Publications
2024
A Pairwise Cytokine Code Explains the Organism-Wide Response to Sepsis
Takahama M, Patil A, Richey G, Cipurko D, Johnson K, Carbonetto P, Plaster M, Pandey S, Cheronis K, Ueda T, Gruenbaum A, Kawamoto T, Stephens M, Chevrier N.
Nature Immunology, 25, 226–239 (2024).
Featured in: Research Briefing
PubMed PMID: 38191855.
2023
A Flexible Model for Correlated Count Data, with Application to Analysis of Gene Expression Differences in Multi-Condition Experiments
Liu Y, Carbonetto P, Takahama M, Gruenbaum A, Xie D, Chevrier N, Stephens M.
Preprint: https://arxiv.org/abs/2210.00697
2020
Pairwise Stimulations of Pathogen-Sensing Pathways Predict Immune Responses to Multi-Adjuvant Combinations
Pandey S, Gruenbaum A, Kashanova T, Mertins P, Cluzel P, Chevrier N.
Cell Systems 11(5):495-508.e10 (2020).
PubMed PMID: 33113356.
A Whole-Tissue RNA-seq Toolkit for Organism-Wide Studies of Gene Expression with PME-seq
Pandey S, Takahama M, Gruenbaum A, Zewde M, Cheronis K, Chevrier N.
Nature Protocols 15(4):1459-1483 (2020).
PubMed PMID: 32076350.
2019
Decoding the Body Language of Immunity: Tackling the Immune System at the Organism Level
Chevrier N.
Current Opinion in Systems Biology 18, 19-26 (2019).
PubMed PMID: 32490290.
2017
Organism-Level Analysis of Vaccination Reveals Networks of Protection Across Tissues.
Kadoki M, Patil A, Thaiss C, Brooks DJ, Pandey S, Deep D, Alvarez D, von Andrian UH, Wagers AJ, Nakai K, Mikkelsen T, Soumillon M, Chevrier N.
Cell 171(2):398-413 (2017).
Featured in: Trends in Immunology, F1000 Faculty, Cell Systems
PubMed PMID: 28942919.
An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling.
Mertins P*, Przybylski D*, Yosef N, Qiao J, Clauser K, Raychowdhury R, Eisenhaure TM, Maritzen T, Haucke V, Satoh T, Akira S, Carr SA, Regev A, Hacohen N, Chevrier N.
Cell Reports 19(13):2853-2866 (2017).
PubMed PMID: 28658630.
2016
Suppression by TFR cells leads to durable and selective inhibition of B cell effector functions.
Sage PT, Ron-Harel N, Juneja V, Sen D, Maleri S, Sungnak W, Kuchroo V, Haining N, Chevrier N, Haigis M, Sharpe A.
Nature Immunology 17(12):1436-1446 (2016).
PubMed PMID: 27695002.
Parsing the Interferon Transcriptional Network and Its Disease Associations.
Mostafavi S, Yoshida H, Moodley D, LeBoité H, Rothamel K, Raj T, Ye CJ, Chevrier N, Zhang SY, Feng T, Lee M, Casanova JL, Clark JD, Hegen M, Telliez JB, Hacohen N, De Jager PL, Regev A, Mathis D, Benoist C; Immunological Genome Project Consortium.
Cell 164(3):564-78 (2016).
PubMed PMID: 26824662.
2015
Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.
Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A.
Science 347(6226):1259038 (2015).
PubMed PMID: 25745177.
Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator.
Maier VK, Feeney CM, Taylor JE, Creech AL, Qiao JW, Szanto A, Das PP, Chevrier N, Cifuentes-Rojas C, Orkin SH, Carr SA, Jaffe JD, Mertins P, Lee JT.
Mol Cell Proteomics 14(6):1435-46 (2015).
PubMed PMID: 25680957.
2013
Bisphosphonates target B cells to enhance humoral immune responses.
Tonti E, Jiménez de Oya N, Galliverti G, Moseman EA, Di Lucia P, Amabile A, Sammicheli S, De Giovanni M, Sironi L, Chevrier N, Sitia G, Gennari L, Guidotti LG, von Andrian UH, Iannacone M.
Cell Reports 5(2):323-30 (2013).
PubMed PMID: 24120862.
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.
Gat-Viks I, Chevrier N, Wilentzik R, Eisenhaure T, Raychowdhury R, Steuerman Y, Shalek A, Hachohen N, Amit I, Regev A.
Nature Biotechnology 31(4):342-9 (2013).
PubMed PMID: 23503680.
Pathogenic Brucellae replicate in human trophoblasts.
Salcedo SP, Chevrier N, Santos Lacerda TL, Ben Amara A, Gerart S, Gorvel VA, de Chastellier C, Blasco JM, Mege JL, Gorvel JP.
Journal of Infectious Diseases 207(7):1075-83 (2013).
PubMed PMID: 23303808.
2012
Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia.
Shalek AK, Gaublomme JT, Wang L, Yosef N, Chevrier N, Andersen MS, Robinson JT, Pochet N, Neuberg D, Gertner RS, Amit I, Brown JR, Hacohen N, Regev A, Wu CJ, Park H.
Nano Letters 12(12):6498-504 (2012).
PubMed PMID: 23190424.
A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals.
Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Chang C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I.
Molecular Cell 47(5):810-22 (2012).
PubMed PMID: 22940246.
B cell maintenance of subcapsular sinus macrophages protects against a fatal viral infection independent of adaptive immunity.
Moseman EA, Iannacone M, Bosurgi L, Tonti E, Chevrier N, Tumanov A, Fu YX, Hacohen N, von Andrian UH.
Immunity 36(3):415-26 (2012).
PubMed PMID: 22386268.
2011
Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits.
Chevrier N, Mertins P, Artyomov MN, Shalek AK, Iannacone M, Ciaccio MF, Gat-Viks I, Tonti E, DeGrace MM, Clauser KR, Garber M, Eisenhaure TM, Yosef N, Robinson JT, Sutton A, Andersen MS, Root DE, von Andrian U, Jones RB, Park H, Carr SA, Regev A*, Amit I*, Hacohen N*.
Cell 147(4):853-67 (2011).
PubMed PMID: 22078882.
Confinement of activating receptors at the plasma membrane controls natural killer cell tolerance.
Guia S, Jaeger BN, Piatek S, Mailfert S, Trombik T, Fenis A, Chevrier N, Walzer T, Kerdiles YM, Marguet D, Vivier E, Ugolini S.
Science Signaling 4(167):ra21 (2011).
PubMed PMID: 21467299.
2009
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses.
Amit I, Garber M*, Chevrier N*, Leite AP*, Donner Y*, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A.
Science 326, 257-263 (2009).
PubMed PMID: 19729616.
2006
Detection of Pathogenic Intestinal Bacteria by Toll-like Receptor 5 on Intestinal CD11c+ Lamina Propria Cells.
Uematsu S*, Jang MH*, Chevrier N, Guo Z, Kumagai Y, Yamamoto M, Kato H, Sougawa N, Matsui H, Kuwata H, Hemmi H, Coban C, Kawai T, Ishii KJ, Takeuchi O, Miyasaka M, Takeda K, Akira S.
Nature Immunology 7(8):868-74 (2006).
PubMed PMID: 16829963.