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Fan Zhang, Ph.D.

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Biography
Broad Institute of Harvard and MIT, USAssociate ScientistCurrentImmunogenomics
Worcester Polytechnic Institute (WPI), USPhD12/2016Computational Biology

Overview
I am a computational biologist working in immunogenomics with Dr. Soumya Raychaudhuri. My research interests lie in the application of bioinformatics and statistics to study autoimmune diseases, medicine, and public health. Recently, I focus on developing accurate and computationally scalable methods to study the single-cell immunogenomics and genetics data to discover potential drug targets in autoimmune diseases.

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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.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. 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.
    Citations:    
  2. Fan Zhang, Chuangqi Wang, Andrew C. Trapp, Patrick Flaherty. A Global Optimization Algorithm for Sparse Mixed Membership Matrix Factorization. Springer Cham. In: Zhang L., Chen DG., Jiang H., Li G., Quan H. (eds). Contemporary Biostatistics with Biopharmaceutical Applications. 2019; 129-156. View Publication.
  3. 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.
    Citations:    
  4. Der E, Suryawanshi H, Morozov P, Kustagi M, Goilav B, Ranabothu S, Izmirly P, Clancy R, Belmont HM, Koenigsberg M, Mokrzycki M, Rominieki H, Graham JA, Rocca JP, Bornkamp N, Jordan N, Schulte E, Wu M, Pullman J, Slowikowski K, Raychaudhuri S, Guthridge J, James J, Buyon J, Tuschl T, Putterman C. Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways. Nat Immunol. 2019 07; 20(7):915-927. PMID: 31110316.
    Citations:    
  5. 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.
    Citations:    
  6. 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.
    Citations:    
  7. Donlin LT, Rao DA, Wei K, Slowikowski K, McGeachy MJ, Turner JD, Meednu N, Mizoguchi F, Gutierrez-Arcelus M, Lieb DJ, Keegan J, Muskat K, Hillman J, Rozo C, Ricker E, Eisenhaure TM, Li S, Browne EP, Chicoine A, Sutherby D, Noma A, Nusbaum C, Kelly S, Pernis AB, Ivashkiv LB, Goodman SM, Robinson WH, Utz PJ, Lederer JA, Gravallese EM, Boyce BF, Hacohen N, Pitzalis C, Gregersen PK, Firestein GS, Raychaudhuri S, Moreland LW, Holers VM, Bykerk VP, Filer A, Boyle DL, Brenner MB, Anolik JH. Methods for high-dimensional analysis of cells dissociated from cryopreserved synovial tissue Arthritis Res Ther. 2018 07 11; 20(1):139. PMID: 29996944.
    Citations: 2     Fields:    
  8. 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.
    Citations:    
  9. 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.
    Citations:    
  10. Zhang F, Chen S, Zhang H, Zhang X, Li G. Bioelectric signal detrending using smoothness prior approach. Med Eng Phys. 2014 Aug; 36(8):1007-13. PMID: 24894030.
    Citations:    
  11. Geng Y, Zhang F, Yang L, Zhang Y, Li G. Reduction of the effect of arm position variation on real-time performance of motion classification. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:2772-5. PMID: 23366500.
    Citations:    
  12. Liang Y, Zhang F, Wang J, Joshi T, Wang Y, Xu D. Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE. PLoS One. 2011; 6(7):e21750. PMID: 21789178.
    Citations:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.