Bonneau, Richard

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

Kurtz, Z. D., Müller, C. L., Miraldi, E. R., Littman, D. R., Blaser, M. J., & Bonneau, R. A. (2015) · PLOS Computational Biology

Gut microbiota and healthMicrobial Community Ecology and Physiology

Cited by 1,799

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

Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., et al. (2017) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 1,532

Tweeting From Left to Right: Is Online Political Communication More Than an Echo Chamber?

Barberá, P., Jost, J. T., Nagler, J., Tucker, J. A., & Bonneau, R. (2015) · Psychological Science

Social Media and PoliticsMisinformation and Its Impacts

Cited by 1,472

A Validated Regulatory Network for Th17 Cell Specification

Ciofani, M., Madar, A., Galan, C., Sellars, M., Mace, K., Pauli, F., Agarwal, A., Huang, W., Parkurst, C. N., Muratet, M., et al. (2012) · Cell

Psoriasis: Treatment and PathogenesisT-cell and B-cell Immunology

Cited by 1,160

High-definition spatial transcriptomics for in situ tissue profiling

Vickovic, S., Eraslan, G., Salmén, F., Klughammer, J., Stenbeck, L., Schapiro, D., Äijö, T., Bonneau, R., Bergenstråhle, L., Navarro, J. F., et al. (2019) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,150

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 888

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

Sano, T., Huang, W., Hall, J. A., Yang, Y., Chen, A., Gavzy, S. J., Lee, J.-Y., Ziel, J. W., Miraldi, E. R., Domingos, A. I., et al. (2015) · Cell

Psoriasis: Treatment and PathogenesisIL-33, ST2, and ILC Pathways

Cited by 547

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

Bonneau, R., Reiss, D. J., Shannon, P., Facciotti, M., Hood, L., Baliga, N. S., & Thorsson, V. (2006) · Genome Biology

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 510

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

Xu, M., Pokrovskii, M., Ding, Y., Yi, R., Au, C., Harrison, O. J., Galan, C., Belkaid, Y., Bonneau, R., & Littman, D. R. (2018) · Nature

T-cell and B-cell ImmunologyInflammatory Bowel Disease

Cited by 498

How Social Media Facilitates Political Protest: Information, Motivation, and Social Networks

Jost, J. T., Barberá, P., Bonneau, R., Langer, M., Metzger, M., Nagler, J., Sterling, J., & Tucker, J. A. (2018) · Political Psychology

Social Media and PoliticsSociopolitical Dynamics in Russia

Cited by 492

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

Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 476

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

Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., et al. (2019) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 452

Airway microbiota is associated with upregulation of the PI3K pathway in lung cancer

Tsay, J.-C. J., Wu, B. G., Badri, M. H., Clemente, J. C., Shen, N., Meyn, P., Li, Y., Yie, T.-A., Lhakhang, T., Olsen, E., et al. (2018) · American Journal of Respiratory and Critical Care Medicine

Oral microbiology and periodontitis researchGut microbiota and health

Cited by 448

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

Ahdritz, G., Bouatta, N., Floristean, C., Kadyan, S., Xia, Q., Gerecke, W., O’Donnell, T. J., Berenberg, D., Fisk, I., Zanichelli, N., et al. (2024) · Nature Methods

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 439

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Maniatis, S., Äijö, T., Vickovic, S., Braine, C., Kang, K., Mollbrink, A., Fagegaltier, D., Andrusivová, Ž., Saarenpää, S., Saiz-Castro, G., et al. (2019) · Science

Amyotrophic Lateral Sclerosis ResearchSingle-cell and spatial transcriptomics

Cited by 429

The Critical Periphery in the Growth of Social Protests

Barberá, P., Wang, N., Bonneau, R., Jost, J. T., Nagler, J., Tucker, J., & González-Bailón, S. (2015) · PLOS ONE

Social Media and PoliticsComplex Network Analysis Techniques

Cited by 348

DREAM4: combining genetic and dynamic information to identify biological networks and dynamical models

Greenfield, A., Madar, A., Ostrer, H., & Bonneau, R. (2010) · PLoS ONE

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 255

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

Jackson, C. A., Castro, D. M., Saldi, G.-A., Bonneau, R., & Gresham, D. (2020) · eLife

Gene Regulatory Network AnalysisSingle-cell and spatial transcriptomics

Cited by 174

An improved protein decoy set for testing energy functions for protein structure prediction

Tsai, J., Bonneau, R., Morozov, A. V., Kuhlman, B., Rohl, C. A., & Baker, D. (2003) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 158

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

Eady, G., Paskhalis, T., Zilinsky, J., Bonneau, R., Nagler, J., & Tucker, J. A. (2023) · Nature Communications

Misinformation and Its ImpactsSocial Media and Politics

Cited by 125

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

SenNet Consortium, Writing Group, Lee, P. J., Benz, C. C., Blood, P., Börner, K., Campisi, J., Chen, F., Daldrup-Link, H., De Jager, P., et al. (2022) · Nature Aging

Telomeres, Telomerase, and SenescenceGenetics, Aging, and Longevity in Model Organisms

Cited by 122

Testing the effects of Facebook usage in an ethnically polarized setting

Asimovic, N., Nagler, J., Bonneau, R., & Tucker, J. A. (2021) · Proceedings of the National Academy of Sciences

Social and Intergroup PsychologySocial Media and Politics

Cited by 85

Elites Tweet to Get Feet Off the Streets: Measuring Regime Social Media Strategies During Protest

Munger, K., Bonneau, R., Nagler, J., & Tucker, J. A. (2019) · Political Science Research and Methods

Social Media and PoliticsMedia Influence and Politics

Cited by 84

Designing Peptides on a Quantum Computer

Mulligan, V. K., Melo, H., Merritt, H. I., Slocum, S., Weitzner, B. D., Watkins, A. M., Renfrew, P. D., Pelissier, C., Arora, P. S., & Bonneau, R. (2019) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsQuantum Computing Algorithms and Architecture

Cited by 67