(6):901-911.

(66) Berman BP, Frenkel B, Coetzee GA, Jia L. Androgen receptor responsive enhancers are flanked by consistently- positioned H3-acetylated nucleosomes. Cell Cycle 2010;9(11):2249-2250.

(67) Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, et al. Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma. Cancer Cell 2010;17(5):510-522.

(68) Scientific workflow applications on amazon EC2. e-science 2009 - Proceedings of the 2009 5th IEEE International Conference on e-Science Workshops; 2009.

(69) Jia L, Landan G, Pomerantz M, Jaschek R, Herman P, Reich D, et al. Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet 2009;5(8).

(70) Berman BP, Frenkel B, Coetzee GA. Location, location, (ChIP-)location! mapping chromatin landscapes one immunoprecipitation at a time. J Cell Biochem 2009;107(1):1-5.

(71) Berman BP, Weisenberger DJ, Laird PW. Locking in on the human methylome. Nat Biotechnol 2009;27(4):341-342.

(72) Jia L, Berman BP, Jariwala U, Yan X, Cogan JP, Walkers A, et al. Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity. PLoS ONE 2008;3(11).

(73) Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, et al. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol 2007;8(7).

(74) Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, et al. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol 2004;5(9).

(75) Gelbart WM, Bayraktaroglu L, Bettencourt B, Campbell K, Crosby M, Emmert D, et al. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res 2003;31(1):172-175.

(76) Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, et al. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 2002;99(2):757-762.

(77) Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, et al. An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol 2002;3(12).

(78) Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, et al. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol 2002;3(12).

(79) Hermesh O, Kalderon B, Berman B, Bar-Tana J. Mitochondrial protonophoric activity induced by a thyromimetic fatty acid analogue. Biochim Biophys Acta Bioenerg 2000;1457(3):166-174.

(80) Hoskins RA, Nelson CR, Berman BP, Laverty TR, George RA, Ciesiolka L, et al. A BAC-based physical map of the major autosomes of Drosophila melanogaster. Science 2000;287(5461):2271-2274.

(81) Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, et al. The genome sequence of Drosophila melanogaster. Science 2000;287(5461):2185-2195.

(82) Fateman RJ, Tokuyasu T, Berman BP, Mitchell N. Optical Character Recognition and Parsing of Typeset Mathematics. J Visual Commun Image Represent 1996;7(1):2-15.

(83) Multimedia Forum Kiosk and SpeakEasy. Proceedings of the ACM International Multimedia Conference & Exhibition; 1995.

(84) Optical character recognition for typeset mathematics. Proceedings of the International Symposium on Symbolic and Algebraic Computation, ISSAC; 1994.

(85) Becker DM, Windsor R, Ockene JK, Berman B, Best JA, Cummings KM, et al. Setting the policy, education, and research agenda to reduce tobacco use: Workshop I. Circulation 1993;88(3):1381-1386.