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Items: 1 to 50 of 55

1.

Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma.

Chen L, Huang M, Plummer J, Pan J, Jiang YY, Yang Q, Silva TC, Gull N, Chen S, Ding LW, An O, Yang H, Cheng Y, Said JW, Doan N, Dinjens WN, Waters KM, Tuli R, Gayther SA, Klempner SJ, Berman BP, Meltzer SJ, Lin DC, Koeffler HP.

Gut. 2019 Aug 13. pii: gutjnl-2019-318325. doi: 10.1136/gutjnl-2019-318325. [Epub ahead of print]

PMID:
31409603
2.

Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data.

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, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z; Genomic Data Analysis Network, Liang H, Noble MS.

Cell Syst. 2019 Jul 24;9(1):24-34.e10. doi: 10.1016/j.cels.2019.06.006.

3.

Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library.

Fert-Bober J, Venkatraman V, Hunter CL, Liu R, Crowgey EL, Pandey R, Holewinski RJ, Stotland A, Berman BP, Van Eyk JE.

J Proteome Res. 2019 May 3;18(5):2270-2278. doi: 10.1021/acs.jproteome.9b00118. Epub 2019 Apr 23.

PMID:
30990720
4.

Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.

Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, Spitsyna VN, Guo Y, Berman BP, Evgrafov OV, Knowles JA, Farnham PJ.

Sci Adv. 2018 Dec 13;4(12):eaav8550. doi: 10.1126/sciadv.aav8550. eCollection 2018 Dec.

5.

Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1.

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, Li J, Berman BP, Yin D, Lin DC, Koeffler HP.

Nucleic Acids Res. 2019 Feb 20;47(3):1255-1267. doi: 10.1093/nar/gky1207.

6.

ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.

Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin DC, Berman BP.

Bioinformatics. 2019 Jun 1;35(11):1974-1977. doi: 10.1093/bioinformatics/bty902.

7.

The chromatin accessibility landscape of primary human cancers.

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, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network, Greenleaf WJ, Chang HY.

Science. 2018 Oct 26;362(6413). pii: eaav1898. doi: 10.1126/science.aav1898.

8.

Discrimination of Pulmonary Nodule Volume Change for Low- and High-contrast Tasks in a Phantom CT Study with Low-dose Protocols.

Gavrielides MA, Li Q, Zeng R, Berman BP, Sahiner B, Gong Q, Myers KJ, DeFilippo G, Petrick N.

Acad Radiol. 2019 Jul;26(7):937-948. doi: 10.1016/j.acra.2018.09.006. Epub 2018 Oct 3.

PMID:
30292564
9.

Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression.

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, Liao LD, Soukiasian HJ, Berman BP, Hao JJ, Xu LY, Li EM, Wang MR, Bi XG, Lin DC, Koeffler HP.

Nat Commun. 2018 Sep 6;9(1):3619. doi: 10.1038/s41467-018-06081-9.

10.

Coronary artery calcium quantification using contrast-enhanced dual-energy computed tomography scans in comparison with unenhanced single-energy scans.

Li Q, Berman BP, Hagio T, Gavrielides MA, Zeng R, Sahiner B, Gong Q, Fang Y, Liu S, Petrick N.

Phys Med Biol. 2018 Aug 30;63(17):175006. doi: 10.1088/1361-6560/aad9be.

11.

Targetable BET proteins- and E2F1-dependent transcriptional program maintains the malignancy of glioblastoma.

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, Dinh HQ, Kappei D, Winter GE, Ding LW, Ang BT, Berman BP, Bradner JE, Tang C, Koeffler HP.

Proc Natl Acad Sci U S A. 2018 May 29;115(22):E5086-E5095. doi: 10.1073/pnas.1712363115. Epub 2018 May 15.

12.

Author Correction: Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A.

Shahid M, Gull N, Yeon A, Cho E, Bae J, Yoon HS, You S, Yoon H, Kim M, Berman BP, Kim J.

Sci Rep. 2018 Apr 16;8(1):6294. doi: 10.1038/s41598-018-24827-9.

13.

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

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

Nat Genet. 2018 Apr;50(4):591-602. doi: 10.1038/s41588-018-0073-4. Epub 2018 Apr 2.

14.

Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A.

Shahid M, Gull N, Yeon A, Cho E, Bae J, Yoon HS, You S, Yoon H, Kim M, Berman BP, Kim J.

Sci Rep. 2018 Mar 14;8(1):4505. doi: 10.1038/s41598-018-22771-2. Erratum in: Sci Rep. 2018 Apr 16;8(1):6294.

15.

Quantitative assessment of nonsolid pulmonary nodule volume with computed tomography in a phantom study.

Gavrielides MA, Berman BP, Supanich M, Schultz K, Li Q, Petrick N, Zeng R, Siegelman J.

Quant Imaging Med Surg. 2017 Dec;7(6):623-635. doi: 10.21037/qims.2017.12.07.

16.

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

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

Immunity. 2017 Nov 21;47(5):890-902.e4. doi: 10.1016/j.immuni.2017.10.021.

17.

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

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, Phillip Koeffler H.

Gut. 2018 Oct;67(10):1769-1779. doi: 10.1136/gutjnl-2017-314607. Epub 2017 Aug 31.

18.

Exosomal MicroRNA Transfer Into Macrophages Mediates Cellular Postconditioning.

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

Circulation. 2017 Jul 11;136(2):200-214. doi: 10.1161/CIRCULATIONAHA.116.024590. Epub 2017 Apr 14.

19.

Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma.

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

Cancer Res. 2017 May 1;77(9):2255-2265. doi: 10.1158/0008-5472.CAN-16-2822. Epub 2017 Feb 20.

20.

Spatial intratumoral heterogeneity 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 Genet. 2016 Dec;48(12):1500-1507. doi: 10.1038/ng.3683. Epub 2016 Oct 17.

21.

The PsychENCODE project.

PsychENCODE Consortium, 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, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N.

Nat Neurosci. 2015 Dec;18(12):1707-12. doi: 10.1038/nn.4156. Review. No abstract available.

22.

FOXC1 Activates Smoothened-Independent Hedgehog Signaling in Basal-like Breast Cancer.

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, Johnson J, Gao B, Hao J, Liu Z, Buttyan R, Ray PS, Hung MC, Giuliano AE, Cui X.

Cell Rep. 2015 Nov 3;13(5):1046-58. doi: 10.1016/j.celrep.2015.09.063.

23.

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.

Yao L, Berman BP, Farnham PJ.

Crit Rev Biochem Mol Biol. 2015;50(6):550-73. doi: 10.3109/10409238.2015.1087961. Epub 2015 Oct 8. Review.

24.

Volumetric MRI of the lungs during forced expiration.

Berman BP, Pandey A, Li Z, Jeffries L, Trouard TP, Oliva I, Cortopassi F, Martin DR, Altbach MI, Bilgin A.

Magn Reson Med. 2016 Jun;75(6):2295-302. doi: 10.1002/mrm.25798. Epub 2015 Jul 3.

PMID:
26140699
25.

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.

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

Genome Biol. 2015 May 21;16:105. doi: 10.1186/s13059-015-0668-3.

26.

Gender-specific postnatal demethylation and establishment of epigenetic memory.

Reizel Y, Spiro A, Sabag O, Skversky Y, Hecht M, Keshet I, Berman BP, Cedar H.

Genes Dev. 2015 May 1;29(9):923-33. doi: 10.1101/gad.259309.115.

27.

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 Res. 2015 Apr;25(4):467-77. doi: 10.1101/gr.183368.114. Epub 2015 Mar 6.

28.

Functional annotation of colon cancer risk SNPs.

Yao L, Tak YG, Berman BP, Farnham PJ.

Nat Commun. 2014 Sep 30;5:5114. doi: 10.1038/ncomms6114.

29.

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes.

Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, Farnham PJ.

Genome Biol. 2014 Sep 20;15(9):469. doi: 10.1186/s13059-014-0469-0.

30.

Multiscale representation of genomic signals.

Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.

Nat Methods. 2014 Jun;11(6):689-94. doi: 10.1038/nmeth.2924. Epub 2014 Apr 13.

31.

Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue.

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, Hutchinson A, Chen PH, Chung BS, Pesatori AC, Consonni D, Bertazzi PA, Bergen AW, Freedman M, Siegmund KD, Berman BP, Borok Z, Chatterjee N, Tucker MA, Caporaso NE, Chanock SJ, Laird-Offringa IA, Landi MT.

Nat Commun. 2014 Feb 27;5:3365. doi: 10.1038/ncomms4365.

32.

Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1.

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, Barry EL, Berman BP, Rice JC, Coetzee GA, Casey G.

Hum Mol Genet. 2014 Apr 15;23(8):2198-209. doi: 10.1093/hmg/ddt584. Epub 2013 Nov 20.

33.

Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation.

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.

PLoS Genet. 2013 Jun;9(6):e1003513. doi: 10.1371/journal.pgen.1003513. Epub 2013 Jun 20.

34.

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 Res. 2012 Dec;22(12):2497-506. doi: 10.1101/gr.143008.112. Epub 2012 Sep 7.

35.

Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data.

Liu Y, Siegmund KD, Laird PW, Berman BP.

Genome Biol. 2012 Jul 11;13(7):R61. doi: 10.1186/gb-2012-13-7-r61.

36.

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs.

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

Nucleic Acids Res. 2012 Oct;40(18):e139. doi: 10.1093/nar/gks542. Epub 2012 Jun 8.

37.

Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion.

Little GH, Noushmehr H, Baniwal SK, Berman BP, Coetzee GA, Frenkel B.

Nucleic Acids Res. 2012 Apr;40(8):3538-47. doi: 10.1093/nar/gkr1219. Epub 2011 Dec 19.

38.

Opposing effects of Runx2 and estradiol on breast cancer cell proliferation: in vitro identification of reciprocally regulated gene signature related to clinical letrozole responsiveness.

Chimge NO, Baniwal SK, Luo J, Coetzee S, Khalid O, Berman BP, Tripathy D, Ellis MJ, Frenkel B.

Clin Cancer Res. 2012 Feb 1;18(3):901-11. doi: 10.1158/1078-0432.CCR-11-1530. Epub 2011 Dec 6.

39.

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 CP, van Dijk CM, Tollenaar RA, Van Den Berg D, Laird PW.

Nat Genet. 2011 Nov 27;44(1):40-6. doi: 10.1038/ng.969.

40.

Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells.

Andreu-Vieyra C, Lai J, Berman BP, Frenkel B, Jia L, Jones PA, Coetzee GA.

Mol Cell Biol. 2011 Dec;31(23):4648-62. doi: 10.1128/MCB.05934-11. Epub 2011 Oct 3.

41.

H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes.

Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, Jones PA.

Mol Cell. 2010 Sep 24;39(6):901-11. doi: 10.1016/j.molcel.2010.08.026.

42.

Vitamin C promotes widespread yet specific DNA demethylation of the epigenome in human embryonic stem cells.

Chung TL, Brena RM, Kolle G, Grimmond SM, Berman BP, Laird PW, Pera MF, Wolvetang EJ.

Stem Cells. 2010 Oct;28(10):1848-55. doi: 10.1002/stem.493.

43.

Androgen receptor responsive enhancers are flanked by consistently-positioned H3-acetylated nucleosomes.

Berman BP, Frenkel B, Coetzee GA, Jia L.

Cell Cycle. 2010 Jun 1;9(11):2249-50. Epub 2010 Jun 1. No abstract available.

44.

Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma.

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, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P, Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW, Aldape K; Cancer Genome Atlas Research Network.

Cancer Cell. 2010 May 18;17(5):510-22. doi: 10.1016/j.ccr.2010.03.017. Epub 2010 Apr 15.

45.

Functional enhancers at the gene-poor 8q24 cancer-linked locus.

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.

PLoS Genet. 2009 Aug;5(8):e1000597. doi: 10.1371/journal.pgen.1000597. Epub 2009 Aug 14.

46.

Locking in on the human methylome.

Berman BP, Weisenberger DJ, Laird PW.

Nat Biotechnol. 2009 Apr;27(4):341-2. doi: 10.1038/nbt0409-341. No abstract available.

PMID:
19352369
47.

Location, location, (ChIP-)location! Mapping chromatin landscapes one immunoprecipitation at a time.

Berman BP, Frenkel B, Coetzee GA.

J Cell Biochem. 2009 May 1;107(1):1-5. doi: 10.1002/jcb.22133.

48.

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;3(11):e3645. doi: 10.1371/journal.pone.0003645. Epub 2008 Nov 10.

49.

Global analysis of patterns of gene expression during Drosophila embryogenesis.

Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker SE, Rubin GM.

Genome Biol. 2007;8(7):R145.

50.

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