Richard Bonneau

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A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell

Amy K. Schmid, William J. R. Longabaugh, Richard Bonneau, 2007, Cell.

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models

Richard Bonneau, Aviv Madar, Alex Greenfield, 2010, PloS one.

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

Richard Bonneau, M. Facciotti, David J. Reiss, 2006, Genome Biology.

Learning biological networks: from modules to dynamics.

Richard Bonneau, 2008, Nature chemical biology.

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

Richard Bonneau, D. Baker, J. Tsai, 2003, Proteins.

Distributions of beta sheets in proteins with application to structure prediction

Richard Bonneau, D. Baker, C. Kooperberg, 2002, Proteins.

Is Online Political Communication More Than an Echo Chamber?

Joshua A. Tucker, Richard Bonneau, J. Jost, 2022 .

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments[OPEN]

Richard Bonneau, Olivia W. Wilkins, Christoph Hafemeister, 2016, Plant Cell.

The Rosetta all-atom energy function for macromolecular modeling and design

Roland L. Dunbrack, Jason W. Labonte, Jeffrey J. Gray, 2017, bioRxiv.

The Critical Periphery in the Growth of Social Protests

Joshua A. Tucker, Richard Bonneau, J. Jost, 2015, PloS one.

Rosetta in CASP4: Progress in ab initio protein structure prediction

Richard Bonneau, D. Baker, C. Strauss, 2001, Proteins.

Ab initio protein structure prediction of CASP III targets using ROSETTA

Richard Bonneau, D. Baker, I. Ruczinski, 1999, Proteins.

A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells

Christopher S. Poultney, Richard Bonneau, Alex Greenfield, 2013, Genome research.

De novo prediction of three-dimensional structures for major protein families.

Richard Bonneau, D. Baker, C. Strauss, 2002, Journal of molecular biology.

Functional inferences from blind ab initio protein structure predictions.

Richard Bonneau, D. Baker, J. Tsai, 2001, Journal of structural biology.

Contact order and ab initio protein structure prediction

Richard Bonneau, D. Baker, J. Tsai, 2002, Protein science : a publication of the Protein Society.

Accurate de novo design of hyperstable constrained peptides

David Baker, James M. Olson, Thomas Szyperski, 2016, Nature.

Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design

Eun Jung Choi, Richard Bonneau, B. Kuhlman, 2012, PloS one.

Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

Brian D. Weitzner, Jeffrey J. Gray, Bryan S. Der, 2013, PloS one.

Structure-Based Function Prediction using Graph Convolutional Networks

Tommi Vatanen, Kyunghyun Cho, Julia Koehler Leman, 2019, bioRxiv.

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

Mario L. Arrieta-Ortiz, Richard Bonneau, Alex Greenfield, 2015, Molecular systems biology.

The Rosetta all-atom energy function for macromolecular modeling and design

Roland L. Dunbrack, Richard Bonneau, P. Douglas Renfrew, 2017, bioRxiv.

A Rotamer Library to Enable Modeling and Design of Peptoid Foldamers

Timothy W. Craven, Richard Bonneau, P. D. Renfrew, 2014, Journal of the American Chemical Society.

Characterizing the epigenetic landscape of cellular populations from bulk and single-cell ATAC-seq information

Nicholas Carriero, Richard Bonneau, Gordon Fishell, 2019, bioRxiv.

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.

Dayanne M. Castro, Richard Bonneau, Aviv Madar, 2019, Genome research.

A Validated Regulatory Network for Th17 Cell Specification

Richard Bonneau, Aviv Madar, Alex Greenfield, 2012, Cell.

Rational Design of Topographical Helix Mimics as Potent Inhibitors of Protein–Protein Interactions

Richard Bonneau, K. Drew, T. Brewer, 2014, Journal of the American Chemical Society.

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.

Min Pan, Paul Shannon, Richard Bonneau, 2004, Genome research.

Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.

Min Pan, Richard Bonneau, Leroy Hood, 2004, Genome research.

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

Dayanne M. Castro, Richard Bonneau, D. Gresham, 2020, eLife.

Multi-species integrative biclustering

Richard Bonneau, Thadeous Kacmarczyk, Peter Waltman, 2010, Genome Biology.

Helminth infection promotes colonization resistance via type 2 immunity

Martin J. Blaser, Zachary D. Kurtz, Kenya Honda, 2016, Science.

Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota

Richard Bonneau, Martin J. Blaser, Zachary D. Kurtz, 2014, PLoS neglected tropical diseases.

For Whom the Bot Tolls: A Neural Networks Approach to Measuring Political Orientation of Twitter Bots in Russia

Joshua A. Tucker, Richard Bonneau, D. Stukal, 2019, SAGE Open.

Normalization methods for microbial abundance data strongly affect correlation estimates

Zachary D. Kurtz, Christian L. Müller, Richard Bonneau, 2018, bioRxiv.

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet

Zachary D. Kurtz, Nicholas A. Bokulich, Christian L. Müller, 2016, Genome Medicine.

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts.

Richard Bonneau, C. Dieterich, Noah Youngs, 2012, Molecular cell.

Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation.

Richard Bonneau, Y. Kluger, V. Snetkova, 2016, Cell reports.

CRISPR-Decryptr reveals cis-regulatory elements from noncoding perturbation screens

Richard Bonneau, N. Carriero, M. Gabitto, 2020, bioRxiv.

Learning accurate representations of microbe-metabolite interactions

James R. Foulds, Se Jin Song, James T. Morton, 2019, Nature Methods.

Revisiting microbe-metabolite interactions: doing better than random

James R. Foulds, Se Jin Song, James T. Morton, 2019, bioRxiv.

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

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2018, Political Science Research and Methods.

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

Joshua A. Tucker, Richard Bonneau, J. Jost, 2018, Political Psychology.

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Catherine E. Braine, Richard Bonneau, J. Lundeberg, 2018, Science.

Social media and political communication: A survey of Twitter users during the 2013 Italian general election

Joshua A. Tucker, Richard Bonneau, J. Jost, 2013 .

De Novo Structure Prediction: Methods and Applications

Richard Bonneau, 2008 .

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity

Zachary D. Kurtz, Christian L. Müller, Richard Bonneau, 2017, Nature Communications.

De novo structure prediction and experimental characterization of folded peptoid oligomers

Jonathan N. Jaworski, Vincent A. Voelz, Richard Bonneau, 2012, Proceedings of the National Academy of Sciences.

Ab initio protein structure prediction: progress and prospects.

Richard Bonneau, D. Baker, D. Baker, 2001, Annual review of biophysics and biomolecular structure.

Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2.

Pedro P. Rocha, Richard Bonneau, D. Reinberg, 2017, Cell reports.

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

Dayanne M. Castro, Richard Bonneau, D. Gresham, 2019, bioRxiv.

Learning global models of transcriptional regulatory networks from data.

Richard Bonneau, Aviv Madar, 2009, Methods in molecular biology.

Protein Structural Alignments From Sequence

Richard Bonneau, C. Strauss, V. Gligorijević, 2020, bioRxiv.

Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology

Richard Bonneau, D. Baker, C. Strauss, 2007, PLoS biology.

Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation

Richard Bonneau, D. Baker, C. Strauss, 2001, Proteins.

The 2010 Rosetta Developers Meeting: Macromolecular Prediction and Design Meets Reproducible Publishing

Richard Bonneau, P. Douglas Renfrew, Charlie E. M. Strauss, 2011, PloS one.

Ab initio methods.

David Baker, Richard Bonneau, Dylan Chivian, 2003, Methods of biochemical analysis.

Robust classification of protein variation using structural modelling and large-scale data integration

Richard Bonneau, Alex E. Lash, Natalia Volfovsky, 2015, bioRxiv.

Robust Classification of Protein Variation Using Structural Modeling and Large-Scale Data Integration

Rebecca F. Alford, Christian L. Müller, Richard Bonneau, 2015, bioRxiv.

FIREWACh: High-throughput Functional Detection of Transcriptional Regulatory Modules in Mammalian Cells

Richard Bonneau, Yuval Kluger, Zuojian Tang, 2014, Nature Methods.

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

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

High-definition spatial transcriptomics for in situ tissue profiling

Richard Bonneau, Aviv Regev, Ludvig Bergenstråhle, 2019, Nature Methods.

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Aaron Watters, Richard Bonneau, Joakim Lundeberg, 2018, Science.

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

Richard Bonneau, Eric Vanden-Eijnden, Aviv Madar, 2010, PloS one.

Diurnally Entrained Anticipatory Behavior in Archaea

Kenia Whitehead, Min Pan, Richard Bonneau, 2009, PloS one.

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

Paul Shannon, Richard Bonneau, Eric W Deutsch, 2004, Genome Biology.

Biophysically motivated regulatory network inference: progress and prospects

Richard Bonneau, Tarmo Äijö, Richard Bonneau, 2016, bioRxiv.

Biophysically motivated regulatory network inference: progress and prospects

Richard Bonneau, Tarmo Äijö, Richard Bonneau, 2016 .

Identification of new therapeutic targets in CRLF2-overexpressing B-ALL through discovery of TF-gene regulatory interactions

Dayanne M. Castro, Richard Bonneau, R. Raviram, 2019, bioRxiv.

Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models

Richard Bonneau, R. Tsien, B. Rudy, 2017, Proceedings of the National Academy of Sciences.

Elites Tweet to get Feet o the Streets: Measuring Elite Reaction to Protest Using Social Media

Joshua A. Tucker, Richard Bonneau, J. Jost, 2015 .

Genome analysis Temporal probabilistic modeling of bacterial compositions derived from 16 S rRNA sequencing

Christian L. Müller, Richard Bonneau, Tarmo Äijö, 2017 .

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

Dayanne M. Castro, Richard Bonneau, Aviv Madar, 2018, bioRxiv.

A physical sciences network characterization of non-tumorigenic and metastatic cells

Christopher S. Poultney, Casey M. Kraning-Rush, Cynthia A. Reinhart-King, 2013, Scientific Reports.

Rotamer libraries for the high-resolution design of β-amino acid foldamers

Timothy W. Craven, Richard Bonneau, P. D. Renfrew, 2016, bioRxiv.

Sequence-Dependent DNA Shape Features Regulate IL-4 Induced Chromatin Accessibility in Alternatively Activated Macrophages

Richard Bonneau, P. Loke, Emily R. Miraldi, 2018, bioRxiv.

Computational-guided determination of the functional role of 447-52D long CDRH3.

Richard Bonneau, X. Kong, Edwin T. Kamau, 2018, Protein engineering, design & selection : PEDS.

Bacillus subtilis Systems Biology: Applications of -Omics Techniques to the Study of Endospore Formation.

Richard Bonneau, P. Eichenberger, Ashley Bate, 2014, Microbiology spectrum.

Side-Chain Conformational Preferences Govern Protein-Protein Interactions.

Richard Bonneau, A. Watkins, P. Arora, 2016, Journal of the American Chemical Society.

Initial Mapping of the New York City Wastewater Virome

Richard Bonneau, E. Ghedin, K. Gulino, 2020, mSystems.

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

Richard Bonneau, D. Koller, L. Iakoucheva, 2012, Cell.

the Halophilic Archaeon Systems Level Insights Into the Stress Response to UV Radiation in

Richard Bonneau, Min Pan, J. DiRuggiero, 2006 .

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells

Richard Bonneau, P. Loke, Ilseung Cho, 2017, Inflammatory bowel diseases.

Environmental gene regulatory influence networks in rice (Oryza sativa):response to water deficit, high temperature and agricultural environments

Richard Bonneau, Olivia W. Wilkins, Christoph Hafemeister, 2016, bioRxiv.

The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families

Richard Bonneau, R. DeSalle, A. Narechania, 2012, Genome biology and evolution.

Sequence-Dependent DNA Shape Features Regulate IL-4 Induced Chromatin Accessibility in Alternatively Activated Macrophages

Richard Bonneau, P. Loke, Emily R. Miraldi, 2018, bioRxiv.

Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility

Richard Bonneau, N. Carriero, Xi Chen, 2016, bioRxiv.

Explicit Modeling of RNA Stability Improves Large-Scale Inference of Transcription Regulation

Richard Bonneau, C. Vogel, Konstantine Tchourine, 2017, bioRxiv.

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops

Christopher R Keefe, Benjamin D. Kaehler, Nicholas A. Bokulich, 2021, PLoS Comput. Biol..

Sequence-structure-function relationships in the microbial protein universe

Julia Koehler Leman, Bryn C. Taylor, Richard Bonneau, 2022, bioRxiv.

Typical development workflow in the Rosetta community.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Rotamer libraries for the high-resolution design of β-amino acid foldamers

Timothy W. Craven, Richard Bonneau, P. D. Renfrew, 2016, bioRxiv.

Values Statement: Equality and Inclusion in the RosettaCommons.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Commercial spin-off companies from the Rosetta community.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

The Gaggle: An open-source software system for integrating bioinformatics software and data sources

David J. Reiss, Nitin S. Baliga, Richard Bonneau, 2006, BMC Bioinformatics.

Multi-study inference of regulatory networks for more accurate models of gene regulation

Richard Bonneau, Emily R. Miraldi, Dayanne M. Castro, 2018, bioRxiv.

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

Richard Bonneau, A. Regev, N. Carriero, 2017, Nature Immunology.

Masked graph modeling for molecule generation

Richard Bonneau, Elman Mansimov, Kyunghyun Cho, 2020, Nature Communications.

Efficient Dual siRNA and Drug Delivery Using Engineered Lipoproteoplexes.

Joseph A. Frezzo, Richard Bonneau, P. D. Renfrew, 2017, Biomacromolecules.

News credibility labels have limited average effects on news diet quality and fail to reduce misperceptions

Joshua A. Tucker, Richard Bonneau, A. Guess, 2022, Science advances.

Viewing the US presidential electoral map through the lens of public health

Richard Bonneau, T. Hamamsy, M. Danziger, 2020, medRxiv.

Quantitative proteomic analysis of the budding yeast cell cycle using acid‐cleavable isotope‐coded affinity tag reagents

Richard Bonneau, Ruedi Aebersold, Parag Mallick, 2006, Proteomics.

Design of Peptoid-peptide Macrocycles to Inhibit the β-catenin TCF Interaction in Prostate Cancer

Timothy W. Craven, Richard Bonneau, K. Kirshenbaum, 2018, Nature Communications.

TM-Vec: template modeling vectors for fast homology detection and alignment

Richard Bonneau, C. Strauss, V. Gligorijević, 2022, bioRxiv.

A novel domain assembly routine for creating full-length models of membrane proteins from known domain structures

Richard Bonneau, J. Leman, 2017, bioRxiv.

Details of Remaining Collective Challenges.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Members of the RosettaCommons Consortium.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Disentangling microbial associations from hidden environmental and technical factors via latent graphical models

Richard Bonneau, Christian Müller, Zachary D. Kurtz, 2019, bioRxiv.

Growth in Rosetta PIs and conference attendees.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Reply to: Examining microbe–metabolite correlations by linear methods

James R. Foulds, Se Jin Song, James T. Morton, 2021, Nature methods.

Intrinsic bioconjugation for site-specific protein PEGylation at N-terminal serine.

Paul M. Levine, Timothy W. Craven, Richard Bonneau, 2014, Chemical communications.

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

Richard Bonneau, Bin Zhang, C. Forst, 2020, Microbiome.

An Assembly Model of Rift Valley Fever Virus

Richard Bonneau, S. Watowich, W. Wriggers, 2012, Front. Microbio..

Engineered multivalent self-assembled binder protein against SARS-CoV-2 RBD

Richard Bonneau, P. D. Renfrew, X. Kong, 2022, Biochemical Engineering Journal.

Election Fraud, YouTube, and Public Perception of the Legitimacy of President Biden

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2022, Journal of Online Trust and Safety.

TM-Vec: template modeling vectors for fast homology detection and alignment

Richard Bonneau, C. Strauss, V. Gligorijević, 2022, bioRxiv.

Critical role of the transcription factors IRF 1 and BATF in preparing the chromatin landscape during Type 1 regulatory cell differentiation

Richard Bonneau, A. Regev, N. Carriero, 2018 .

An Automatic Framework to Continuously Monitor Multi-Platform Information Spread

Joshua A. Tucker, Richard Bonneau, J. Freire, 2021, MISINFO@WWW.

Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs

Richard Bonneau, P. Loke, Emily R. Miraldi, 2020, The Journal of Immunology.

Using Social Media Data to Reveal Patterns of Policy Engagement in State Legislatures

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2022, State Politics & Policy Quarterly.

The Effects of Legislators ’ Communication with their Constituents

Joshua A. Tucker, Richard Bonneau, J. Jost, 2013 .

Semisynthesis of peptoid-protein hybrids by chemical ligation at serine.

Paul M. Levine, Timothy W. Craven, Richard Bonneau, 2014, Organic letters.

Masked graph modeling for molecule generation

Elman Mansimov, Richard Bonneau, Omar Mahmood, 2020, Nature Communications.

Cracking Open the News Feed

Joshua A. Tucker, Richard Bonneau, A. Guess, 2021, Journal of Quantitative Description: Digital Media.

News Sharing on Social Media: Mapping the Ideology of News Media Content, Citizens, and Politicians

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2020 .

PPII Helical Peptidomimetics Templated by Cation–π Interactions

Timothy W. Craven, Richard Bonneau, K. Kirshenbaum, 2016, Chembiochem : a European journal of chemical biology.

N-Naphthyl peptoid foldamers exhibiting atropisomerism.

Richard Bonneau, K. Kirshenbaum, G. L. Butterfoss, 2012, Organic letters.

Tweeting identity? Ukrainian, Russian, and #Euromaidan

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2016 .

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

Chang S. Chan, Richard Bonneau, A. Levine, 2018 .

Dictionary-Assisted Supervised Contrastive Learning

Patrick Y. Wu, Joshua A. Tucker, Richard Bonneau, 2022, EMNLP.

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

Philip D. Blood, Ellen M. Quardokus, Matthew A. Wyczalkowski, 2022, Nature aging.

Modeling host-pathogen interactions: Computational biology and bioinformatics for infectious disease research

Richard Bonneau, P. Braun, D. Hyduke, 2011 .

Sequence-structure-function relationships in the microbial protein universe

Bryn C. Taylor, Richard Bonneau, T. Vatanen, 2022, bioRxiv.

A novel domain assembly routine for creating full-length models of membrane proteins from known domain structures

Richard Bonneau, Julia Koehler Leman, Richard Bonneau, 2017, bioRxiv.

Oligo(N-alkoxy glycines): trans substantiating peptoid conformations.

Richard Bonneau, P. D. Renfrew, K. Kirshenbaum, 2011, Biopolymers.

Oligo(N-aryl glycines): a new twist on structured peptoids.

Richard Bonneau, Khanh Nguyen, Glenn L. Butterfoss, 2008, Journal of the American Chemical Society.

Racemization barriers of atropisomeric 3,3′-bipyrroles: an experimental study with theoretical verification

Richard Bonneau, G. L. Butterfoss, S. Chatterjee, 2016 .

A preliminary survey of the peptoid folding landscape.

Richard Bonneau, Brian Kuhlman, Kent Kirshenbaum, 2009, Journal of the American Chemical Society.

Evaluating the Conformations and Dynamics of Peptoid Macrocycles.

Richard Bonneau, P. D. Renfrew, K. Kirshenbaum, 2022, The journal of physical chemistry. B.

Short of Suspension: How Suspension Warnings Can Reduce Hate Speech on Twitter

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2021, Perspectives on Politics.

What’s Not to Like? Facebook Page Likes Reveal Limited Polarization in Lifestyle Preferences

Joshua A. Tucker, Richard Bonneau, A. Guess, 2021, Political Communication.

Tweeting Beyond Tahrir

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2021, World Politics.

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

Jason W. Labonte, Timothy W. Craven, Stephen A. Rettie, 2021, Proceedings of the National Academy of Sciences.

Lower airway dysbiosis affects lung cancer progression.

Richard Bonneau, J. Clemente, G. Michaud, 2020, Cancer discovery.

Thermoresponsive Protein-Engineered Coiled-coil Hydrogel for Sustained Small Molecule Release.

Richard Bonneau, P. D. Renfrew, R. Tu, 2019, Biomacromolecules.

ICOS-based chimeric antigen receptors program bipolar TH17/TH1 cells.

Matthew J. Frigault, Richard Bonneau, Aviv Madar, 2014, Blood.

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

Christian L. Müller, Richard Bonneau, Martin J. Blaser, 2014, PLoS Comput. Biol..

Supramolecular Assembly and Small-Molecule Binding by Protein-Engineered Coiled-Coil Fibers.

Richard Bonneau, P. D. Renfrew, J. Montclare, 2022, Biomacromolecules.

Engineered coiled-coil protein microfibers.

Richard Bonneau, P. D. Renfrew, J. Montclare, 2014, Biomacromolecules.

Tuning a coiled-coil hydrogel via computational design of supramolecular fiber assembly

Richard Bonneau, P. D. Renfrew, J. Montclare, 2022, Molecular Systems Design & Engineering.

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

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2023, Nature Communications.

Detecting Bots on Russian Political Twitter

Richard Bonneau, Joshua A. Tucker, Denis Stukal, 2017, Big Data.

NetTIME: Improving Multitask Transcription Factor Binding Site Prediction with Base-pair Resolution

Richard Bonneau, Kyunghyun Cho, Ren Yi, 2021 .

GABA-receptive microglia selectively sculpt developing inhibitory circuits

S. R. Datta, Richard Bonneau, G. Fishell, 2020, Cell.

Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility

Nicholas Carriero, Richard Bonneau, Bowen Yu, 2016, bioRxiv.

UniPep - a database for human N-linked glycosites: a resource for biomarker discovery

Ning Zhang, Richard Bonneau, Ruedi Aebersold, 2006, Genome Biology.

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

Kyunghyun Cho, Richard Bonneau, A. Tjaernberg, 2020, bioRxiv.

Automated prediction of CASP‐5 structures using the Robetta server

Lars Malmström, David Baker, Timothy Robertson, 2003, Proteins.

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling

Richard Bonneau, G. Fishell, N. Carriero, 2020, Nature Communications.

Collier/OLF/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors.

Richard Bonneau, Wei Wang, Lionel Christiaen, 2014, Developmental cell.

General transcription factor specified global gene regulation in archaea

Richard Bonneau, M. Facciotti, David J. Reiss, 2007, Proceedings of the National Academy of Sciences.

Specificities of modeling membrane proteins using multi-template homology modeling

Richard Bonneau, Julia Koehler Leman, Richard Bonneau, 2020, bioRxiv.

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27

Krishna Praneeth Kilambi, Richard Bonneau, Jason W. Labonte, 2013, Proteins.

High-definition spatial transcriptomics for in situ tissue profiling

Patrik L. Ståhl, Richard Bonneau, A. Regev, 2019, Nature Methods.

Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks

Richard Bonneau, Christine Vogel, Konstantine Tchourine, 2018, Cell reports.

Interleukin‐17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin‐25–Driven Intestinal Inflammation

Richard Bonneau, J. Clemente, P. Dorrestein, 2019, Arthritis & rheumatology.

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

Arnold J Levine, Hua Ke, Chang S. Chan, 2017, Cell Death and Differentiation.

Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing

Christian L. Müller, Richard Bonneau, Tarmo Äijö, 2016, bioRxiv.

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

Richard Bonneau, Dan Knights, Gabriel A Al-Ghalith, 2018, eLife.

A convolutional neural network for common coordinate registration of high-resolution histology images

Aidan C. Daly, Krzysztof J. Geras, Richard A. Bonneau, 2020, bioRxiv.

Scalable estimation of microbial co-occurrence networks with Variational Autoencoders

Richard Bonneau, G. Tikhonov, J. Silverman, 2021, bioRxiv.

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity

Zachary D. Kurtz, Christian L. Müller, Richard Bonneau, 2017, Nature Communications.

Designing Peptides on a Quantum Computer

Brian D. Weitzner, Andrew M. Watkins, P. Douglas Renfrew, 2019, bioRxiv.

Structure-based protein function prediction using graph convolutional networks

Bryn C. Taylor, Richard Bonneau, T. Vatanen, 2021, Nature Communications.

Towards region-specific propagation of protein functions

Richard Bonneau, Da Chen Emily Koo, Da Chen Emily Koo, 2018, bioRxiv.

Liberal and Conservative Values: What We Can Learn From Congressional Tweets

Joshua A. Tucker, Richard Bonneau, J. Jost, 2018 .

deepNF: deep network fusion for protein function prediction

Richard Bonneau, Vladimir Gligorijevic, Meet Barot, 2017, bioRxiv.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Lars Malmström, Karen R. Khar, 2020, Nature Methods.

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

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

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

Tapio Salakoski, Paolo Fontana, Silvio C. E. Tosatto, 2016, Genome Biology.

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets

Christian L. Müller, Richard Bonneau, Edward M. Marcotte, 2017, PLoS Comput. Biol..

One third of dynamic protein expression profiles can be predicted by a simple rate equation.

Christopher S. Poultney, Richard Bonneau, C. Vogel, 2014, Molecular bioSystems.

NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity

Kyunghyun Cho, Richard Bonneau, Meet Barot, 2020, bioRxiv.

Somatodendritic microRNAs identified by laser capture and multiplex RT-PCR.

Sasha F. Levy, Richard Bonneau, Tsunglin Liu, 2007, RNA.

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms

Richard Bonneau, Sean Davey, Jay H. Konieczka, 2009, BMC Genomics.

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

Katherine H. Huang, Joshua A. Tucker, Richard Bonneau, 2021, Science of The Total Environment.

SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

Richard Bonneau, M. Santillana, S. Wuertz, 2020, medRxiv.

Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters

Richard Bonneau, Thadeous Kacmarczyk, Peter Waltman, 2011, PLoS Comput. Biol..

Generative Models for Quantification of DNA Modifications.

Richard Bonneau, Harri Lähdesmäki, Tarmo Äijö, 2018, Methods in molecular biology.

Managing and Analyzing Big-Data in Genomics

Ashish Agarwal, Kristin C. Gunsalus, Richard Bonneau, 2012 .

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

Richard Bonneau, Christoph Hafemeister, Alex Greenfield, 2013, Bioinform..

The Proteome Folding Project: proteome-scale prediction of structure and function.

Lars Malmström, Richard Bonneau, Trisha N Davis, 2011, Genome research.

Generalized Stability Approach for Regularized Graphical Models

Richard Bonneau, Zachary D. Kurtz, Christian L. Muller, 2016, 1605.07072.

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

Lilia M. Iakoucheva, Richard Bonneau, Kahn Rhrissorrakrai, 2008, Cell.

OutPredict: multiple datasets can improve prediction of expression and inference of causality

G. Coruzzi, D. Shasha, Richard Bonneau, 2020, Scientific Reports.

SlrA/SinR/SlrR inhibits motility gene expression upstream of a hypersensitive and hysteretic switch at the level of σD in Bacillus subtilis

Richard Bonneau, P. Eichenberger, Ashley Bate, 2012, Molecular microbiology.

Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks

Richard Bonneau, Nitin S. Baliga, Patrick Eichenberger, 2019, mSystems.

Macromolecular Modeling and Design in Rosetta: New Methods and Frameworks

Brian D. Weitzner, Steven M. Lewis, Richard Bonneau, 2019 .

Integrated inference and analysis of regulatory networks from multi-level measurements.

Richard Bonneau, Christopher S. Poultney, Alex Greenfield, 2012, Methods in cell biology.

Modeling gene regulation and spatial organization of sequence based motifs

Andreas Zell, Klaus Harter, Jochen Supper, 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

Rachel S. Meyer, Christian L. Müller, Richard Bonneau, 2015, eLife.

Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa

Richard Bonneau, A. Narechania, D. Robinson, 2019, Proceedings of the National Academy of Sciences.

Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice.

Kelly V. Ruggles, Richard Bonneau, F. Bäckhed, 2021, Cell host & microbe.

Conformational preferences of peptide–peptoid hybrid oligomers

Richard Bonneau, Kent Kirshenbaum, P Douglas Renfrew, 2014, Biopolymers.

Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function.

Richard Bonneau, Roni Barak Ventura, P. D. Renfrew, 2017, Molecular bioSystems.

The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis

Richard Bonneau, Peter T. McKenney, P. Eichenberger, 2009, Molecular microbiology.

CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer.

Dayanne M. Castro, Richard Bonneau, G. Freeman, 2019, Cancer cell.

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet

Zachary D. Kurtz, Christian L. Müller, Richard Bonneau, 2016, Genome Medicine.

Who Leads? Who Follows? Measuring Issue Attention and Agenda Setting by Legislators and the Mass Public Using Social Media Data

Richard Bonneau, Jonathan Nagler, John T. Jost, 2019, American Political Science Review.

Cracking Open the News Feed

Joshua A. Tucker, Richard Bonneau, A. Guess, 2021 .

Text Classification for Automatic Detection of E-Cigarette Use and Use for Smoking Cessation from Twitter: A Feasibility Pilot

Richard Bonneau, Yin Aphinyanaphongs, Duncan Penfold-Brown, 2016, PSB.

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

David J. Reiss, Nitin S. Baliga, Richard Bonneau, 2006, BMC Bioinformatics.

Twitter flagged Donald Trump’s tweets with election misinformation: They continued to spread both on and off the platform

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2021, Harvard Kennedy School Misinformation Review.

YouTube Recommendations and Effects on Sharing Across Online Social Platforms

Cody Buntain, Richard Bonneau, Jonathan Nagler, 2020, Proc. ACM Hum. Comput. Interact..

Fungi stabilize connectivity in the lung and skin microbial ecosystems

Zachary D. Kurtz, Christian L. Müller, Richard Bonneau, 2018, Microbiome.

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

Richard Bonneau, J. Clemente, M. Blaser, 2018, American journal of respiratory and critical care medicine.

Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stability

Richard Bonneau, C. Bystroff, G. L. Butterfoss, 2016, Proteins.

Moderating with the Mob: Evaluating the Efficacy of Real-Time Crowdsourced Fact-Checking

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2021, Journal of Online Trust and Safety.

Why Botter: How Pro-Government Bots Fight Opposition in Russia

Joshua A. Tucker, Richard Bonneau, D. Stukal, 2022, American Political Science Review.

Digital Dissent: An Analysis of the Motivational Contents of Tweets From an Occupy Wall Street Demonstration

Richard Bonneau, J. Jost, D. Penfold-Brown, 2018, Motivation Science.

Political Expression and Action on Social Media: Exploring the Relationship Between Lower- and Higher-Threshold Political Activities Among Twitter Users in Italy

Richard Bonneau, Augusto Valeriani, Jonathan Nagler, 2015, J. Comput. Mediat. Commun..

Political psycholinguistics: A comprehensive analysis of the language habits of liberal and conservative social media users.

Richard Bonneau, J. Jost, Joanna Sterling, 2020, Journal of personality and social psychology.

High-density spatial transcriptomics arrays for in situ tissue profiling

Richard Bonneau, Aviv Regev, Ludvig Bergenstråhle, 2019, bioRxiv.

Social Media Data Reveal Patterns of Policy Engagement in State Legislatures

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2020 .

Translating microbiome futures

Richard Bonneau, Jun Wang, Curtis Huttenhower, 2018, Nature Biotechnology.

Splotch: Robust estimation of aligned spatial temporal gene expression data

Richard Bonneau, Joakim Lundeberg, Tarmo Äijö, 2019, bioRxiv.

Improved Stability and Half‐Life of Fluorinated Phosphotriesterase Using Rosetta

Richard Bonneau, P. D. Renfrew, J. Montclare, 2014, Chembiochem : a European journal of chemical biology.

Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks

Richard Bonneau, Patrick Eichenberger, Christoph Hafemeister, 2020, mSystems.

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

Richard Bonneau, Bin Zhang, C. Forst, 2020, Microbiome.

Negative Example Selection for Protein Function Prediction: The NoGO Database

Dennis Shasha, Richard Bonneau, Noah Youngs, 2014, PLoS Comput. Biol..

Parametric Bayesian priors and better choice of negative examples improve protein function prediction

Dennis Shasha, Richard Bonneau, Kevin Drew, 2013, Bioinform..

Tweeting Beyond Tahrir: Ideological Diversity and Political Intolerance in Egyptian Twitter Networks

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2021 .

Author response: Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

Benjamin M Hillmann, Robin R. Shields-Cutler, Richard Bonneau, 2018 .

Shrinkage improves estimation of microbial associations under different normalization methods

Christian L. Müller, Richard Bonneau, Zachary D. Kurtz, 2020, NAR genomics and bioinformatics.

Tweeting From Left to Right

Joshua A. Tucker, Richard Bonneau, J. Jost, 2015, Psychological science.

The Mechanisms of Protest Recruitment through Social Media Networks∗

Jennifer M. Larson, Joshua A. Tucker, Richard Bonneau, 2020 .

Echo Chambers, Rabbit Holes, and Algorithmic Bias: How YouTube Recommends Content to Real Users

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2022, SSRN Electronic Journal.

Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions.

Richard Bonneau, Andrew M Watkins, Paramjit S Arora, 2017, Methods in molecular biology.

Testing the effects of Facebook usage in an ethnically polarized setting

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2021, Proceedings of the National Academy of Sciences.

Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints

Jens Meiler, Julia Koehler Leman, Richard Bonneau, 2019, bioRxiv.

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

Andrew Watkins, Krishna Praneeth Kilambi, P. Douglas Renfrew, 2013, PloS one.

Fused Regression for Multi-source Gene Regulatory Network Inference

Christian L. Müller, Richard Bonneau, Lionel Christiaen, 2016, bioRxiv.

Chemoselective fragment condensation between peptide and peptidomimetic oligomers.

Paul M. Levine, Timothy W. Craven, Richard Bonneau, 2013, Organic & biomolecular chemistry.

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet

Zachary D. Kurtz, Christian L. Müller, Richard Bonneau, 2016, Genome Medicine.

Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ

Zachary D. Kurtz, Richard Bonneau, R. Condos, 2017, ERJ Open Research.

Systems Biology Experimental Design - Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems

Marc T. Facciotti, Richard Bonneau, Nitin S. Baliga, 2004 .

CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection

Richard Bonneau, G. Kuan, A. Gordon, 2022, Microbiome.

Classification of the Molecular Defects Associated with Pathogenic Variants of the SLC6A8 Creatine Transporter.

Richard Bonneau, Julia Koehler Leman, Wesley D. Penn, 2020, Biochemistry.

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP

Julia Koehler Leman, Sergey Lyskov, Richard Bonneau, 2016, BMC Bioinformatics.

Trumping Hate on Twitter? Online Hate Speech in the 2016 U.S. Election Campaign and its Aftermath

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2021, Quarterly Journal of Political Science.

A Comparison of Methods in Political Science Text Classification: Transfer Learning Language Models for Politics

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2020 .

Better together: Elements of successful scientific software development in a distributed collaborative community

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020, PLoS Comput. Biol..

Multi-species integrative biclustering

Richard Bonneau, David J. Reiss, Peter Waltman, 2010 .

Measuring the Ideology of Audiences for Web Links and Domains Using Differentially Private Engagement Data

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2023, Proceedings of the International AAAI Conference on Web and Social Media.

Is There Anybody Out There? The Eects of Legislators' Communication with their Constituents.

Richard Bonneau, Jonathan Nagler, John T. Jost, 2013 .

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Jason W. Labonte, Jeffrey J. Gray, Johanna K. S. Tiemann, 2021, Nature Communications.

Androgen receptor antagonism by divalent ethisterone conjugates in castrate-resistant prostate cancer cells.

Richard Bonneau, Paul M. Levine, Kent Kirshenbaum, 2012, ACS chemical biology.

Fungi stabilize connectivity in the lung and skin microbial ecosystems

Richard Bonneau, Zachary D. Kurtz, Elodie Ghedin, 2018, Microbiome.

A Miniature Protein Stabilized by a Cation-π Interaction Network.

Timothy W. Craven, Richard Bonneau, K. Kirshenbaum, 2016, Journal of the American Chemical Society.

Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins

Richard Bonneau, M. Ulmschneider, Julia Koehler Leman, 2018, Scientific Reports.

The inferelator 2.0: A scalable framework for reconstruction of dynamic regulatory network models

Richard Bonneau, Eric Vanden-Eijnden, Aviv Madar, 2009, 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts.

Richard Bonneau, C. Dieterich, Noah Youngs, 2012, Molecular cell.

Inter-species pathway perturbation prediction via data-driven detection of functional homology

Erhan Bilal, Pablo Meyer, Raquel Norel, 2015, Bioinform..

BioNetBuilder: automatic integration of biological networks

David J. Reiss, Richard Bonneau, Kevin Drew, 2006, Bioinform..

GABA-receptive microglia selectively sculpt developing inhibitory circuits

S. R. Datta, Richard Bonneau, G. Fishell, 2021, Cell.

Structure-based protein function prediction using graph convolutional networks

Bryn C. Taylor, Richard Bonneau, T. Vatanen, 2021, Nature Communications.

An adaptive geometric search algorithm for macromolecular scaffold selection

Richard Bonneau, Noah Youngs, P. D. Renfrew, 2017, bioRxiv.

Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stability

Richard Bonneau, C. Bystroff, G. L. Butterfoss, 2016, Proteins.

Parametric Bayesian priors and better choice of negative examples improve protein function prediction

Richard Bonneau, Noah Youngs, K. Drew, 2013, Bioinform..

The inferelator 2.0: A scalable framework for reconstruction of dynamic regulatory network models

Richard Bonneau, Aviv Madar, Alex Greenfield, 2009, 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Learning biological networks: from modules to dynamics.

Richard Bonneau, 2008, Nature chemical biology.

Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks

Cláudio T. Silva, Mario L. Arrieta-Ortiz, Richard Bonneau, 2014, IEEE Transactions on Visualization and Computer Graphics.

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction

Richard Bonneau, Christopher S. Poultney, Kristin C. Gunsalus, 2011, PloS one.

Tweeting From Left to Right

Joshua A. Tucker, Richard Bonneau, J. Jost, 2015, Psychological science.

Testing the Effect of Information on Discerning the Veracity of News in Real Time

Joshua A. Tucker, Richard Bonneau, Jonathan Nagler, 2023, Journal of Experimental Political Science.

Twitter activity about treatments during the COVID-19 pandemic: case studies of remdesivir, hydroxychloroquine, and convalescent plasma.

Richard Bonneau, T. Hamamsy, 2020, medRxiv.

Session introduction

Richard Bonneau, Jason E. McDermott, Daniel R. Hyduke, 2011, Pacific Symposium on Biocomputing.

Bacillus subtilis Systems Biology: Applications of -Omics Techniques to the Study of Endospore Formation.

Richard Bonneau, P. Eichenberger, Ashley Bate, 2014, Microbiology spectrum.

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

Richard Bonneau, D. Koller, L. Iakoucheva, 2008, Cell.

OutPredict: multiple datasets can improve prediction of expression and inference of causality

Gloria M. Coruzzi, Richard Bonneau, Jacopo Cirrone, 2020, Scientific Reports.

The Aquila Digital Community The Aquila Digital Community

Silvio C. E. Tosatto, Karin M. Verspoor, David A. Lee, 2022 .

Macromolecular Modeling and Design in Rosetta: New Methods and Frameworks

Brian D. Weitzner, Steven M. Lewis, Richard Bonneau, 2019 .

Helminth infection promotes colonization resistance via type 2 immunity

Zachary D. Kurtz, Richard Bonneau, M. Blaser, 2016, Science.

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling

Nicholas Carriero, Richard Bonneau, Anders Rasmussen, 2020, Nature Communications.

PSR volume 116 issue 3 Cover and Front matter

Richard Bonneau, D. Stukal, Sergey Sanovich, 2022, American Political Science Review.