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High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0.
Skok Gibbs C, Jackson CA, Saldi GA, Tjärnberg A, Shah A, Watters A, De Veaux N, Tchourine K, Yi R, Hamamsy T, Castro DM, Carriero N, Gorissen BL, Gresham D, Miraldi ER, Bonneau R. Skok Gibbs C, et al. Among authors: bonneau r. Bioinformatics. 2022 Apr 28;38(9):2519-2528. doi: 10.1093/bioinformatics/btac117. Bioinformatics. 2022. PMID: 35188184 Free PMC article.
A validated regulatory network for Th17 cell specification.
Ciofani M, Madar A, Galan C, Sellars M, Mace K, Pauli F, Agarwal A, Huang W, Parkhurst CN, Muratet M, Newberry KM, Meadows S, Greenfield A, Yang Y, Jain P, Kirigin FK, Birchmeier C, Wagner EF, Murphy KM, Myers RM, Bonneau R, Littman DR. Ciofani M, et al. Among authors: bonneau r. Cell. 2012 Oct 12;151(2):289-303. doi: 10.1016/j.cell.2012.09.016. Epub 2012 Sep 25. Cell. 2012. PMID: 23021777 Free PMC article.
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.
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.
326 results