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

Phone: 

(212) 992-9516

Fax: 

(212) 995-4015

Lab Homepage: 

http://bonneaulab.bio.nyu.edu

Areas of Research/Interest: 

Systems Biology and Protein Modeling

List of Publications from Pubmed

List of citations from Google Scholar

Research:

Biclustering / Transparent Probabilistic Data Integration: Grouping genes into functionally related and putatively co-regulated clusters is an essential first step for the inference of regulatory networks (one could think of many reasons for doing this but network inference is a good problem to start with). It is widely known that regulatory relationships among genes can vary under diverse environmental settings, and that co-expressed genes are trivially under control of the same regulator(s). This leads to patterns of co-expression that are valid under some, not all, observed conditions. With such considerations in mind, we have developed cMonkey, an unsupervised learning procedure for detecting putatively co-regulated gene clusters by integrating diverse systems biology data including: (1) mRNA and/or protein expression levels, (2) cis-regulatory sequences, and (3) functional association and physical interaction networks.

Network inference: We have also developed a methodology for deriving transcriptional regulatory interactions on a genomewide scale, and apply the method to predict a large portion of the gene regulatory network of the archaea, Halobacterium NRC-1. A small portion of the halobacterium learned network is shown below. The learned network is predictive, and was used to successfully predict the global expression of Halobacterium under novel perturbations (not part of the original training set) with predictive power similar to that seen over the training set. Methodological advancements over earlier work include an explicit treatment of time such that the network model can be fit using both steady-state measurements and heterogeneous time series simultaneously. The method contains a novel means for learning binary logic interactions between regulators that requires no discretization of data.

Rosetta de novo structure prediction: methods development for extracting functional information fro de novo structure predictions. Recent progress in de novo structure prediction methods has resulted in methods with increased accuracy that are applicable to greater numbers of proteins. When combined intelligently with other structure prediction methods, de novo structure prediction can contribute to systems biology in several ways. While still highly experimental such applications include 1) structural annotation on a genome wide scale and 2) synergy with experimental approaches to structural genomics such as the derivation of distance constraints from mass spectroscopy. I will describe the underlying methodologies common to current de novo prediction methods, focusing on core concepts rather than specific implementations, groups or methods. Possible applications of de novo structure prediction will also be reviewed. For more information, view our latest results on 80 complete genomes including many model organisms being actively studied at NYU. This work is being carried out in collaboration with David Baker.

Cytoscape: Cytoscape is a computer program designed to visualize systems biology data. This began initially as a program to map expression data onto networks and has evolved parallel to the field to encompass several other functionalities. We are involved in cytoscape development with a focus on providing immersive tools that can be used to view the data created by the HPF project (in collaboration with Iliana Avila-Campillo at the ISB). BioNetBuilder is a tool developed by Iliana to automatically build networks in cytoscape for any organism comprised of edges derived from protein-protein, protein-DNA, evolutionary comparison and metabolic/signaling pathways. For more information on Cytoscape see cytoscape.org.

Employment Opportunities

The Center for Genomics and Systems Biology at NYU Abu Dhabi is currently inviting applications for multiple Bioinformatics Software Engineer positions. These personnel will form the nucleus of a new bioinformatics core group to support multiple large-scale projects in the new NYU Abu Dhabi Center for Genomics and Systems Biology as part of a larger NYUAD Research Institute initiative. These position are NOT located in the United States. You must be willing to RELOCATE TO ABU DHABI, UNITED ARAB EMIRATES. NYU Abu Dhabi is an Equal Oppurtunity/Affirmative Action Employer.

Fellowships/Honors:

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:

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells.
Nat Methods   (2014 Mar 23);   PMID: 24658142
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);   PMID: 24123494
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
 
Updated on 04/05/2014