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Fan Zhang - Publications

Affiliations: 
University of Colorado at Denver, Denver, CO, United States 
Website:
https://medschool.cuanschutz.edu/rheumatology/faculty2/fan-zhang-phd
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29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 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, et al. Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution. Nature Genetics. PMID 38036787 DOI: 10.1038/s41588-023-01586-6  0.626
2023 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, et al. Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes. Nature. PMID 37938773 DOI: 10.1038/s41586-023-06708-y  0.759
2023 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, et al. Associations between rheumatoid arthritis clinical factors with synovial cell types and states. Arthritis & Rheumatology (Hoboken, N.J.). PMID 37791989 DOI: 10.1002/art.42726  0.541
2023 Wang X, Gao Y, Li CJ, Fang L, Liu GE, Zhao X, Zhang Y, Cai G, Xue G, Liu Y, Wang L, Zhang F, Wang K, Zhang M, Li R, et al. The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese holstein cattle. Bmc Genomic Data. 24: 39. PMID 37550629 DOI: 10.1186/s12863-023-01139-0  0.358
2023 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, ... ... Zhang F, et al. Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis. Biorxiv : the Preprint Server For Biology. PMID 37461737 DOI: 10.1101/2023.07.03.547507  0.556
2023 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, et al. Adipocytes regulate fibroblast function, and their loss contributes to fibroblast dysfunction in inflammatory diseases. Biorxiv : the Preprint Server For Biology. PMID 37292637 DOI: 10.1101/2023.05.16.540975  0.472
2023 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 : the Preprint Server For Biology. PMID 37066336 DOI: 10.1101/2023.04.07.536026  0.542
2023 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, et al. 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 : the Preprint Server For Biology. PMID 36993527 DOI: 10.1101/2023.03.18.533282  0.596
2023 Kang JB, Shen AZ, Sakaue S, Luo Y, Gurajala S, Nathan A, Rumker L, Aguiar VRC, Valencia C, Lagattuta K, Zhang F, Jonsson AH, Yazar S, Alquicira-Hernandez J, Khalili H, et al. Mapping the dynamic genetic regulatory architecture of genes at single-cell resolution. Medrxiv : the Preprint Server For Health Sciences. PMID 36993194 DOI: 10.1101/2023.03.14.23287257  0.626
2023 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. 13: 1076700. PMID 36685542 DOI: 10.3389/fimmu.2022.1076700  0.314
2022 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, et al. Granzyme K CD8 T cells form a core population in inflamed human tissue. Science Translational Medicine. 14: eabo0686. PMID 35704599 DOI: 10.1126/scitranslmed.abo0686  0.535
2022 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 Reports. 39: 110766. PMID 35508128 DOI: 10.1016/j.celrep.2022.110766  0.302
2022 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 Rheumatology. PMID 35014221 DOI: 10.1002/acr2.11381  0.484
2021 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. Nature Communications. 12: 5890. PMID 34620862 DOI: 10.1038/s41467-021-25957-x  0.525
2021 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. FcγR engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity. Nature Communications. 12: 4791. PMID 34373452 DOI: 10.1038/s41467-021-24591-x  0.537
2021 Zhang F, Mears JR, Shakib L, Beynor JI, Shanaj S, Korsunsky I, Nathan A, Donlin LT, Raychaudhuri S. IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation. Genome Medicine. 13: 64. PMID 33879239 DOI: 10.1186/s13073-021-00881-3  0.475
2020 Fan J, Slowikowski K, Zhang F. Single-cell transcriptomics in cancer: computational challenges and opportunities. Experimental & Molecular Medicine. PMID 32929226 DOI: 10.1038/S12276-020-0422-0  0.697
2020 Zhang F, Mears JR, Shakib L, Beynor JI, Shanaj S, Korsunsky I, Nathan A, Donlin LT, Raychaudhuri S. IFN- and TNF- drive a + + macrophage phenotype expanded in severe COVID-19 and other diseases with tissue inflammation. Biorxiv : the Preprint Server For Biology. PMID 32793902 DOI: 10.1101/2020.08.05.238360  0.521
2020 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. The New England Journal of Medicine. 383: 218-228. PMID 32668112 DOI: 10.1056/Nejmoa2004114  0.578
2020 Cahill LA, Guo F, Nguyen J, Zhang F, Seshadri A, Keegan J, Hauser CJ, Otterbein LE, Robson S, Shaefi S, Yaffe MB, Lederer JA. Circulating Factors in Trauma Plasma Activate Specific Human Immune Cell Subsets. Injury. PMID 32171537 DOI: 10.1016/J.Injury.2020.03.009  0.323
2019 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. Nature Methods. PMID 31740819 DOI: 10.1038/S41592-019-0619-0  0.739
2019 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, et al. Publisher Correction: The immune cell landscape in kidneys of patients with lupus nephritis. Nature Immunology. PMID 31409923 DOI: 10.1038/S41590-019-0473-3  0.699
2019 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, et al. The immune cell landscape in kidneys of patients with lupus nephritis. Nature Immunology. PMID 31209404 DOI: 10.1038/S41590-019-0398-X  0.753
2019 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, et al. HBEGF macrophages in rheumatoid arthritis induce fibroblast invasiveness. Science Translational Medicine. 11. PMID 31068444 DOI: 10.1126/Scitranslmed.Aau8587  0.581
2019 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, et al. Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry. Nature Immunology. PMID 31061532 DOI: 10.1038/S41590-019-0378-1  0.71
2017 Zhang F, Flaherty P. Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data. Bmc Bioinformatics. 18: 45. PMID 28103803 DOI: 10.1186/S12859-016-1451-5  0.647
2016 Dordea AC, Vandenwijngaert S, Garcia V, Tainsh RE, Nathan DI, Allen K, Raher MJ, Tainsh LT, Zhang FF, Lieb WS, Mikelman S, Kirby A, Stevens C, Thoonen R, Hindle AG, et al. ANDROGEN-SENSITIVE HYPERTENSION ASSOCIATED WITH SOLUBLE GUANYLATE CYCLASE ALPHA1 DEFICIENCY IS MEDIATED BY 20-HETE. American Journal of Physiology. Heart and Circulatory Physiology. ajpheart.00877.2015. PMID 27199131 DOI: 10.1152/Ajpheart.00877.2015  0.309
2015 He Y, Zhang F, Flaherty P. RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data Bioinformatics. 31: 2785-2793. PMID 25931517 DOI: 10.1093/Bioinformatics/Btv275  0.651
2014 Mahajan A, Go MJ, Zhang W, Below JE, Gaulton KJ, Ferreira T, Horikoshi M, Johnson AD, Ng MC, Prokopenko I, ... ... Zhang F, et al. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nature Genetics. 46: 234-44. PMID 24509480 DOI: 10.1038/Ng.2897  0.418
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