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Richard Bonneau
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Wisdom of crowds for robust gene network inference
D Marbach, JC Costello, R Küffner, NM Vega, RJ Prill, DM Camacho, ...
Nature methods 9 (8), 796-804, 2012
15312012
Tweeting from left to right: Is online political communication more than an echo chamber?
P Barberá, JT Jost, J Nagler, JA Tucker, R Bonneau
Psychological science 26 (10), 1531-1542, 2015
14732015
The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts
AG Baltz, M Munschauer, B Schwanhäusser, A Vasile, Y Murakawa, ...
Molecular cell 46 (5), 674-690, 2012
11212012
A validated regulatory network for Th17 cell specification
M Ciofani, A Madar, C Galan, ML Sellars, K Mace, F Pauli, A Agarwal, ...
Cell 151 (2), 289-303, 2012
10382012
Sparse and compositionally robust inference of microbial ecological networks
ZD Kurtz, CL Müller, ER Miraldi, DR Littman, MJ Blaser, RA Bonneau
PLoS computational biology 11 (5), e1004226, 2015
8322015
Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome
EA Miao, DP Mao, N Yudkovsky, R Bonneau, CG Lorang, SE Warren, ...
Proceedings of the National Academy of Sciences 107 (7), 3076-3080, 2010
8222010
The Rosetta all-atom energy function for macromolecular modeling and design
RF Alford, A Leaver-Fay, JR Jeliazkov, MJ O’Meara, FP DiMaio, H Park, ...
Journal of chemical theory and computation 13 (6), 3031-3048, 2017
7422017
Ab initio protein structure prediction of CASP III targets using ROSETTA
KT Simons, R Bonneau, I Ruczinski, D Baker
Proteins: Structure, Function, and Bioinformatics 37 (S3), 171-176, 1999
6991999
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
R Bonneau, DJ Reiss, P Shannon, M Facciotti, L Hood, NS Baliga, ...
Genome biology 7 (5), 1-16, 2006
6162006
Structural bioinformatics
J Gu, PE Bourne
John Wiley & Sons, 2009
4962009
An IL-23R/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses
T Sano, W Huang, JA Hall, Y Yang, A Chen, SJ Gavzy, JY Lee, JW Ziel, ...
Cell 163 (2), 381-393, 2015
4442015
High-definition spatial transcriptomics for in situ tissue profiling
S Vickovic, G Eraslan, F Salmén, J Klughammer, L Stenbeck, D Schapiro, ...
Nature methods 16 (10), 987-990, 2019
4382019
Ab initio protein structure prediction: progress and prospects
R Bonneau, D Baker
Annual review of biophysics and biomolecular structure 30 (1), 173-189, 2001
4252001
Rosetta in CASP4: progress in ab initio protein structure prediction
R Bonneau, J Tsai, I Ruczinski, D Chivian, C Rohl, CEM Strauss, D Baker
Proteins: Structure, Function, and Bioinformatics 45 (S5), 119-126, 2001
3872001
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea
NS Baliga, R Bonneau, MT Facciotti, M Pan, G Glusman, EW Deutsch, ...
Genome research 14 (11), 2221-2234, 2004
3722004
Automated prediction of CASP‐5 structures using the Robetta server
D Chivian, DE Kim, L Malmström, P Bradley, T Robertson, P Murphy, ...
Proteins: Structure, Function, and Bioinformatics 53 (S6), 524-533, 2003
3472003
How social media facilitates political protest: Information, motivation, and social networks
JT Jost, P Barberá, R Bonneau, M Langer, M Metzger, J Nagler, J Sterling, ...
Political psychology 39, 85-118, 2018
3402018
ICOS-based chimeric antigen receptors program bipolar TH17/TH1 cells
S Guedan, X Chen, A Madar, C Carpenito, SE McGettigan, MJ Frigault, ...
Blood, The Journal of the American Society of Hematology 124 (7), 1070-1080, 2014
3372014
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ...
Genome biology 17 (1), 1-19, 2016
3362016
A predictive model for transcriptional control of physiology in a free living cell
R Bonneau, MT Facciotti, DJ Reiss, AK Schmid, M Pan, A Kaur, ...
Cell 131 (7), 1354-1365, 2007
3342007
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