Richard Bonneau
Encyclopedia
Richard Bonneau is an American computational biologist
who studies methods to analyze systems biology
datasets and methods to predict
the three-dimensional structures
of protein
s. 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
.
; 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 proteome
s.
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.
Computational biology
Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems...
who studies methods to analyze systems biology
Systems biology
Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
datasets and methods to predict
Protein structure prediction
Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
the three-dimensional structures
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
of protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s. He is an Assistant Professor in the New York University
New York University
New York University is a private, nonsectarian research university based in New York City. NYU's main campus is situated in the Greenwich Village section of Manhattan...
Department of Biology and the Courant Institute for Mathematical Sciences. He studied under David Baker
David Baker (biochemist)
David Baker is an American biochemist and computational biologist who studies methods to predict the three-dimensional structures of proteins. He is a Professor of Biochemistry at the University of Washington, where he is the principal investigator of the 30+ member...
at the University of Washington in Seattle, where he was an early contributor to the Rosetta
Rosetta
Rosetta is a port city on the Mediterranean coast of Egypt. It is located east of Alexandria, in Beheira governorate. It was founded around AD 800....
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
Systems biology
Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
data analysis with Nitin Baliga and Leroy Hood
Leroy Hood
Leroy Hood is an American biologist. He won the 2011 Fritz J. and Dolores H. Russ Prize “for automating DNA sequencing that revolutionized biomedicine and forensic science” and the 2003 Lemelson-MIT Prize for inventing "four instruments that have unlocked much of the mystery of human biology" by...
at the Institute for Systems Biology
Institute for Systems Biology
The Institute for Systems Biology is a non-profit research institution, located in Seattle, Washington, United States. Leroy Hood co-founded the Institute with Alan Aderem and Ruedi Aebersold in 2000....
in Seattle. In 2008 he was selected as one of the top twenty scientists under 40 by Discover
Discover (magazine)
Discover is an American science magazine that publishes articles about science for a general audience. The monthly magazine was launched in October 1980 by Time Inc. It was sold to Family Media, the owners of Health, in 1987. Walt Disney Company bought the magazine when Family Media went out of...
magazine.
Richard is married and lives in Greenwich Village
Greenwich Village
Greenwich Village, , , , .in New York often simply called "the Village", is a largely residential neighborhood on the west side of Lower Manhattan in New York City. A large majority of the district is home to upper middle class families...
, in New York City
New York City
New York is the most populous city in the United States and the center of the New York Metropolitan Area, one of the most populous metropolitan areas in the world. New York exerts a significant impact upon global commerce, finance, media, art, fashion, research, technology, education, and...
.
Structure prediction
Bonneau trained in the Baker laboratory where he contributed to the development of the Rosetta algorithm for ab initio protein structure predictionProtein structure prediction
Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
; he continued this work at the Institute for Systems Biology
Institute for Systems Biology
The Institute for Systems Biology is a non-profit research institution, located in Seattle, Washington, United States. Leroy Hood co-founded the Institute with Alan Aderem and Ruedi Aebersold in 2000....
where he began the Human Proteome Folding Project
Human Proteome Folding Project
The Human Proteome Folding Project is a collaborative effort between New York University , the Institute for Systems Biology and the University of Washington , using the Rosetta software developed by the Rosetta Commons....
(with Robin Wilner, Bill Boverman and Viktors Berstis, IBM) on the World Community Grid
World Community Grid
World Community Grid is an effort to create the world's largest public computing grid to tackle scientific research projects that benefit humanity...
. 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 proteome
Proteome
The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome.The term has been...
s.
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 CellCell (journal)
Cell is a peer-reviewed scientific journal publishing research papers across a broad range of disciplines within the life sciences. Areas covered include molecular biology, cell biology, systems biology, stem cells, developmental biology, genetics and genomics, proteomics, cancer research,...
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.
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.