Richard Bonneau
Richard Bonneau is an American computational biologist who studies methods to analyze systems biology datasets and methods to predict the three-dimensional structures of proteins. He is an Assistant Professor in the New York University Department of Biology and the Courant Institute for Mathematical Sciences. He studied under David Baker at the University of Washington in Seattle, where he was an early contributor to the Rosetta protein structure prediction code. He was an HHMI pre-doctoral fellow during the inception of this work. Before joining NYU, he developed new algorithms for systems biology data analysis with Nitin Baliga and Leroy Hood at the Institute for Systems Biology in Seattle. In 2008 he was selected as one of the top twenty scientists under 40 by Discover magazine.
Richard is married and lives in Greenwich Village, in New York City.
Structure prediction
Bonneau trained in the Baker laboratory where he contributed to the development of the Rosetta algorithm for ab initio protein structure prediction; he continued this work at the Institute for Systems Biology where he began the Human Proteome Folding Project (with Robin Wilner, Bill Boverman and Viktors Berstis, IBM) on the World Community Grid. The project was the first project run on the World Community Grid and a second phase of the project (HPF2) is currently running. These projects aim to predict the fold and function of unknown proteins in more than 100 complete proteomes.
Network inference and systems biology
Along with Vestienn Thorsson, David Reiss and Nitin Baliga he developed the Inferelator and cMonkey, two algorithms that were critical to an effort to learn a genome-wide model of the Halobacterium regulatory network. Dr. Nitin Baliga and Dr. Bonneau demonstrated that their model was capable of predicting the genome-wide transcriptional dynamics of the cell’s response to new environments (a work that resulted in publication in Cell in December 2007). This work represents the first fully data driven reconstruction of a cells regulatory network to include learning of kinetic/dynamical parameters as well as network topology.
References
Structure prediction
- Bonneau, R & Baker, D. (2001). Ab Initio Protein Structure Prediction: Progress and Prospects. Annu. Rev. Biophys. Biomol. Struct. 30, 173-89.
- 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, 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
- 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. A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis. (2008) Cell, 134(3) pp. 534 – 545.
- Andersen-Nissen E, Smith KD, Bonneau R, Strong RK, Aderem A. A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin. (2007) J Exp Med. Feb 19;204(2):393-403.
Genomics and systems biology
- Bonneau, Richard. Learning biological networks: from modules to dynamics. Nature Chemical Biology 4, 658 - 664 (2008)
- Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson T, Shannon P, Johnson MH, Bare CJ, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, DiRuggiero J, Johnson CH, Hood L, Baliga NS. A predictive model for transcriptional control of physiology in a free living cell. Cell. 2007 Dec 28; 131 (7): 1354-65.
- Bonneau R, Reiss DJ, Shannon P, Hood L, Baliga NS, Thorsson V (2006) The Inferelator: a procedure for learning parsimonious regulatory networks from systems-biology data-sets de novo. Genome Biol. 7(5):R36.
- David J Reiss, Nitin S Baliga, Bonneau R. (2006) Integrated biclustering of heterogeneous genome-wide datasets. BMC Bioinformatics. 7(1):280.
External links