Richard A Bonneau (Richard Bonneau)

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 28

Top Topics

Transcription Factor

Amyotrophic Lateral Sclerosis

Saccharomyces Cerevisiae

Top Venues

Nature communications

bioRxiv : the preprint server for biology

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

Dong-Min Jin, James T Morton, Richard A Bonneau
Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. mSystems 9 (8) (2024)
Dong-Min Jin, James T Morton, Richard A Bonneau
Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. mSystems 9 (8) (2024)
Dong-Min Jin, James T Morton, Richard A Bonneau
Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. mSystems 9 (8) (2024)
Dong-Min Jin, James T Morton, Richard A Bonneau
Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. mSystems (2024)
Dong-Min Jin, James T Morton, Richard A Bonneau
Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. mSystems (2024)
Gregory Eady, Tom Paskhalis, Jan Zilinsky, Richard A Bonneau, Jonathan Nagler, Joshua A Tucker
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. Nature communications 14 (1) (2023)
Tymor Hamamsy, James T Morton, Robert Blackwell, Daniel Berenberg, Nicholas Carriero, Vladimir Gligorijevic, Charlie E M Strauss, Julia Koehler Leman, Kyunghyun Cho, Richard A Bonneau
Protein remote homology detection and structural alignment using deep learning. Nature biotechnology (2023)
Christopher A Jackson, Maggie Beheler-Amass, Andreas Tj Rnberg, Ina Suresh, Angela Shang-Mei Hickey, Richard A Bonneau, David Gresham
Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression. bioRxiv : the preprint server for biology (2023)
Andreas Tj Rnberg, Maggie Beheler-Amass, Christopher A Jackson, Lionel A Christiaen, David Gresham, Richard A Bonneau
Structure Primed Embedding on the Transcription Factor Manifold Enables Transparent Model Architectures for Gene Regulatory Network and Latent Activity Inference. bioRxiv : the preprint server for biology (2023)
Gregory Eady, Tom Paskhalis, Jan Zilinsky, Richard A Bonneau, Jonathan Nagler, Joshua A Tucker
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. Nature communications 14 (1) (2023)
Andreas Tj Rnberg, Maggie Beheler-Amass, Christopher A Jackson, Lionel A Christiaen, David Gresham, Richard A Bonneau
Structure Primed Embedding on the Transcription Factor Manifold Enables Transparent Model Architectures for Gene Regulatory Network and Latent Activity Inference. bioRxiv : the preprint server for biology (2023)
Gregory Eady, Tom Paskhalis, Jan Zilinsky, Richard A Bonneau, Jonathan Nagler, Joshua A Tucker
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. Nature communications 14 (1) (2023)
Gregory Eady, Tom Paskhalis, Jan Zilinsky, Richard A Bonneau, Jonathan Nagler, Joshua A Tucker
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. Nature communications 14 (1) (2023)
Andreas Tj Rnberg, Maggie Beheler-Amass, Christopher A Jackson, Lionel A Christiaen, David Gresham, Richard A Bonneau
Structure Primed Embedding on the Transcription Factor Manifold Enables Transparent Model Architectures for Gene Regulatory Network and Latent Activity Inference. bioRxiv : the preprint server for biology (2023)
Kevin Aslett, Andrew M Guess, Richard A Bonneau, Jonathan Nagler, Joshua A Tucker
News credibility labels have limited average effects on news diet quality and fail to reduce misperceptions. Science advances 8 (18) (2022)
Mehmet Neset Özel, Claudia Skok Gibbs, Isabel Holguera, Mennah Soliman, Richard A Bonneau, Claude Desplan
Coordinated control of neuronal differentiation and wiring by sustained transcription factors. Science (New York, N.Y.) (2022)
Lindsay K Hill, Dustin Britton, Teeba Jihad, Kamia Punia, Xuan Xie, Erika Delgado-Fukushima, Che Fu Liu, Orin Mishkit, Chengliang Liu, Chunhua Tony Hu, Michael Meleties, P Douglas Renfrew, Richard A Bonneau, Youssef Zaim Wadghiri, Jin Kim Montclare
Engineered Protein-Iron Oxide Hybrid Biomaterial for MRI-traceable Drug Encapsulation. Molecular systems design & engineering 7 (8) (2022)
Kathryn C Allaway, Mariano I Gabitto, Orly Wapinski, Giuseppe-Antonio Saldi, Chen-Yu Wang, Rachel C Bandler, Sherry Jingjing Wu, Richard A Bonneau, Gordon Fishell
Genetic and epigenetic coordination of cortical interneuron development. Nature 597 (7878) (2021)
Julia Koehler Leman, Sergey Lyskov, Steven M Lewis, Jared Adolf-Bryfogle, Rebecca F Alford, Kyle A Barlow, Ziv Ben-Aharon, Daniel P Farrell, Jason S Fell, William A Hansen, Ameya Harmalkar, Jeliazko R Jeliazkov, Georg Kuenze, Justyna Dorota Kryś, Ajasja Ljubetič, Amanda L Loshbaugh, Jack Maguire, Rocco Moretti, Vikram Khipple Mulligan, Morgan L Nance, Phuong T Nguyen, Shane Ó Conchúir, Shourya S Roy Burman, Rituparna Samanta, Shannon T Smith, Frank Teets, Johanna K S Tiemann, Andrew Watkins, Hope Woods, Brahm J Yachnin, Christopher D Bahl, Chris Bailey-Kellogg, Julien S Baker, Rachel J Hagey, Frank DiMaio, Sagar D Khare, Tanja Kortemme, Jason W Labonte, Kresten Lindorff-Larsen, Jens Meiler, William R Schief, Ora Schueler-Furman, Justin B Siegel, Amelie Stein, Vladimir Yarov-Yarovoy, Brian Kuhlman, Andrew Leaver-Fay, Dominik Gront, Jeffrey J Gray, Richard A Bonneau
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature communications 12 (1) (2021)
Vladimir Gligorijević, P Douglas Renfrew, Tomasz Kosciolek, Julia Koehler Leman, Daniel Berenberg, Tommi Vatanen, Chris Chandler, Bryn C Taylor, Ian M Fisk, Hera Vlamakis, Ramnik J Xavier, Rob Knight, Kyunghyun Cho, Richard A Bonneau
Structure-based protein function prediction using graph convolutional networks. Nature communications 12 (1) (2021)
Matthew R Dillon, Evan Bolyen, Anja Adamov, Aeriel D Belk, Emily Borsom, Zachary Burcham, Justine W Debelius, Heather Deel, Alexandra L Emmons, Mehrbod Estaki, Chloe Herman, Christopher R Keefe, Jamie T Morton, Renato Renison Moreira Oliveira, Andrew Sanchez, Anthony Simard, Yoshiki Vázquez-Baeza, Michal Ziemski, Hazuki E Miwa, Terry A Kerere, Carline Coote, Richard A Bonneau, Rob Knight, Guilherme Corrêa de Oliveira, Piraveen Gopalasingam, Benjamin D Kaehler, Emily K Cope, Jessica L Metcalf, Michael Scott Robeson, Nicholas A Bokulich, J Gregory Caporaso
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS computational biology 17 (6) (2021)
Andreas Tj Rnberg, Omar Mahmood, Christopher A Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel A Christiaen, Richard A Bonneau
Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data. PLoS computational biology 17 (1) (2021)
Omar Mahmood, Elman Mansimov, Richard A Bonneau, Kyunghyun Cho
Masked graph modeling for molecule generation. Nature communications 12 (1) (2021)
Julia Koehler Leman, Brian D Weitzner, Steven M Lewis, Jared Adolf-Bryfogle, Nawsad Alam, Rebecca F Alford, Melanie Aprahamian, Julien S Baker, Kyle A Barlow, Patrick Barth, Benjamin Basanta, Brian J Bender, Kristin Blacklock, Jaume Bonet, Scott E Boyken, Philip G Bradley, Chris Bystroff, Patrick Conway, Seth Cooper, Bruno E Correia, Brian Coventry, Rachel J Hagey, René M De Jong, Frank DiMaio, Lorna Dsilva, Roland L Dunbrack, Alexander S Ford, Brandon Frenz, Darwin Y Fu, Caleb Geniesse, Lukasz Goldschmidt, Ragul Gowthaman, Jeffrey J Gray, Dominik Gront, Sharon Guffy, Scott Horowitz, Po-Ssu Huang, Thomas Huber, Tim M Jacobs, Jeliazko R Jeliazkov, David K Johnson, Kalli Kappel, John Karanicolas, Hamed Khakzad, Karen R Khar, Sagar D Khare, Firas Khatib, Alisa Khramushin, Indigo C King, Robert Kleffner, Brian Koepnick, Tanja Kortemme, Georg Kuenze, Brian Kuhlman, Daisuke Kuroda, Jason W Labonte, Jason K Lai, Gideon Lapidoth, Andrew Leaver-Fay, Steffen Lindert, Thomas Linsky, Nir London, Joseph H Lubin, Sergey Lyskov, Jack Maguire, Lars Malmström, Enrique Marcos, Orly Marcu, Nicholas A Marze, Jens Meiler, Rocco Moretti, Vikram Khipple Mulligan, Santrupti Nerli, Christoffer Norn, Shane Ó'Conchúir, Noah Ollikainen, Sergey Ovchinnikov, Michael S Pacella, Xingjie Pan, Hahnbeom Park, Ryan E Pavlovicz, Manasi Pethe, Brian G Pierce, Kala Bharath Pilla, Barak Raveh, P Douglas Renfrew, Shourya S Roy Burman, Aliza Rubenstein, Marion F Sauer, Andreas Scheck, William R Schief, Ora Schueler-Furman, Yuval Sedan, Alexander M Sevy, Nikolaos G Sgourakis, Lei Shi, Justin B Siegel, Daniel-Adriano Silva, Shannon Smith, Yifan Song, Amelie Stein, Maria Szegedy, Frank D Teets, Summer B Thyme, Ray Yu-Ruei Wang, Andrew Watkins, Lior Zimmerman, Richard A Bonneau
Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature methods 17 (7) (2020)
Christopher A Jackson, Dayanne M Castro, Giuseppe-Antonio Saldi, Richard A Bonneau, David Gresham
Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. eLife 9 (2020)
Dayanne M Castro, Nicholas R de Veaux, Emily R Miraldi, Richard A Bonneau
Multi-study inference of regulatory networks for more accurate models of gene regulation. PLoS computational biology 15 (1) (2019)
Priscillia Lhoumaud, Sana Badri, Javier Rodriguez-Hernaez, Theodore Sakellaropoulos, Gunjan Sethia, Andreas Kloetgen, MacIntosh Cornwell, Sourya Bhattacharyya, Ferhat Ay, Richard A Bonneau, Aristotelis Tsirigos, Jane A Skok
NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains. Nature communications 10 (1) (2019)
Silas Maniatis, Tarmo Äijö, Sanja Vickovic, Catherine Braine, Kristy Kang, Annelie Mollbrink, Delphine Fagegaltier, Žaneta Andrusivová, Sami Saarenpää, Gonzalo Saiz-Castro, Miguel Cuevas, Aaron Watters, Joakim Lundeberg, Richard A Bonneau, Hemali Phatnani
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. Science (New York, N.Y.) 364 (6435) (2019)