2026 Richard Bonneau: Biology and Biochemistry Researcher – H-Index, Publications & Awards

Discipline name	D-Index	World Ranking	Current World Ranking	National Ranking	Current National Ranking	Publications	Citations
Biology and Biochemistry	88	2657	2441	1382	1244	295	35514

Overview

Richard Bonneau is affiliated with New York University in the United States. Their research primarily focuses on Biochemistry, Genetics, and Molecular Biology, with significant contributions to Molecular Biology as a central subfield. Other notable subfields include Sociology and Political Science, Communication, Materials Chemistry, and Artificial Intelligence.

Bonneau's work spans a range of topics, including:

Protein Structure and Dynamics
Machine Learning in Bioinformatics
Social Media and Politics
Single-cell and Spatial Transcriptomics
Gut Microbiota and Health
RNA and Protein Synthesis Mechanisms
Genomics and Phylogenetic Studies

Their publication record features frequent contributions to venues such as bioRxiv (Cold Spring Harbor Laboratory), SSRN Electronic Journal, arXiv (Cornell University), OPAL (Open@LaTrobe) from La Trobe University, and Nature Communications.

Several recent papers illustrate the range and focus of Bonneau's research. These include:

Structure-based protein function prediction using graph convolutional networks, 2021, Nature Communications
SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases, 2021, The Science of The Total Environment
GABA-receptive microglia selectively sculpt developing inhibitory circuits, 2021, Cell
OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization, 2024, Nature Methods
Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments, 2020, eLife

Collaborations are an important aspect of their scholarly activity. Notable frequent coauthors include Vladimir Gligorijević, Jonathan Nagler, Joshua A. Tucker, Kyunghyun Cho, and P. Douglas Renfrew.

Best Publications

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

Zachary D. Kurtz;Christian L. Müller;Emily R. Miraldi;Dan R. Littman

1764
Citations
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

Rebecca F. Alford;Andrew Leaver-Fay;Jeliazko R. Jeliazkov;Matthew J. O’Meara

1306
Citations
The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

Alexander G. Baltz;Mathias Munschauer;Björn Schwanhäusser;Alexandra Vasile

1306
Citations
A Validated Regulatory Network for Th17 Cell Specification

Maria Ciofani;Aviv Madar;Aviv Madar;Carolina Galan;MacLean Sellars

1238
Citations
Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome

Edward A. Miao;Dat P. Mao;Natalya Yudkovsky;Richard Bonneau

946
Citations
High-definition spatial transcriptomics for in situ tissue profiling.

Sanja Vickovic;Sanja Vickovic;Gökcen Eraslan;Fredrik Salmén;Johanna Klughammer

887
Citations
Macromolecular modeling and design in Rosetta: recent methods and frameworks

Julia Koehler Leman;Brian D. Weitzner;Brian D. Weitzner;Steven M. Lewis;Steven M. Lewis;Jared Adolf-Bryfogle

847
Citations
Structure-based protein function prediction using graph convolutional networks.

Vladimir Gligorijević;P. Douglas Renfrew;Tomasz Kosciolek;Tomasz Kosciolek;Julia Koehler Leman

828
Citations
Ab initio protein structure prediction of CASP III targets using ROSETTA

Kim T. Simons;Rich Bonneau;Ingo Ruczinski;David Baker

740
Citations
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

Richard A. Bonneau;Richard A. Bonneau;David J Reiss;Paul Shannon;Marc T. Facciotti

652
Citations
An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses

Teruyuki Sano;Wendy Huang;Jason A. Hall;Yi Yang

549
Citations
Why are there hotspot mutations in the TP53 gene in human cancers

Evan H Baugh;Hua Ke;Arnold J Levine;Richard A Bonneau

542
Citations
Accurate de novo design of hyperstable constrained peptides.

Gaurav Bhardwaj;Vikram Khipple Mulligan;Christopher D. Bahl;Jason M. Gilmore

483
Citations
An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Yuxiang Jiang;Tal Ronnen Oron;Wyatt T. Clark;Asma R. Bankapur

453
Citations
Helminth infection promotes colonization resistance via type 2 immunity

Deepshika Ramanan;Rowann Bowcutt;Soo Ching Lee;Mei San Tang

443
Citations
Ab Initio Protein Structure Prediction: Progress and Prospects

Richard Bonneau;David Baker

440
Citations
c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont

Mo Xu;Maria Pokrovskii;Yi Ding;Ren Yi

435
Citations
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).

Sergey Lyskov;Fang Chieh Chou;Shane Ó Conchúir;Bryan S. Der

432
Citations
Rosetta in CASP4: Progress in ab initio protein structure prediction

Richard Bonneau;Jerry Tsai;Ingo Ruczinski;Dylan Chivian

429
Citations
Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea

Nitin S. Baliga;Richard Bonneau;Marc T. Facciotti;Min Pan

386
Citations