Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Fan Zhang

TitleAssistant Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-MED
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 https://fanzhanglab.org/ 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 https://fanzhanglab.org/ for more recent research and publications!

    Collapse Research 
    Collapse research activities and funding
    Arthritis Foundation     (Fan Zhang)Jan 2, 2025 - Dec 31, 2026
    Arthritis Foundation
    Uncovering dynamic immunophenotypes by developing novel AI methods to predict RA onset
    Role: PI
    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
    PhRMA
    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 - Dec 31, 2026
    NIH
    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. Inamo J, Keegan J, Griffith A, Ghosh T, Horisberger A, Howard K, Pulford JF, Murzin E, Hancock B, Dominguez ST, Gurra MG, Gurajala S, Jonsson AH, Seifert JA, Feser ML, Norris JM, Cao Y, Apruzzese W, Bridges SL, Bykerk VP, Goodman S, Donlin LT, Firestein GS, Bathon JM, Hughes LB, Filer A, Pitzalis C, Anolik JH, Moreland L, Hacohen N, Guthridge JM, James JA, Cuda CM, Perlman H, Brenner MB, Raychaudhuri S, Sparks JA, Holers VM, Deane KD, Lederer J, Rao DA, Zhang F. Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis. J Clin Invest. 2025 Mar 17; 135(6). PMID: 40091833.
      View in: PubMed
    2. Reynoso S, Schiebout C, Krishna R, Zhang F. STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance. bioRxiv. 2025 Feb 19. PMID: 40027655.
      View in: PubMed
    3. Donado CA, Theisen E, Zhang F, Nathan A, Fairfield ML, Rupani KV, Jones D, Johannes KP, Raychaudhuri S, Dwyer DF, Jonsson AH, Brenner MB. Granzyme K activates the entire complement cascade. Nature. 2025 May; 641(8061):211-221. PMID: 39914456.
      View in: PubMed
    4. Young J, Inamo J, Caterer Z, Krishna R, Zhang F. CellPhenoX: An eXplainable Cell-specific machine learning method to predict clinical Phenotypes using single-cell multi-omics. bioRxiv. 2025 Jan 27. PMID: 39975336.
      View in: PubMed
    5. Davidson NR, Zhang F, Greene CS. BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. PLoS Comput Biol. 2025 Jan; 21(1):e1012742. PMID: 39823522.
      View in: PubMed
    6. Townsend HA, Rosenberger KJ, Vanderlinden LA, Inamo J, Zhang F. Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity. Front Immunol. 2024; 15:1454263. PMID: 39703500.
      View in: PubMed
    7. Faust HJ, Cheng TY, Korsunsky I, Watts GFM, Gal-Oz ST, Trim WV, Kongthong S, Jonsson AH, Simmons DP, Zhang F, Padera R, Chubinskaya S, Wei K, Raychaudhuri S, Lynch L, Moody DB, Brenner MB. Adipocyte associated glucocorticoid signaling regulates normal fibroblast function which is lost in inflammatory arthritis. Nat Commun. 2024 11 14; 15(1):9859. PMID: 39543086.
      View in: PubMed
    8. Thomas T, Friedrich M, Rich-Griffin C, Pohin M, Agarwal D, Pakpoor J, Lee C, Tandon R, Rendek A, Aschenbrenner D, Jainarayanan A, Voda A, Siu JHY, Sanches-Peres R, Nee E, Sathananthan D, Kotliar D, Todd P, Kiourlappou M, Gartner L, Ilott N, Issa F, Hester J, Turner J, Nayar S, Mackerodt J, Zhang F, Jonsson A, Brenner M, Raychaudhuri S, Kulicke R, Ramsdell D, Stransky N, Pagliarini R, Bielecki P, Spies N, Marsden B, Taylor S, Wagner A, Klenerman P, Walsh A, Coles M, Jostins-Dean L, Powrie FM, Filer A, Travis S, Uhlig HH, Dendrou CA, Buckley CD. A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease. Nat Immunol. 2024 Nov; 25(11):2152-2165. PMID: 39438660.
      View in: PubMed
    9. Holers VM, Demoruelle KM, Buckner JH, James EA, Firestein GS, Robinson WH, Steere AC, Zhang F, Norris JM, Kuhn KA, Deane KD. Distinct mucosal endotypes as initiators and drivers of rheumatoid arthritis. Nat Rev Rheumatol. 2024 Oct; 20(10):601-613. PMID: 39251771.
      View in: PubMed
    10. Kamiya M, Carter H, Espindola MS, Doyle TJ, Lee JS, Merriam LT, Zhang F, Kawano-Dourado L, Sparks JA, Hogaboam CM, Moore BB, Oldham WM, Kim EY. Immune mechanisms in fibrotic interstitial lung disease. Cell. 2024 Jul 11; 187(14):3506-3530. PMID: 38996486.
      View in: PubMed
    11. Dunlap G, Wagner A, Meednu N, Wang R, Zhang F, Ekabe JC, 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, Thakar J, McDavid A, Rao DA, Anolik JH. Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nat Commun. 2024 Jun 11; 15(1):4991. PMID: 38862501.
      View in: PubMed
    12. Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Al Suqri M, 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. Nat Commun. 2024 May 31; 15(1):4650. PMID: 38821936.
      View in: PubMed
    13. Guo N, Vargas J, Reynoso S, Fritz D, Krishna R, Wang C, Zhang F. Uncover spatially informed variations for single-cell spatial transcriptomics with STew. Bioinform Adv. 2024; 4(1):vbae064. PMID: 38827413.
      View in: PubMed
    14. Bai Z, Bartelo N, Aslam M, Murphy EA, Hale CR, Blachere NE, Parveen S, Spolaore E, DiCarlo E, Gravallese EM, Smith MH, Frank MO, Jiang CS, Zhang H, Pyrgaki C, Lewis MJ, Sikandar S, Pitzalis C, Lesnak JB, Mazhar K, Price TJ, Malfait AM, Miller RE, Zhang F, Goodman S, Darnell RB, Wang F, Orange DE. Synovial fibroblast gene expression is associated with sensory nerve growth and pain in rheumatoid arthritis. Sci Transl Med. 2024 04 10; 16(742):eadk3506. PMID: 38598614.
      View in: PubMed
    15. 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
    16. 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 02; 23(2):e14043. PMID: 38111237.
      View in: PubMed
    17. 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
    18. 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
    19. 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
    20. 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
    21. 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
    22. 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
    23. 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
    24. 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
    25. 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
    26. 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
    27. 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
    28. 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
    29. 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
    30. 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
    31. 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
    32. 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
    33. 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
    34. 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
    35. 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
    36. Diallo D, Paulsen BS, Liljeb?ck TH, Michaelsen TE. Polysaccharides from the roots of Entada africana Guill. et Perr., Mimosaceae, with complement fixing activity. J Ethnopharmacol. 2001 Feb; 74(2):159-71. PMID: 11167034.
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