Bonneau R - Search Results

1

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments.

Jackson CA, Castro DM, Saldi GA, Bonneau R, Gresham D. Jackson CA, et al. Among authors: bonneau r. Elife. 2020 Jan 27;9:e51254. doi: 10.7554/eLife.51254. Elife. 2020. PMID: 31985403 Free PMC article.

2

Rational design of temperature-sensitive alleles using computational structure prediction.

Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE, Bonneau R. Poultney CS, et al. Among authors: bonneau r. PLoS One. 2011;6(9):e23947. doi: 10.1371/journal.pone.0023947. Epub 2011 Sep 2. PLoS One. 2011. PMID: 21912654 Free PMC article.

3

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.

Arrieta-Ortiz ML, Hafemeister C, Bate AR, Chu T, Greenfield A, Shuster B, Barry SN, Gallitto M, Liu B, Kacmarczyk T, Santoriello F, Chen J, Rodrigues CD, Sato T, Rudner DZ, Driks A, Bonneau R, Eichenberger P. Arrieta-Ortiz ML, et al. Among authors: bonneau r. Mol Syst Biol. 2015 Nov 17;11(11):839. doi: 10.15252/msb.20156236. Mol Syst Biol. 2015. PMID: 26577401 Free PMC article.

4

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions.

Plessis A, Hafemeister C, Wilkins O, Gonzaga ZJ, Meyer RS, Pires I, Müller C, Septiningsih EM, Bonneau R, Purugganan M. Plessis A, et al. Among authors: bonneau r. Elife. 2015 Nov 26;4:e08411. doi: 10.7554/eLife.08411. Elife. 2015. PMID: 26609814 Free PMC article.

5

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments.

Wilkins O, Hafemeister C, Plessis A, Holloway-Phillips MM, Pham GM, Nicotra AB, Gregorio GB, Jagadish SV, Septiningsih EM, Bonneau R, Purugganan M. Wilkins O, et al. Among authors: bonneau r. Plant Cell. 2016 Oct;28(10):2365-2384. doi: 10.1105/tpc.16.00158. Epub 2016 Sep 21. Plant Cell. 2016. PMID: 27655842 Free PMC article.

6

Fused Regression for Multi-source Gene Regulatory Network Inference.

Lam KY, Westrick ZM, Müller CL, Christiaen L, Bonneau R. Lam KY, et al. Among authors: bonneau r. PLoS Comput Biol. 2016 Dec 6;12(12):e1005157. doi: 10.1371/journal.pcbi.1005157. eCollection 2016 Dec. PLoS Comput Biol. 2016. PMID: 27923054 Free PMC article.

7

Biophysically Motivated Regulatory Network Inference: Progress and Prospects.

Äijö T, Bonneau R. Äijö T, et al. Among authors: bonneau r. Hum Hered. 2016;81(2):62-77. doi: 10.1159/000446614. Epub 2017 Jan 12. Hum Hered. 2016. PMID: 28076866 Free article. Review.

8

Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks.

Tchourine K, Vogel C, Bonneau R. Tchourine K, et al. Among authors: bonneau r. Cell Rep. 2018 Apr 10;23(2):376-388. doi: 10.1016/j.celrep.2018.03.048. Cell Rep. 2018. PMID: 29641998 Free PMC article.

9

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.

10

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.

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