Bonneau R - Search Results

1

Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice.

Miraldi ER, Sharfi H, Friedline RH, Johnson H, Zhang T, Lau KS, Ko HJ, Curran TG, Haigis KM, Yaffe MB, Bonneau R, Lauffenburger DA, Kahn BB, Kim JK, Neel BG, Saghatelian A, White FM. Miraldi ER, et al. Among authors: bonneau r. Integr Biol (Camb). 2013 Jul 24;5(7):940-63. doi: 10.1039/c3ib40013a. Epub 2013 May 20. Integr Biol (Camb). 2013. PMID: 23685806 Free PMC article.

2

CX₃CR1⁺ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22.

Longman RS, Diehl GE, Victorio DA, Huh JR, Galan C, Miraldi ER, Swaminath A, Bonneau R, Scherl EJ, Littman DR. Longman RS, et al. Among authors: bonneau r. J Exp Med. 2014 Jul 28;211(8):1571-83. doi: 10.1084/jem.20140678. Epub 2014 Jul 14. J Exp Med. 2014. PMID: 25024136 Free PMC article.

3

Sparse and compositionally robust inference of microbial ecological networks.

Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Kurtz ZD, et al. Among authors: bonneau ra. PLoS Comput Biol. 2015 May 7;11(5):e1004226. doi: 10.1371/journal.pcbi.1004226. eCollection 2015 May. PLoS Comput Biol. 2015. PMID: 25950956 Free PMC article.

4

An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses.

Sano T, Huang W, Hall JA, Yang Y, Chen A, Gavzy SJ, Lee JY, Ziel JW, Miraldi ER, Domingos AI, Bonneau R, Littman DR. Sano T, et al. Among authors: bonneau r. Cell. 2015 Oct 8;163(2):381-93. doi: 10.1016/j.cell.2015.08.061. Epub 2015 Sep 24. Cell. 2015. PMID: 26411290 Free PMC article.

5

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.

Raviram R, Rocha PP, Müller CL, Miraldi ER, Badri S, Fu Y, Swanzey E, Proudhon C, Snetkova V, Bonneau R, Skok JA. Raviram R, et al. Among authors: bonneau r. PLoS Comput Biol. 2016 Mar 3;12(3):e1004780. doi: 10.1371/journal.pcbi.1004780. eCollection 2016 Mar. PLoS Comput Biol. 2016. PMID: 26938081 Free PMC article.

6

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.

Karwacz K, Miraldi ER, Pokrovskii M, Madi A, Yosef N, Wortman I, Chen X, Watters A, Carriero N, Awasthi A, Regev A, Bonneau R, Littman D, Kuchroo VK. Karwacz K, et al. Among authors: bonneau r. Nat Immunol. 2017 Apr;18(4):412-421. doi: 10.1038/ni.3683. Epub 2017 Feb 6. Nat Immunol. 2017. PMID: 28166218 Free PMC article.

7

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate.

Raviram R, Rocha PP, Luo VM, Swanzey E, Miraldi ER, Chuong EB, Feschotte C, Bonneau R, Skok JA. Raviram R, et al. Among authors: bonneau r. Genome Biol. 2018 Dec 13;19(1):216. doi: 10.1186/s13059-018-1598-7. Genome Biol. 2018. PMID: 30541598 Free PMC article.

8

Multi-study inference of regulatory networks for more accurate models of gene regulation.

Castro DM, de Veaux NR, Miraldi ER, Bonneau R. Castro DM, et al. Among authors: bonneau r. PLoS Comput Biol. 2019 Jan 24;15(1):e1006591. doi: 10.1371/journal.pcbi.1006591. eCollection 2019 Jan. PLoS Comput Biol. 2019. PMID: 30677040 Free PMC article.

9

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.

Miraldi ER, Pokrovskii M, Watters A, Castro DM, De Veaux N, Hall JA, Lee JY, Ciofani M, Madar A, Carriero N, Littman DR, Bonneau R. Miraldi ER, et al. Among authors: bonneau r. Genome Res. 2019 Mar;29(3):449-463. doi: 10.1101/gr.238253.118. Epub 2019 Jan 29. Genome Res. 2019. PMID: 30696696 Free PMC article.

10

Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells.

Pokrovskii M, Hall JA, Ochayon DE, Yi R, Chaimowitz NS, Seelamneni H, Carriero N, Watters A, Waggoner SN, Littman DR, Bonneau R, Miraldi ER. Pokrovskii M, et al. Among authors: bonneau r. Immunity. 2019 Jul 16;51(1):185-197.e6. doi: 10.1016/j.immuni.2019.06.001. Epub 2019 Jul 2. Immunity. 2019. PMID: 31278058 Free PMC article.

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