PUBLICATIONS
Pan-cancer mapping of single CD8+ T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity
Tooley K, Jerby L, Escobar G, Krovi SH, Mangani D, Dandekar G, Cheng H, Madi A, Goldschmidt E, Lambden C, Krishnan RK, Rozenblatt-Rosen O, Regev A, Anderson AC. Cell Rep Med. 2024 Jul 16;5(7):101640. doi: 10.1016/j.xcrm.2024.101640. Epub 2024 Jul 2. Pubmed
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors
Sheinin R, Salomon K, Yeini E, Dulberg S, Kaminitz A, Satchi-Fainaro R, Sharan R+, Madi A+. NPJ. Systems Biology and Apl. 2024 Jun 10;10(1):66. doi: 10.1038/s41540-024-00391-z. Pubmed (+ corresponding author)
Itan M*, Dulberg S*, Kaminitz A, Munitz A+, Madi A+. J Leukoc Biol. 2024 Mar 13;qiae063. doi: 10.1093/jleuko/qiae063. Pubmed (* equal contribution, + corresponding author)
Targeting PGLYRP1 promotes antitumor immunity while inhibiting autoimmune neuroinflammation
Schnell A, Huang L, Regan BML, Singh V, Vonficht D, Bollhagen A, Wang M, Hou Y, Bod L, Sobel RA, Chihara N, Madi A, Anderson AC, Regev A, Kuchroo VK. Nat Immunol. 2023 Nov;24(11):1908-1920. doi: 10.1038/s41590-023-01645-4. Epub 2023 Oct 12. Pubmed
Viral infection reveals hidden sharing of TCR CDR3 sequences between individuals
Mark M, Reich-Zeliger S, Greenstein E, Biram A, Chain B, Friedman N, Madi A. Front Immunol. 2023 May 30;14:1199064. doi: 10.3389/fimmu.2023.1199064. eCollection 2023. Pubmed
Kilian M*, Sheinin R*, Tan CL, Friedrich M, Krämer C, Kaminitz A, Sanghvi K, Lindner K, Chih YC, Cichon F, Richter B, Jung S, Jähne K, Ratliff M, Prins RM, Etminan N, von Deimling A, Wick W, Madi A+, Bunse L+, Platten M+. Cancer Cell. 2022 Dec 30:S1535-6108(22)00593-1. doi: 10.1016/j.ccell.2022.12.007. Online ahead of print. Pubmed (* equal contribution, + corresponding author)
Transient cell-in-cell formation underlies tumor relapse and resistance to immunotherapy
Gutwillig A, Santana-Magal N, Farhat-Younis L, Rasoulouniriana D, Madi A, Luxenburg C, Cohen J, Padmanabhan K, Shomron N, Shapira G, Gleiberman A, Parikh R, Levy C, Feinmesser M, Hershkovitz D, Zemser-Werner V, Zlotnik O, Kroon S, Hardt WD, Debets R, Reticker-Flynn NE, Rider P, Carmi Y. Elife. 2022 Sep 20;11:e80315. doi: 10.7554/eLife.80315. Pubmed
Pozzi S, Scomparin A, Ben-Shushan D, Yeini E, Ofek P, Nahmad AD, Soffer S, Ionescu A, Ruggiero A, Barzel A, Brem H, Hyde TM, Barshack I, Sinha S, Ruppin E, Weiss T, Madi A, Perlson E, Slutsky I, Florindo HF, Satchi-Fainaro R. JCI Insight. 2022 Sep 8;7(17):e154804. doi: 10.1172/jci.insight.154804. Pubmed
A hierarchy of selection pressures determines the organization of the T cell receptor repertoire.
Mark M, Reich-Zeliger S, Greenstein E, Reshef D, Madi A, Chain B, Friedman N. Front Immunol. 2022 Jul 29;13:939394. doi: 10.3389/fimmu.2022.939394. eCollection 2022. Pubmed
Perelroizen R, Philosof B, Budick-Harmelin N, Chernobylsky T, Ron A, Katzir R, Shimon D, Tessler A, Adir O, Gaoni-Yogev A, Meyer T, Krivitsky A, Shidlovsky N, Madi A, Ruppin E, Mayo L. Brain. 2022 Sep 14;145(9):3288-3307. doi: 10.1093/brain/awac222. Pubmed
Frequent aneuploidy in primary human T cells after CRISPR-Cas9 cleavage
Nahmad AD*, Reuveni E*, Goldschmidt E*, Tenne T, Liberman M, Horovitz-Fried M, Khosravi R, Kobo H, Reinstein E, Madi A+, Ben-David U+, Barzel A+. Nat Biotechnol. 2022 Jun 30. doi: 10.1038/s41587-022-01377-0. Pubmed (* equal contribution, + corresponding author)
Sumida TS*,+, Dulberg S*, Schupp J, Stillwell HA, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A+, Kuchroo VK, Hafler DA. Nature Immunology. 2022 March 17. Pubmed (* equal contribution, + corresponding author)
Metastasis-Entrained Eosinophils Enhance Lymphocyte-Mediated Antitumor Immunity
Grisaru-Tal S, Dulberg S, Beck L, Zhang C, Itan M, Hediyeh-Zadeh S, Caldwell J, Rozenberg P, Dolitzky A, Avlas S, Hazut I, Gordon Y, Shani O, Tsuriel S, Gerlic M, Erez N, Jacquelot N, Belz GT, Rothenberg ME, Davis MJ, Yu H, Geiger T, Madi A, Munitz A. Cancer Res. 2021 Nov 1;81(21):5555-5571. doi: 10.1158/0008-5472.CAN-21-0839. Pubmed
Neufeld L, Yeini E, Reisman N, Shtilerman Y, Ben-Shushan D, Pozzi S, Madi A, Tiram G, Eldar-Boock A, Ferber S, Grossman R, Ram Z, Satchi-Fainaro R. Sci Adv. 2021 Aug 18;7(34):eabi9119. doi: 10.1126/sciadv.abi9119. Print 2021 Aug. Pubmed
Shani O, Raz Y, Monteran L, Scharff Y, Levi-Galibov O, Megides O, Shacham H, Cohen N, Silverbush D, Avivi C, Sharan R, Madi A, Scherz-Shouval R, Barshack I, Tsarfaty I, Erez N. Elife. 2021 Jun 25;10:e60745. doi: 10.7554/eLife.60745. Pubmed
Holla P, Dizon B, Ambegaonkar AA, Rogel N, Goldschmidt E, Boddapati AK,
Sohn H, Sturdevant D, Austin JW, Kardava L, Yuesheng L, Liu P, Moir S, Pierce SK* and Madi A*. Science Adv. 2021: Vol. 7, no. 22, eabg8384 doi: 10.1126/sciadv.abg8384. Pubmed
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P-selectin axis plays a key role in microglia immunophenotype and glioblastoma progression.
Yeini E, Ofek P, Pozzi S, Albeck N, Ben-Shushan D, Tiram G, Golan S, Kleiner R, Sheinin R, Israeli Dangoor S, Reich-Zeliger S, Grossman R, Ram Z, Brem H, Hyde TM, Magod P, Friedmann-Morvinski D, Madi A & Satchi-Fainaro R. Nature Commun. 2021 12, 1912 . doi.org/10.1038/s41467-021-22186-0. Pubmed
Zhang H, Madi A*, Yosef N, Chihara N, Awasthi A, Pot C, Lambden C, Srivastava A, Burkett PR, Nyman J, Christian E, Etminan Y, Lee A, Stroh H, Xia J, Karwacz K, Thakore PI, Acharya N, Schnell A, Wang C, Apetoh L, Rozenblatt-Rosen O, Anderson AC, Regev A*, Kuchroo VK*. Cell Rep. 2020 Nov 24;33(8):108433. doi: 10.1016/j.celrep.2020.108433. (* corresponding author) Pubmed
Endogenous Glucocorticoid Signaling Regulates CD8+ T Cell Differentiation and Development of Dysfunction in the Tumor Microenvironment
Acharya N*, Madi A*, Zhang H, Klapholz M, Escobar G, Dulberg S, Christian H,Ferreira M, Dixon KO, Fell G, Tooley K, Mangani D, Xia J, Singer M, Bosenberg M, Neuberg D, Rozenblatt-Rosen O, Regev A, Kuchroo VK and Anderson AC: Immunity 2020 (* equal contribution) doi.org/10.1016/j.immuni.2020.08.005
Checkpoint Receptor TIGIT Expressed on Tim-1+ B Cells Regulates Tissue Inflammation.
Xiao S, Bod L, Pochet N, Kota SB, Hu D, Madi A, Kilpatrick J, Shi J, Ho A, Zhang H, Sobel R, Weiner HL, Strom TB, Quintana FJ, Joller N, Kuchroo VK: Cell Rep. 2020 Jul; 33(2) doi: 10.1016/j.celrep.2020.107892. Pubmed
The yin and yang of co-inhibitory receptors: toward anti-tumor immunity without autoimmunity.
Schnell A*, Bod L*, Madi A, Kuchroo VK: Cell Res. 2020 (* equal contribution) doi: https://doi.org/10.1038/s41422-020-0277-x
Challenges in the implementation of MIRIBEL criteria on nanobiomed manuscripts.
Florindo H.F., Madi A & Satchi-Fainaro R: Nature Nanotechnology 2019 Jul;14(7):627-628 doi: 10.1038/s41565-019-0498-7 Nature
Checkpoint blockade immunotherapy induces dynamic changes in novel subsets of PD-1-CD8+ tumor-infiltrating T cells.
Kurtulus S*, Madi A*, Escobar J, Klapholz M, Nyman J, Pawlak M, Dionne D, Xia J, Rozenblatt-Rosen O, Kuchroo VK, Regev A, Anderson AC: Immunity 2019 Jan 15;50(1):181-194.e6. (* equal contribution) Pubmed
Acute microglia ablation induces neurodegeneration in the somatosensory system.
Rubino SJ, Mayo L, Wimmer I, Siedler V, Brunner F, Hametner S, Madi A, Lanser A, Moreira T, Donnelly D, Cox L, Rezende RM, Butovsky O, Lassmann H, Weiner HL: Nat Commun. 2018 Nov 1;9(1):4578. doi: 10.1038/s41467-018-05929-4. Pubmed
Induction and transcriptional regulation of a “co-inhibitory” gene module in T cells.
Chihara N*, Madi A*, Kondo T, Singer M, Marjanovic ND, Kowalczyk MS, Wang C, Kurtulus S, Zhang H, Nyman J, Nevin J, Burkett PR, Rozenblatt-Rosen O, Anderson AC, Regev A, Kuchroo VK: Nature 2018, 558(7710):454-459. DOI: 10.1038/s41586-018-0206-z. (* equal contribution) Pubmed
SGK1 Governs the Reciprocal Development of Th17 and Regulatory T Cells.
Wu C, Chen Z, Xiao S, Thalhamer T, Madi A, Han T, Kuchroo VK: Cell Rep. 2018, 16;22(3):653-665. doi: 10.1016/j.celrep.2017.12.068.
The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.
Krasemann S, Madore C, Cialic R, Baufeld C, Calcagno N, El Fatimy R, Beckers L, O'Loughlin E, Xu Y, Fanek Z, Greco DJ, Smith ST, Tweet G, Humulock Z, Zrzavy T, Conde-Sanroman P, Gacias M, Weng Z, Chen H, Tjon E, Mazaheri F, Hartmann K, Madi A, Ulrich JD, Glatzel M, Worthmann A, Heeren J, Budnik B, Lemere C, Ikezu T, Heppner FL, Litvak V, Holtzman DM, Lassmann H, Weiner HL, Ochando J, Haass C, Butovsky O: Immunity 2017 Sep 19;47(3):566-581.e9. doi: 10.1016/j.immuni.2017.08.008. Pubmed
T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences.
Madi A*, Poran A*, Shifrut E, Reich-Zeliger S, Zaretsky I, Arnon T, Van Laethem F, Singer A, Lu J, Sun DP, Cohen IR and Friedman N: eLife 2017, 6:e22057 DOI: 10.7554/eLife.22057. (* equal contribution) Pubmed
Critical role of IRF1 and BATF in forming the chromatin landscape during Tr1 differentiation.
Karwacz K, Miraldi E, Pokrovskii M, Madi A, Yosef N, Wortman I, Chen X, Watters A, Carriero N, Awasthi A, Regev A, Bonneau R, Littman D, Kuchroo VK: Nature Immunol. 2017 Feb 6. doi: 10.1038/ni.3683. Pubmed
Targeting latency-associated peptide promotes anti-tumor immunity.
Gabriely G, Pires da Cunha A, Rezende RM, Kenyon B, Madi A, Vandeventer T, Rubino S, Garo L, Kolypetri P, Lanser A, Moreira T, Caetano Faria AM, Lassmann H, Kuchroo V, Murugaiyan G and Weiner HL: Science Immunol. 2017, 2(11): eaaj1738 Pubmed
Musculin promotes unidirectional development of peripheral Treg by suppressing the Th2 transcriptional program.
Wu C, Chen Z, Dardalhon V, Xiao S, Thalhamer T, Liao M, Madi A, Franca RF, Han T, Oukka M, and Kuchroo VK: Nature Immunol. 2017 Mar;18(3):344-353. Pubmed
IL-10-dependent Tr1 cells attenuate astrocyte activation and ameliorate chronic central nervous system inflammation.
Mayo L, Pires Da Cunha A, Madi A, Beynon V, Patel B, Alvarez JI, Prat A, Sobel R, Kuchroo KV, Lassmann H, Quintana FJ and Weiner HL: Brain 2016, 139(7):1939-57. Pubmed
TIM3 Mediates T Cell Exhaustion during Mycobacterium tuberculosis Infection.
Jayaraman P, Jacques MK, Zhu C, Steblenko MK, Stowell LB, Madi A, Anderson AC, Kuchroo VK, Behar SM: PLoS Pathog. 2016, 12(3): e1005490. Pubmed
CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity.
Wang C, Yosef N, Gaublomme J, Wu C, Lee Y, Clish CB, Kaminski J, Xiao S, Meyer Zu Horste G, Pawlak M, Kishi Y, Joller N, Karwacz K, Zhu C, Ordovas-Montanes M, Madi A, Wortman I, Miyazaki T, Sobel RA, Park H, Regev A, Kuchroo VK: Cell 2015, 163(6):1413-27. Pubmed
Human neonatal thymectomy induces altered B cell auto-reactivity later in life.
van den Broek T, Madi A, Delemarre EM, Schadenberg AWL, Tesselaar K, Borghans JA, Redegeld FA, Otten HG, Sorek R, Prakken B, M.D., Cohen IR, Jansen NJG: European Journal of Immunol. 2017, doi: 10.1002/eji.201746971. Pubmed
Tumor-Associated and Disease-Associated Autoantibody Repertoires in Healthy Colostrum and Maternal and Newborn Cord Sera.
Madi A, Bransburg-Zabary S, Maayan-Metzger A, Dar G, Ben-Jacob E, Cohen IR: J Immunol. 2015, 194(11):5272-81. Pubmed
T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity.
Madi A*, Shifrut E*, Reich-Zeliger S, Gal H, Best K, Ndifon W, Chain B, Cohen IR, Friedman N: Genome Res. 2014, 24(10):1603-12. (* equal contribution) Pubmed
Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence.
Thomas N, Best K, Cinelli M, Reich-Zeliger S, Gal H, Shifrut E, Madi A, Friedman N, Shawe-Taylor J, Chain B: Bioinformatics. 2014, 30(22):3181-8. Pubmed
Analyses of antigen dependency networks unveil immune system reorganization between birth and adulthood.
Madi A, Kenett DY, Bransburg-Zabary S, Merbl Y, Quintana FJ, Boccaletti S, Tauber AI, Cohen IR, Ben-Jacob E: Chaos 2011, 21(1):016109. Pubmed
Network theory analysis of antibody-antigen reactivity data: the immune trees at birth and adulthood.
Madi A, Kenett DY, Bransburg-Zabary S, Merbl Y, Quintana FJ, Tauber AI, Cohen IR, Ben-Jacob E: PLoS One 2011, 6(3):e17445. Pubmed
Organization of the autoantibody repertoire in healthy newborns and adults revealed by system level informatics of antigen microarray data.
Madi A, Hecht I, Bransburg-Zabary S, Merbl Y, Pick A, Zucker-Toledano M, Quintana FJ, Tauber AI, Cohen IR, Ben-Jacob E: Proc Natl Acad Sci U S A 2009, 106(34):14484-14489. Pubmed
Genome holography: deciphering function-form motifs from gene expression data.
Madi A, Friedman Y, Roth D, Regev T, Bransburg-Zabary S, Ben Jacob E: PLoS One 2008, 3(7):e2708. Pubmed