Past Projects - Joint Bioinformatics and Computational Core

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Example of a Principle Component Analysis of T cell DNA methylation comparing peripheral blood and synovial T cells in rheumatoid arthritis and osteoarthritis

All publications, grants, and presentations resulting from research funded by the MARC or using MARC resources must cite the P30 grant as a contributing source of support and indicate the NIH grant title and number: Resource-based Center for the study of the joint microenvironment in rheumatology; University of California San Diego, NIH Grant P30AR073761.

Selected Publications related to Joint Bioinformatics and Computation

Ai R, Laragione T, Hammaker D, Boyle DL, Wildberg A, Maeshima K, Palescandolo E, Krishna V, Pocalyko D, Whitaker JW, Bai Y, Nagpal S, Bachman KE, Ainsworth RI, Wang M, Ding B, Gulko PS, Wang W, Firestein GS. Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes. Nat Commun. 2018 May 15;9(1):1921. doi: 10.1038/s41467-018-04310-9. PMID: 29765031; PMCID: PMC5953939.

Zhang K, Wang M, Zhao Y, Wang W. Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development. Sci Adv. 2019 Mar 27;5(3):eaav3262. doi: 10.1126/sciadv.aav3262. PMID: 30944857; PMCID: PMC6436936.

Ai R, Boyle DL, Wang W, Firestein GS. Distinct DNA Methylation Patterns of Rheumatoid Arthritis Peripheral Blood and Synovial Tissue T Cells.ACR Open Rheumatol. 2021 Mar;3(3):127-132. doi: 10.1002/acr2.11231. Epub 2021 Feb 5. PMID: 33544432; PMCID: PMC7966880.

Whitaker JW, Shoemaker R, Boyle DL, Hillman J, Anderson D, Wang W, Firestein GS. An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype. Genome Med. 2013 Apr 30;5(4):40. doi: 10.1186/gm444. PMID: 23631487; PMCID: PMC3706831.

Whitaker JW, Boyle DL, Bartok B, Ball ST, Gay S, Wang W, Firestein GS. Integrative omics analysis of rheumatoid arthritis identifies non-obvious therapeutic targets. PLoS One. 2015 Apr 22;10(4):e0124254. doi: 10.1371/journal.pone.0124254. Erratum in: PLoS One. 2015;10(8):e0136334. PMID: 25901943; PMCID: PMC4406750.

Ai R, Whitaker JW, Boyle DL, Tak PP, Gerlag DM, Wang W, Firestein GS. DNA Methylome Signature in Synoviocytes From Patients With Early Rheumatoid Arthritis Compared to Synoviocytes From Patients With Longstanding Rheumatoid Arthritis. Arthritis Rheumatol. 2015 Jul;67(7):1978-80. doi: 10.1002/art.39123. PMID: 25808728; PMCID: PMC4485541.

Wang Z, Zhao Y, Phipps-Green A, Liu-Bryan R, Ceponis A, Boyle DL, Wang J, Merriman TR, Wang W, Terkeltaub R. Differential DNA Methylation of Networked Signalling, Transcriptional, Innate and Adaptive Immunity, and Osteoclastogenesis Genes and Pathways in Gout. Arthritis Rheumatol. 2020 May;72(5):802-814. doi: 10.1002/art.41173. Epub 2020 Mar 23. PMID: 31738005; PMCID: PMC7323903.

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