Recent Publications

[Our lab members are in bold]

Highlighted 2025 Publications: 

• Reynoso, S., Schiebout, C., Krishna, R., Zhang, F. STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance, https://doi.org/10.1101/2025.02.17.636505, bioRxiv, 2025. Corresponding

• Young, J., Inamo, J., Caterer, Z., Krishna, R., Zhang, F. CellPhenoX: An eXplainable Cell-specific machine learning method to predict clinical Phenotypes using single-cell multi-omics, https://doi.org/10.1101/2025.01.24.634132, bioRxiv, 2025. Corresponding

• Inamo, J., Keegan, J., Griffith, A., Ghosh, T., Horisberger, A., Howard, K., Pulford, J.F., Murzin, E., Hancock, B., Dominguez S.T., Gurra, M.G., Gurra, M.G., Gurajala, S., Jonsson, A.H., Seifert, J.A.,, Feser, M.L., Morris, J.M., Cao, Y., Apruzzese, W., Bridges, S.L., Bykerk, V., Goodman, S., Donlin, L.T., Firestein, G.S., Bathon, J.M., Hughes, B.L., Filer, A., Pitzalis, C., Anolik, J.H., Moreland, L., Hacohen, N., Guthridge, J.M., James, J.A., Cuda, C.M., Perlman, H., Brenner, M.B., Raychaudhuri, S., Sparks, J.A., AMP RA/SLE Network, Holers, V.M., Deane, K.D., Lederer, J.A., Rao, D.A., Zhang, F. Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis, JCI (Journal of Clinical Investigation), 135(6):e185217, 2025. Corresponding

• Donado, C.A., Theisen, E., Zhang, F., Nathan, A., Rupani, K.V., Jones, D., Fairfield, M.L., Johannes, K.P., AMP RA/SLE, Raychaudhurit, S., Dwyer, D.F., Jonsson, A.H., Brenner, M.B. Granzyme K activates a newly-identified complement pathway, Nature, In press, 2025  

Highlighted 2024 Publications: 

• Townsend, H.A., Rosenberger, K., Vanderlinden, L., Inamo, J., Zhang, F. , Evaluating Methods for Integrating Single-Cell Data and Genetics to Understand Inflammatory Disease Complexity, Frontiers in Immunology, 15, 1454263, 2024. Corresponding 

• Guo, N., Vargas, J., Reynoso, S., Fritz, D., Krishna, R., Wang, C., Zhang, F. Uncover spatially informed variations for single-cell spatial transcriptomics with STew, Bioinformatics Advances, https://doi.org/10.1093/bioadv/vbae064, 2024. Corresponding

• Holers, V.M., Demoruelle, M.K., Buckner, J.H., James, E.A., Firestein, G.S., Robinson, W.H., Steere, A.C., Zhang, F., Norris, J.M., Kuhn, K.A., Deane, K.D. Distinct mucosal endotypes as initiators and drivers of rheumatoid arthritis, Nature Review Rheumatology, 1-13, 2024 

• Kamiya, M., Carter, H., …, Zhang, F., …, Oldham, W.M., Kim, E.Y. Immune mechanisms in fibrotic interstitial lung disease, Cell, https://doi.org/10.1016/j.cell.2024.05.015, 2024

• 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. J.H.Y., 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.H., Brenner, M.B., 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, F.M., Filer, A., Travis, S., Uhlig, H.H., Dendrou, C.A., Buckley, C.D. A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease, Nature Immunology, 1-14, 2024

• Bai, Z., Bartelo, N., Aslam, M., Hale, C., Blachere, N., Parveen, S., Spolaore, E., DiCarlo, E., Gravallese, E., Smith, M.H., …, Pitzalis, C., Malfait, A., Miller, R.E., Zhang, F., Goodman, S., Darnell, R., Wang, F., Orange, D.E. Synovial fibroblast gene expression is associated with sensory nerve growth and pain in rheumatoid arthritis, Science Translational Medicine, DOI: 10.1126/scitranslmed.adk3506, 2024 [Cover Article]

• Horisberger, A., Griffith, A., Keegan, J., Arazi, A., Pulford, J., Murzin, E., Howard, K., Hancock, B., Fava, A., Sasaki, T., Ghosh, T., Inamo, J., Beuschel, R., Cao, Y., Preisinger, K., Gutierrez-Arcelus, M., Eisenhaure, T.M., Guthridge, J., Hoover, P.J., Dall’Era, M., Wofsy, D., Kamen, D.L., Kalunian, K.C., Furie, R., Belmont, M., Izmirly, P., Clancy, R., Hildeman, D., Woodle, E.S., Apruzzese, W., McMahon, M.Z., Grossman, J., Barnas, J.L., Payan-Schober, F., Ishimori, M., Weisman, M., Kretzler, M., Berthier, C.C., Hodgin, J.B., Demeke, D.S., Putterman, C., AMP RA/SLE Network, Brenner, M.B., Anolik, J.H., Raychaudhuri, S., Hacohen, N., James, J.A., Davidson, A., Petri, M.A., Buyon, J.P., Diamond, B., Zhang, F., Lederer, J.A., Rao, D.A. Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis. bioRxiv, in review, 2024. Co-senior

• Dunlap, G.S.*, Wagner, A.*, Meednu, N.*, Zhang, F., …, McDavid, A., Rao, D.A., Anolik, J.H., Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium, Nature Communications, 2024

• Weinand, K., Sakaue, S., Nathan, A., Jonsson, A.H., Zhang, F., Watts, GFM, et al, The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis, Nature Communications, 2024

• Ahmed, Z., Wan, S., Zhang, F., Zhong, W. Artificial intelligence for omics data analysis. BMC Methods 1, 4, 2024

Highlighted 2023 Publications:

• Zhang, F.*, Jonsson, A.H.*, Nathan, A.*, Millard, N.*, et al, Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes, Nature, 2023

• Kang, J.B., Shen, A.Z., Sakaue, S., Luo, Y., Gurajala, S., Natha, A., Rumker, L., Aguiar, V.R.C., Valencia, C., Lagattuta, K., Zhang, F., Jonsson, A.H., Yazar, S., …, Raychaudhuri, S., Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution, Nature Genetics, 2023

• Guo, N., Vargas, J., Fritz, F., Krishna, R., Zhang, F., Uncover spatially informed shared variations for single-cell spatial transcriptomics with STew, bioRxiv, 2023.

• Iijima, H., Zhang, F., Ambrosio, F., Matsui, Y., Network-based cytokine inference implicates Oncostatin M as a driver for inflammation phenotype of knee osteoarthritis. Aging Cell, https://doi.org/10.1111/acel.14043, 2023

• Weisenfeld, D., Zhang, F., Donlin, L., Jonsson, A.H., Apruzzese, W., Campbell, D., ..., Liao, K.P., Associations between rheumatoid arthritis clinical factors with synovial cell types and states, Arthritis & Rheumatology, 2023 

• Bai, Z., Bartelo, N., Aslam, M., Hale, C., Blachere, N., Parveen, S., Spolaore, E., DiCarlo, E., Gravallese, E., Smith, M.H., …, Pitzalis, C., Malfait, A., Miller, R.E., Zhang, F., Goodman, S., Darnell, R., Wang, F., Orange, D.E., Machine Learning Reveals Synovial Fibroblast Genes Associated with Pain Affect Sensory Nerve Growth in Rheumatoid Arthritis, medRxiv, 2023

• Iijima, H., Zhang, F., Ambrosio, F., Matsui, Y., Network-based cytokine inference implicates Oncostatin M as a driver for inflammation phenotype of knee osteoarthritis, bioRxiv, 2023

Highlighted 2022 Publications:

• 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, 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, 2022

• Liu. S.*, Li, L.*, Zhang, F.*, et al, Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC, In review, 2022

• Jonsson, A.H.*, Zhang, F.*, Dunlap, G., Gomez-Rivas, E., Watts, G.F.M., Faust, H., Rupani, K., Rupani, K.V., Mears, J.R., Meednu, N., Wang, R., Keras, G., Coblyn J., Massarotti, E., Todd, D., Anolik, J.H., McDavid, A., AMP RA/SLE, Wei, K., Rao, D.A., Raychaudhuri, S.*, Brenner, M.B.*. Granzyme K+ CD8 T cells form a core population in inflamed human tissue Science Translational Medicine, 2022 [Cover article!]

• Meednu, N., Rangel-Moreno, J., Zhang, F., Escaiera-Rivera, K., Corsiero, E., …, McDavid, A., Anolik, J.H. Dynamic spectrum of ectopic lymphoid B cell activation and hypermutation in the RA synovium characterized by NR4A nuclear receptor expression, Cell Reports, 2022

• Guan, S., Mehta, B., Slater, D., Thompson, J., DiCarlo, E., Pannellini, T., Pearce-Fisher, D., Zhang, F. Raychaudhuri, S., Hale, C., Jiang, C.S., Goodman, S., Orange, D. Rheumatoid arthritis synovial inflammation quantification using computer vision. ACR Open Rheumatology, 2022

Highlighted Publications before 2021:

• Kang, J.B., Nathan, A., Weinand, K., Zhang, F., Millard, N., Rumker, L., Moody, D.B., Korsunsky, I., Raychaudhuri, S. Efficient and precise single-cell reference atlas mapping with Symphony. Nature Communications, 12, 5890, 2021

• Mysore, V., Cullere, X., Mears, J., Rosetti, F., Okubo, K., Liew, P. X., Zhang, F., Madera-Salcedo, I., …, Raychaudhuri, Mayadas, TN. FcγR engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity. Nature Communications, 12(1), 1-23, 2021

• Fan, J., Slowikowski, K, Zhang, F. Single-cell transcriptomics in cancer: computational challenges and opportunities. Nature Experimental & Molecular Medicine, 2020

• Orange, D., Yao, V., Sawicka, K., Jak, J., Frank, M.O., Parveen, S., Blachere, N.E., Hale, C., Zhang, F., Raychaudhuri, S., Troyanskya, O.G., Darnell, R.B. RNA identification of PRIME cells predicting rheumatoid arthritis flares. New England Journal of Medicine (NEJM), 2020

• Kuo, D.*, Ding J.*, Cohn, I., Zhang, F., Wei, K., Rao, D., Rozo. C., Sokhi U.K., Shanaj, S., Oliver, D., Echeverria, A.P., DiCarlo E.F., Brenner, M.B., Bykerk, V.P., Goodman, S.M., Raychaudhuri, S., Ratsch, G., Ivashkiv, L.B., Donlin, L.T. HBEGF+ macrophages in rheumatoid arthritis induce fibroblast invasiveness. Science Translational Medicine, 2019

• Korsunsky, I., Millard, N., Fan, J., Slowikowski, K., Zhang, F., Wei, K., ..., Loh, P., Raychaudhuri, S. Fast, sensitive and accurate integration of single-cell data with Harmony. Nature Methods, 2019

• Arazi, A.*, Rao, D.A.*, Berthier, C.C.*, Davidson, A., Liu, Y., Hoover, P.J., Chicoine, A., Eisenhaure, T.M., Jonsson, A.H., Li, S., Lieb, D.J., Zhang, F., Slowikovski K, …, Raychaudhuri S., Kretzler, M., Anolik, J.H., Brenner, M.B., Wofsy D., Hacohen, N.*, Diamond, B.*, the AMP RA/SLE. The immune cell landscape in kidneys of patients with lupus nephritis. Nature Immunology, 2019