Professional Titles
- Assistant Professor
Research Interests
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!
Publications
- 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
- 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
- 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, Frontiers in Immunology, In press, doi: 10.3389/fimmu.2022.1076700, 2022
- 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
Practice Locations
Personal Interests
Hiking
Public Speaking
Yes
Hiking
Public Speaking
Yes
General Information
Graduate Schools:
- PhD, Worcester Polytechnic Institute (2017)