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R

Richard Bonneau

roche

90H-index
500Paper Count
3.7WCitation Count
Published Papers 136
Publication Date
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Distinct cellular phenotypes of language and executive decline in amyotrophic lateral sclerosis
errCell
IF42.5
err2026-08-04
err0
errOAAI
errJoana Petrescu; Cláudio Gouveia Roque; Christopher A. Jackson; Aidan C. Daly; Zoé Butti; Kristy Kang; Obadele Casel; Matthew Leung; Luke Reilly; Jacqueline Eschbach; Brhan Gebremedhin; Karina McDade; Jenna M. Gregory; Richard Bonneau; Colin Smith; Hemali Phatnani
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errSave
Conformation-aware structure prediction of antigen-recognizing immune proteins
errMABS
IF7.3
err2026-01-06
err0
PREAI
errDreyer, Frederic A.; Ludwiczak, Jan; Martinkus, Karolis; Abanades, Brennan; Alberstein, Robert G.; Kessel, Pan; Rao, Pranav; Lee, Jae Hyeon; Bonneau, Richard; Watkins, Andrew M.; Seeger, Franziska
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errSave
Tissue and cellular spatiotemporal dynamics in colon aging
errNature Biotechnology
IF41.7
err2025-10-22
err0
errOAAI
errAidan C. Daly; Francesco Cambuli; Tarmo Äijö; Britta Lötstedt; Nemanja Despot Marjanovic; Sara Fernandez; Olena Kuksenko; Matthew Smith-Erb; Daniel Domovic; Nicholas Van Wittenberghe; Eugene Drokhlyansky; Gabriel K. Griffin; Hemali Phatnani; Richard Bonneau; Aviv Regev; Sanja Vickovic
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errSave
A Validated Regulatory Network for Th17 Cell Specification
errCell
IF42.5
err2025-09-23
err0
PREAI
errMaria 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. Murphy; Richard M. Myers; Richard Bonneau; Dan R. Littman
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errSave
deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning
errBIOINFORMATICS
IF5.4
err2025-09-01
err0
PREAI
errMohammadipeyhani, Homa; Lee, Edith; Bonneau, Richard; Gligorijevic, Vladimir; Lee, Jae Hyeon
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errSave
Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans
errNature Communications
IF15.7
err2025-07-24
err0
errOAAI
errSteven A. Sullivan; Jordan C. Orosco; Francisco Callejas-Hernández; Frances Blow; Hayan Lee; T. Rhyker Ranallo-Benavidez; Andrew Peters; Shane R. Raidal; Yvette A. Girard; Christine K. Johnson; Krysta H. Rogers; Richard Gerhold; Hayley Mangelson; Ivan Liachko; Harsh Srivastava; Chris Chandler; Daniel Berenberg; Richard A. Bonneau; Po-Jung Huang; Yuan-Ming Yeh; Chi-Ching Lee; Hsuan Liu; Ting-Wen Chen; Petrus Tang; Cheng-Hsun Chiu; Michael C. Schatz; Jane M. Carlton
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errSave
Measuring receptivity to misinformation at scale on a social media platform
errPNAS NEXUS
IF3.8
err2024-09-10
err1
errOAAI
errTokita, Christopher K.; Aslett, Kevin; Godel, William P.; Sanderson, Zeve; Tucker, Joshua A.; Nagler, Jonathan; Persily, Nathaniel; Bonneau, Richard
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errSave
Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases
errMSYSTEMS
IF4.6
err2024-08-20
err1
errOAAI
errJin, Dong-Min; Morton, James T.; Bonneau, Richard
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errSave
OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
errNATURE METHODS
IF32.1
err2024-05-14
err37
errOAAI
errAhdritz, Gustaf; Bouatta, Nazim; Floristean, Christina; Kadyan, Sachin; Xia, Qinghui; Gerecke, William; O'Donnell, Timothy J.; Berenberg, Daniel; Fisk, Ian; Zanichelli, Niccolo; Zhang, Bo; Nowaczynski, Arkadiusz; Wang, Bei; Stepniewska-Dziubinska, Marta M.; Zhang, Shang; Ojewole, Adegoke; Guney, Murat Efe; Biderman, Stella; Watkins, Andrew M.; Ra, Stephen; Lorenzo, Pablo Ribalta; Nivon, Lucas; Weitzner, Brian; Ban, Yih-En Andrew; Chen, Shiyang; Zhang, Minjia; Li, Conglong; Song, Shuaiwen Leon; He, Yuxiong; Sorger, Peter K.; Mostaque, Emad; Zhang, Zhao; Bonneau, Richard; AlQuraishi, Mohammed
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errSave
Computational Prediction of Coiled-Coil Protein Gelation Dynamics and Structure (vol 25, pg 258, 2024)
errBIOMACROMOLECULES
IF5.4
err2024-04-17
err0
errOAAI
errBritton, Dustin; Christians, Luc F.; Liu, Chengliang; Legocki, Jakub; Xiao, Yingxin; Meleties, Michael; Yang, Lin; Cammer, Michael; Jia, Sihan; Zhang, Zihan; Mahmoudinobar, Farbod; Kowalski, Zuzanna; Renfrew, P. Douglas; Bonneau, Richard; Pochan, Darrin J.; Pak, Alexander J.; Montclare, Jin Kim
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errSave
PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization
errGENOME BIOLOGY
IF9.4
err2024-04-08
err1
errOAAI
errGibbs, Claudia Skok; Mahmood, Omar; Bonneau, Richard; Cho, Kyunghyun
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errSave
Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop
errJOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
IF11.2
err2024-04-01
err2
PREAI
errBunyavanich, Supinda; Becker, Patrice M.; Altman, Matthew C.; Lasky-Su, Jessica; Ober, Carole; Zengler, Karsten; Berdyshev, Evgeny; Bonneau, Richard; Chatila, Talal; Chatterjee, Nilanjan; Chung, Kian Fan; Cutcliffe, Colleen; Davidson, Wendy; Dong, Gang; Fang, Gang; Fulkerson, Patricia; Himes, Blanca E.; Liang, Liming; Mathias, Rasika A.; Ogino, Shuji; Petrosino, Joseph; Price, Nathan D.; Schadt, Eric; Schofield, James; Seibold, Max A.; Steen, Hanno; Wheatley, Lisa; Zhang, Hongmei; Togias, Alkis; Hasegawa, Kohei
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errSave
Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference
errGENOME BIOLOGY
IF9.4
err2024-01-18
err2
errOAAI
errTjarnberg, Andreas; Beheler-Amass, Maggie; Jackson, Christopher A.; Christiaen, Lionel A.; Gresham, David; Bonneau, Richard
errShare
errSave
Computational Prediction of Coiled-Coil Protein Gelation Dynamics and Structure
errBIOMACROMOLECULES
IF5.4
err2023-12-18
err9
errOAAI
errBritton, Dustin; Christians, Luc F.; Liu, Chengliang; Legocki, Jakub; Xiao, Yingxin; Meleties, Michael; Yang, Lin; Cammer, Michael; Jia, Sihan; Zhang, Zihan; Mahmoudinobar, Farbod; Kowalski, Zuzanna; Renfrew, P. Douglas; Bonneau, Richard; Pochan, Darrin J.; Pak, Alexander J.; Montclare, Jin Kim
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errSave
Testing the Effect of Information on Discerning the Veracity of News in Real Time
errJOURNAL OF EXPERIMENTAL POLITICAL SCIENCE
IF3.4
err2023-11-08
err0
errOAAI
errAslett, Kevin; Sanderson, Zeve; Godel, William; Persily, Nathaniel; Nagler, Jonathan; Bonneau, Richard; Tucker, Joshua A.
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errSave
Protein remote homology detection and structural alignment using deep learning
errNATURE BIOTECHNOLOGY
IF41.7
err2023-09-07
err22
errOAAI
errHamamsy, Tymor; Morton, James T.; Blackwell, Robert; Berenberg, Daniel; Carriero, Nicholas; Gligorijevic, Vladimir; Strauss, Charlie E. M.; Leman, Julia Koehler; Cho, Kyunghyun; Bonneau, Richard
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errSave
CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection
errMICROBIOME
IF12.7
err2023-06-17
err5
errOAAI
errZhang, Lingdi; Rahman, Jahan; Chung, Matthew; Lashua, Lauren; Gordon, Aubree; Balmaseda, Angel; Kuan, Guillermina; Bonneau, Richard; Ghedin, Elodie
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errSave
Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method
errMSYSTEMS
IF4.6
err2023-04-27
err14
errOAAI
errMaranga, Mary; Szczerbiak, Pawel; Bezshapkin, Valentyn; Gligorijevic, Vladimir; Chandler, Chris; Bonneau, Richard; Xavier, Ramnik J.; Vatanen, Tommi; Kosciolek, Tomasz
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errSave
Sequence-structure-function relationships in the microbial protein universe
errNATURE COMMUNICATIONS
IF15.7
err2023-04-26
err23
errOAAI
errLeman, Julia Koehler; Szczerbiak, Pawel; Renfrew, P. Douglas; Gligorijevic, Vladimir; Berenberg, Daniel; Vatanen, Tommi; Taylor, Bryn C.; Chandler, Chris; Janssen, Stefan; Pataki, Andras; Carriero, Nick; Fisk, Ian; Xavier, Ramnik J.; Knight, Rob; Bonneau, Richard; Kosciolek, Tomasz
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errSave
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
errNATURE COMMUNICATIONS
IF15.7
err2023-01-09
err40
errOAAI
errEady, Gregory; Paskhalis, Tom; Zilinsky, Jan; Bonneau, Richard; Nagler, Jonathan; Tucker, Joshua A.
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errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
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Ramnik J. Xavier
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Dan R. Littman
H-index: 169 · Papers: 501
L
Leroy Hood
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