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The cis-Regulatory Atlas of the Mouse Immune System.

Yoshida H, Lareau CA, Ramirez RN, Rose SA, Maier B, Wroblewska A, Desland F, Chudnovskiy A, Mortha A, Dominguez C, Tellier J, Kim E, Dwyer D, Shinton S, Nabekura T, Qi Y, Yu B, Robinette M, Kim KW, Wagers A, Rhoads A, Nutt SL, Brown BD, Mostafavi S, Buenrostro JD, Benoist C; Immunological Genome Project.

Cell. 2019 Feb 7;176(4):897-912.e20. doi: 10.1016/j.cell.2018.12.036. Epub 2019 Jan 24.


Age-related tumor growth in mice is related to integrin α 4 in CD8+ T cells.

Oh J, Magnuson A, Benoist C, Pittet MJ, Weissleder R.

JCI Insight. 2018 Nov 2;3(21). pii: 122961. doi: 10.1172/jci.insight.122961. [Epub ahead of print]


Identification and validation of a tumor-infiltrating Treg transcriptional signature conserved across species and tumor types.

Magnuson AM, Kiner E, Ergun A, Park JS, Asinovski N, Ortiz-Lopez A, Kilcoyne A, Paoluzzi-Tomada E, Weissleder R, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):E10672-E10681. doi: 10.1073/pnas.1810580115. Epub 2018 Oct 22.


Molecular profiling of hormone receptor-positive, HER2-negative breast cancers from patients treated with neoadjuvant endocrine therapy in the CARMINA 02 trial (UCBG-0609).

Liang X, Briaux A, Becette V, Benoist C, Boulai A, Chemlali W, Schnitzler A, Baulande S, Rivera S, Mouret-Reynier MA, Bouvet LV, De La Motte Rouge T, Lemonnier J, Lerebours F, Callens C.

J Hematol Oncol. 2018 Oct 11;11(1):124. doi: 10.1186/s13045-018-0670-9.


Molecular diversification of regulatory T cells in nonlymphoid tissues.

DiSpirito JR, Zemmour D, Ramanan D, Cho J, Zilionis R, Klein AM, Benoist C, Mathis D.

Sci Immunol. 2018 Sep 14;3(27). pii: eaat5861. doi: 10.1126/sciimmunol.aat5861.


Genetic determinants of co-accessible chromatin regions in activated T cells across humans.

Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, De Jager PL, Chang HY, Aiden EL, Benoist C, Beer MA, Ye CJ, Regev A.

Nat Genet. 2018 Aug;50(8):1140-1150. doi: 10.1038/s41588-018-0156-2. Epub 2018 Jul 9.


TCR Transgenic Mice Reveal Stepwise, Multi-site Acquisition of the Distinctive Fat-Treg Phenotype.

Li C, DiSpirito JR, Zemmour D, Spallanzani RG, Kuswanto W, Benoist C, Mathis D.

Cell. 2018 Jul 12;174(2):285-299.e12. doi: 10.1016/j.cell.2018.05.004. Epub 2018 Jun 7.


Publisher Correction: Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR.

Zemmour D, Zilionis R, Kiner E, Klein AM, Mathis D, Benoist C.

Nat Immunol. 2018 Jun;19(6):645. doi: 10.1038/s41590-018-0104-4.


Relevance of a molecular tumour board (MTB) for patients' enrolment in clinical trials: experience of the Institut Curie.

Basse C, Morel C, Alt M, Sablin MP, Franck C, Pierron G, Callens C, Melaabi S, Masliah-Planchon J, Bataillon G, Gardrat S, Lavigne M, Bonsang B, Vaflard P, Pons Tostivint E, Dubot C, Loirat D, Marous M, Geiss R, Clément N, Schleiermacher G, Kamoun C, Girard E, Ardin M, Benoist C, Bernard V, Mariani O, Rouzier R, Tresca P, Servois V, Vincent-Salomon A, Bieche I, Le Tourneau C, Kamal M.

ESMO Open. 2018 Apr 6;3(3):e000339. doi: 10.1136/esmoopen-2018-000339. eCollection 2018.


Treg cells limit IFN-γ production to control macrophage accrual and phenotype during skeletal muscle regeneration.

Panduro M, Benoist C, Mathis D.

Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):E2585-E2593. doi: 10.1073/pnas.1800618115. Epub 2018 Feb 23.


Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR.

Zemmour D, Zilionis R, Kiner E, Klein AM, Mathis D, Benoist C.

Nat Immunol. 2018 Mar;19(3):291-301. doi: 10.1038/s41590-018-0051-0. Epub 2018 Feb 12. Erratum in: Nat Immunol. 2018 May 3;:.


FoxP3 scanning mutagenesis reveals functional variegation and mild mutations with atypical autoimmune phenotypes.

Kwon HK, Chen HM, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):E253-E262. doi: 10.1073/pnas.1718599115. Epub 2017 Dec 21. Erratum in: Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):E10515.


Vitamin D and Its Analogues Decrease Amyloid-β (Aβ) Formation and Increase Aβ-Degradation.

Grimm MOW, Thiel A, Lauer AA, Winkler J, Lehmann J, Regner L, Nelke C, Janitschke D, Benoist C, Streidenberger O, Stötzel H, Endres K, Herr C, Beisswenger C, Grimm HS, Bals R, Lammert F, Hartmann T.

Int J Mol Sci. 2017 Dec 19;18(12). pii: E2764. doi: 10.3390/ijms18122764.


The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.


Different molecular complexes that mediate transcriptional induction and repression by FoxP3.

Kwon HK, Chen HM, Mathis D, Benoist C.

Nat Immunol. 2017 Nov;18(11):1238-1248. doi: 10.1038/ni.3835. Epub 2017 Sep 11.


Imaging the emergence and natural progression of spontaneous autoimmune diabetes.

Mohan JF, Kohler RH, Hill JA, Weissleder R, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7776-E7785. doi: 10.1073/pnas.1707381114. Epub 2017 Aug 24.


Protective major histocompatibility complex allele prevents type 1 diabetes by shaping the intestinal microbiota early in ontogeny.

Silverman M, Kua L, Tanca A, Pala M, Palomba A, Tanes C, Bittinger K, Uzzau S, Benoist C, Mathis D.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9671-9676. doi: 10.1073/pnas.1712280114. Epub 2017 Aug 22.


Flicr, a long noncoding RNA, modulates Foxp3 expression and autoimmunity.

Zemmour D, Pratama A, Loughhead SM, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):E3472-E3480. doi: 10.1073/pnas.1700946114. Epub 2017 Apr 10.


An Intestinal Organ Culture System Uncovers a Role for the Nervous System in Microbe-Immune Crosstalk.

Yissachar N, Zhou Y, Ung L, Lai NY, Mohan JF, Ehrlicher A, Weitz DA, Kasper DL, Chiu IM, Mathis D, Benoist C.

Cell. 2017 Mar 9;168(6):1135-1148.e12. doi: 10.1016/j.cell.2017.02.009. Epub 2017 Mar 2.


T Regulatory Cells Support Plasma Cell Populations in the Bone Marrow.

Glatman Zaretsky A, Konradt C, Dépis F, Wing JB, Goenka R, Atria DG, Silver JS, Cho S, Wolf AI, Quinn WJ, Engiles JB, Brown DC, Beiting D, Erikson J, Allman D, Cancro MP, Sakaguchi S, Lu LF, Benoist CO, Hunter CA.

Cell Rep. 2017 Feb 21;18(8):1906-1916. doi: 10.1016/j.celrep.2017.01.067.


Mining the Human Gut Microbiota for Immunomodulatory Organisms.

Geva-Zatorsky N, Sefik E, Kua L, Pasman L, Tan TG, Ortiz-Lopez A, Yanortsang TB, Yang L, Jupp R, Mathis D, Benoist C, Kasper DL.

Cell. 2017 Feb 23;168(5):928-943.e11. doi: 10.1016/j.cell.2017.01.022. Epub 2017 Feb 16.


The transcriptional regulator Aire binds to and activates super-enhancers.

Bansal K, Yoshida H, Benoist C, Mathis D.

Nat Immunol. 2017 Mar;18(3):263-273. doi: 10.1038/ni.3675. Epub 2017 Jan 30.


Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice.

Tan TG, Sefik E, Geva-Zatorsky N, Kua L, Naskar D, Teng F, Pasman L, Ortiz-Lopez A, Jupp R, Wu HJ, Kasper DL, Benoist C, Mathis D.

Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):E8141-E8150. Epub 2016 Nov 23.


Singular role for T-BET+CXCR3+ regulatory T cells in protection from autoimmune diabetes.

Tan TG, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):14103-14108. Epub 2016 Nov 21.


Aire Inhibits the Generation of a Perinatal Population of Interleukin-17A-Producing γδ T Cells to Promote Immunologic Tolerance.

Fujikado N, Mann AO, Bansal K, Romito KR, Ferre EMN, Rosenzweig SD, Lionakis MS, Benoist C, Mathis D.

Immunity. 2016 Nov 15;45(5):999-1012. doi: 10.1016/j.immuni.2016.10.023.


Combination of COX-2 expression and PIK3CA mutation as prognostic and predictive markers for celecoxib treatment in breast cancer.

Tury S, Becette V, Assayag F, Vacher S, Benoist C, Kamal M, Marangoni E, Bièche I, Lerebours F, Callens C.

Oncotarget. 2016 Dec 20;7(51):85124-85141. doi: 10.18632/oncotarget.13200.


Network pharmacology of JAK inhibitors.

Moodley D, Yoshida H, Mostafavi S, Asinovski N, Ortiz-Lopez A, Symanowicz P, Telliez JB, Hegen M, Clark JD, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9852-7. doi: 10.1073/pnas.1610253113. Epub 2016 Aug 11.


Tissue Tregs.

Panduro M, Benoist C, Mathis D.

Annu Rev Immunol. 2016 May 20;34:609-33. doi: 10.1146/annurev-immunol-032712-095948. Review.


Promiscuity Promotes Tolerance.

Mathis D, Benoist C.

J Immunol. 2016 Apr 1;196(7):2913-4. doi: 10.4049/jimmunol.1600225. No abstract available.


Poor Repair of Skeletal Muscle in Aging Mice Reflects a Defect in Local, Interleukin-33-Dependent Accumulation of Regulatory T Cells.

Kuswanto W, Burzyn D, Panduro M, Wang KK, Jang YC, Wagers AJ, Benoist C, Mathis D.

Immunity. 2016 Feb 16;44(2):355-67. doi: 10.1016/j.immuni.2016.01.009. Epub 2016 Feb 9.


Fibroblast Growth Factor 21 (FGF21) Protects against High Fat Diet Induced Inflammation and Islet Hyperplasia in Pancreas.

Singhal G, Fisher FM, Chee MJ, Tan TG, El Ouaamari A, Adams AC, Najarian R, Kulkarni RN, Benoist C, Flier JS, Maratos-Flier E.

PLoS One. 2016 Feb 12;11(2):e0148252. doi: 10.1371/journal.pone.0148252. eCollection 2016.


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. 2016 Jan 28;164(3):564-78. doi: 10.1016/j.cell.2015.12.032.


Unstable FoxP3+ T regulatory cells in NZW mice.

Dépis F, Kwon HK, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1345-50. doi: 10.1073/pnas.1524660113. Epub 2016 Jan 14.


Imbalanced signal transduction in regulatory T cells expressing the transcription factor FoxP3.

Yan D, Farache J, Mingueneau M, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14942-7. doi: 10.1073/pnas.1520393112. Epub 2015 Nov 16. Erratum in: Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):E256. Mingueneau, Michael [added].


Constitutive Stringent Response Restores Viability of Bacillus subtilis Lacking Structural Maintenance of Chromosome Protein.

Benoist C, Guérin C, Noirot P, Dervyn E.

PLoS One. 2015 Nov 5;10(11):e0142308. doi: 10.1371/journal.pone.0142308. eCollection 2015.


Rapid, high efficiency isolation of pancreatic ß-cells.

Clardy SM, Mohan JF, Vinegoni C, Keliher EJ, Iwamoto Y, Benoist C, Mathis D, Weissleder R.

Sci Rep. 2015 Sep 2;5:13681. doi: 10.1038/srep13681.


MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells.

Sefik E, Geva-Zatorsky N, Oh S, Konnikova L, Zemmour D, McGuire AM, Burzyn D, Ortiz-Lopez A, Lobera M, Yang J, Ghosh S, Earl A, Snapper SB, Jupp R, Kasper D, Mathis D, Benoist C.

Science. 2015 Aug 28;349(6251):993-7. doi: 10.1126/science.aaa9420. Epub 2015 Aug 13.


Aire controls gene expression in the thymic epithelium with ordered stochasticity.

Meredith M, Zemmour D, Mathis D, Benoist C.

Nat Immunol. 2015 Sep;16(9):942-9. doi: 10.1038/ni.3247. Epub 2015 Aug 3.


Brd4 bridges the transcriptional regulators, Aire and P-TEFb, to promote elongation of peripheral-tissue antigen transcripts in thymic stromal cells.

Yoshida H, Bansal K, Schaefer U, Chapman T, Rioja I, Proekt I, Anderson MS, Prinjha RK, Tarakhovsky A, Benoist C, Mathis D.

Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):E4448-57. doi: 10.1073/pnas.1512081112. Epub 2015 Jul 27.


A pharmacogenetic study implicates SLC9a9 in multiple sclerosis disease activity.

Esposito F, Sorosina M, Ottoboni L, Lim ET, Replogle JM, Raj T, Brambilla P, Liberatore G, Guaschino C, Romeo M, Pertel T, Stankiewicz JM, Martinelli V, Rodegher M, Weiner HL, Brassat D, Benoist C, Patsopoulos NA, Comi G, Elyaman W, Martinelli Boneschi F, De Jager PL.

Ann Neurol. 2015 Jul;78(1):115-27. doi: 10.1002/ana.24429. Epub 2015 May 14.


Antigen- and cytokine-driven accumulation of regulatory T cells in visceral adipose tissue of lean mice.

Kolodin D, van Panhuys N, Li C, Magnuson AM, Cipolletta D, Miller CM, Wagers A, Germain RN, Benoist C, Mathis D.

Cell Metab. 2015 Apr 7;21(4):543-57. doi: 10.1016/j.cmet.2015.03.005.


ImmVar project: Insights and design considerations for future studies of "healthy" immune variation.

De Jager PL, Hacohen N, Mathis D, Regev A, Stranger BE, Benoist C.

Semin Immunol. 2015 Feb;27(1):51-7. doi: 10.1016/j.smim.2015.03.003. Epub 2015 Mar 25. Review.


Immune tolerance. Regulatory T cells generated early in life play a distinct role in maintaining self-tolerance.

Yang S, Fujikado N, Kolodin D, Benoist C, Mathis D.

Science. 2015 May 1;348(6234):589-94. doi: 10.1126/science.aaa7017. Epub 2015 Mar 19.


Noninvasive mapping of pancreatic inflammation in recent-onset type-1 diabetes patients.

Gaglia JL, Harisinghani M, Aganj I, Wojtkiewicz GR, Hedgire S, Benoist C, Mathis D, Weissleder R.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2139-44. doi: 10.1073/pnas.1424993112. Epub 2015 Feb 3.


Population dynamics of islet-infiltrating cells in autoimmune diabetes.

Magnuson AM, Thurber GM, Kohler RH, Weissleder R, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1511-6. doi: 10.1073/pnas.1423769112. Epub 2015 Jan 20.


Appearance and disappearance of the mRNA signature characteristic of Treg cells in visceral adipose tissue: age, diet, and PPARγ effects.

Cipolletta D, Cohen P, Spiegelman BM, Benoist C, Mathis D.

Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):482-7. doi: 10.1073/pnas.1423486112. Epub 2014 Dec 30.


Genomic responses to inflammation in mouse models mimic humans: we concur, apples to oranges comparisons won't do.

Shay T, Lederer JA, Benoist C.

Proc Natl Acad Sci U S A. 2015 Jan 27;112(4):E346. doi: 10.1073/pnas.1416629111. Epub 2014 Dec 24. No abstract available.


Epigenetic modulation of type-1 diabetes via a dual effect on pancreatic macrophages and β cells.

Fu W, Farache J, Clardy SM, Hattori K, Mander P, Lee K, Rioja I, Weissleder R, Prinjha RK, Benoist C, Mathis D.

Elife. 2014 Nov 19;3:e04631. doi: 10.7554/eLife.04631.


Single-cell mass cytometry of TCR signaling: amplification of small initial differences results in low ERK activation in NOD mice.

Mingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe'er D, Mathis D, Nolan GP, Benoist C.

Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16466-71. doi: 10.1073/pnas.1419337111. Epub 2014 Oct 31.


Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains.

Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, Mathis D, Benoist C; Immunological Genome Consortium.

J Immunol. 2014 Nov 1;193(9):4485-96. doi: 10.4049/jimmunol.1401280. Epub 2014 Sep 29.

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