Richard Bonneau

Richard A. Bonneau

Associate Professor of Biology, Computer Science; Faculty Director of Bioinformatics

Ph.D. 2001 (Biochemistry), University of Washington; B.A. 1997 (Biochemistry), Florida State University.

Office Address: 

New York University
Department of Biology
Center for Genomics and Systems Biology
12 Waverly Place, Room 406
New York, NY 10003


(212) 992-9516


(212) 995-4015

Lab Homepage:

Areas of Research/Interest: 

Systems Biology and Protein Modeling

List of Publications from Pubmed

List of citations from Google Scholar

Dr. Bonneau focuses on two main categories of computational biology: learning networks from functional genomics data and predicting and designing protein and peptoid structure. In both areas he has played key roles in achieving critical field-wide milestones. In the area of structure prediction he was one of the early authors on the Rosetta code, which was one of the first codes to demonstrate accurate and comprehensive ability to predict protein structure in the absence of sequence homology. His lab has also made key contributions to the areas of genomics data analysis. They focus on two main areas: 1) methods for network inference that learn dynamics and topology from data (the Inferelator) , and 2) methods that learn condition dependent co-regulated groups from integrations of different genomics data-types (integrative biclustering). His lab strives to develop new methods that let systems-biologists derive functional forms from relevant biology and parameters from data automatically. Dr. Bonneau has also helped to start a new project with political scientists and experimental psychologists to apply methods for learning network structure from time series to social media time series data (using Twitter, online blogs about politics, and Facebook as our initial data sources (recently funded by NSF INSPIRE, ).


Howard Hughes Medical Institute pre-doctoral Fellowship in the Biological Sciences, 1998-2001; Magna Cum Laude, Biochemistry, FSU, 1996; American Cancer Society – James Jay Fisher Fellowship, 1996; Florida Academic Scholars Award, 1993; International Baccalaureate Degree, 1993.

Selected Works:

PubMed Search Results:

Tweeting From Left to Right: Is Online Political Communication More Than an Echo Chamber?
Psychol Sci   (2015 Aug 21);   PMID: 26297377
Barbera P, Jost JT, Nagler J, Tucker JA, Bonneau R
Breaking TADs: insights into hierarchical genome organization.
Epigenomics   (2015);   PMID: 26111025
Rocha PP, Raviram R, Bonneau R, Skok JA
Sparse and compositionally robust inference of microbial ecological networks.
PLoS Comput Biol   (2015 May);  PMC4423992 free full-text archive
Kurtz ZD, Muller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA
Interpreting 4C-Seq data: how far can we go?
Epigenomics   (2014);  PMC4406053 free full-text archive
Raviram R, Rocha PP, Bonneau R, Skok JA
Inter-species pathway perturbation prediction via data-driven detection of functional homology.
Bioinformatics   (2015 Feb 15);  PMC4325539 free full-text archive
Hafemeister C, Romero R, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Bonneau R, Tarca AL
One third of dynamic protein expression profiles can be predicted by a simple rate equation.
Mol Biosyst   (2014 Nov);  PMC4183714 free full-text archive
Tchourine K, Poultney CS, Wang L, Silva GM, Manohar S, Mueller CL, Bonneau R, Vogel C
Improved stability and half-life of fluorinated phosphotriesterase using Rosetta.
Chembiochem   (2014 Aug 18);   PMID: 25066940
Yang CY, Renfrew PD, Olsen AJ, Zhang M, Yuvienco C, Bonneau R, Montclare JK
CX(3)CR1(+) mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22.
J Exp Med   (2014 Jul 28);  PMC4113938 free full-text archive
Longman RS, Diehl GE, Victorio DA, Huh JR, Galan C, Miraldi ER, Swaminath A, Bonneau R, Scherl EJ, Littman DR
ICOS-based chimeric antigen receptors program bipolar TH17/TH1 cells.
Blood   (2014 Aug 14);  PMC4133482 free full-text archive
Guedan S, Chen X, Madar A, Carpenito C, McGettigan SE, Frigault MJ, Lee J, Posey AD Jr, Scholler J, Scholler N, Bonneau R, June CH
Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions.
J Am Chem Soc   (2014 Jun 4);  PMC4353027 free full-text archive
Lao BB, Drew K, Guarracino DA, Brewer TF, Heindel DW, Bonneau R, Arora PS
Engineered coiled-coil protein microfibers.
Biomacromolecules   (2014 Oct 13);   PMID: 24941228
Hume J, Sun J, Jacquet R, Renfrew PD, Martin JA, Bonneau R, Gilchrist ML, Montclare JK
Negative example selection for protein function prediction: the NoGO database.
PLoS Comput Biol   (2014 Jun);  PMC4055410 free full-text archive
Youngs N, Penfold-Brown D, Bonneau R, Shasha D
Conformational preferences of peptide-peptoid hybrid oligomers.
Biopolymers   (2014 Sep);   PMID: 24919990
Butterfoss GL, Drew K, Renfrew PD, Kirshenbaum K, Bonneau R
Helminth colonization is associated with increased diversity of the gut microbiota.
PLoS Negl Trop Dis   (2014 May);  PMC4031128 free full-text archive
Lee SC, Tang MS, Lim YA, Choy SH, Kurtz ZD, Cox LM, Gundra UM, Cho I, Bonneau R, Blaser MJ, Chua KH, Loke P
Intrinsic bioconjugation for site-specific protein PEGylation at N-terminal serine.
Chem Commun (Camb)   (2014 Jul 4);   PMID: 24840103
Levine PM, Craven TW, Bonneau R, Kirshenbaum K
A rotamer library to enable modeling and design of peptoid foldamers.
J Am Chem Soc   (2014 Jun 18);  PMC4227732 free full-text archive
Renfrew PD, Craven TW, Butterfoss GL, Kirshenbaum K, Bonneau R
Collier/OLF/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors.
Dev Cell   (2014 May 12);  PMC4045103 free full-text archive
Razy-Krajka F, Lam K, Wang W, Stolfi A, Joly M, Bonneau R, Christiaen L
Bacillus subtilis Systems Biology: Applications of -Omics Techniques to the Study of Endospore Formation.
Microbiol Spectr   (2014 Apr);   PMID: 26105826
Bate AR, Bonneau R, Eichenberger P
FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells.
Nat Methods   (2014 May);  PMC4020622 free full-text archive
Murtha M, Tokcaer-Keskin Z, Tang Z, Strino F, Chen X, Wang Y, Xi X, Basilico C, Brown S, Bonneau R, Kluger Y, Dailey L
Semisynthesis of peptoid-protein hybrids by chemical ligation at serine.
Org Lett   (2014 Jan 17);   PMID: 24393000
Levine PM, Craven TW, Bonneau R, Kirshenbaum K
Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27.
Proteins   (2013 Dec);  PMC4037910 free full-text archive
Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.
PLoS One   (2013);  PMC3712014 free full-text archive
Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, Kirshenbaum K, Arora PS, Das R, Bonneau R
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).
PLoS One   (2013);  PMC3661552 free full-text archive
Lyskov S, Chou FC, Conchuir SO, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R
Chemoselective fragment condensation between peptide and peptidomimetic oligomers.
Org Biomol Chem   (2013 Jul 7);   PMID: 23715215
Levine PM, Craven TW, Bonneau R, Kirshenbaum K
Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice.
Integr Biol (Camb)   (2013 Jul 24);  PMC3759823 free full-text archive
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
A physical sciences network characterization of non-tumorigenic and metastatic cells.
Sci Rep   (2013);  PMC3636513 free full-text archive
Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, Damania D, Davies PC, Decuzzi P, Dickinson L, Estevez-Salmeron L, Estrella V, Ferrari M, Fischbach C, Foo J, Fraley SI, Frantz C, Fuhrmann A, Gascard P, Gatenby RA, Geng Y, Gerecht S, Gillies RJ, Godin B, Grady WM, Greenfield A, Hemphill C, Hempstead BL, Hielscher A, Hillis WD, Holland EC, Ibrahim-Hashim A, Jacks T, Johnson RH, Joo A, Katz JE, Kelbauskas L, Kesselman C, King MR, Konstantopoulos K, Kraning-Rush CM, Kuhn P, Kung K, Kwee B, Lakins JN, Lambert G, Liao D, Licht JD, Liphardt JT, Liu L, Lloyd MC, Lyubimova A, Mallick P, Marko J, McCarty OJ, Meldrum DR, Michor F, Mumenthaler SM, Nandakumar V, O'Halloran TV, Oh S, Pasqualini R, Paszek MJ, Philips KG, Poultney CS, Rana K, Reinhart-King CA, Ros R, Semenza GL, Senechal P, Shuler ML, Srinivasan S, Staunton JR, Stypula Y, Subramanian H, Tlsty TD, Tormoen GW, Tseng Y, van Oudenaarden A, Verbridge SS, Wan JC, Weaver VM, Widom J, Will C, Wirtz D, Wojtkowiak J, Wu PH
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks.
Bioinformatics   (2013 Apr 15);  PMC3624811 free full-text archive
Greenfield A, Hafemeister C, Bonneau R
Parametric Bayesian priors and better choice of negative examples improve protein function prediction.
Bioinformatics   (2013 May 1);  PMC3634187 free full-text archive
Youngs N, Penfold-Brown D, Drew K, Shasha D, Bonneau R
A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells.
Genome Res   (2013 Apr);  PMC3613576 free full-text archive
Imberg-Kazdan K, Ha S, Greenfield A, Poultney CS, Bonneau R, Logan SK, Garabedian MJ
A validated regulatory network for Th17 cell specification.
Cell   (2012 Oct 12);  PMC3503487 free full-text archive
Ciofani M, Madar A, Galan C, Sellars M, Mace K, Pauli F, Agarwal A, Huang W, Parkurst 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
De novo structure prediction and experimental characterization of folded peptoid oligomers.
Proc Natl Acad Sci U S A   (2012 Sep 4);  PMC3437879 free full-text archive
Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill KA, Zuckermann RN, Bonneau R, Kirshenbaum K, Voelz VA
Androgen receptor antagonism by divalent ethisterone conjugates in castrate-resistant prostate cancer cells.
ACS Chem Biol   (2012 Oct 19);  PMC3874888 free full-text archive
Levine PM, Lee E, Greenfield A, Bonneau R, Logan SK, Garabedian MJ, Kirshenbaum K
An assembly model of rift valley Fever virus.
Front Microbiol   (2012);  PMC3400131 free full-text archive
Rusu M, Bonneau R, Holbrook MR, Watowich SJ, Birmanns S, Wriggers W, Freiberg AN
Wisdom of crowds for robust gene network inference.
Nat Methods   (2012 Aug);  PMC3512113 free full-text archive
Marbach D, Costello JC, Kuffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G
The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts.
Mol Cell   (2012 Jun 8);   PMID: 22681889
Baltz AG, Munschauer M, Schwanhausser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, Wyler E, Bonneau R, Selbach M, Dieterich C, Landthaler M
Integrated inference and analysis of regulatory networks from multi-level measurements.
Methods Cell Biol   (2012);   PMID: 22482944
Poultney CS, Greenfield A, Bonneau R
Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design.
PLoS One   (2012);  PMC3303795 free full-text archive
Renfrew PD, Choi EJ, Bonneau R, Kuhlman B
Dynamic microRNA gene transcription and processing during T cell development.
J Immunol   (2012 Apr 1);  PMC3934760 free full-text archive
Kirigin FF, Lindstedt K, Sellars M, Ciofani M, Low SL, Jones L, Bell F, Pauli F, Bonneau R, Myers RM, Littman DR, Chong MM
The plant proteome folding project: structure and positive selection in plant protein families.
Genome Biol Evol   (2012);  PMC3318447 free full-text archive
Pentony MM, Winters P, Penfold-Brown D, Drew K, Narechania A, DeSalle R, Bonneau R, Purugganan MD
SlrA/SinR/SlrR inhibits motility gene expression upstream of a hypersensitive and hysteretic switch at the level of sigma(D) in Bacillus subtilis.
Mol Microbiol   (2012 Mar);  PMC3303961 free full-text archive
Cozy LM, Phillips AM, Calvo RA, Bate AR, Hsueh YH, Bonneau R, Eichenberger P, Kearns DB
N-Naphthyl peptoid foldamers exhibiting atropisomerism.
Org Lett   (2012 Feb 3);   PMID: 22272975
Paul B, Butterfoss GL, Boswell MG, Huang ML, Bonneau R, Wolf C, Kirshenbaum K
Oligo(N-alkoxy glycines): trans substantiating peptoid conformations.
Biopolymers   (2011);   PMID: 22180909
Jordan PA, Paul B, Butterfoss GL, Renfrew PD, Bonneau R, Kirshenbaum K
Comparative microbial modules resource: generation and visualization of multi-species biclusters.
PLoS Comput Biol   (2011 Dec);  PMC3228777 free full-text archive
Kacmarczyk T, Waltman P, Bate A, Eichenberger P, Bonneau R
Rational design of temperature-sensitive alleles using computational structure prediction.
PLoS One   (2011);  PMC3166291 free full-text archive
Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE, Bonneau R
The 2010 Rosetta developers meeting: macromolecular prediction and design meets reproducible publishing.
PLoS One   (2011);  PMC3166131 free full-text archive
Renfrew PD, Campbell G, Strauss CE, Bonneau R
The Proteome Folding Project: proteome-scale prediction of structure and function.
Genome Res   (2011 Nov);  PMC3205581 free full-text archive
Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmstrom L, Bonneau R
Peptoid atropisomers.
J Am Chem Soc   (2011 Jul 20);   PMID: 21634437
Paul B, Butterfoss GL, Boswell MG, Renfrew PD, Yeung FG, Shah NH, Wolf C, Bonneau R, Kirshenbaum K
DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models.
PLoS One   (2010);  PMC2963605 free full-text archive
Greenfield A, Madar A, Ostrer H, Bonneau R
Multi-species integrative biclustering.
Genome Biol   (2010);  PMC2965388 free full-text archive
Waltman P, Kacmarczyk T, Bate AR, Kearns DB, Reiss DJ, Eichenberger P, Bonneau R
DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator.
PLoS One   (2010);  PMC2842436 free full-text archive
Madar A, Greenfield A, Vanden-Eijnden E, Bonneau R
Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome.
Proc Natl Acad Sci U S A   (2010 Feb 16);  PMC2840275 free full-text archive
Miao EA, Mao DP, Yudkovsky N, Bonneau R, Lorang CG, Warren SE, Leaf IA, Aderem A
The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models.
Conf Proc IEEE Eng Med Biol Soc   (2009);   PMID: 19964678
Madar A, Greenfield A, Ostrer H, Vanden-Eijnden E, Bonneau R
A preliminary survey of the peptoid folding landscape.
J Am Chem Soc   (2009 Nov 25);   PMID: 19919145
Butterfoss GL, Renfrew PD, Kuhlman B, Kirshenbaum K, Bonneau R
The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis.
Mol Microbiol   (2009 Nov);  PMC2806667 free full-text archive
Wang KH, Isidro AL, Domingues L, Eskandarian HA, McKenney PT, Drew K, Grabowski P, Chua MH, Barry SN, Guan M, Bonneau R, Henriques AO, Eichenberger P
BioNetBuilder2.0: bringing systems biology to chicken and other model organisms.
BMC Genomics   (2009);  PMC2966329 free full-text archive
Konieczka JH, Drew K, Pine A, Belasco K, Davey S, Yatskievych TA, Bonneau R, Antin PB
2,5-Dimethyl-2,4-hexadiene induced photodechlorination of 9,10-dichloroanthracene.
Photochem Photobiol Sci   (2009 Jun);   PMID: 19492114
Saltiel J, Smothers WK, Schanze KS, Charman SA, Bonneau R
Diurnally entrained anticipatory behavior in archaea.
PLoS One   (2009);  PMC2675056 free full-text archive
Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS
Learning global models of transcriptional regulatory networks from data.
Methods Mol Biol   (2009);   PMID: 19381524
Madar A, Bonneau R
Oligo(N-aryl glycines): a new twist on structured peptoids.
J Am Chem Soc   (2008 Dec 10);   PMID: 19049458
Shah NH, Butterfoss GL, Nguyen K, Yoo B, Bonneau R, Rabenstein DL, Kirshenbaum K
Learning biological networks: from modules to dynamics.
Nat Chem Biol   (2008 Nov);   PMID: 18936750
Bonneau R
A protein domain-based interactome network for C. elegans early embryogenesis.
Cell   (2008 Aug 8);  PMC2596478 free full-text archive
Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, de Smet AS, Wang H, Schlaitz AL, Hao T, Milstein S, Fan C, Tipsword M, Drew K, Galli M, Rhrissorrakrai K, Drechsel D, Koller D, Roth FP, Iakoucheva LM, Dunker AK, Bonneau R, Gunsalus KC, Hill DE, Piano F, Tavernier J, van den Heuvel S, Hyman AA, Vidal M
Dissecting the quorum-sensing receptor LuxN.
Cell   (2008 Aug 8);   PMID: 18692463
Bonneau R
A predictive model for transcriptional control of physiology in a free living cell.
Cell   (2007 Dec 28);   PMID: 18160043
Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga NS
Somatodendritic microRNAs identified by laser capture and multiplex RT-PCR.
RNA   (2007 Aug);  PMC1924896 free full-text archive
Kye MJ, Liu T, Levy SF, Xu NL, Groves BB, Bonneau R, Lao K, Kosik KS
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.
PLoS Biol   (2007 Apr);  PMC1828141 free full-text archive
Malmstrom L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D
General transcription factor specified global gene regulation in archaea.
Proc Natl Acad Sci U S A   (2007 Mar 13);  PMC1838652 free full-text archive
Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS
A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin.
J Exp Med   (2007 Feb 19);  PMC2118731 free full-text archive
Andersen-Nissen E, Smith KD, Bonneau R, Strong RK, Aderem A
BioNetBuilder: automatic integration of biological networks.
Bioinformatics   (2007 Feb 1);   PMID: 17138585
Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R
Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents.
Proteomics   (2006 Dec);   PMID: 17133367
Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Morris DR, Aebersold R
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery.
Genome Biol   (2006);  PMC1779586 free full-text archive
Zhang H, Loriaux P, Eng J, Campbell D, Keller A, Moss P, Bonneau R, Zhang N, Zhou Y, Wollscheid B, Cooke K, Yi EC, Lee H, Peskind ER, Zhang J, Smith RD, Aebersold R
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.
BMC Bioinformatics   (2006);  PMC1502140 free full-text archive
Reiss DJ, Baliga NS, Bonneau R
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo.
Genome Biol   (2006);  PMC1779511 free full-text archive
Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V
The Gaggle: an open-source software system for integrating bioinformatics software and data sources.
BMC Bioinformatics   (2006);  PMC1464137 free full-text archive
Shannon PT, Reiss DJ, Bonneau R, Baliga NS
THUMP: an immersive haptic console for surgical simulation and training.
Stud Health Technol Inform   (2004);   PMID: 15544287
Niemeyer G, Kuchenbecker KJ, Bonneau R, Mitra P, Reid AM, Fiene J, Weldon G
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.
Genome Res   (2004 Nov);  PMC525680 free full-text archive
Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV
Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp.
Cold Spring Harb Symp Quant Biol   (2003);   PMID: 15338636
Weston AD, Baliga NS, Bonneau R, Hood L
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.
Genome Biol   (2004);  PMC507877 free full-text archive
Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L
Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.
Genome Res   (2004 Jun);  PMC419780 free full-text archive
Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J
Automated prediction of CASP-5 structures using the Robetta server.
Proteins   (2003);   PMID: 14579342
Chivian D, Kim DE, Malmstrom L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D
An improved protein decoy set for testing energy functions for protein structure prediction.
Proteins   (2003 Oct 1);   PMID: 12945051
Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D
Photoprotodesilylation of 9-trimethylsilylanthracene in alcohols.
Photochem Photobiol Sci   (2003 Mar);   PMID: 12713230
Desvergne JP, Bonneau R, Dorr G, Bouas-Laurent H
Ab initio methods.
Methods Biochem Anal   (2003);   PMID: 12647404
Chivian D, Robertson T, Bonneau R, Baker D
Zinc status modulates bronchopulmonary eosinophil infiltration in a murine model of allergic inflammation.
Chest   (2003 Mar);   PMID: 12629032
Richter M, Bonneau R, Girard MA, Beaulieu C, Larivee P
De novo prediction of three-dimensional structures for major protein families.
J Mol Biol   (2002 Sep 6);   PMID: 12215415
Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmstrom L, Robertson T, Baker D
Contact order and ab initio protein structure prediction.
Protein Sci   (2002 Aug);  PMC2373674 free full-text archive
Bonneau R, Ruczinski I, Tsai J, Baker D
Distributions of beta sheets in proteins with application to structure prediction.
Proteins   (2002 Jul 1);   PMID: 12012340
Ruczinski I, Kooperberg C, Bonneau R, Baker D
Rosetta in CASP4: progress in ab initio protein structure prediction.
Proteins   (2001);   PMID: 11835488
Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D
Photochemistry of methoxyhydroquinone and methoxy-p-benzoquinone in solution related to the photoyellowing of the lignocellulosics.
Photochem Photobiol   (2001 Oct);   PMID: 11683033
Bearnais-Barbry S, Bonneau R, Castellan A
Functional inferences from blind ab initio protein structure predictions.
J Struct Biol   (2001 May-Jun);   PMID: 11551178
Bonneau R, Tsai J, Ruczinski I, Baker D
Ab initio protein structure prediction: progress and prospects.
Annu Rev Biophys Biomol Struct   (2001);   PMID: 11340057
Bonneau R, Baker D
Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.
Proteins   (2001 Apr 1);   PMID: 11170209
Bonneau R, Strauss CE, Baker D
Ab initio protein structure prediction of CASP III targets using ROSETTA.
Proteins   (1999);   PMID: 10526365
Simons KT, Bonneau R, Ruczinski I, Baker D
Spatial distribution of DNA ploidy in colorectal carcinoma.
Anal Cell Pathol   (1994 Dec);   PMID: 7696154
Bigras G, Bonneau R, Dumont A
[No title available]
Can Fam Physician   (1992 Sep);  PMC2145484 free full-text archive
Bonneau R
Plexiform fibrohistiocytic tumor.
Dermatologica   (1991);   PMID: 1667100
Giard F, Bonneau R, Raymond GP
[Merkel's tumor].
Union Med Can   (1984 Jun);   PMID: 6485160
Bonneau R, Bluteau P
[Is Goodpasture's syndrome always a triad?].
Union Med Can   (1984 Jan);   PMID: 6710693
Bonneau R, Giroux L
Neuromuscular choristoma. A clinicopathologic study of two cases.
Am J Surg Pathol   (1983 Sep);   PMID: 6625049
Bonneau R, Brochu P
Complications of water-soluble contrast lumbar myelography. Review of the literature and case report.
Spine (Phila Pa 1976)   (1978 Dec);   PMID: 741241
Bonneau R, Morris JM
Stomal recurrence following laryngectomy.
Arch Otolaryngol   (1975 Jul);   PMID: 1147823
Bonneau RA, Lehman RH
pH dependence of singlet oxygen production in aqueous solutions using toluidine blue as a photosensitizer.
Photochem Photobiol   (1975 Jul-Aug);   PMID: 242021
Pottier R, Bonneau R, Joussot-Dubien J
Mechanism of photoreduction of thiazine dyes by EDTA studied by flash photolysis III. Consequences of a newly found pKT of thionine on the mechanism in basic solutions.
Photochem Photobiol   (1975 Mar);   PMID: 806084
Bonneau R, Pereyre J
pH dependence of singlet oxygen production in aqueous solutions using thiazine dyes as photosensitizers.
Photochem Photobiol   (1975 Mar);   PMID: 237293
Bonneau R, Pottier R, Bagno O, Joussot-Dubien J
[Light spectroscopic study of thiazine dyes in aqueous solution].
Photochem Photobiol   (1967 May);   PMID: 6042949
Faure J, Bonneau R, Joussot-Dubien J
[Not Available].
Talanta   (1967 Jan);   PMID: 18960074
Bonneau R, Faure J, Joussot-Dubien J
[The temporomandibular joint; its false radiological individualization].
Odontologie   (1951 Jul-Aug);   PMID: 14863823
Updated on 09/01/2015