Mission
The Integrative Bioinformatics (IB) Core provides PREMIER researchers with access to a full range of services to facilitate successful study design, data analysis and integration for basic, translational, and clinical research studies in rheumatic disease. The IB Core uses a data-driven approach to advance precision medicine in rheumatology by offering services in study design, molecular-omics data analysis, leveraging publicly available datasets, integrating molecular and clinical data and facilitating data dissemination.
Specifically, the IB Core will:
- 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.
- 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.
- 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.
- 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.
Publications and Preprints:
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):e176963. doi: 10.1172/jci.insight.176963. PMID:
38743491; PMCID: PMC11383589.
2. 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. PMID: 39999839; PMCID: PMC11970322.
3. Narendra R, Phan HV, Patterson SL, Almonte Loya AL, Lanata C, Love C, Park J, Lydon EC, Shimoda MA, Barcellos L, Mekonen H, Detweiler A, Deosthale P, Neff
N, Criswell LA, Maliskova L, Eckalbar W, Fragiadakis G, Yazdany J, Dall'Era M, Katz P, Ye CJ, Sirota M, Langelier CR. Epigenetic attenuation of interferon signaling drives aging-related improvements in systemic lupus. medRxiv [Preprint]. 2025 Jan 28:2025.01.27.25321143. doi: 10.1101/2025.01.27.25321143. PMID: 39974140; PMCID: PMC11838985.
4. 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.
5. Tang AS, Woldemariam SR, Miramontes S, Norgeot B, Oskotsky TT, Sirota M. Harnessing EHR data for health research. Nat Med. 2024 Jul;30(7):1847-1855. doi: 10.1038/s41591-024-03074-8. Epub 2024 Jul 4. PMID: 38965433.
6. 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. PMID: 39531917; PMCID: PMC11603005.
7. Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M,
Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG.
Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. Nat Commun. 2024 Feb 19;15(1):1493. doi: 10.1038/s41467-024-45665-6. PMID: 38374043; PMCID: PMC10876948.
8. 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 May 11;1:e25. doi: 10.1017/pcm.2023.14. PMID: 38550937; PMCID: PMC10953750.
9. Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye C, Dall'Era M, Yazdany J, Criswell L, 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.PMID: 39143499 PMCID: PMC11557995.
10. 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 Jan 25;15:1326922. doi: 10.3389/fimmu.2024.1326922. PMID: 38348044; PMCID: PMC10859856.
11. Mennillo E, Lotstein ML, Lee G, Johri V, Ekstrand C, Tsui J, Hou J, Leet DE, He JY, Mahadevan U, Eckalbar W, Oh DY, Fragiadakis GK, Kattah MG, Combes AJ.
Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks. bioRxiv [Preprint]. 2024 Nov 11:2024.11.11.623014. doi: 10.1101/2024.11.11.623014. PMID: 39605355; PMCID: PMC11601222.
12. Babdor J, Patel RK, Davidson B, Noecker C, Rahim M, Bisanz JE, Tenvooren I, Marquez D, Calvo M, Johri V, McCarthy E, Shaheed A, Ekstrand C, Weakley AM, Yu
FB, Fiehn O, Turnbaugh PJ, Combes AJ, Fragiadakis GK, Spitzer MH. Coordinated variation in the immune systems and microbiomes of healthy humans is linked to
tonic interferon states. bioRxiv [Preprint]. 2024 Dec 3:2024.11.27.625750. doi: 10.1101/2024.11.27.625750. PMID: 39677657; PMCID: PMC11642739.
13. 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. PMID: 37159875; PMCID: PMC11146013.
14. Patel RK, Jaszczak RG, Kwok I, Carey ND, Courau T, Bunis D, Samad B, Avanesyan L, Chew NW, Stenske S, Jespersen JM, Publicover J, Edwards A, Naser M, Rao AA, Lupin-Jimenez L, Krummel MF, Cooper S, Baron J, Combes AJ, Fragiadakis GK. Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data. Front Immunol. 2023 Sep 4;14:1167241. doi: 10.3389/fimmu.2023.1167241. PMID: 37731497; PMCID: PMC10507399.
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