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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, MAStatistician12/2021Single-cell data integration
    Worcester Polytechnic Institute, Worcester, MAPhD02/2017Computational Biology
    Broad Institute, 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
         (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 Description: The goal is to develop integrative analytical strategies for cross-tissue single-cell omics data integration to delineate promising targets for the joint-lung axis for rheumatoid arthritis.
    Role: PI

    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. 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 Jun 15; 14(649):eabo0686. PMID: 35704599.
      View in: PubMed
    2. 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
    3. 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
    4. 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
    5. 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
    6. 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
    7. 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
    8. 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
    9. 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
    10. 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
    11. 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, Rätsch 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
    12. 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
    13. 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
    14. 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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