Berman Laboratory

 

 
 
 

Ben Berman, PhD - Associate Professor - Center for Bioinformatics and Functional Genomics at Cedars-Sinai Medical Center (benjamin.berman@cshs.org)

Ben Berman, PhD - Associate Professor

I earned a Bachelor’s in Computer Science and a PhD in Molecular & Cell Biology, both from UC Berkeley. There, I participated in the sequencing of the complete Drosophila genome, and was the first to show that transcriptional enhancers could be identified at genome-wide significance using a purely computational approach. I did a postdoctoral fellowship in molecular epidemiology at the University of Southern California, where I developed computational tools to understand the function of enhancer polymorphisms identified in large genome-wide association studies.  

From 2008-2014, I was Director of Bioinformatics for the USC/Norris Comprehensive Cancer Center Sequencing Core, where my group developed software pipelines to analyze Whole-Genome Bisulfite-Seq (WGBS), ChIP-seq, RNA-seq, and other NGS methods. I led a project to sequence the first complete DNA methylation map of any cancer using WGBS, and collaborated to generate and analyze sequence data as part of the ENCODE and PsychENCODE Consortia (Farnham, PI), and TCGA Consortium (Laird, PI). 

I am currently Co-Director of the Center for Bioinformatics & Functional Genomics (BFG) at Cedars-Sinai, an integrated, interdisciplinary group with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient samples. My key interest is in how variation and alterations in non-coding transcriptional regulatory regions lead to disease, and my lab develops computational tools to address these questions in large, patient focused datasets. I currently develop cancer genomics software tools as a PI in the NCI Informatics Technology for Cancer Research (ITCR) Consortium, and integrated cancer epigenomics pipelines as a PI in the NCI Genomic Data Analysis Network (GDAN) Consortium.  

 

Simon Coetzee - Research Bioinformatician II - Center for Bioinformatics and Functional Genomics at Cedars-Sinai Medical Center (Simon.Coetzee@cshs.org)

  Simon Coetzee Research Bioinformatician II

Simon Coetzee
Research Bioinformatician II

I began my career doing bioinformatics analysis of GWAS data as part of the U19 GAME-ONconsortium at USC. Since then, I have focused on the functional consequences of non-proteincoding risk regions within the context of many complex diseases. To this end, we developed asoftware program called FunciSNP, which is an R/Bioconductor tool integrating functional non-coding datasets with genetic association studies to identify candidate regulatory SNPs (Coetzeeet al., 2012). I have worked on analyzing and interpretation of large genomic datasets, includingnext-generation sequencing from internal collaborations and downloaded from public datasetssuch as 1000 genomes, The Encyclopedia of DNA Elements (ENCODE), NIH EpigenomicsRoadmap, and The Cancer Genome Atlas. At Cedars-Sinai, I am working with Dr. Ben Bermanand Dr. Dennis Hazelett to develop automation tools for analysis and functional annotation ofgenetic variants from large genome and epigenome sequencing projects. I am also continuingmy development of novel algorithms for the analysis of gene regulatory sequences.

 

Nicole Yeager - Graduate Student - Center for Bioinformatics and Functional Genomics at Cedars-Sinai Medical Center (nicole.yeager@cshs.org)

 Nicole Yeager Graduate Student  

Nicole Yeager
Graduate Student
 

Nicole Yeager graduated from Carnegie Mellon University, earning her bachelor's degree in Biological Sciences and Psychology.  She worked at Cedars-Sinai Medical Center in the Regenerative Medicine Institute where her research focused on the use of stem cells to gain insights into the pathogenesis of inflammatory bowel disease.  She is currently a graduate student working under Benjamin Berman using next-generation sequencing (NGS) methods to investigate epigenomic & genomic changes that can lead to dysregulation of cancer pathways. 

 

Publications

Lin D, Dinh HQ, Xie J, et al.Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas. Gut Published Online First: 31 August 2017. DOI: 10.1136/gutjnl-2017-314607

The Cancer Genome Atlas Research Network et al. (2010): “Integrated Genomic Analyses of Ovarian Carcinoma” Nature, 2010 v.474, pp. 609–615. PMCID: PMC3163504  

Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CPE, van Dijk CM, Tollenaar R, Van Den Berg D, Laird PW (2011) “Regions of Focal DNA Hypermethylation and Long-Range Hypomethylation in Colorectal Cancer Coincide with Nuclear Lamina-Associated Domains.” Nature Genetics. 2011 Nov 27;44(1):40-6. PMCID: PMC4309644  

The Cancer Genome Atlas Research Network et al. (2012): “Comprehensive Molecular Characterization of Human Colon and Rectal Cancer.” Nature, 2012 Jul 18;487(7407):330-7. PMCID: PMC3401966  

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, 2012 Dec;22(12):2497-506. PMCID: PMC3514679  

The Cancer Genome Atlas Research Network et al. (2012): “Comprehensive molecular portraits of human breast tumours.” Nature, 2012 Oct 4;490(7418):61-70. PMCID: PMC3465532  

Liu Y, Siegmund KD, Laird PW, Berman BP (2012) “Bis-SNP: Combined cytosine methylation and SNP calling for bisulfite sequence data.” Genome Biology, 2012 Jul 11;13(7):R61. PMCID: PMC3491382  

Marconett CN, Zhou B, Rieger ME, Selamat SA, Dubourd M, Fang X, Lynch SK, Siegmund KD, Berman BP, Borok Z, Laird-Offringa IA (2013): “Integrated Transcriptomic and Epigenomic Analysis of Primary Human Lung Epithelial Cell Differentiation.” PLoS Genetics, 2013 Jun 9(6):e1003513. PMCID: PMC3688557  

The Cancer Genome Atlas Research Network et al (2013): “Comprehensive molecular characterization of clear cell renal cell carcinoma.” Nature, 2013 Jul 4; 499(7456):43-9. PMCID: PMC3771322  

The Cancer Genome Atlas Research Network et al. (2013): “The Cancer Genome Atlas Pan-Cancer analysis project.” Nature Genetics. 2013 Sep 26;45(10):1113-20. PMCID: PMC3919969  

Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. (2015) “The role of DNA methylation in directing the functional organization of the cancer epigenome”. Genome Research Advance online publication March 6, 2015, doi:10.1101/gr.183368.114 

Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. (2002). “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 99(2): 757-62. PMCID: PMC117378   

Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE. (2004). “Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.” Genome Biology 5(9):R61. PMCID: PMC522868  

Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker SE, Rubin GM. (2007). “Global analysis of patterns of gene expression during Drosophila embryogenesis.” Genome Biology 8(7):R145. PMCID: PMC2323238  

Jia L, Berman BP, Jariwala U, Yan X, Cogan JP, Walters A, Chen T, Buchanan G, Frenkel B, Coetzee GA. (2008). “Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity”. PLoS ONE 2008 vol. 3 (11) pp. e3645. PMCID: PMC2577007  

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, Freedman M, Tanay A, Coetzee GA. (2009) “Functional enhancers at the gene-poor 8q24 cancer-linked locus”. PLoS Genetics 5(8):e1000597. PMCID: PMC2717370