2018

DNA methylation loss in late-replicating domains is linked to mitotic cell divisions

Zhou W*, Dinh HQ*, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H**, Laird PW**, Berman BP**

Nat. Genetics 2018 April 2;50(4):591. PMID: 29610480

Apr. 2018; Nat. Genetics

 


Asparagine availability governs metastasis in a model of breast cancer.

Knott SRV*, Wagenblast E*, Kim SY, Soto M, Khan S, Gable AL, Maceli AR, Dickopf S, Erard N, Harrell C, Perou CM, Wilkinson JE, Hannon GJ. (*first author)
Nature. 2018 Feb 7. doi: 10.1038/nature25465 PMID:29414946

Feb. 2018; Nature


2017

Identification of distinct mutational patterns and new driver genes in esophageal squamous cell carcinomas and adenocarcinomas

Lin DC*, Dinh HQ*, Xie JJ**, Mayakonda A, Jiang YY, Ding LW, He JZ, Xu XE, Hao JJ, Wang MR, Xu LY, Li EM**, Berman BP** and Koeffler HP**

Gut, 2017 Aug 31. PMID:28860350

Aug. 2017; Gut


Exosomal microRNA Transfer into Macrophages Mediates Cellular Postconditioning

de Couto G, Gallet R, Cambier L, Makkar N, Jaghatspanyan E, Dawkins J, Berman BP**, Marbán E**

Circulation, 2017 Jul 11;136(2):200-214. PMID: 28411247  

Jul. 2017; Circulation

 


A CRISPR Resource for Individual, Combinatorial, or Multiplexed Gene Knockout.

Erard N, Knott SRV**, Hannon GJ**.
Mol Cell. 2017 Jul 20;67(2):348-354.e3. doi: 10.1016/j.molcel.2017.06.030. PMID:28732207

Jul. 2017; Mol Cell


Genomic and epigenomic heterogeneity of hepatocellular carcinoma

Lin DC*, Mayakonda A*, Dinh HQ*, Lin L, Huang P, Liu X, Ding L, Wang J, Berman BP**, Yin D**, Song EW**, Koeffler HP**

Cancer Res., 2017 May 1;77(9):2255-2265. PMID: 28302680

May 2017; Cancer Res.

 


2017; Oncotarget

 The PAX8 Cistrome in Epithelial Ovarian Cancer

Emily K. Adler*, Rosario I. Corona*, Janet M. Lee, Norma Rodriguez-Malave, Paulette Mhawech-Fauceglia, Heidi Sowter, Dennis J. Hazelett**, Kate Lawrenson**, and Simon A. Gayther**

Oncotarget 2017 8(65):108316—108332. PMID:29312534


2017; Immunity

Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocyte

Yáñez A, Coetzee SG, Olsson A, Muench DE, Berman BP, Hazelett DJ, Salomonis N, Grimes HL, and Goodridge HS

Immunity 47(5):890—902. PMID:29166589


2017; Nature Genetics

Identification of twelve new susceptibility loci for different histotypes of epithelial ovarian cancer

Phelan C, Kuchenbaeker KB, Tyrer JP, Kar S, Lawrenson K, Winham SJ, …~100+additional authors…, Hazelett DJ, Offit K, Simard J, Schmutzler RK, Monteiro AN, Couch FJ, Berchuck A, Chenevix-Trench G, Goode EL, Sellers TA, Gayther SA, Anoniou AC, Pharoah PDP

Nature Genetics 2017. PMID:28346442


2017; J Natl Cancer Inst

Two Novel Susceptibility Loci for Prostate Cancer in Men of African Ancestry

Conti DV, Wang K, Sheng X, Bensen JT, Hazelett DJ, et al.

J Natl Cancer Inst 2017. PMCID: PMC5448553


2016

Spatial intratumor heterogeneity of genetic, epigenetic alterations and temporal clonal evolution in esophageal squamous cell carcinoma

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**, Wang MR**, Koeffler HP**

Nat. Genetics. 2016 Dec; 48(12):1500-1507. PMCID: PMC5127772

Dec. 2016;Nat. Genetics


Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

Lawrenson K, Kar S [...] Gayther SA

Nat Commun. 2016 7:12675

2016; Nat Commun


2016; CEBP

The OncoArray Consortium: a Network for Understanding the Genetic Architecture of Common Cancers

Amos C, Dennis J, Wang Z, 17 additional authors, Hazelett DJ, and 63 additional authors

 CEBP 2016. PMID:27697780


2016; British Journal of Cancer

Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci

Kar S, Adler E, Tyrer J, Hazelett D and 19 other authors

British Journal of Cancer 2016. PMID:28103614


2016; Scientific Reports

Parkinson’s Disease Risk Functionality

Coetzee SG, Brundin P, Hazelett DJ, Coetzee G

Scientific Reports 2016 6:30509. PMID:27461410


2016; CEBP

A meta-analysis of multiple myeloma risk regions in African and European ancestry populations identifies putatively functional loci.

Rand KA, Song C, Dean E, Serie DJ, Curtin K, + 99 additional authors, Hazelett DJ, Cozen W,Haiman CA

CEBP 2016 PMID:27587788


2016; J Natl Cancer Inst

Prostate Cancer Susceptibility in Men of African Ancestry at 8q24

Han Y, Rand KA, Hazelett DJ and 62 additional authors

J Natl Cancer Inst 2016 108 (7):pii PMID: 26823525


2016; Cell Cycle

Reducing GWAS complexity

Hazelett DJ, Conti DV, Han Y, Al Oloma AA, Easton D, Eeles RA, Kote-Jarai Z, Haiman CA and Coetzee GA

Cell Cycle 2016 vol. 15 (1):22-24. PMID: 26771711


2015; Invest Opthalmol Vis Sci

Identification of a novel mucin gene HCG22 associated with steroid-induced ocular hypertension

Jeong S, Patel N, Edlund C, Hartiala J, Hazelett DJ, Itakura T, Avery RL, Davis JL, Flynn HW, Lalwani G, Puliafito C, Wafapoor H, Hijikata M, Keicho N, Gao X, Argueso P, Allayee H, Coetzee GA, Pletcher MT, Conti DV, Schwartz SG, Eaton AM, Fini ME

Invest Opthalmol Vis Sci 2015 vol. 56 (4):2737-48. PMID: 25813999


2015

May 2015; Genome Biology

Inferring Regulatory Element Landscapes and Transcription Factor Networks from Cancer Methylomes

Yao L, Shen H, Laird PW, Farnham PJ, Berman BP

Genome Biology. 2015 May 21; 16(1):105. PMCID: PMC4460959


The role of DNA methylation in directing the functional organization of the cancer epigenome

Lay FD*, Liu Y*, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP  

Genome Research 2015 Apr; 25(4):467. PMCID: PMC4381519

Apr. 2015; Genome Research

 


A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis.

Wagenblast E, Soto M, Gutiérrez-Ángel S, Hartl CA, Gable AL, Maceli AR, Erard N, Williams AM, Kim SY, Dickopf S, Harrell JC, Smith AD, Perou CM, Wilkinson JE, Hannon GJ, Knott SR.
Nature. 2015 Apr 16;520(7547):358-62. doi: 10.1038/nature14403. Epub 2015 Apr 8.
PMID: 25855289

Apr. 2015; Nature


Fine mapping and regulatory profiling of ovarian cancer susceptibility loci discovered by GWAS

Coetzee S, Shen H, Hazelett D, Lawrenson K, Li Q, Freedman MF, Pharoah PDP, Noushmehr H, Coetzee G. Gayther SA

Hum Mol Genet. 2015 24(13):3595-607

2015; Hum Mol Genet


Genome-wide significant risk associations for mucinous epithelial ovarian carcinoma

Kelemen LE*, Lawrenson K* Tyrer J, Li Q, The Ovarian Cancer Association Consortium, Freedman M, Pharoah PDP, Gayther SA*, Andrew Berchuck A*

Nat Genet. 2015 47(8):888-97

2015; Nat Genet


Contribution of germline mutations in the RAD51B, RAD51C and RAD51D genes to ovarian cancer in the population

Song H, Dicks E [...] Gayther SA*, Pharoah PD* 

J Clin Oncol. 2015 33(26):2901-7

2015; J Clin Oncol


2015; J Natl Cancer Inst.


Cis-eQTL Analysis And Functional Validation Of Candidate Susceptibility Genes For High-Grade Serous Ovarian Cancer

Lawrenson K, Li Q, Kar S …. Monteiro A, Pharoah PD, Gayther SA*, Freedman ML* 

Nat Commun. 2015 Sep 22;6:823

2015; Nat Commun


CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

Spisák S, Lawrenson K, Fu Y … Gayther SA*, Joung JK*, Freedman ML*

Nat Med. 2015 21(11):1357-63

2015; Nat Med


2015; Carcinogenesis

Common variants at the CHEK2 gene locus and risk of epithelial ovarian cancer

Lawrenson K, Iversen ES, Tyrer J, Weber RP, Concannon P, Hazelett DJ, and 152 additional authors

Carcinogenesis 2015 vol. 36 (11):1341-53. PMID: 26424751


2015; Bioinformatician

MotifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites

Coetzee SG, Coetzee GA, Hazelett DJ

Bioinformatics 2015 vol. 31 (23):3847-9. PMID: 26272984


2015; Hum Mol Gen

Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions

Han Y*, Hazelett DJ* and 80 additional authors

Hum Mol Gen 2015 vol. 24 (19):5603-18. PMID: 26823525


2015; Hum Mel Gen

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Al Olama AA, Dadaev T, Hazelett DJ and 74 additional authors

Hum Mol Gen 2015 vol. 24 (19):5589-602. PMID: 26025378


2015; Nat Gent

Identification of six novel, common variant susceptibility loci for invasive epithelial ovarian cancer

Kuchenbaecker K, Ramus S, Tyrer J, Shen H, Lawrenson K, Beesley J, Lee J, Spindler T, Lin Y, Pejovic T, Bean Y, Li Q, Coetzee S, Hazelett D, and 68 additional authors

Nat Genet 2015 vol. 47 pp. 164-71. PMID: 25581431


2014

A computational algorithm to predict shRNA potency.

Knott SR, Maceli AR, Erard N, Chang K, Marran K, Zhou X, Gordon A, El Demerdash O, Wagenblast E, Kim S, Fellmann C, Hannon GJ.

Mol Cell. 2014 Dec 18;56(6):796-807. doi: 10.1016/j.molcel.2014.10.025. Epub 2014 Nov 26. PMID: 25435137

Dec. 2014;
Mol Cell


2014; Nat Genet

A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer

Al Olama AA, Kote-Jarai Z, Berndt SI, Conti D, Schumacher F, Han Y, Benlloch S, Hazelett DJ and 160 additional authors

Nat Genet 2014 vol. 46 pp. 1103-9. PMID: 25217961


2014; Nat Commun

A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus

Cozen W*, Timofeeva MN*, Li D*, Diepstra A*, Hazelett D*, Delahaye-Sourdeix M* and 59 additionla authors

Nat Commun 2014 vol. 5 pp. 3856. PMID: 24920014


2014; BMC Genomics

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells

Rhie SK, Hazelett DJ, Coetzee SG, Yan C, Noushmehr H, Coetzee GA 

BMC Genomics 2014 vol. 15 (1) pp. 331. PMID: 24885402


2014; PLoS Gen

Comprehensive functional annotation of 77 prostate cancer risk loci.

Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG; Ellipse/GAME-ON consortium; Practical consortium, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA

PLoS Gen 2014 vol. 10 e1004102. PMID: 24497837


2013

Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31

Permuth-Wey J, Lawrenson K [...] Gayther SA

Nat Commun. 2013 4:1627 23535648

2013; Nat Commun


A rare variant, which destroys a FoxA1 site at 8q24, is associated with prostate cancer risk.

Hazelett DJ, Coetzee SG, Coetzee GA

Cell Cycle 2013 vol. 12 pp. 379-80. PMID: 23255135

2013; Cell Cycle


2012

Genome-wide Mapping of Nucleosome Positioning and DNA Methylation Within Individual DNA Molecules

Kelly TK*, Liu Y*, Lay FD, Liang G, Berman BP, Jones PA

Genome Research 2012 Dec;22(12):2497-506. PMID: 22960375

Dec. 2012; Genome Research

 


FunciSNP An R/Bioconductor Tool Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H

Nucleic Acids Research. 2012 Oct;40(18):e139. PMCID: PMC3467035

Oct. 2012;Nucleic Acids Research


Bis-SNP: Combined cytosine methylation and SNP calling for bisulfite sequence data

Liu Y, Siegmund KD, Laird PW, Berman BP

Genome Biology. 2012 Jul 11;13(7):R61. PMID: 22784381

Jul. 2012;Genome Biology


Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae.

Knott SR, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavaré S, Aparicio OM.
Cell. 2012 Jan 20;148(1-2):99-111. doi: 10.1016/j.cell.2011.12.012.
PMID: 22265405

Jan. 2012; Cell


2011

Regions of Focal DNA Hypermethylation and Long-Range Hypomethylation in Colorectal Cancer Coincide with Nuclear Lamina-Associated Domains

Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CPE, van Dijk CM, Tollenaar RAEM, Van Den Berg D, Laird PW

Nat. Genetics. 2011 v.44(1):40-6. PMCID: PMC4309644

2011;Nat.Genetics


2010

2010; Nat Genet

Common variants at 19p13 are associated with susceptibility to ovarian cancer

Bolton KL, Tyrer J [...] Gayther SA

Nat Genet 2010; 42:880-884. 20852633


 A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24

Goode EL, Chenevix-Trench G [...] Gayther SA*, Pharoah PD*

Nat Genet 2010; 42:874-879. 20852632

2010; Nat Genet


A three-dimensional microenvironment alters protein expression & chemosensitivity of epithelial ovarian cancer cells in vitro 

Lee J, Mhawech-Fauceglia P, Lee N, Parsanian JC, Lin YG, Gayther SA*, Lawrenson K*

2013 Lab Invest. 2013 93:528-42 23459371

2010; Lab Invest


Sellers TA* GWAS meta-analysis and replication identifies three novel common susceptibility loci for ovarian cancer

Pharoah PD, Tsai YY [...] Gayther SA*, Schildkraut JM*

Nat Genet. 2013 45:362-70. 23535730

2010; Nat Genet


2009

2009;IEEE Conference on E-Science

Scientific workflow applications on Amazon EC2

Juve G, Deelman E, Vahi K, Mehta G, Berriman B, Berman BP, Maechling P

IEEE Conference on E-Science. 2009 Dec. 9-11, pp. 59-66. arXiv ID:1005.2718 DOI:10.1109/ESCIW.2009.5408002


Functional complementation studies identify candidate Genes and Common Genetic Variants Associated with Ovarian Cancer Survival

Quaye L, Dafou D, Ramus SJ, Song, H, Gentry-Maharaj A, Notaridou M, Högdall E, Kruger Kjaer S, Christensen L, Högdall C, Easton DF, Jacobs IJ, Menon U, Pharoah PDP, Gayther SA

Hum Mol Genet 2009; 18:1869–1878. 19270026

2009; Hum Mol Genet


A genome-wide association study identifies a novel ovarian cancer susceptibility locus on 9p22.2

Song H, Ramus SJ [...] Gayther SA

Nat Genet 2009; 41:996-1000. 19648919

2009; Nat Genet


Affinity density: a novel genomic approach to the identification of transcription factor regulatory targets

Hazelett DJ, Lakeland DL, Weiss JB

Bioinformatics 2009 vol. 25 (13) pp. 1617-24. PMID: 19401399

2009; Bioinformatics


2008

2008;PLoS ONE

Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity

Jia L*, Berman BP*, Jariwala U, Yan X, Cogan JP, Walters A, Chen T, Buchanan G, Frenkel B, Coetzee GA 

PLoS ONE 2008 vol. 3 (11) pp. e3645.PMID: 18997859


Effects of common germline genetic variation in cell cycle genes on ovarian cancer survival

Song H, Högdall E, Ramus SJ, Dicioccio RA, Högdall C, Quaye L, McGuire V, Whittemore AS, Shah M, Greenberg D, Easton DF, Kjaer SK, Pharoah PD, Gayther SA

 Clin Cancer Res 2008; 14:1090-1095 18281541

2008; Clin Cancer Res