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Fan Zhang

TitleAsst Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
ORCID ORCID Icon0000-0002-6102-2970 Additional info

    Collapse Biography 
    Collapse education and training
    Harvard Medical School, Boston, MAPostdoc12/2021Immunogenomics modeling
    Brigham and Women's Hospital, Boston, MAResearch Scientist12/2021Single-cell data integration
    Worcester Polytechnic Institute, Worcester, MAPhD02/2017Computational Biology
    Broad Institute of MIT and Harvard, Boston, MAAssociate Scientist12/2021Computational Biology

    Collapse Overview 
    Collapse overview
    We are a Computational Omics and Systems Immunology (COSI) lab in the Department of Medicine Division of Rheumatology and the Center for Health AI, University of Colorado Anschutz Campus.

    We develop and use statistical machine learning methods, single-cell multi-omics, and systems immunology to study inflammatory diseases through deep collaborations with immunologists, rheumatologists, and clinicians.

    We are actively recruiting motivated computational biologists who are interested in dynamic and interdisciplinary research for translational medicine. Check our website for more recent research and publications!

    Collapse Research 
    Collapse research activities and funding
    CU Orthopedics-DBMI Dyads Award     (Fan Zhang)Nov 1, 2023 - Oct 31, 2024
    CU Orthopedics-Department of Biomedical Informatics (DBMI) Dyads Award
    Multi-Omics Integration with Machine Learning to Reveal Synovium Phenotypes in Ankle Osteoarthritis
    Role: Co-PI

    NIH NIAID Autoimmunity Centers of Excellence (ACE)     (Kevin Deane)Oct 1, 2023 - Sep 30, 2024
    NIH NIAID Autoimmunity Centers of Excellence (ACE)
    ARA08/StopRA: Collaborative Mechanistic Study
    Role: Co-Investigator

    Translational Research Scholars     (Fan Zhang)Jul 1, 2023 - Jun 30, 2027
    The University of Colorado School of Medicine
    Using AI to elucidate novel pathogenic programs underlying chronic inflammatory diseases for precision medicine
    Role: PI

    Arthritis National Research Foundation     (Fan Zhang)Jul 1, 2023 - Jun 30, 2025
    Arthritis National Research Foundation
    Deciphering complement-dependent phagocytic myeloid phenotypes in human autoimmune arthritis using single-cell computational omics
    Role: PI

    PhRMA     (Fan Zhang)Jul 1, 2022 - Jun 30, 2023
    Deciphering shared inflammatory myeloid phenotypes between rheumatoid arthritis (RA) and RA-associated interstitial lung disease by Computational Omics
    Role: PI

    Spondylitis Association of America     (Kristine Kuhn)Jul 1, 2022 - Jun 30, 2023
    Spondylitis Association of America
    Gene regulation of gut-trafficking T cells during SpA
    Role: Co-Investigator

    R01DK076690     (THURMAN, JOSHUA M)Dec 1, 2006 - May 31, 2022
    Complement-mediated injury of the kidney: New mechanisms and novel therapies
    Role: Co-Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Bai Z, Bartelo N, Aslam M, Murphy EA, Hale CR, Blachere NE, Parveen S, Spolaore E, DiCarlo E, Gravallese EM, Smith MH. Synovial fibroblast gene expression is associated with sensory nerve growth and pain in rheumatoid arthritis. Sci Transl Med. 2024 Apr 10; 16(742):eadk3506. PMID: 38598614.
      View in: PubMed
    2. Weisenfeld D, Zhang F, Donlin L, Jonsson AH, Apruzzese W, Campbell D, Rao DA, Wei K, Holers VM, Gravallese E, Moreland L, Goodman S, Brenner M, Raychaudhuri S, Filer A, Anolik J, Bykerk V, Liao KP. Associations Between Rheumatoid Arthritis Clinical Factors and Synovial Cell Types and States. Arthritis Rheumatol. 2024 Mar; 76(3):356-362. PMID: 37791989.
      View in: PubMed
    3. Iijima H, Zhang F, Ambrosio F, Matsui Y. Network-based cytokine inference implicates Oncostatin M as a driver of an inflammation phenotype in knee osteoarthritis. Aging Cell. 2024 Feb; 23(2):e14043. PMID: 38111237.
      View in: PubMed
    4. Kang JB, Shen AZ, Gurajala S, Nathan A, Rumker L, Aguiar VRC, Valencia C, Lagattuta KA, Zhang F, Jonsson AH, Yazar S, Alquicira-Hernandez J, Khalili H, Ananthakrishnan AN, Jagadeesh K, Dey K, Daly MJ, Xavier RJ, Donlin LT, Anolik JH, Powell JE, Rao DA, Brenner MB, Gutierrez-Arcelus M, Luo Y, Sakaue S, Raychaudhuri S. Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution. Nat Genet. 2023 Dec; 55(12):2255-2268. PMID: 38036787.
      View in: PubMed
    5. Zhang F, Jonsson AH, Nathan A, Millard N, Curtis M, Xiao Q, Gutierrez-Arcelus M, Apruzzese W, Watts GFM, Weisenfeld D, Nayar S, Rangel-Moreno J, Meednu N, Marks KE, Mantel I, Kang JB, Rumker L, Mears J, Slowikowski K, Weinand K, Orange DE, Geraldino-Pardilla L, Deane KD, Tabechian D, Ceponis A, Firestein GS, Maybury M, Sahbudin I, Ben-Artzi A, Mandelin AM, Nerviani A, Lewis MJ, Rivellese F, Pitzalis C, Hughes LB, Horowitz D, DiCarlo E, Gravallese EM, Boyce BF, Moreland LW, Goodman SM, Perlman H, Holers VM, Liao KP, Filer A, Bykerk VP, Wei K, Rao DA, Donlin LT, Anolik JH, Brenner MB, Raychaudhuri S. Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes. Nature. 2023 Nov; 623(7987):616-624. PMID: 37938773.
      View in: PubMed
    6. Davidson NR, Greene CS. BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. bioRxiv. 2023 Oct 05. PMID: 37503097.
      View in: PubMed
    7. Inamo J, Keegan J, Griffith A, Ghosh T, Horisberger A, Howard K, Pulford J, Murzin E, Hancock B, Jonsson AH, Seifert J, Feser ML, Norris JM, Cao Y, Apruzzese W, Louis Bridges S, Bykerk V, Goodman S, Donlin L, Firestein GS, Perlman H, Bathon JM, Hughes LB, Tabechian D, Filer A, Pitzalis C, Anolik JH, Moreland L, Guthridge JM, James JA, Brenner MB, Raychaudhuri S, Sparks JA, Michael Holers V, Deane KD, Lederer JA, Rao DA, Zhang F. Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis. bioRxiv. 2023 Jul 04. PMID: 37461737.
      View in: PubMed
    8. Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis. bioRxiv. 2023 Apr 08. PMID: 37066336.
      View in: PubMed
    9. Dunlap G, Wagner A, Meednu N, Zhang F, Jonsson AH, Wei K, Sakaue S, Nathan A, Bykerk VP, Donlin LT, Goodman SM, Firestein GS, Boyle DL, Holers VM, Moreland LW, Tabechian D, Pitzalis C, Filer A, Raychaudhuri S, Brenner MB, McDavid A, Rao DA, Anolik JH. Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium. bioRxiv. 2023 Mar 21. PMID: 36993527.
      View in: PubMed
    10. Fritz D, Inamo J, Zhang F. Single-cell computational machine learning approaches to immune-mediated inflammatory disease: New tools uncover novel fibroblast and macrophage interactions driving pathogenesis. Front Immunol. 2022; 13:1076700. PMID: 36685542.
      View in: PubMed
    11. Jonsson AH, Zhang F, Dunlap G, Gomez-Rivas E, Watts GFM, Faust HJ, Rupani KV, Mears JR, Meednu N, Wang R, Keras G, Coblyn JS, Massarotti EM, Todd DJ, Anolik JH, McDavid A, Wei K, Rao DA, Raychaudhuri S, Brenner MB. Granzyme K+ CD8 T cells form a core population in inflamed human tissue. Sci Transl Med. 2022 06 15; 14(649):eabo0686. PMID: 35704599.
      View in: PubMed
    12. Meednu N, Rangel-Moreno J, Zhang F, Escalera-Rivera K, Corsiero E, Prediletto E, DiCarlo E, Goodman S, Donlin LT, Raychauduri S, Bombardieri M, Pitzalis C, Orange DE, McDavid A, Anolik JH. Dynamic spectrum of ectopic lymphoid B cell activation and hypermutation in the RA synovium characterized by NR4A nuclear receptor expression. Cell Rep. 2022 05 03; 39(5):110766. PMID: 35508128.
      View in: PubMed
    13. Guan S, Mehta B, Slater D, Thompson JR, DiCarlo E, Pannellini T, Pearce-Fisher D, Zhang F, Raychaudhuri S, Hale C, Jiang CS, Goodman S, Orange DE. Rheumatoid Arthritis Synovial Inflammation Quantification Using Computer Vision. ACR Open Rheumatol. 2022 Apr; 4(4):322-331. PMID: 35014221.
      View in: PubMed
    14. Kang JB, Nathan A, Weinand K, Zhang F, Millard N, Rumker L, Moody DB, Korsunsky I, Raychaudhuri S. Efficient and precise single-cell reference atlas mapping with Symphony. Nat Commun. 2021 10 07; 12(1):5890. PMID: 34620862.
      View in: PubMed
    15. Mysore V, Cullere X, Mears J, Rosetti F, Okubo K, Liew PX, Zhang F, Madera-Salcedo I, Rosenbauer F, Stone RM, Aster JC, von Andrian UH, Lichtman AH, Raychaudhuri S, Mayadas TN. Fc?R engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity. Nat Commun. 2021 08 09; 12(1):4791. PMID: 34373452.
      View in: PubMed
    16. Zhang F, Mears JR, Shakib L, Beynor JI, Shanaj S, Korsunsky I, Nathan A, Donlin LT, Raychaudhuri S. IFN-? and TNF-a drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation. Genome Med. 2021 04 20; 13(1):64. PMID: 33879239.
      View in: PubMed
    17. Fan J, Slowikowski K, Zhang F. Single-cell transcriptomics in cancer: computational challenges and opportunities. Exp Mol Med. 2020 09; 52(9):1452-1465. PMID: 32929226.
      View in: PubMed
    18. Orange DE, Yao V, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB. RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares. N Engl J Med. 2020 07 16; 383(3):218-228. PMID: 32668112.
      View in: PubMed
    19. Korsunsky I, Millard N, Fan J, Slowikowski K, Zhang F, Wei K, Baglaenko Y, Brenner M, Loh PR, Raychaudhuri S. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods. 2019 12; 16(12):1289-1296. PMID: 31740819.
      View in: PubMed
    20. Arazi A, Rao DA, Berthier CC, Davidson A, Liu Y, Hoover PJ, Chicoine A, Eisenhaure TM, Jonsson AH, Li S, Lieb DJ, Zhang F, Slowikowski K, Browne EP, Noma A, Sutherby D, Steelman S, Smilek DE, Tosta P, Apruzzese W, Massarotti E, Dall'Era M, Park M, Kamen DL, Furie RA, Payan-Schober F, Pendergraft WF, McInnis EA, Buyon JP, Petri MA, Putterman C, Kalunian KC, Woodle ES, Lederer JA, Hildeman DA, Nusbaum C, Raychaudhuri S, Kretzler M, Anolik JH, Brenner MB, Wofsy D, Hacohen N, Diamond B. The immune cell landscape in kidneys of patients with lupus nephritis. Nat Immunol. 2019 07; 20(7):902-914. PMID: 31209404.
      View in: PubMed
    21. Kuo D, Ding J, Cohn IS, Zhang F, Wei K, Rao DA, Rozo C, Sokhi UK, Shanaj S, Oliver DJ, Echeverria AP, DiCarlo EF, Brenner MB, Bykerk VP, Goodman SM, Raychaudhuri S, R?tsch G, Ivashkiv LB, Donlin LT. HBEGF+ macrophages in rheumatoid arthritis induce fibroblast invasiveness. Sci Transl Med. 2019 05 08; 11(491). PMID: 31068444.
      View in: PubMed
    22. Zhang F, Wei K, Slowikowski K, Fonseka CY, Rao DA, Kelly S, Goodman SM, Tabechian D, Hughes LB, Salomon-Escoto K, Watts GFM, Jonsson AH, Rangel-Moreno J, Meednu N, Rozo C, Apruzzese W, Eisenhaure TM, Lieb DJ, Boyle DL, Mandelin AM, Boyce BF, DiCarlo E, Gravallese EM, Gregersen PK, Moreland L, Firestein GS, Hacohen N, Nusbaum C, Lederer JA, Perlman H, Pitzalis C, Filer A, Holers VM, Bykerk VP, Donlin LT, Anolik JH, Brenner MB, Raychaudhuri S. Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry. Nat Immunol. 2019 07; 20(7):928-942. PMID: 31061532.
      View in: PubMed
    23. Zhang F, Flaherty P. Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data. BMC Bioinformatics. 2017 Jan 19; 18(1):45. PMID: 28103803.
      View in: PubMed
    24. He Y, Zhang F, Flaherty P. RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data. Bioinformatics. 2015 Sep 01; 31(17):2785-93. PMID: 25931517.
      View in: PubMed
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