Selected Publications
Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers BA, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint. Immunity 2024 PMID: 38697118, DOI: 10.1016/j.immuni.2024.04.009.
Sex and prior exposure jointly shape innate immune responses to a live herpesvirus vaccine
Cheung F, Apps R, Dropulic L, Kotliarov Y, Chen J, Jordan T, Langweiler M, Candia J, Biancotto A, Han K, Rachmaninoff N, Pietz H, Wang K, Tsang JS, Cohen J. Sex and prior exposure jointly shape innate immune responses to a live herpesvirus vaccine. ELife 2023, 12: e80652. PMID: 36648132, PMCID: PMC9844983, DOI: 10.7554/elife.80652.
Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19
Sparks R*, Lau W*, Liu C*, Han K, Vrindten K, Sun G, Cox M, Andrews S, Bansal N, Failla L, Manischewitz J, Grubbs G, King L, Koroleva G, Leimenstoll S, Snow L, Chen J, Tang J, Mukherjee A, Sellers B, Apps R, McDermott A, Martins A, Bloch E, Golding H, Khurana S, Tsang JS. Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19. Nature 2023, 614: 752-761. PMID: 36599369, PMCID: PMC10481789, DOI: 10.1038/s41586-022-05670-5. (* co-first authors)
Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children
Xu Q, Milanez-Almeida P, Martins A, Radtke A, Hoehn K, Oguz C, Chen J, Liu C, Tang J, Grubbs G, Stein S, Ramelli S, Kabat J, Behzadpour H, Karkanitsa M, Spathies J, Kalish H, Kardava L, Kirby M, Cheung F, Preite S, Duncker P, Kitakule M, Romero N, Preciado D, Gitman L, Koroleva G, Smith G, Shaffer A, McBain I, McGuire P, Pittaluga S, Germain R, Apps R, Schwartz D, Sadtler K, Moir S, Chertow D, Kleinstein S, Khurana S, Tsang JS, Mudd P, Schwartzberg P, Manthiram K. Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children. Nature Immunology 2022, 24: 186-199. PMID: 36536106, PMCID: PMC10777159, DOI: 10.1038/s41590-022-01367-z.
Considering innate immune responses in SARS-CoV-2 infection and COVID-19
Diamond M, Lambris J, Ting J, Tsang JS. Considering innate immune responses in SARS-CoV-2 infection and COVID-19. Nature Reviews Immunology 2022, 22: 465-470. PMID: 35788185, PMCID: PMC9252555, DOI: 10.1038/s41577-022-00744-x.
Normalizing and denoising protein expression data from droplet-based single cell profiling
Mulè M, Martins A, Tsang JS. Normalizing and denoising protein expression data from droplet-based single cell profiling. Nature Communications 2022, 13: 2099. PMID: 35440536, PMCID: PMC9018908, DOI: 10.1038/s41467-022-29356-8.
Sacco K*, Castagnoli R*, Vakkilainen S*, Liu C*, Delmonte OM, Oguz C, Kaplan IM, Alehashemi S, Burbelo PD, Bhuyan F, de Jesus AA, Dobbs K, Rosen LB, Cheng A, Shaw E, Vakkilainen MS, Pala F, Lack J, Zhang Y, Fink DL, Oikonomou V, Snow AL, Dalgard CL, Chen J, Sellers BA, Montealegre Sanchez GA, Barron K, Rey-Jurado E, Vial C, Poli MC, Licari A, Montagna D, Marseglia GL, Licciardi F, Ramenghi U, Discepolo V, Lo Vecchio A, Guarino A, Eisenstein EM, Imberti L, Sottini A, Biondi A, Mató S, Gerstbacher D, Truong M, Stack MA, Magliocco M, Bosticardo M, Kawai T, Danielson JJ, Hulett T, Askenazi M, Hu S, Cohen J, Su H, Kuhns D, Lionakis M, Snyder T, Holland S, Goldbach-Mansky R, Tsang JS, Notarangelo L. Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19. Nature Medicine 2022, 28: 1050-1062. PMID: 35177862, PMCID: PMC9119950, DOI: 10.1038/s41591-022-01724-3. (* co-first authors)
Wong H, Park K, Gola A, Baptista A, Miller C, Deep D, Lou M, Boyd L, Rudensky A, Savage P, Altan-Bonnet G, Tsang JS, Germain R. A local regulatory T cell feedback circuit maintains immune homeostasis by pruning self-activated T cells. Cell 2021, 184: 3981-3997.e22. PMID: 34157301, PMCID: PMC8390950, DOI: 10.1016/j.cell.2021.05.028.
Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children. Immunity 2021, 54: 1083-1095.e7. PMID: 33891889, PMCID: PMC8043654, DOI: 10.1016/j.immuni.2021.04.003.
Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19
Liu C*, Martins AJ*, Lau WW*, Rachmaninoff N*, Chen J, Imberti L, Mostaghimi D, Fink DL, Burbelo PD, Dobbs K, Delmonte OM, Bansal N, Failla L, Sottini A, Quiros-Roldan E, Han KL, Sellers BA, Cheung F, Sparks R, Chun TW, Moir S, Lionakis MS; NIAID COVID Consortium; COVID Clinicians; Rossi C, Su HC, Kuhns DB, Cohen JI, Notarangelo LD, Tsang JS. Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19. Cell. 2021 Apr 1;184(7):1836-1857.e22. doi: 10.1016/j.cell.2021.02.018. Epub 2021 Feb 10. PMID: 33713619; PMCID: PMC7874909. (* co-first authors)
Intravenous nanoparticle vaccination generates stem-like TCF1+ neoantigen-specific CD8+ T cells
Baharom F, Ramirez-Valdez RA, Tobin KKS, Yamane H, Dutertre CA, Khalilnezhad A, Reynoso GV, Coble VL, Lynn GM, Mulè MP, Martins AJ, Finnigan JP, Zhang XM, Hamerman JA, Bhardwaj N, Tsang JS, Hickman HD, Ginhoux F, Ishizuka AS, Seder RA. Intravenous nanoparticle vaccination generates stem-like TCF1+ neoantigen-specific CD8+ T cells. Nature Immunology 2020, 22: 41-52. PMID: 33139915, PMCID: PMC7746638, DOI: 10.1038/s41590-020-00810-3.
Improving Vaccine-Induced Immunity: Can Baseline Predict Outcome?
Tsang JS, Dobaño C, VanDamme P, Moncunill G, Marchant A, Othman R, Sadarangani M, Koff W, Kollmann T. Improving Vaccine-Induced Immunity: Can Baseline Predict Outcome? Trends In Immunology 2020, 41: 457-465. PMID: 32340868, PMCID: PMC7142696, DOI: 10.1016/j.it.2020.04.001.
Kotliarov Y*, Sparks R*, Martins A, Mulè M, Lu Y, Goswami M, Kardava L, Banchereau R, Pascual V, Biancotto A, Chen J, Schwartzberg P, Bansal N, Liu C, Cheung F, Moir S, Tsang JS. Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nature Medicine 2020, 26: 618-629. PMID: 32094927, PMCID: PMC8392163, DOI: 10.1038/s41591-020-0769-8. (* co-first authors)
Cancer prognosis with shallow tumor RNA sequencing
Milanez-Almeida P, Martins A, Germain R, Tsang JS. Cancer prognosis with shallow tumor RNA sequencing. Nature Medicine 2020, 26: 188-192. PMID: 32042193, DOI: 10.1038/s41591-019-0729-3.
Austin JW, Buckner CM, Kardava L, Wang W, Zhang X, Melson VA, Swanson RG, Martins AJ, Zhou JQ, Hoehn KB, Fisk JN, Dimopoulos Y, Chassiakos A, O'Dell S, Smelkinson MG, Seamon CA, Kwan RW, Sneller MC, Pittaluga S, Doria-Rose NA, McDermott A, Li Y, Chun TW, Kleinstein SH, Tsang JS, Petrovas C, Moir S. Overexpression of T-bet in HIV infection is associated with accumulation of B cells outside germinal centers and poor affinity maturation. Science Translational Medicine 2019, 11 PMID: 31776286, PMCID: PMC7479651, DOI: 10.1126/scitranslmed.aax0904.
Resident Macrophages Cloak Tissue Microlesions to Prevent Neutrophil-Driven Inflammatory Damage
Uderhardt S, Martins A, Tsang JS, Lämmermann T, Germain R. Resident Macrophages Cloak Tissue Microlesions to Prevent Neutrophil-Driven Inflammatory Damage. Cell 2019, 177: 541-555.e17. PMID: 30955887, PMCID: PMC6474841, DOI: 10.1016/j.cell.2019.02.028.
Machine learning of stochastic gene network phenotypes
Machine learning of stochastic gene network phenotypes Kyemyung Park, Thorsten Prüstel, Yong Lu, John S. Tsang bioRxiv 825943; doi: https://doi.org/10.1101/825943
Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network
Martins A*, Narayanan M*, Prüstel T, Fixsen B, Park K, Gottschalk R, Lu Y, Andrews-Pfannkoch C, Lau W, Wendelsdorf K, Tsang JS. Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network. Cell Systems 2017, 4: 379-392.e12. PMID: 28365150, PMCID: PMC8392141, DOI: 10.1016/j.cels.2017.03.002. (* co-first authors)
Vodovotz Y, Xia A, Read EL, Bassaganya-Riera J, Hafler DA, Sontag E, Wang J, Tsang JS, Day JD, Kleinstein SH, Butte AJ, Altman MC, Hammond R, Sealfon SC. Solving Immunology? Trends In Immunology 2016, 38: 116-127. PMID: 27986392, PMCID: PMC5695553, DOI: 10.1016/j.it.2016.11.006.
Lu Y, Biancotto A, Cheung F, Remmers E, Shah N, McCoy J, Tsang JS. Systematic Analysis of Cell-to-Cell Expression Variation of T Lymphocytes in a Human Cohort Identifies Aging and Genetic Associations. Immunity 2016, 45: 1162-1175. PMID: 27851916, PMCID: PMC6532399, DOI: 10.1016/j.immuni.2016.10.025.
A crowdsourcing approach for reusing and meta-analyzing gene expression data
Shah N, Guo Y, Wendelsdorf K, Lu Y, Sparks R, Tsang JS. A crowdsourcing approach for reusing and meta-analyzing gene expression data. Nature Biotechnology 2016, 34: 803-806. PMID: 27323300, PMCID: PMC6871002, DOI: 10.1038/nbt.3603.
Utilizing population variation, vaccination, and systems biology to study human immunology
Tsang JS. Utilizing population variation, vaccination, and systems biology to study human immunology. Trends In Immunology 2015, 36: 479-493. PMID: 26187853, PMCID: PMC4979540, DOI: 10.1016/j.it.2015.06.005.
Abnormal B cell memory subsets dominate HIV-specific responses in infected individuals
Kardava L, Moir S, Shah N, Wang W, Wilson R, Buckner CM, Santich BH, Kim LJ, Spurlin EE, Nelson AK, Wheatley AK, Harvey CJ, McDermott AB, Wucherpfennig KW, Chun TW, Tsang JS, Li Y, Fauci AS. Abnormal B cell memory subsets dominate HIV-specific responses in infected individuals. Journal Of Clinical Investigation 2014, 124: 3252-3262. PMID: 24892810, PMCID: PMC4071400, DOI: 10.1172/jci74351.
Global Analyses of Human Immune Variation Reveal Baseline Predictors of Postvaccination Responses
Tsang JS*, Schwartzberg P*, Kotliarov Y, Biancotto A, Xie Z, Germain R, Wang E, Olnes M, Narayanan M, Golding H, Moir S, Dickler H, Perl S, Cheung F, Center T, Consortium T, Obermoser G, Chaussabel D, Palucka K, Chen J, Fuchs J, Ho J, Khurana S, King L, Langweiler M, Liu H, Manischewitz J, Pos Z, Posada J, Schum P, Shi R, Valdez J, Wang W, Zhou H, Kastner D, Marincola F, McCoy J, Trinchieri G, Young N. Global Analyses of Human Immune Variation Reveal Baseline Predictors of Postvaccination Responses. Cell 2014, 157: 499-513. PMID: 24725414, PMCID: PMC4139290, DOI: 10.1016/j.cell.2014.03.031. (* senior and corresponding authors)