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Items: 1 to 20 of 57

1.

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
2.

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.

3.

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.

4.

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.

5.

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.

6.

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
7.

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.

8.

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.

PMID:
30101756
9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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