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Richard Bonneau

Active 2001–2025

184
Papers
31,411
Citations
88
h-index
160
i10-index

Citations

Citations per year for Richard Bonneau1978: 2 citations1985: 1 citations1988: 1 citations1989: 3 citations1992: 1 citations1995: 2 citations1996: 2 citations1997: 1 citations1998: 1 citations2000: 1 citations2001: 14 citations2002: 32 citations2003: 54 citations2004: 45 citations2005: 54 citations2006: 78 citations2007: 123 citations2008: 137 citations2009: 132 citations2010: 172 citations2011: 167 citations2012: 171 citations2013: 243 citations2014: 234 citations2015: 301 citations2016: 340 citations2017: 416 citations2018: 445 citations2019: 1,068 citations2020: 1,442 citations2021: 1,684 citations2022: 1,513 citations2023: 1,246 citations2024: 1,729 citations2025: 1,022 citations2026: 113 citations2027: 1 citations1979–1984: no citations, so these years are not shown1986–1987: no citations, so these years are not shown1990–1991: no citations, so these years are not shown1993–1994: no citations, so these years are not shown1999: no citations, so this year is not shown

Citation sources

Countries

World map of the countries and regions citing this authorUnited States: 5,436 citing papers, 30.8% of this breakdownChina: 2,205 citing papers, 12.5% of this breakdownUnited Kingdom: 1,139 citing papers, 6.4% of this breakdownGermany: 1,132 citing papers, 6.4% of this breakdownCanada: 569 citing papers, 3.2% of this breakdownFrance: 559 citing papers, 3.2% of this breakdownItaly: 498 citing papers, 2.8% of this breakdownAustralia: 421 citing papers, 2.4% of this breakdownSpain: 389 citing papers, 2.2% of this breakdownJapan: 385 citing papers, 2.2% of this breakdownSwitzerland: 374 citing papers, 2.1% of this breakdownNetherlands: 350 citing papers, 2% of this breakdown
0%30.8%Other 23.8%

Institutions

Fields

  • Biochemistry, Genetics and Molecular Biology53.8%
  • Medicine15.3%
  • Immunology and Microbiology9.1%
  • Social Sciences6.1%
  • Computer Science4.7%
  • Neuroscience2.8%
  • Other8.2%

Topics

  • Gut microbiota and health4%
  • Protein Structure and Dynamics3.4%
  • Bioinformatics and Genomic Networks3%
  • RNA and protein synthesis mechanisms2.6%
  • Single-cell and spatial transcriptomics2.5%
  • Machine Learning in Bioinformatics2.2%
  • Other82.3%

Coauthors

All papers

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  1. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

    Authors: Rebecca F. Alford, Andrew Leaver‐Fay, Jeliazko R. Jeliazkov, Matthew J. O’Meara, Frank DiMaio, Hahnbeom Park, Maxim V. Shapovalov, P. Douglas Renfrew, Vikram Khipple Mulligan, Kalli Kappel, Jason W. Labonte, Michael S. Pacella, Richard Bonneau, Philip Bradley, Roland L. Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J. Gray - Journal of Chemical Theory and Computation 2017 cited by 1,570

  2. High-definition spatial transcriptomics for in situ tissue profiling

    Authors: Sanja Vicković, Gökçen Eraslan, Fredrik Salmén, Johanna Klughammer, Linnea Stenbeck, Denis Schapiro, Tarmo Äijö, Richard Bonneau, Ludvig Bergenstråhle, José Fernández Navarro, Joshua Gould, Gabriel K. Griffin, Åke Borg, Mostafa Ronaghi, Jonas Frisén, Joakim Lundeberg, Aviv Regev, Patrik L. Ståhl - Nature Methods 2019 cited by 1,221

  3. OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

    Authors: Gustaf Ahdritz, Nazim Bouatta, Christina Floristean, Sachin Kadyan, Qinghui Xia, William Gerecke, Timothy J. O’Donnell, Daniel Berenberg, I. Fisk, Niccolò Zanichelli, Bo Zhang, Arkadiusz Nowaczynski, Bei Wang, Marta M. Stepniewska-Dziubinska, Shang Zhang, Adegoke A. Ojewole, Murat Efe Guney, Stella Biderman, Andrew M. Watkins, Stephen Ra, Pablo Ribalta Lorenzo, Lucas G. Nivón, Brian D. Weitzner, Yih‐En Andrew Ban, Shiyang Chen, Minjia Zhang, Conglong Li, Shuaiwen Leon Song, Yuxiong He, Peter K. Sorger, Emad Mostaque, Zhao Zhang, Richard Bonneau, Mohammed AlQuraishi - Nature Methods 2024 cited by 289

  4. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

    Authors: Naihui Zhou, Yuxiang Jiang, Timothy Bergquist, Alexandra Lee, Balint Z Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George P. Georghiou, Huy Nguyen, Md-Nafiz Hamid, L. Taylor Davis, Tunca Doğan, Volkan Atalay, Ahmet Süreyya Rifaioğlu, Alperen Dalkıran, Rengül Çetin-Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemović, Vladimir Perović, Radoslav Davidović, Neven Šumonja, Nevena Veljković, Ehsaneddin Asgari, Mohammad R. K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fábio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan Medlar, Elaine Zosa, Itamar Borukhov, Ilya B. Novikov, Angela D. Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Sašo Džeroski, Ian Sillitoe, Sayoni Das, Jonathan Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, José Manuel Rodrı́guez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Ré, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie‐Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo and 67 more - Genome biology 2019 cited by 482

  5. Tweeting From Left to Right

    Authors: Pablo Barberá, John T. Jost, Jonathan Nagler, Joshua A. Tucker, Richard Bonneau - Psychological Science 2015 cited by 1,431

  6. Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles

    Authors: James T. Morton, Dong-Min Jin, Robert H. Mills, Yan Shao, Gibraan Rahman, Daniel McDonald, Qiyun Zhu, Metin Balaban, Yueyu Jiang, Kalen Cantrell, Antonio González, Julie Carmel, Linoy Mia Frankiensztajn, Sandra Martin‐Brevet, Kirsten Berding, Brittany D. Needham, María Fernanda Zurita, Maude M. David, О. В. Аверина, Alexey S. Kovtun, Antonio Noto, Michele Mussap, Mingbang Wang, Daniel N. Frank, Ellen Li, Wenhao Zhou, Vassilios Fanos, В. Н. Даниленко, Dennis P. Wall, Paúl Cárdenas, Manuel E. Baldeón, Sébastien Jacquemont, Omry Koren, Evan Elliott, Ramnik J. Xavier, Sarkis K. Mazmanian, Rob Knight, Jack A. Gilbert, Sharon M. Donovan, Trevor D. Lawley, Bob Carpenter, Richard Bonneau, Gaspar Taroncher‐Oldenburg - Nature Neuroscience 2023 cited by 209

  7. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

    Authors: Adrian Tett, Kun D. Huang, Francesco Asnicar, Hannah Fehlner-Peach, Edoardo Pasolli, Nicolai Karcher, Federica Armanini, Paolo Manghi, Kevin S. Bonham, Moreno Zolfo, Francesca De Filippis, Cara Magnabosco, Richard Bonneau, John Lusingu, John Amuasi, Karl J. Reinhard, Thomas Rattei, Fredrik Boulund, Lars Engstrand, Albert Zink, María Carmen Collado, Dan R. Littman, Daniel Eibach, Danilo Ercolini, Omar Rota‐Stabelli, Curtis Huttenhower, Frank Maixner, Nicola Segata - Cell Host & Microbe 2019 cited by 502

  8. Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer

    Authors: Jun-Chieh J. Tsay, Benjamin G. Wu, Michelle Badri, José C. Clemente, Nan Shen, Peter Meyn, Yonghua Li, Ting-An Yie, Tenzin Lhakhang, Evan Olsen, Vivek Murthy, Gaëtane Michaud, Imran Sulaiman, Aristotelis Tsirigos, Adriana Heguy, Harvey I. Pass, Michael D. Weiden, William N. Rom, Daniel H. Sterman, Richard Bonneau, Martin J. Blaser, Leopoldo N. Segal - American Journal of Respiratory and Critical Care Medicine 2018 cited by 457

  9. GABA-receptive microglia selectively sculpt developing inhibitory circuits

    Authors: Emilia Favuzzi, Shuhan Huang, Giuseppe-Antonio Saldi, Loïc Binan, Leena A. Ibrahim, Marian Fernández-Otero, Yuqing Cao, Ayman Zeine, Adwoa Sefah, Karen Zheng, Qingru Xu, Elizaveta Khlestova, Samouil L. Farhi, Richard Bonneau, Sandeep Robert Datta, Beth Stevens, Gord Fishell - Cell 2021 cited by 327

  10. Lower Airway Dysbiosis Affects Lung Cancer Progression

    Authors: Jun-Chieh J. Tsay, Benjamin G. Wu, Imran Sulaiman, Katherine Gershner, Rosemary Schluger, Yonghua Li, Ting-An Yie, Peter Meyn, Evan Olsen, Luisannay Perez, Brendan Franca, Joseph Carpenito, Tadasu Iizumi, Mariam El-Ashmawy, Michelle Badri, James T. Morton, Nan Shen, Linchen He, Gaetane Michaud, Samaan Rafeq, Jamie L. Bessich, Robert L. Smith, Harald Sauthoff, Kevin Felner, Ray Pillai, Anastasia-Maria Zavitsanou, Sergei B. Koralov, Valeria Mezzano, Cynthia A. Loomis, Andre L. Moreira, William Moore, Aristotelis Tsirigos, Adriana Heguy, William N. Rom, Daniel H. Sterman, Harvey I. Pass, Jose C. Clemente, Huilin Li, Richard Bonneau, Kwok-Kin Wong, Thales Papagiannakopoulos, Leopoldo N. Segal - Cancer Discovery 2020 cited by 305

  11. Why are there hotspot mutations in the TP53 gene in human cancers?

    Authors: Evan H. Baugh, Hua Zhu Ke, Arnold J. Levine, Richard Bonneau, Chang S. Chan - Cell Death and Differentiation 2017 cited by 627

  12. A Validated Regulatory Network for Th17 Cell Specification

    Authors: Maria Ciofani, Aviv Madar, Carolina Galan, MacLean Sellars, Kieran Mace, Florencia Pauli, Ashish Agarwal, Wendy Huang, Christopher N. Parkurst, Michael Muratet, Kim Newberry, Sarah K. Meadows, Alex Greenfield, Yi Yang, Preti Jain, Francis K. Kirigin, Carmen Birchmeier, Erwin F. Wagner, Kenneth M. Murphy, R Myers, Richard Bonneau, Dan R. Littman - Cell 2012 cited by 1,192

  13. Accurate de novo design of hyperstable constrained peptides

    Authors: Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl, Jason M. Gilmore, Peta J. Harvey, Olivier Cheneval, Garry W. Buchko, Surya V. S. R. K. Pulavarti, Quentin Kaas, Alexander Eletsky, Po-Ssu Huang, William A. Johnsen, Per Greisen, Gabriel J. Rocklin, Yifan Song, Thomas W. Linsky, Andrew M. Watkins, Stephen A. Rettie, Xianzhong Xu, Lauren P. Carter, Richard Bonneau, James M. Olson, Evangelos A. Coutsias, Colin E. Correnti, Thomas Szyperski, David J. Craik, David Baker - Nature, Nat. 2016 cited by 467

  14. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

    Authors: Silas Maniatis, Tarmo Äijö, Sanja Vicković, Catherine Braine, Kristy Kang, Annelie Mollbrink, Delphine Fagegaltier, Žaneta Andrusivová, Sami Saarenpää, Gonzalo Saiz-Castro, Miguel Cuevas, Aaron Watters, Joakim Lundeberg, Richard Bonneau, Hemali Phatnani - Science 2019 cited by 454

  15. The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

    Authors: Alexander G. Baltz, Mathias Munschauer, Björn Schwanhäußer, Alexandra Iulia Vasile, Yasuhiro Murakawa, Markus Schueler, Noah Youngs, Duncan Penfold-Brown, Kevin Drew, Miha Milek, Emanuel Wyler, Richard Bonneau, Matthias Selbach, Christoph Dieterich, Markus Landthaler - Molecular Cell 2012 cited by 1,280

  16. c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont

    Authors: Mo Xu, Maria Pokrovskii, Yi Ding, Ren Yi, Christy Au, Oliver J. Harrison, Carolina Galan, Yasmine Belkaid, Richard Bonneau, Dan R. Littman - Nature 2018 cited by 516

  17. Protein remote homology detection and structural alignment using deep learning

    Authors: Tymor Hamamsy, James T. Morton, Robert Blackwell, Daniel Berenberg, Nicholas Carriero, Vladimir Gligorijević, Charlie E. M. Strauss, Julia Koehler Leman, Kyunghyun Cho, Richard Bonneau - Nature Biotechnology 2023 cited by 150

  18. NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

    Authors: Writing Group, Patty J. Lee, Christopher C. Benz, Philip D. Blood, Katy Börner, Judith Campisi, Feng Chen, Heike E. Daldrup‐Link, Phil De Jager, Li Ding, Francesca E. Duncan, Oliver Eickelberg, Rong Fan, Toren Finkel, David Furman, Vesna D. Garovic, Nils Gehlenborg, Carolyn Glass, Indra Heckenbach, Ziv-Bar Joseph, Pragati Katiyar, Sojin Kim, Mélanie Königshoff, George A. Kuchel, Haesung Lee, Jun Hee Lee, Jian Ma, Qin Ma, Simon Melov, Kay Metis, Ana L. Mora, Nicolas Musi, Nicola Neretti, João F. Passos, Irfan Rahman, Juan Carlos Rivera‐Mulia, Paul Robson, Mauricio Rojas, Ananda L. Roy, Morten Scheibye‐Knudsen, Birgit Schilling, Pixu Shi, Jonathan C. Silverstein, Vidyani Suryadevara, Jichun Xie, Jinhua Wang, A. Ian Wong, Laura J. Niedernhofer, Siyuan Wang, Hannah Anvari, Julia L. Balough, Christopher C. Benz, Joanna Bons, Boris Brenerman, William J. Evans, Akos A. Gerencser, Heather Gregory, Malene Hansen, Jamie N. Justice, Pankaj Kapahi, Natália Faraj Murad, Amy O’Broin, Mary Ellen Pavone, Mark Powell, Gary K. Scott, Elisheva D. Shanes, Mahalakshmi Shankaran, Eric Verdin, Daniel A. Winer, Fei Wu, Andrew I. Adams, Philip D. Blood, Andreas Bueckle, Ivan Cao-Berg, Hao Chen, Michael J. Davis, Shane Filus, Yuhan Hao, Austin Hartman, Euxhen Hasanaj, Jesse Helfer, Bruce Herr, Ziv Bar‐Joseph, Gesmira Molla, Gloria Mou, Juan Puerto, Ellen M. Quardokus, Alexander J. Ropelewski, Matt Ruffalo, Rahul Satija, Melissa Schwenk, Robin Scibek, William Shirey, Max Sibilla, Joel Welling, Yuan Zhou, Columbia TMC, Richard Bonneau, Angela M. Christiano, Benjamin Izar and 149 more - Nature Aging 2022 cited by 128

  19. OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

    Authors: Gustaf Ahdritz, Nazim Bouatta, Christina Floristean, Sachin Kadyan, Qinghui Xia, William Gerecke, Timothy J. O’Donnell, Daniel Berenberg, I. Fisk, Niccolò Zanichelli, Bo Zhang, Arkadiusz Nowaczynski, Bei Wang, Marta M. Stepniewska-Dziubinska, Shang Zhang, Adegoke A. Ojewole, Murat Efe Guney, Stella Biderman, Andrew M. Watkins, Stephen Ra, Pablo Ribalta Lorenzo, Lucas G. Nivón, Brian D. Weitzner, Yih‐En Andrew Ban, Peter K. Sorger, Emad Mostaque, Zhao Zhang, Richard Bonneau, Mohammed AlQuraishi - 2022 cited by 169

  20. Learning representations of microbe–metabolite interactions

    Authors: James T. Morton, Alexander A. Aksenov, Louis‐Félix Nothias, James R. Foulds, Robert A. Quinn, Michelle Badri, Tami L. Swenson, Marc W. Van Goethem, Trent R. Northen, Yoshiki Vázquez‐Baeza, Mingxun Wang, Nicholas A. Bokulich, Aaron Watters, Se Jin Song, Richard Bonneau, Pieter C. Dorrestein, Rob Knight - Nature Methods 2019 cited by 308

  21. SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

    Authors: Fuqing Wu, Amy Xiao, Jianbo Zhang, Katya Moniz, Noriko Endo, Federica Armas, Richard Bonneau, Megan A. Brown, Mary Bushman, Peter R. Chai, Claire Duvallet, Timothy B. Erickson, Katelyn Foppe, Newsha Ghaeli, Xiaoqiong Gu, William P. Hanage, Katherine Huang, Wei Lin Lee, Mariana Matus, Kyle A. McElroy, Jonathan Nagler, Steven F Rhode, Mauricio Santillana, Joshua A. Tucker, Stefan Wuertz, Shijie Zhao, Janelle R. Thompson, Eric J. Alm - The Science of The Total Environment 2021 cited by 304

  22. An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses

    Authors: Teruyuki Sano, Wendy Huang, Jason A. Hall, Yi Yang, Alessandra Chen, Samuel J. Gavzy, June‐Yong Lee, Joshua W. Ziel, Emily R. Miraldi, Ana I. Domingos, Richard Bonneau, Dan R. Littman - Cell 2015 cited by 555

  23. Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates

    Authors: Hannah Fehlner-Peach, Cara Magnabosco, Varsha Raghavan, José U. Scher, Adrian Tett, Laura M. Cox, Claire Gottsegen, Aaron Watters, John D. Wiltshire-Gordon, Nicola Segata, Richard Bonneau, Dan R. Littman - Cell Host & Microbe 2019 cited by 224

  24. An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    Authors: Yuxiang Jiang, Tal Oron, Wyatt T. Clark, Asma Bankapur, Daniel D’Andrea, Rosalba Lepore, Christopher S. Funk, Indika Kahanda, Karin Verspoor, Asa Ben‐Hur, Da Chen Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra J. Lin, Sayed Mohammad Ebrahim Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio, Renzhi Cao, Zhaolong Zhong, Jianlin Cheng, Adrian Altenhoff, Nives Škunca, Christophe Dessimoz, Tunca Doğan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt E. Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching-Tai Chen, Wen−Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T. Jones, Samuel Chapman, Dukka Bkc, Ishita Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrián–Uhalte, Paul Denny, Rebecca E. Foulger, Reija Hieta, Duncan Legge, Ruth C. Lovering, Michele Magrane, Anna N. Melidoni, Prudence Mutowo, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon-Charles Tranchevent, Sayoni Das, Natalie L. Dawson, David Lee, Jonathan Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E. Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, Jesse Gillis, Adriana E. Sedeño-Cortés, Paul Pavlidis, Shou Feng, Juan Miguel Cejuela, Tatyana Goldberg, Tobias Hamp, Lothar Richter, Asaf Salamov, Toni Gabaldón, Marina Marcet‐Houben, Fran Supek, Qingtian Gong, Wei Ning, Yuanpeng Zhou, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Stefano Toppo, Carlo Ferrari, Manuel Giollo and 47 more - Genome biology 2016 cited by 452