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Richard A. Bonneau, Ph.D.

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
protein structure prediction
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Parents

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David Baker grad student 2001 University of Washington
 (Gene annotation using ab initio protein structure prediction: Method, development and application to major protein families.)

Children

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Evan Baugh grad student NYU Courant
Xi Chen grad student NYU Courant
Kevin Drew grad student UT Austin
Alex Greenfield grad student NYU Courant
Christophe Hafemeister grad student NYU
Leif Halvorsen grad student NYU
Zachary Kurtz grad student NYU Courant
Kari Lam grad student NYU
Aviv Madar grad student NYU
Emily Miraldi grad student Cincinati Children's Hospital
Mario Arrieta Ortiz grad student NYU
Christopher S. Poultney grad student NYU Courant
Thadeous J. Kacmarczyk grad student 2012 NYU
Peter Waltman grad student 2012 NYU
Dalton Conley grad student 2014 NYU (SocTree)
Noah Youngs grad student 2014 NYU
Ramya Raviram grad student 2011-2017 NYU Langone Medical Center

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Publications

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Alford RF, Leaver-Fay A, Jeliazkov JR, et al. (2022) Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation
Gibbs CS, Jackson CA, Saldi GA, et al. (2022) High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0. Bioinformatics (Oxford, England)
Koehler Leman J, Lyskov S, Lewis SM, et al. (2021) Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947
Wu F, Xiao A, Zhang J, et al. (2021) SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. The Science of the Total Environment. 805: 150121
Lee SC, Tang MS, Lim YAL, et al. (2021) Correction: Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota. Plos Neglected Tropical Diseases. 15: e0009325
Badri M, Kurtz ZD, Bonneau R, et al. (2020) Shrinkage improves estimation of microbial associations under different normalization methods. Nar Genomics and Bioinformatics. 2: lqaa100
Cirrone J, Brooks MD, Bonneau R, et al. (2020) Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality. Scientific Reports. 10: 14141
Tang MS, Miraldi ER, Girgis NM, et al. (2020) Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs. Journal of Immunology (Baltimore, Md. : 1950)
Wu F, Xiao A, Zhang J, et al. (2020) SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. Medrxiv : the Preprint Server For Health Sciences
Arrieta-Ortiz ML, Hafemeister C, Shuster B, et al. (2020) Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks. Msystems. 5
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