 Connection
Fan Zhang to Humans
This is a "connection" page, showing publications Fan Zhang has written about Humans.
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Connection Strength |
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0.298 |
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Young J, Inamo J, Caterer Z, Krishna R, Zhang F. CellPhenoX: An Explainable Machine Learning Method for Identifying Cell Phenotypes To Predict Clinical Outcomes from Single-Cell Multi-Omics. Adv Sci (Weinh). 2025 Nov; 12(42):e03289.
Score: 0.024
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Reynoso S, Schiebout C, Krishna R, Zhang F. STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance. Brief Bioinform. 2025 Aug 31; 26(5).
Score: 0.024
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Inamo J, Keegan J, Griffith A, Ghosh T, Horisberger A, Howard K, Pulford JF, Murzin E, Hancock B, Dominguez ST, Gurra MG, Gurajala S, Jonsson AH, Seifert JA, Feser ML, Norris JM, Cao Y, Apruzzese W, Bridges SL, Bykerk VP, Goodman S, Donlin LT, Firestein GS, Bathon JM, Hughes LB, Filer A, Pitzalis C, Anolik JH, Moreland L, Hacohen N, Guthridge JM, James JA, Cuda CM, Perlman H, Brenner MB, Raychaudhuri S, Sparks JA, Holers VM, Deane KD, Lederer J, Rao DA, Zhang F. Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis. J Clin Invest. 2025 Mar 17; 135(6).
Score: 0.023
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Townsend HA, Rosenberger KJ, Vanderlinden LA, Inamo J, Zhang F. Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity. Front Immunol. 2024; 15:1454263.
Score: 0.023
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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, 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 11; 623(7987):616-624.
Score: 0.021
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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.
Score: 0.020
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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.
Score: 0.018
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Fan J, Slowikowski K, Zhang F. Single-cell transcriptomics in cancer: computational challenges and opportunities. Exp Mol Med. 2020 09; 52(9):1452-1465.
Score: 0.017
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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.
Score: 0.016
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He Z, Glass MC, Venkatesan P, Feser ML, Lazaro L, Okada LY, Tran NTT, He YD, Zaim SR, Bennett CE, Ravisankar P, Dornisch EM, Ferrannini AC, Arishi NA, Asamoah AG, Barzideh S, Becker LA, Bemis EA, Buckner JH, Collora CE, Criley MAL, Demoruelle MK, Fleischer CL, Garber J, Genge PC, Gong Q, Graybuck LT, Gustafson CE, Hattel BC, Hernandez V, Heubeck AT, Kawelo EK, Krishnan U, Kuan EL, Kuhn KA, LaFrance CM, Lee KJ, Li R, Lord C, Mettey RR, Moss L, Musgrove B, Nguyen KH, Ochoa A, Parthasarathy V, Pebworth MP, Pedrick C, Peng T, Phalen CG, Reading J, Roll CR, Seifert JA, Siedschlag MD, Speake C, Striebich CC, Stuckey TJ, Swanson EG, Takada H, Thai T, Thomson ZJ, Trieu N, Tsaltskan V, Wang W, Weiss MDA, Westermann A, Zhang F, Boyle DL, Goldrath AW, Bumol TF, Li XJ, Holers VM, Skene PJ, Savage AK, Firestein GS, Deane KD, Torgerson TR, Gillespie MA. Progression to rheumatoid arthritis in at-risk individuals is defined by systemic inflammation and by T and B cell dysregulation. Sci Transl Med. 2025 Sep 24; 17(817):eadt7214.
Score: 0.006
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Liu S, Li L, Zhang F, Garcia-Corral M, Meyer K, Fortuna PRJ, van Sambeek B, Appleton E, Ng AHM, Khoshakhlagh P, Lu YR, Cameron J, Ramirez RN, Chen Y, Wu CT, Huang JY, Tan Y, Chao G, Aach J, Lim ET, Tam JM, Raychaudhuri S, Church GM. Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC. Nat Commun. 2025 Jun 10; 16(1):5136.
Score: 0.006
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Donado CA, Theisen E, Zhang F, Nathan A, Fairfield ML, Rupani KV, Jones D, Johannes KP, Raychaudhuri S, Dwyer DF, Jonsson AH, Brenner MB. Granzyme K activates the entire complement cascade. Nature. 2025 May; 641(8061):211-221.
Score: 0.006
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Davidson NR, Zhang F, Greene CS. BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. PLoS Comput Biol. 2025 Jan; 21(1):e1012742.
Score: 0.006
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Faust HJ, Cheng TY, Korsunsky I, Watts GFM, Gal-Oz ST, Trim WV, Kongthong S, Jonsson AH, Simmons DP, Zhang F, Padera R, Chubinskaya S, Wei K, Raychaudhuri S, Lynch L, Moody DB, Brenner MB. Adipocyte associated glucocorticoid signaling regulates normal fibroblast function which is lost in inflammatory arthritis. Nat Commun. 2024 11 14; 15(1):9859.
Score: 0.006
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Thomas T, Friedrich M, Rich-Griffin C, Pohin M, Agarwal D, Pakpoor J, Lee C, Tandon R, Rendek A, Aschenbrenner D, Jainarayanan A, Voda A, Siu JHY, Sanches-Peres R, Nee E, Sathananthan D, Kotliar D, Todd P, Kiourlappou M, Gartner L, Ilott N, Issa F, Hester J, Turner J, Nayar S, Mackerodt J, Zhang F, Jonsson A, Brenner M, Raychaudhuri S, Kulicke R, Ramsdell D, Stransky N, Pagliarini R, Bielecki P, Spies N, Marsden B, Taylor S, Wagner A, Klenerman P, Walsh A, Coles M, Jostins-Dean L, Powrie FM, Filer A, Travis S, Uhlig HH, Dendrou CA, Buckley CD. A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease. Nat Immunol. 2024 Nov; 25(11):2152-2165.
Score: 0.006
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Holers VM, Demoruelle KM, Buckner JH, James EA, Firestein GS, Robinson WH, Steere AC, Zhang F, Norris JM, Kuhn KA, Deane KD. Distinct mucosal endotypes as initiators and drivers of rheumatoid arthritis. Nat Rev Rheumatol. 2024 Oct; 20(10):601-613.
Score: 0.006
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Kamiya M, Carter H, Espindola MS, Doyle TJ, Lee JS, Merriam LT, Zhang F, Kawano-Dourado L, Sparks JA, Hogaboam CM, Moore BB, Oldham WM, Kim EY. Immune mechanisms in fibrotic interstitial lung disease. Cell. 2024 Jul 11; 187(14):3506-3530.
Score: 0.006
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Dunlap G, Wagner A, Meednu N, Wang R, Zhang F, Ekabe JC, 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, Thakar J, McDavid A, Rao DA, Anolik JH. Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nat Commun. 2024 Jun 11; 15(1):4991.
Score: 0.006
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Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Al Suqri M, 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. Nat Commun. 2024 May 31; 15(1):4650.
Score: 0.006
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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 04 10; 16(742):eadk3506.
Score: 0.005
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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 and Synovial Cell Types and States. Arthritis Rheumatol. 2024 Mar; 76(3):356-362.
Score: 0.005
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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 12; 55(12):2255-2268.
Score: 0.005
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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 06 15; 14(649):eabo0686.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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).
Score: 0.004
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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.
Score: 0.003
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Connection Strength
The connection strength for concepts is the sum of the scores for each matching publication.
Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
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