Richard Bonneau

36.7k citations

243 papers · 19.1k indexed · 15 hit papers · h-index 67

Molecular Biology top 0.2%
Immunology top 1%
Sociology and Political Science top 0.5%
Communication top 0.2%
Genetics top 1%

Co-authors: Joshua A. Tucker Jonathan Nagler David Baker John T. Jost Dan R. Littman Pablo Barberá Emily R. Miraldi Zachary Kurtz
Topics: Protein Structure and Dynamics (35 papers)Bioinformatics and Genomic Networks (30 papers)Social Media and Politics (28 papers)
Cited by: Communication Molecular Biology Immunology
Journals: Nature Science Cell
Partner nations: United States Germany United Kingdom

In The Last Decade

Richard Bonneau

239 papers receiving 18.8k citations

Hit Papers

5 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

2015 1.1k citations Zachary Kurtz, Christian L. Müller et al. profile →
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

2017 942 citations Rebecca F. Alford, Andrew Leaver‐Fay et al. Journal of Chemical Theory and Computation profile →
The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

2012 923 citations Richard Bonneau et al. profile →
Tweeting From Left to Right

2015 922 citations Richard Bonneau et al. profile →
High-definition spatial transcriptomics for in situ tissue profiling

2019 705 citations Sanja Vicković, Tarmo Äijö et al. profile →
Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome

2010 629 citations Edward A. Miao, Dat P. Mao et al. Proceedings of the National Academy of Sciences profile →
Structure-based protein function prediction using graph convolutional networks

2021 467 citations Vladimir Gligorijević, P. Douglas Renfrew et al. Nature Communications profile →
An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses

2015 440 citations Emily R. Miraldi, Richard Bonneau et al. Cell profile →
Why are there hotspot mutations in the TP53 gene in human cancers?

2017 398 citations Richard Bonneau et al. profile →
Helminth infection promotes colonization resistance via type 2 immunity

2016 300 citations Zachary Kurtz, Martin J. Blaser et al. Science profile →
Who Leads? Who Follows? Measuring Issue Attention and Agenda Setting by Legislators and the Mass Public Using Social Media Data

2019 282 citations Richard Bonneau et al. profile →
How Social Media Facilitates Political Protest: Information, Motivation, and Social Networks

2018 281 citations Richard Bonneau et al. profile →
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

2019 276 citations Silas Maniatis, Tarmo Äijö et al. Science profile →
GABA-receptive microglia selectively sculpt developing inhibitory circuits

2021 193 citations Emilia Favuzzi, Shuhan Huang et al. Cell profile →
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

2023 54 citations Richard Bonneau et al. Nature Communications profile →

Peers

Countries citing papers authored by Richard Bonneau

Since Specialization

Citations

This map shows the geographic impact of Richard Bonneau's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Richard Bonneau with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Richard Bonneau more than expected).

Fields of papers citing papers by Richard Bonneau

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Richard Bonneau. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Richard Bonneau. The network helps show where Richard Bonneau may publish in the future.

Co-authorship network of co-authors of Richard Bonneau

This figure shows the co-authorship network connecting the top 25 collaborators of Richard Bonneau. A scholar is included among the top collaborators of Richard Bonneau based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Richard Bonneau. Richard Bonneau is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

#	Work	Indexed citations
1	Conformation-aware structure prediction of antigen-recognizing immune proteins 2025 ·mAbs ·Frédéric A. Dreyer,Jan Ludwiczak,(unknown),Brennan Abanades,Robert G. Alberstein,Pan Kessel,Priya Rao,(unknown),Richard Bonneau,Andrew M. Watkins,(unknown)	0
2	Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases 2024 ·mSystems ·(unknown),James T. Morton,Richard Bonneau	7
3	Computational Design of Phosphotriesterase Improves V‐Agent Degradation Efficiency 2024 ·ChemistryOpen ·(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),(unknown),Tamara C. Otto,P. Douglas Renfrew,Richard Bonneau,Jin Kim Montclare	4
4	High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0 2022 ·Bioinformatics ·(unknown),Christopher A. Jackson,Giuseppe-Antonio Saldi,Andreas Tjärnberg,(unknown),Aaron Watters,(unknown),(unknown),Ren Yi,Tymor Hamamsy,Dayanne M. Castro,Nicholas Carriero,Bram L. Gorissen,David Gresham,Emily R. Miraldi,Richard Bonneau	37
5	NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction 2022 ·Bioinformatics ·Ren Yi,Kyunghyun Cho,Richard Bonneau	1
6	Tuning a coiled-coil hydrogel via computational design of supramolecular fiber assembly 2022 ·Molecular Systems Design & Engineering ·(unknown),(unknown),(unknown),(unknown),Farbod Mahmoudinobar,P. Douglas Renfrew,Richard Bonneau,Jin Kim Montclare	8
7	A convolutional neural network for common coordinate registration of high-resolution histology images 2021 ·Bioinformatics ·(unknown),Krzysztof J. Geras,Richard Bonneau	7
8	NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity 2021 ·Bioinformatics ·Meet Barot,Vladimir Gligorijević,Kyunghyun Cho,Richard Bonneau	14
9	GABA-receptive microglia selectively sculpt developing inhibitory circuitsbreakdown → 2021 ·Cell ·Emilia Favuzzi,Shuhan Huang,Giuseppe-Antonio Saldi,Loïc Binan,Leena A. Ibrahim,Marian Fernández-Otero,Yuqing Cao,Ayman Zeine,(unknown),Karen Zheng,Qing Xu,(unknown),Samouil L. Farhi,Richard Bonneau,Sandeep Robert Datta,Beth Stevens,Gord Fishell	193
10	Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks 2020 ·mSystems ·Mario L. Arrieta‐Ortiz,Christoph Hafemeister,(unknown),Nitin S. Baliga,Richard Bonneau,Patrick Eichenberger	11
11	Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling 2020 ·Nature Communications ·Mariano I. Gabitto,(unknown),Orly L. Wapinski,Kathryn Allaway,Nicholas Carriero,Gord Fishell,Richard Bonneau	7
12	Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosisbreakdown → 2019 ·Science ·Silas Maniatis,Tarmo Äijö,Sanja Vicković,Catherine Braine,Kristy Kang,Annelie Mollbrink,Delphine Fagegaltier,Žaneta Andrusivová,Sami Saarenpää,(unknown),Miguel Cuevas,Aaron Watters,Joakim Lundeberg,Richard Bonneau,Hemali Phatnani	276
13	deepNF: deep network fusion for protein function prediction 2018 ·Bioinformatics ·Vladimir Gligorijević,Meet Barot,Richard Bonneau	151
14	Towards region-specific propagation of protein functions 2018 ·Bioinformatics ·Da Chen Emily Koo,Richard Bonneau	8
15	Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing 2017 ·Bioinformatics ·Tarmo Äijö,Christian L. Müller,Richard Bonneau	42
16	Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function 2017 ·Molecular BioSystems ·(unknown),(unknown),(unknown),(unknown),(unknown),P. Douglas Renfrew,Richard Bonneau,Jin Kim Montclare	5
17	The Rosetta All-Atom Energy Function for Macromolecular Modeling and Designbreakdown → 2017 ·Journal of Chemical Theory and Computation ·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	942
18	A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity 2017 ·Nature Communications ·Victoria Ruiz,Thomas Battaglia,Zachary Kurtz,Luc Bijnens,(unknown),(unknown),Xuhui Zheng,Tadasu Iizumi,(unknown),Christian L. Müller,Ken Cadwell,Richard Bonneau,(unknown),Martin J. Blaser	102
19	One third of dynamic protein expression profiles can be predicted by a simple rate equation 2014 ·Molecular BioSystems ·(unknown),Christopher S. Poultney,Li Wang,Gustavo M. Silva,(unknown),(unknown),Richard Bonneau,Christine Vogel	19
20	Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasomebreakdown → 2010 ·Proceedings of the National Academy of Sciences ·Edward A. Miao,Dat P. Mao,Natalya Yudkovsky,Richard Bonneau,Cynthia G. Lorang,Sarah Warren,Irina A. Leaf,Alan Aderem	629

About Richard Bonneau

Richard Bonneau is a scholar working on Communication, Molecular Biology and General Social Sciences, having authored 243 papers that have together received 19.1k indexed citations. Recurring topics across this work include Protein Structure and Dynamics (35 papers), Bioinformatics and Genomic Networks (30 papers) and Social Media and Politics (28 papers). The work is most often cited by research in Communication (1.5k citations), Molecular Biology (12.2k citations) and Immunology (2.2k citations). Richard Bonneau has collaborated with scholars based in United States, Germany and United Kingdom. Frequent co-authors include Joshua A. Tucker, Jonathan Nagler, David Baker, John T. Jost, Dan R. Littman, Pablo Barberá, Emily R. Miraldi, Zachary Kurtz, Christian L. Müller and Martin J. Blaser. Their work appears in journals such as Nature, Science and Cell.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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