Integrative Bioinformatics Core

Mission

The Integrative Bioinformatics core provides analytical consulting on study design and develops novel tools for all stages of data management, including analysis, visualization, and integration. The use of centralized data management and existing UCSF partnerships facilitates precision medicine by providing an economy of scale in computational analysis.  

IB Core Figure

 

Specifically, the IB Core will:

  1. Provide analytical consulting services in study design, data analysis and data integration with public datasets in order to advance precision medicine in rheumatic disease research.
  2. Develop novel tools, software and analytical pipelines for the integration, annotation, analysis, retrieval, and presentation of data from clinical and molecular studies of rheumatic diseases.  As a result of this aim, we have established and maintain a technologically up-to-date toolset that can be readily used for systems-level analyses of the data.
  3. Integrate molecular and clinical data and leverage collaborations between the GT and CDI Cores and facilitate integrative computational analysis for a wide range of clinical, translational and basic research studies to enable precision medicine in rheumatology.
  4. Provide centralized data management and storage including assistance in dissemination of data for P30 associated projects including use of the UCSF Data Library developed by the Data Science CoLab.

Recent Publications:

  1. Tang AS, Wei ML, Haemel A, La C, Sirota M, Lee EY. Artificial intelligence-enabled precision medicine for inflammatory skin diseases. J Invest Dermatol. 2026 May;146(5):1195-1209.e4. doi: 10.1016/j.jid.2025.10.596. Epub 2026 Feb 14. Review. PubMed PMID: 41689579; PubMed Central PMCID: PMC13005173.

  1. Neely J, Sabbagh SE, Dvergsten J, Madubata C, Berthier CC, Zheng Z, Goudsmit C, Matossian S, Ferris SP, Fragiadakis GK, Sirota M, Kahlenberg JM, Kim H, Turnier JL, CARRA Registry Investigators and CARRA Translational Medicine for Juvenile Myositis Working Group. Discovery of tissue-specific proteomic signatures in juvenile dermatomyositis highlights pathways reflecting persistent disease activity, clinical heterogeneity, and myositis-specific autoantibody subtype. Ann Rheum Dis. 2025 Nov;84(11):1836-1851. doi: 10.1016/j.ard.2025.07.020. Epub 2025 Sep 6. PubMed PMID: 40915939; PubMed Central PMCID: PMC12925510.

  1. Narendra R, Van Phan H, Patterson SL, Almonte-Loya A, Lydon EC, Lanata C, Love C, Park J, Shimoda M, Barcellos L, Mekonen H, Detweiler A, Deosthale P, Neff N, Criswell LA, Maliskova L, Eckalbar W, Fragiadakis GK, Yazdany J, Dall'Era M, Katz P, Ye CJ, Sirota M, Langelier CR. Epigenetic attenuation of interferon signaling is associated with aging-related improvements in systemic lupus erythematosus. Sci Transl Med. 2025 Jun 25;17(804):eadt5550. doi: 10.1126/scitranslmed.adt5550. Epub 2025 Jun 25. PubMed PMID: 40561001; PubMed Central PMCID: PMC13012812.

  1. Ramey GD, Tang A, Phongpreecha T, Yang MM, Woldemariam SR, Oskotsky TT, Montine TJ, Allen I, Miller ZA, Aghaeepour N, Capra JA, Sirota M. Exposure to autoimmune disorders is associated with increased Alzheimer's disease risk in a multi-site electronic health record analysis. Cell Rep Med. 2025 Mar 18;6(3):101980. doi: 10.1016/j.xcrm.2025.101980. Epub 2025 Feb 24. PubMed PMID: 39999839; PubMed Central PMCID: PMC11970322.

  1. Patterson SL, Van Phan H, Ye CJ, Lanata C, González SC, Park J, Criswell LA, Barbour KE, Yazdany J, Dall'Era M, Sirota M, Katz P, Langelier CR. Physical inactivity exacerbates pathologic inflammatory signalling at the single cell level in patients with systemic lupus. EBioMedicine. 2024 Dec;110:105432. doi: 10.1016/j.ebiom.2024.105432. Epub 2024 Nov 11. PubMed PMID: 39531917; PubMed Central PMCID: PMC11603005.

  1. Jia BB, Sun BK, Lee EY, Ren B. Emerging Techniques in Spatial Multiomics: Fundamental Principles and Applications to Dermatology. J Invest Dermatol. 2025 May;145(5):1017-1032. doi: 10.1016/j.jid.2024.09.006. Epub 2024 Nov 5. Review. PubMed PMID: 39503694; PubMed Central PMCID: PMC13003203.

  1. Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye CJ, Dall'Era M, Yazdany J, Criswell LA, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes. ACR Open Rheumatol. 2024 Nov;6(11):769-779. doi: 10.1002/acr2.11713. Epub 2024 Aug 14. PubMed PMID: 39143499; PubMed Central PMCID: PMC11557995.

  1. Binvignat M, Miao BY, Wibrand C, Yang MM, Rychkov D, Flynn E, Nititham J, Tamaki W, Khan U, Carvidi A, Krueger M, Niemi E, Sun Y, Fragiadakis GK, Sellam J, Mariotti-Ferrandiz E, Klatzmann D, Gross AJ, Ye CJ, Butte AJ, Criswell LA, Nakamura MC, Sirota M. Single-cell RNA-Seq analysis reveals cell subsets and gene signatures associated with rheumatoid arthritis disease activity. JCI Insight. 2024 Jul 2;9(16). doi: 10.1172/jci.insight.178499. PubMed PMID: 38954480; PubMed Central PMCID: PMC11343607.

  1. Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Madubata C, Fragiadakis GK, Ye CJ, Kim S, Gartner ZJ, Sirota M, Neely J. Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics. JCI Insight. 2024 May 14;9(12). doi: 10.1172/jci.insight.176963. PubMed PMID: 38743491; PubMed Central PMCID: PMC11383589.

  1. Yang MM, Lee S, Neely J, Hinchcliff M, Wolters PJ, Sirota M. Gene expression meta-analysis reveals aging and cellular senescence signatures in scleroderma-associated interstitial lung disease. Front Immunol. 2024;15:1326922. doi: 10.3389/fimmu.2024.1326922. eCollection 2024. PubMed PMID: 38348044; PubMed Central PMCID: PMC10859856. 

  1. Hédou J, Marić I, Bellan G, Einhaus J, Gaudillière DK, Ladant FX, Verdonk F, Stelzer IA, Feyaerts D, Tsai AS, Ganio EA, Sabayev M, Gillard J, Amar J, Cambriel A, Oskotsky TT, Roldan A, Golob JL, Sirota M, Bonham TA, Sato M, Diop M, Durand X, Angst MS, Stevenson DK, Aghaeepour N, Montanari A, Gaudillière B. Discovery of sparse, reliable omic biomarkers with Stabl. Nat Biotechnol. 2024 Oct;42(10):1581-1593. doi: 10.1038/s41587-023-02033-x. Epub 2024 Jan 2. PubMed PMID: 38168992; PubMed Central PMCID: PMC11217152.

  1. Patel RK, Jaszczak RG, Im K, Carey ND, Courau T, Bunis DG, Samad B, Avanesyan L, Chew NW, Stenske S, Jespersen JM, Publicover J, Edwards AW, Naser M, Rao AA, Lupin-Jimenez L, Krummel MF, Cooper S, Baron JL, Combes AJ, Fragiadakis GK. Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data. Front Immunol. 2023;14:1167241. doi: 10.3389/fimmu.2023.1167241. eCollection 2023. PubMed PMID: 37731497; PubMed Central PMCID: PMC10507399. 

  1. Baglaenko Y, Wagner C, Bhoj VG, Brodin P, Gershwin ME, Graham D, Invernizzi P, Kidd KK, Korsunsky I, Levy M, Mammen AL, Nizet V, Ramirez-Valle F, Stites EC, Williams MS, Wilson M, Rose NR, Ladd V, Sirota M. Making inroads to precision medicine for the treatment of autoimmune diseases: Harnessing genomic studies to better diagnose and treat complex disorders. Camb Prism Precis Med. 2023;1:e25. doi: 10.1017/pcm.2023.14. eCollection 2023. Review. PubMed PMID: 38550937; PubMed Central PMCID: PMC10953750. 

  1. Adams C, Nair N, Plant D, Verstappen SMM, Quach HL, Quach DL, Carvidi A, Nititham J, Nakamura M, Graf J, Barton A, Criswell LA, Barcellos LF. Identification of Cell-Specific Differential DNA Methylation Associated With Methotrexate Treatment Response in Rheumatoid Arthritis. Arthritis Rheumatol. 2023 Jul;75(7):1088-1097. doi: 10.1002/art.42464. Epub 2023 May 9. PubMed PMID: 36716083; PubMed Central PMCID: PMC10313739. 

  1. Flynn E, Almonte-Loya A, Fragiadakis GK. Single-Cell Multiomics. Annu Rev Biomed Data Sci. 2023 Aug 10;6:313-337. doi: 10.1146/annurev-biodatasci-020422-050645. Epub 2023 May 9. Review. PubMed PMID: 37159875; PubMed Central PMCID: PMC11146013.

  1. Tang A, Woldemariam S, Roger J, Sirota M. Translational Bioinformatics to Enable Precision Medicine for All: Elevating Equity across Molecular, Clinical, and Digital Realms. Yearb Med Inform. 2022 Aug;31(1):106-115. doi: 10.1055/s-0042-1742513. Epub 2022 Dec 4. Review. PubMed PMID: 36463867; PubMed Central PMCID: PMC9719766. 

  1. Neely J, Sabbagh SE, Dvergsten J, Madubata C, Berthier CC, Zheng Z, Goudsmit C, Matossian S, Ferris SP, Fragiadakis GK, Sirota M, Kahlenberg JM, Kim H, Turnier JL, CARRA Registry Investigators and CARRA Translational Medicine for Juvenile Myositis Working Group. Discovery of tissue-specific proteomic signatures in juvenile dermatomyositis highlights pathways reflecting persistent disease activity, clinical heterogeneity, and myositis-specific autoantibody subtype. Ann Rheum Dis. 2025 Nov;84(11):1836-1851. doi: 10.1016/j.ard.2025.07.020. Epub 2025 Sep 6. PubMed PMID: 40915939; PubMed Central PMCID: PMC12925510. 

  1. Perez RK, Gordon MG, Subramaniam M, Kim MC, Hartoularos GC, Targ S, Sun Y, Ogorodnikov A, Bueno R, Lu A, Thompson M, Rappoport N, Dahl A, Lanata CM, Matloubian M, Maliskova L, Kwek SS, Li T, Slyper M, Waldman J, Dionne D, Rozenblatt-Rosen O, Fong L, Dall'Era M, Balliu B, Regev A, Yazdany J, Criswell LA, Zaitlen N, Ye CJ. Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus. Science. 2022 Apr 8;376(6589):eabf1970. doi: 10.1126/science.abf1970. Epub 2022 Apr 8. PubMed PMID: 35389781; PubMed Central PMCID: PMC9297655.