Richard Bonneau, Marc T. Facciotti, David J. Reiss, Amy K. Schmid, Min Pan, Amardeep Kaur, Vesteinn Thorsson, Paul Shannon, Michael H. Johnson, J. Christopher Bare, William Longabaugh, Madhavi Vuthoori, Kenia Whitehead, Aviv Madar, Lena Suzuki, Tetsuya Mori, Dong-Eun Chang, Jocelyne DiRuggiero, Carl H. Johnson, Leroy Hood, and Nitin S. Baliga (2007) A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell, Cell, Vol 131, 1354-1365, 28 December 2007

Bonneau R, Reiss DJ, Shannon P, Hood L, Baliga NS, Thorsson V (2005) The Inferelator: a procedure for learning parsimonious regulatory networks from systems-biology data-sets de novo [Submitted].

David J Reiss, Nitin S Baliga, Bonneau R. (2005) Integrated biclustering of heterogeneous genome-wide datasets [Submitted]

Malmstrom L, Riffle M., Strauss CEM, Chivian D, Davis TN, Bonneau R, Baker D. (2005) Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology. PLoS Biol. 2007 Mar 20;5 (4):e76 17373854

Shannon P, Reiss DJ, Bonneau R, Baliga NS (2005) The Gaggle: A system for integrating
bioinformatics and computational biology software and data sources. [Submitted].

Bonneau, R. (2005) De Novo Structure Prediction: methods and applications. Chapter 12 in Bioinformatics: From genomes to therapies. Wiley-VCH. [In press]

Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L. (2004) Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.Genome Biology. 5(8):R52-68

Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. (2004) Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 14(6):1025-35. Epub 2004 May 12.

Weston, A.D.*, Baliga, N.S.*, Bonneau, R.*, Hood, L. (2003) Systems Approaches Applied to the Study of Saccharomyces cerevisiae and Halobacterium sp. Cold Spring Harbor Symposia on Quantitative Biology LVIII 68:345-57 * equal authorship

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 sequence of Haloarcula marismortui –a halophilic archaeon from the Dead Sea. Genome Res. 5(8):R52

Facciotti, M.T., Bonneau, R., Hood, L., and Baliga, N.S. (2004) Systems Biology Experimental Design - Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems. Current Genomics [In Press]

Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Goodlett D, Morris D, Aebersold R. (2005) Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotopecoded affinity tag reagents. Proteomics [Submitted].

Bonneau, R., Dylan Chivian, Charlie EM Strauss, Carol Rohl, David Baker. (2002)De Novo Prediction of Three Dimensional Structures for Major Protein Families. JMB, 322(1):65-78.

Bonneau, R., Ingo Ruczinski, Jerry Tsai, David Baker. (2002) Contact Order and ab initio Structure Prediction. Protein Science, 11(8):1937-44.

Bonneau, R., Jerry Tsai, Ingo Ruczinski, Dylan Chivian, Carol Rohl, Charlie EM Strauss, David Baker. (2001) Rosetta in CASP4: Progress in ab initio protein structure prediction. Proteins. 45(S5)119-126.

Bonneau, R., Jerry Tsai, Ingo Ruczinski, David Baker. (2001) Functional inferences from blind ab initio protein structure predictions. J. Struct. Biol. 134(2-3),186-90.

Bonneau, R., Strauss, C. & Baker, D. (2001). Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins 43(1), 1-11.

Bonneau, R & Baker, D. (2001). Ab Initio Protein Structure Prediction: Progress and Prospects. Annu. Rev. Biophys. Biomol. Struct. 30, 173-89. Review.

Chivian D, Kim DE, Malmstrom L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. (2003) Automated prediction of CASP-5 structures using the Robetta server. Proteins. 53 Suppl 6:524-33.

Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins.53(1):76-87.

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

Chivian, D., Bonneau, R., Baker, D. et al. (2003) Chapter 27: Ab initio structure prediction. (In)Bourne, P.E. (2003) Structural Bioinformatics(Methods of Biochemical Analysis, V. 44). New York: John Wiley & Sons; ISBN: 0471201995.

Ruczinski, I., Kooperberg, C., Bonneau, R., Baker, D. (2001) Distributions of beta sheets in proteins with application to structure prediction. Proteins 48(1), 85-97.

Simons, K. T., Bonneau, R., Ruczinski, I. & Baker, D. (1999). Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 37(S3), 171-176.