John W. Whitaker
John W. Whitaker
Bioinformatics Director, San Diego
Verified email at - Homepage
Cited by
Cited by
Integrative analysis of 111 reference human epigenomes
Nature 518 (7539), 317-330, 2015
Expanded encyclopaedias of DNA elements in the human and mouse genomes
JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ...
Nature 583 (7818), 699-710, 2020
Epigenomic analysis of multilineage differentiation of human embryonic stem cells
W Xie, MD Schultz, R Lister, Z Hou, N Rajagopal, P Ray, JW Whitaker, ...
Cell 153 (5), 1134-1148, 2013
Human body epigenome maps reveal noncanonical DNA methylation variation
MD Schultz, Y He, JW Whitaker, M Hariharan, EA Mukamel, D Leung, ...
Nature 523 (7559), 212–216, 2015
DNA methylome signature in rheumatoid arthritis
K Nakano, JW Whitaker, DL Boyle, W Wang, GS Firestein
Annals of the rheumatic diseases 72 (1), 110-117, 2013
Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes
R Ai, T Laragione, D Hammaker, DL Boyle, A Wildberg, K Maeshima, ...
Nature communications 9 (1), 1921, 2018
Predicting enhancer transcription and activity from chromatin modifications
Y Zhu, L Sun, Z Chen, JW Whitaker, T Wang, W Wang
Nucleic acids research 41 (22), 10032-10043, 2013
Constructing 3D interaction maps from 1D epigenomes
Y Zhu, Z Chen, K Zhang, M Wang, D Medovoy, JW Whitaker, B Ding, N Li, ...
Nature communications 7, 10812, 2016
Predicting the human epigenome from DNA motifs
JW Whitaker, Z Chen, W Wang
Nature methods 12, 265–272, 2014
An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype
JW Whitaker, R Shoemaker, DL Boyle, J Hillman, D Anderson, W Wang, ...
Genome Medicine 5 (4), 40, 2013
Perspectives on ENCODE
MP Snyder, TR Gingeras, JE Moore, Z Weng, MB Gerstein, B Ren, ...
Nature 583 (7818), 693-698, 2020
DNA Methylome Signature in Synoviocytes From Patients With Early Rheumatoid Arthritis Compared to Synoviocytes From Patients With Longstanding Rheumatoid Arthritis
R Ai, JW Whitaker, DL Boyle, PP Tak, DM Gerlag, W Wang, GS Firestein
Arthritis & Rheumatology 67 (7), 1978–1980, 2015
Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations
AM Walsh, JW Whitaker, CC Huang, Y Cherkas, SL Lamberth, ...
Genome biology 17, 1-16, 2016
The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes
JW Whitaker, GA McConkey, DR Westhead
Genome biology 10 (4), R36, 2009
The Rheumatoid Arthritis Risk Gene LBH Regulates Growth in Fibroblast‐like Synoviocytes
AKH Ekwall, JW Whitaker, D Hammaker, WD Bugbee, W Wang, ...
Arthritis & rheumatology 67 (5), 1193-1202, 2015
Integrative omics analysis of rheumatoid arthritis identifies non-obvious therapeutic targets
JW Whitaker, DL Boyle, B Bartok, ST Ball, S Gay, W Wang, GS Firestein
PLoS ONE 10 (4), e0124254, 2015
Abnormal PTPN11 enhancer methylation promotes rheumatoid arthritis fibroblast-like synoviocyte aggressiveness and joint inflammation
K Maeshima, SM Stanford, D Hammaker, C Sacchetti, L Zeng, R Ai, ...
JCI insight 1 (7), 2016
Limb Bud and Heart Development Gene Transcription is Regulated by the Interplay of an Enhancer Risk Allele and DNA Methylation in Rheumatoid Arthritis
D Hammaker, JW Whitaker, K Maeshima, DL Boyle, AKH Ekwall, W Wang, ...
Arthritis & Rheumatology 68, 2637–2645, 2016
metaTIGER: a metabolic evolution resource
JW Whitaker, I Letunic, GA McConkey, DR Westhead
Nucleic acids research 37 (suppl 1), D531-D538, 2009
Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse
V Ngo, Z Chen, K Zhang, JW Whitaker, M Wang, W Wang
Proceedings of the National Academy of Sciences 116 (9), 3668-3677, 2019
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