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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.
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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 Simonis, Anne-Lore Schlaitz, Murat Cokol, Muhammed A. Yildirim, Tong Hao, Changyu Fan, Chenwei Lin, Mike Tipsword, Kevin Drew, Matilde Galli,
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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.
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The proteome folding project: Proteome-scale prediction of structure and function (2011) Kevin Drew, Patrick
Winters, GlennL. Butterfoss, Viktors Berstis, Keith Uplinger, Jonathan Armstrong, MichaelRiffle, Erik Schweighofer, Bill Bovermann, David R. Goodlett, Trisha N. Davis, Dennis Shasha, Lars
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His group has made key contributions to the areas of genomics data analysis, focusing on two primary areas: 1. methods for network inference that uncover dynamics and topology from data and 2. methods that learn condition dependent co-regulated groups from integrations of different genomics
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is an
American computational biologist and data scientist whose primary research is in the following areas: learning networks from functional genomics data, predicting and designing protein and peptiodomimetic structure and applying data science to social networks. A professor at
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In the area of structure prediction, Bonneau was one of the early authors on the
Rosetta code, one of the first codes to demonstrate the ability to predict protein structure in the absence of sequence homology. Using IBM's
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In 2013, he and his colleagues at NYU started a project to examine the impact of social media use on political attitudes and participation by applying methods from a range of academic disciplines. The project--
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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.
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Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R., Genome Res. 2011 Nov; 21(11):1981-94.
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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
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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.
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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
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Renfrew PD, Choi EJ, Bonneau R, Kuhlman B (2012) Incorporation of Noncanonical AminoAcids into Rosetta and Use in Computational Protein-Peptide Interface Design.PLoS ONE 7(3): e32637.
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Bonneau, R, Facciotti, MT, Reiss, DJ, Madar A, Baliga, NS, et al. A predictive model for transcriptional control of physiology in a free living cell. (2007) Cell. Dec 131:1354-1365
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Renfrew PD, Campbell G, Strauss CEM, Bonneau R (2011) The 2010 Rosetta Developers Meeting: Macromolecular Prediction and Design Meets Reproducible Publishing. PLoS ONE 6(8): e22431
80:(SMaPP) --relies on both survey data and publicly available social media data to address a range of questions concerning the causal processes that shape political participation.
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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.
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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.
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regulatory network. Baliga and Bonneau used their model to predict the genome-wide transcriptional dynamics of the cell’s response to new environments (publication in
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Bonneau, R & Baker, D. (2001). Ab Initio Protein Structure Prediction: Progress and Prospects. Annu. Rev. Biophys. Biomol. Struct. 30, 173-89.
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David J Reiss, Nitin S Baliga, Bonneau R. (2006) Integrated biclustering of heterogeneous genome-wide datasets. BMC Bioinformatics. 7(1):280.
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to carry out folding of whole proteomes, his group has also applied structure prediction to the problem of genome and proteome annotation.
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Bonneau, Richard. Learning biological networks: from modules to dynamics. Nature Chemical Biology 4, 658 - 664 (2008)
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Murphy, Richard M. Myers, Richard Bonneau, Dan R. Littman. Cell, October 12, 2012 (Vol. 151, Issue 2, pp. 289-303)
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Malmstrom, and Richard Bonneau. Genome Research, August 8, 2011)
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