Fan Zhang, PhD
Assistant Professor, Medicine-Rheumatology

Professional Titles

• Assistant Professor

Recognition & Awards

• Arthritis National Research Foundation, Deciphering complement-dependent phagocytic myeloid phenotypes in human autoimmune arthritis using single-cell computational omics (2023)
• Translational Research Scholar Program (TRSP) CU School of Medicine, Using AI to elucidate novel pathogenic programs underlying chronic inflammatory diseases for precision medicine (2023)
• CU Orthopedics-Department of Biomedical Informatics (DBMI) Dyads Award, Multi-Omics Integration with Machine Learning to Reveal Synovium Phenotypes in Ankle Osteoarthritis (2023)
• PhRMA Research Starter Grant, Deciphering shared inflammatory myeloid phenotypes between rheumatoid arthritis (RA) and RA-associated interstitial lung disease by Computational Omics (2022)

Research Interests

Teaching

Publications

• 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 Apr 10;16(742):eadk3506. PubMed PMID: 38598614
• Davidson NR, Zhang F, Greene CS. BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. bioRxiv. 2024 Apr 4. PubMed PMID: 37503097
• 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. PubMed PMID: 36993527
• Faust HJ, Cheng TY, Korsunsky I, Watts GFM, Gal-Oz ST, Trim W, Kongthong K, Jonsson AH, Simmons DP, Zhang F, Padera R, Chubinskaya S, Wei K, Raychaudhuri S, Lynch L, Moody DB, Brenner MB. Adipocytes regulate fibroblast function, and their loss contributes to fibroblast dysfunction in inflammatory diseases. bioRxiv. 2023 May 18. PubMed PMID: 37292637
• 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 8. PubMed PMID: 37066336
• 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 2nd, 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. PubMed PMID: 37938773
• 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. PubMed PMID: 38036787
• 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. 2023 Dec 18;:e14043. [Epub ahead of print] PubMed PMID: 38111237
• 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 with synovial cell types and states. Arthritis Rheumatol. 2023 Oct 4. [Epub ahead of print] PubMed PMID: 37791989
• 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 with synovial cell types and states. Arthritis Rheumatol. 2023 Oct 4. [Epub ahead of print] PubMed PMID: 37791989
• 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 2nd, 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. PubMed PMID: 37938773
• 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. PubMed PMID: 38036787
• 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. 2023 Dec 18;:e14043. [Epub ahead of print] PubMed PMID: 38111237
• 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 4. PubMed PMID: 37461737
• 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 8. PubMed PMID: 37066336
• 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. PubMed PMID: 36993527
• 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. PubMed PMID: 35014221
• 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 May 3;39(5):110766. PubMed PMID: 35508128
• 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. PubMed PMID: 35704599
• 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 May 3;39(5):110766. PubMed PMID: 35508128
• 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. PubMed PMID: 35014221
• 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. PubMed PMID: 36685542
• 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 Apr 20;13(1):64. PubMed PMID: 33879239
• 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 Aug 9;12(1):4791. PubMed PMID: 34373452
• 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 Oct 7;12(1):5890. PubMed PMID: 34620862
• 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 Jul 16;383(3):218-228. PubMed PMID: 32668112
• 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 May 8;11(491). PubMed PMID: 31068444
• 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 2nd, 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 Jul;20(7):928-942. PubMed PMID: 31061532
• 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 Dec;16(12):1289-1296. PubMed PMID: 31740819
• 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 3rd, 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. Publisher Correction: The immune cell landscape in kidneys of patients with lupus nephritis. Nat Immunol. 2019 Oct;20(10):1404. PubMed PMID: 31409923
• 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. PubMed PMID: 28103803
• He Y, Zhang F, Flaherty P. RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data. Bioinformatics. 2015 Sep 1;31(17):2785-93. PubMed PMID: 25931517
• Zhang, F.*, Jonsson, A.H.*, Nathan, A.*, Wei, K.*, Millard, N.*, et al, Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritis, bioRxiv, In review, 2022
• Liu, S.*, Li, L.*, Zhang, F*, …, Church, G., Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC, bioRxiv, In review, 2022

Professional Memberships

• The Federation of Clinical Immunology Societies (FOCIS), Member
• American College of Rheumatology (ACR), Member
• Intelligent Systems for Molecular Biology (ISMB), Member