Richard Bonneau

Richard Bonneau 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 New York University, he holds appointments in the department of biology, the Center for Data Science and the Courant Institute of Mathematical Sciences. Provided by Wikipedia
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  1. 1
    Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks

    Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks by Konstantine Tchourine, Christine Vogel, Richard Bonneau

    Published 2018-04-01
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  2. 2
    Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases

    Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases by Dong-Min Jin, James T. Morton, Richard Bonneau

    Published 2024-08-01
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  3. 3
    PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization

    PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization by Claudia Skok Gibbs, Omar Mahmood, Richard Bonneau, Kyunghyun Cho

    Published 2024-04-01
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  4. 4
    Negative example selection for protein function prediction: the NoGO database.

    Negative example selection for protein function prediction: the NoGO database. by Noah Youngs, Duncan Penfold-Brown, Richard Bonneau, Dennis Shasha

    Published 2014-06-01
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  5. 5
    DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator.

    DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator. by Aviv Madar, Alex Greenfield, Eric Vanden-Eijnden, Richard Bonneau

    Published 2010-03-01
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  6. 6
    The 2010 Rosetta developers meeting: macromolecular prediction and design meets reproducible publishing.

    The 2010 Rosetta developers meeting: macromolecular prediction and design meets reproducible publishing. by P Douglas Renfrew, Gabrielle Campbell, Charlie E M Strauss, Richard Bonneau

    Published 2011-01-01
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  7. 7
    Exposure to the Russian Internet Research Agency foreign influence campaign on Twitter in the 2016 US election and its relationship to attitudes and voting behavior

    Exposure to the Russian Internet Research Agency foreign influence campaign on Twitter in the 2016 US election and its relationship to attitudes and voting behavior by Gregory Eady, Tom Paskhalis, Jan Zilinsky, Richard Bonneau, Jonathan Nagler, Joshua A. Tucker

    Published 2023-01-01
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  8. 8
    Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks

    Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks by Mario L. Arrieta-Ortiz, Christoph Hafemeister, Bentley Shuster, Nitin S. Baliga, Richard Bonneau, Patrick Eichenberger

    Published 2020-06-01
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  9. 9
    Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference

    Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference by Andreas Tjärnberg, Maggie Beheler-Amass, Christopher A. Jackson, Lionel A. Christiaen, David Gresham, Richard Bonneau

    Published 2024-01-01
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  10. 10
    CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection

    CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection by Lingdi Zhang, Jahan Rahman, Matthew Chung, Lauren Lashua, Aubree Gordon, Angel Balmaseda, Guillermina Kuan, Richard Bonneau, Elodie Ghedin

    Published 2023-06-01
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  11. 11
    Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method

    Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method by Mary Maranga, Pawel Szczerbiak, Valentyn Bezshapkin, Vladimir Gligorijevic, Chris Chandler, Richard Bonneau, Ramnik J. Xavier, Tommi Vatanen, Tomasz Kosciolek

    Published 2023-04-01
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  12. 12
    Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

    Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions by Anne Plessis, Christoph Hafemeister, Olivia Wilkins, Zennia Jean Gonzaga, Rachel Sarah Meyer, Inês Pires, Christian Müller, Endang M Septiningsih, Richard Bonneau, Michael Purugganan

    Published 2015-11-01
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  13. 13
    Correction: Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota.

    Correction: Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota. by Soo Ching Lee, Mei San Tang, Yvonne A L Lim, Seow Huey Choy, Zachary D Kurtz, Laura M Cox, Uma Mahesh Gundra, Ilseung Cho, Richard Bonneau, Martin J Blaser, Kek Heng Chua, P'ng Loke

    Published 2021-04-01
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  14. 14
    Sequence-structure-function relationships in the microbial protein universe

    Sequence-structure-function relationships in the microbial protein universe by Julia Koehler Leman, Pawel Szczerbiak, P. Douglas Renfrew, Vladimir Gligorijevic, Daniel Berenberg, Tommi Vatanen, Bryn C. Taylor, Chris Chandler, Stefan Janssen, Andras Pataki, Nick Carriero, Ian Fisk, Ramnik J. Xavier, Rob Knight, Richard Bonneau, Tomasz Kosciolek

    Published 2023-04-01
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  15. 15
    An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

    An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network by Mario L Arrieta‐Ortiz, Christoph Hafemeister, Ashley Rose Bate, Timothy Chu, Alex Greenfield, Bentley Shuster, Samantha N Barry, Matthew Gallitto, Brian Liu, Thadeous Kacmarczyk, Francis Santoriello, Jie Chen, Christopher DA Rodrigues, Tsutomu Sato, David Z Rudner, Adam Driks, Richard Bonneau, Patrick Eichenberger

    Published 2015-11-01
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  16. 16
    Computational Design of Phosphotriesterase Improves V‐Agent Degradation Efficiency

    Computational Design of Phosphotriesterase Improves V‐Agent Degradation Efficiency by Jacob Kronenberg, Stanley Chu, Andrew Olsen, Dustin Britton, Leif Halvorsen, Shengbo Guo, Ashwitha Lakshmi, Jason Chen, Maria Jinu Kulapurathazhe, Cetara A. Baker, Benjamin C. Wadsworth, Cynthia J. Van Acker, John G. Lehman III, Tamara C. Otto, P. Douglas Renfrew, Richard Bonneau, Jin Kim Montclare

    Published 2024-07-01
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