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Items: 1 to 20 of 28

1.

Epipolymorphisms associated with the clinical outcome of autoimmune arthritis affect CD4+ T cell activation pathways.

Spreafico R, Rossetti M, Whitaker JW, Wang W, Lovell DJ, Albani S.

Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13845-13850. Epub 2016 Nov 14.

2.

LBH Gene Transcription Regulation by the Interplay of an Enhancer Risk Allele and DNA Methylation in Rheumatoid Arthritis.

Hammaker D, Whitaker JW, Maeshima K, Boyle DL, Ekwall AH, Wang W, Firestein GS.

Arthritis Rheumatol. 2016 Nov;68(11):2637-2645. doi: 10.1002/art.39746.

PMID:
27159840
3.

The Transcriptional Response to DNA-Double-Strand Breaks in Physcomitrella patens.

Kamisugi Y, Whitaker JW, Cuming AC.

PLoS One. 2016 Aug 18;11(8):e0161204. doi: 10.1371/journal.pone.0161204. eCollection 2016.

4.

Effects of Enrichment and Litter Parity on Reproductive Performance and Behavior in BALB/c and 129/Sv Mice.

Whitaker JW, Moy SS, Pritchett-Corning KR, Fletcher CA.

J Am Assoc Lab Anim Sci. 2016;55(4):387-99.

5.

Abnormal PTPN11 enhancer methylation promotes rheumatoid arthritis fibroblast-like synoviocyte aggressiveness and joint inflammation.

Maeshima K, Stanford SM, Hammaker D, Sacchetti C, Zeng LF, Ai R, Zhang V, Boyle DL, Aleman Muench GR, Feng GS, Whitaker JW, Zhang ZY, Wang W, Bottini N, Firestein GS.

JCI Insight. 2016 May 19;1(7). pii: e86580.

6.

Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations.

Walsh AM, Whitaker JW, Huang CC, Cherkas Y, Lamberth SL, Brodmerkel C, Curran ME, Dobrin R.

Genome Biol. 2016 Apr 30;17:79. doi: 10.1186/s13059-016-0948-6.

7.

Constructing 3D interaction maps from 1D epigenomes.

Zhu Y, Chen Z, Zhang K, Wang M, Medovoy D, Whitaker JW, Ding B, Li N, Zheng L, Wang W.

Nat Commun. 2016 Mar 10;7:10812. doi: 10.1038/ncomms10812.

8.

Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation.

Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, Ren B, Sejnowski TJ, Wang W, Ecker JR.

Nature. 2016 Feb 11;530(7589):242. doi: 10.1038/nature16179. Epub 2015 Nov 25. No abstract available.

PMID:
26605523
9.

Correction: Integrative Omics Analysis of Rheumatoid Arthritis Identifies Non-Obvious Therapeutic Targets.

Whitaker JW, Boyle DL, Bartok B, Ball ST, Gay S, Wang W, Firestein GS.

PLoS One. 2015 Aug 19;10(8):e0136334. doi: 10.1371/journal.pone.0136334. eCollection 2015. No abstract available.

10.

Human body epigenome maps reveal noncanonical DNA methylation variation.

Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, Ren B, Sejnowski TJ, Wang W, Ecker JR.

Nature. 2015 Jul 9;523(7559):212-6. doi: 10.1038/nature14465. Epub 2015 Jun 1. Erratum in: Nature. 2016 Feb 11;530(7589):242.

11.

Integrative omics analysis of rheumatoid arthritis identifies non-obvious therapeutic targets.

Whitaker JW, Boyle DL, Bartok B, Ball ST, Gay S, Wang W, Firestein GS.

PLoS One. 2015 Apr 22;10(4):e0124254. doi: 10.1371/journal.pone.0124254. eCollection 2015. Erratum in: PLoS One. 2015;10(8):e0136334.

12.

DNA Methylome Signature in Synoviocytes From Patients With Early Rheumatoid Arthritis Compared to Synoviocytes From Patients With Longstanding Rheumatoid Arthritis.

Ai R, Whitaker JW, Boyle DL, Tak PP, Gerlag DM, Wang W, Firestein GS.

Arthritis Rheumatol. 2015 Jul;67(7):1978-80. doi: 10.1002/art.39123. No abstract available.

13.

The Rheumatoid Arthritis Risk Gene LBH Regulates Growth in Fibroblast-like Synoviocytes.

Ekwall AK, Whitaker JW, Hammaker D, Bugbee WD, Wang W, Firestein GS.

Arthritis Rheumatol. 2015 May;67(5):1193-202. doi: 10.1002/art.39060.

14.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium., Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

15.

Computational schemes for the prediction and annotation of enhancers from epigenomic assays.

Whitaker JW, Nguyen TT, Zhu Y, Wildberg A, Wang W.

Methods. 2015 Jan 15;72:86-94. doi: 10.1016/j.ymeth.2014.10.008. Epub 2014 Oct 15. Review.

16.

Predicting the human epigenome from DNA motifs.

Whitaker JW, Chen Z, Wang W.

Nat Methods. 2015 Mar;12(3):265-72, 7 p following 272. doi: 10.1038/nmeth.3065. Epub 2014 Sep 21.

17.

STAR: an integrated solution to management and visualization of sequencing data.

Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W.

Bioinformatics. 2013 Dec 15;29(24):3204-10. doi: 10.1093/bioinformatics/btt558. Epub 2013 Sep 27.

18.

Predicting enhancer transcription and activity from chromatin modifications.

Zhu Y, Sun L, Chen Z, Whitaker JW, Wang T, Wang W.

Nucleic Acids Res. 2013 Dec;41(22):10032-43. doi: 10.1093/nar/gkt826. Epub 2013 Sep 12.

19.

Epigenomic analysis of multilineage differentiation of human embryonic stem cells.

Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B.

Cell. 2013 May 23;153(5):1134-48. doi: 10.1016/j.cell.2013.04.022. Epub 2013 May 9.

20.

An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype.

Whitaker JW, Shoemaker R, Boyle DL, Hillman J, Anderson D, Wang W, Firestein GS.

Genome Med. 2013 Apr 30;5(4):40. doi: 10.1186/gm444. eCollection 2013.

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