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Recent and Pending Publications

CELL: A Validated Regulatory Network for Th17 Cell Specification

Maria Ciofani, Aviv Madar, Carolina Galan, MacLean Sellars, Kieran Mace, Florencia Pauli, Ashish Agarwal, Wendy Huang, Christopher N. Parkurst, Michael Muratet, Kim M. Newberry, Sarah Meadows, Alex Greenfield, Yi Yang, Preti Jain, Francis K. Kirigin, Carmen Birchmeier, Erwin F. Wagner, Kenneth M. Murphy, Richard M. Myers, Richard Bonneau, Dan R. Littman. A Validated Regulatory Network for Th17 Cell Specification. Cell - 25 September 2012.

Abstract [+/-] Paper link

Organic Letters: N-Naphthyl peptoid foldamers exhibiting atropisomerism

Bishwajit Paul, Glenn L. Butterfoss, Mikki G. Boswell, Mia L. Huang, Richard Bonneau, Christian Wolf, and Kent Kirshenbaum. N-Naphthyl Peptoid Foldamers Exhibiting Atropisomerism. Organic Letters 2012 14 (3), 926-929.

Abstract [+/-] Paper link

GBE: The Plant Proteome Folding Project: Structure and positive selection in plant protein families

M. M. Pentony, P. Winters, D. Penfold-Brown, K. Drew, A. Narechania, R. DeSalle, R. Bonneau, and M. D. Purugganan. The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families. Genome Biol Evol (2012) Vol. 4 360-371 first published online February 16, 2012 doi:10.1093/gbe/evs015

Abstract [+/-] Paper link

2011 Publications

The proteome folding project: proteome-scale prediction of structure and function

Kevin Drew, Patrick Winters, Glenn L. Butterfoss, Viktors Berstis, Keith Uplinger, Jonathan Armstrong, Michael Riffle, Erik Schweighofer, Bill Bovermann, David R. Goodlett, Trisha N. Davis, Dennis Shasha, Lars Malmström and Richard Bonneau. The Proteome Folding Project: Proteome-scale prediction of structure and function. Genome Res. 2011. 21: 1981-1994.

Abstract [+/-] Paper link

Structure based prediction of temperature sensitive mutations

Christopher S. Poultney, David Gresham, Nathan J. Brandt, Glenn L. Butterfoss, Michelle R. Gutwein, Kevin Drew, Kristin C. Gunsalus, Dennis E. Shasha, Richard Bonneau.

Invited submission to PLoS one special collection: RosettaCon 2010: Worked examples of macromolecular modeling and design.

Oligo(N-alkoxy glycines): Trans substantiating peptoid conformation

Peter Jordan, Glenn L. Butterfoss, P. Douglas Renfrew, Rich Bonneau, Kent Kirshenbaum.

Submitted to Biopolymers.

The Rosetta Developers Meeting, 2010 special collection: state of the art macromolecular modeling meets reproducible publishing

Charlie EM Strauss, P. Douglas Renfrew, Richard Bonneau.

Invited introduction to the RosettaCon 2010 PLoS one special collection.

Peptoid Atropisomers

Paul B, Butterfoss GL, Boswell MG, Renfrew PD, Yeung FG, Shah NH, Wolf C, Bonneau R, Kirshenbaum K. Peptoid atropisomers. J Am Chem Soc. 2011 Jul 20;133(28):10910-9. Epub 2011 Jun 22.

Abstract [+/-] Paper link

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P. Methods Enzymol. 2011;487:545-74.

Abstract [+/-] Paper link

2010 Publications

Multi-species integrative biclustering

Waltman P, Kacmarczyk T, Bate AR, Kearns DB, Reiss DJ, Eichenberger P, Bonneau R. Genome Biol. 2010;11(9):R96. Epub 2010, Sep 29. PubMed PMID: 20920250

Abstract [+/-] Paper link

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models

Greenfield A, Madar, A, Bonneau R. DREAM4 top performers special collection. PLoS ONE 2010, 5(10): e13397. doi:10.1371/journal.pone.0013397

Abstract [+/-] Paper link

Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome

Miao EA, Mao DP, Yudkovsky N, Bonneau R, Lorang CG, Warren SE, Leaf IA, Aderem A. Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):3076-80. Epub 2010 Feb 1. PubMed PMID: 20133635.

Abstract [+/-] Paper link

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

Madar A, Greenfield A, Vanden-Eijnden E, Bonneau R. PLoS ONE, 2010, 5(3): e9803. doi:10.1371/journal.pone.0009803

Abstract [+/-] Paper link

2009 Publications

The Inferelator 2.0: A scalable framework for reconstruction of dynamic regulatory network models

Madar A, Greenfield A, Ostrer H, Vanden-Eijnden E, Bonneau R. Conf Proc IEEE Eng Med Biol Soc. 2009;1:5448-51. PubMed PMID: 19964678.

Abstract [+/-] Paper link

A preliminary survey of the peptoid folding landscape

Butterfoss GL, Renfrew PD, Kuhlman B, Kirshenbaum K, Bonneau R. J Am Chem Soc. 2009 Nov 25;131(46):16798-807. PubMed PMID: 19919145.

Abstract [+/-] Paper link

The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis

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. Mol Microbiol. 2009 Nov;74(3):634-49. Epub 2009 Sep 22. PubMed PMID: 19775244; PubMed Central PMCID: PMC2806667.

Abstract [+/-] Paper link

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms

Konieczka JH, Drew K, Pine A, Belasco K, Davey S, Yatskievych TA, Bonneau R, Antin PB. BMC Genomics. 2009 Jul 14;10 Suppl 2:S6. PubMed PMID: 19607657; PubMed Central PMCID: PMC2709267.

Abstract [+/-] Paper link

Diurnally entrained anticipatory behavior in archaea

Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS. PLoS One. 2009;4(5):e5485. Epub 2009 May 8. PubMed PMID: 19424498; PubMed Central PMCID: PMC2675056.

Abstract [+/-] Paper link

2008 Publications

Oligo(N-aryl glycines): a new twist on structured peptoids

Shah NH, Butterfoss GL, Nguyen K, Yoo B, Bonneau R, Rabenstein DL, Kirshenbaum K. J Am Chem Soc. 2008 Dec 10;130(49):16622-32. PubMed PMID: 19049458.

Abstract [+/-] Paper link

Modeling gene regulation and spatial organization of sequence based motifs

Jochen Supper, Claas aufm Kampe, Dierk Wanke, Kenneth W. Berendzen, Klaus Harter, Richard Bonneau, and Andreas Zell. 8th IEEE international conference on BioInformatics and BioEngineering (BIBE 2008).

Abstract [+/-] Paper link

A protein domain-based interactome network for C. elegans early embryogenesis

Mike Boxem, Zoltan Maliga, Niels J. Klitgord, Na Li, Irma Lemmens, Miyeko Mana, Lorenzo De Lichtervelde, Joram Mul, Diederik van de Peut, Maxime Devos, Nicolas Si-monis, Anne-Lore Schlaitz, Murat Cokol, Muhammed A. Yildirim, Tong Hao, Changyu Fan, Chenwei Lin, Mike Tipsword, Kevin Drew, Matilde Galli, Kahn Rhrissorrakrai, David Drech-sel, David E. Hill, Richard Bonneau, Kristin C. Gunsalus, Frederick P. Roth, Fabio Piano, Jan Tavernier, Sander van den Heuvel, Anthony A. Hyman, Marc Vidal. Cell, 2008 134(3) pp. 534 - 545.

Abstract [+/-] Paper link

2007 Publications

A predictive model for transcriptional control of physiology in a free living cell

Bonneau, R*, Facciotti, MT, Reiss, DJ, Madar A, et al., Baliga, NS*. (2007) Cell. Dec 131:1354-1365

Abstract [+/-] Paper link

BioNetBuilder, an automatic network interface

Iliana Avila-Campillo*, Kevin Drew*, John Lin, David J. Reiss, Richard Bonneau. (2007) Bioinformatics. Feb 1;23(3):392-3.

Abstract [+/-] Paper link

A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin

Andersen-Nissen E, Smith KD, Bonneau R, Strong RK, Aderem A. (2007) J Exp Med. Feb 19;204(2):393-403.

Abstract [+/-] Paper link

Genome-wide superfamily assignments for Saccharomyces cerevisiae protein domains through integration of de novo structure prediction with the gene ontology

Malmström L, Riffle M., Strauss CEM, Chivian, D, Davis TN., Bonneau R.3 Baker D.. PLoS Biol. (2007) Apr;5(4):e76.

Abstract [+/-] Paper link

General transcription factor specified global gene regulation in archaea

Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS. Proc Natl Acad Sci U S A. (2007) Mar 13;104(11):4630-5.

Abstract [+/-] Paper link

Somatodendritic microRNAs identified by laser capture and multiplex RT-PCR

Kye MJ, Liu T, Levy SF, Xu NL, Groves BB, Bonneau R, Lao K, Kosik KS. RNA. (2007) Aug;13(8):1224-34.

Abstract [+/-] Paper link

Earlier Publications

The Inferelator: a procedure for learning parsimonious regulatory networks from systems-biology data-sets de novo

Bonneau R, Reiss DJ, Shannon P, Hood L, Baliga NS, Thorsson V (2006). Genome Biol. 7(5):R36.

Abstract [+/-] Paper link

Integrated biclustering of heterogeneous genome-wide datasets

David J Reiss, Nitin S Baliga, Bonneau R. (2006) BMC Bioinformatics. 7(1):280.

Abstract [+/-] Paper link

The Gaggle: A system for integrating bioinformatics and computational biology software and data sources

Shannon P, Reiss DJ, Bonneau R, Baliga NS. (2006) BMC Bioinformatics. 7:176.

Abstract [+/-] Paper link

Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotopecoded affinity tag reagents

Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Goodlett D, Morris D, Aebersold R. (2006) Proteomics Dec;6(23):6146-57.

Abstract [+/-] Paper link

UniPep, a database for human N-linked glycosites: A resource for biomarker discovery

Zhang, H., Loriaux, P., Eng, J., Bonneau, R., Smith, R & Aebersold, R. Genome Biology, (2006), 7:114

Abstract [+/-] Paper link

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L. (2004) Genome Biology. 5(8):R52-68

Abstract [+/-] Paper link

Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1

Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. (2004) Genome Res. 14(6):1025-35. Epub 2004 May 12.

Abstract [+/-] Paper link

Genome sequence of Haloarcula marismortui–a halophilic archaeon from the Dead Sea

Baliga NS., Bonneau R., Facciotti M, Pan M, Deutsch E, Glusman G, Shannon P, Chiu Y, Weng RS, Kan JR, Hung P, Date S, Marcotte E, Hood L, Ng V. (2004) Genome Res. 5(8):R52

Abstract [+/-] Paper link

Automated prediction of CASP-5 structures using the Robetta server

Chivian D, Kim DE, Malmstrom L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. (2003) Proteins. 53 Suppl 6:524-33.

Abstract [+/-] Paper link

An improved protein decoy set for testing energy functions for protein structure prediction

Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. (2003) Proteins. 53(1):76-87.

Abstract [+/-] Paper link

De Novo Prediction of Three Dimensional Structures for Major Protein Families

Bonneau, R., Dylan Chivian, Charlie EM Strauss, Carol Rohl, David Baker. (2002) JMB, 322(1):65-78.

Abstract [+/-] Paper link

Contact Order and ab initio Structure Prediction

Bonneau, R., Ingo Ruczinski, Jerry Tsai, David Baker. (2002) Protein Science, 11(8):1937-44.

Abstract [+/-] Paper link

Rosetta in CASP4: Progress in ab initio protein structure prediction

Bonneau, R., Jerry Tsai, Ingo Ruczinski, Dylan Chivian, Carol Rohl, Charlie EM Strauss, David Baker. (2001) Proteins. 45(S5)119-126.

Abstract [+/-] Paper link

Distributions of beta sheets in proteins with application to structure prediction

Ruczinski, I., Kooperberg, C., Bonneau, R., Baker, D. (2001) Proteins 48(1), 85-97.

Abstract [+/-] Paper link

Functional inferences from blind ab initio protein structure predictions

Bonneau, R., Jerry Tsai, Ingo Ruczinski, David Baker. (2001) J. Struct. Biol. 134(2-3),186-90.

Abstract [+/-] Paper link

Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation

Bonneau, R., Strauss, C. & Baker, D. (2001) Proteins 43(1), 1-11.

Abstract [+/-] Paper link

Ab initio protein structure prediction of CASP III targets using ROSETTA

Simons, K. T., Bonneau, R., Ruczinski, I. & Baker, D. (1999) Proteins 37(S3), 171-176.

Abstract [+/-] Paper link

Book Chapters, Reviews, and Perspectives

De novo protein structure prediction: methods and application

Kevin Drew, Dylan Chivian and Richard Bonneau. (2007) Structural Bioinformatics 2nd Edition. Wiley-Liss (Book Chapter).

Learning biological networks: from modules to dynamics

Bonneau, Richard. Nature Chemical Biology 4, 2008, 658 - 664

Prokaryotic Systems Biology

Waltman P, Kacmarczyk T, Bonneau R. In Plant Systems Biology, Annual Plant Reviews. 1st edition. Edited by: Coruzzi G, Gutierrez RA. Ames, Iowa: Blackwell Publishers; 2009:67-136

Learning global models of transcriptional regulatory networks from data

Madar A, Bonneau R. Methods Mol Biol. 2009;541:181. Review. PubMed PMID:19381524.

De novo structure prediction: methods and applications

Kevin Drew, Dylan Chivian, Richard Bonneau. Structural Bioinformatics, Second Edition. (2009), Edited by: Jenny Gu and Philip E. Bourne, p. 755- 781, John Wiley and Sons. ISBN-10: 0470181052

Dissecting the Quorum-Sensing Receptor LuxN

Richard Bonneau. (2008) Cell, 134(3):390-391, ISSN 0092-8674

Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium

Weston AD, Baliga NS, Bonneau R, Hood L. Cold Spring Harb Symp Quant Biol. 2003;68:345-57. PubMed PMID: 15338636.

Ab initio methods

Chivian D, Robertson T, Bonneau R, Baker D. (2003) Methods Biochem Anal. 44:547-57.

Ab Initio Protein Structure Prediction: Progress and Prospects

Bonneau, R & Baker, D. (2001). Annu. Rev. Biophys. Biomol. Struct. 30, 173-89. Review.