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List of works by Richard Bonneau

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

scientific article

A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV

scientific article published on 01 January 2020

A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination

scientific article published on 15 June 2016

A Miniature Protein Stabilized by a Cation-π Interaction Network

scientific article published on 26 January 2016

A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures

scientific article published on 29 November 2017

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

A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin

scientific article

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

scientific article published on 12 February 2013

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

scientific article published on January 2013

A predictive model for transcriptional control of physiology in a free living cell.

scientific article published in December 2007

A preliminary survey of the peptoid folding landscape

scientific article published on 01 November 2009

A protein domain-based interactome network for C. elegans early embryogenesis

scientific article

A rotamer library to enable modeling and design of peptoid foldamers

scientific article

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

scientific article published on 11 September 2017

A validated regulatory network for Th17 cell specification

scientific journal article

Ab initio methods.

scientific article

Ab initio protein structure prediction of CASP III targets using ROSETTA

scientific article (publication date: 1999)

Accurate de novo design of hyperstable constrained peptides

scientific article

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

scientific article published on 25 May 2016

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design

scientific article (publication date: 2013)

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

scientific article published on 01 November 2018

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

scientific article

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

scientific article published on 14 January 2016

An adaptive geometric search algorithm for macromolecular scaffold selection

scientific article published on 01 September 2018

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

scientific article

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

scientific article published on 17 November 2015

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

scientific article

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

article

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

scientific article published on 07 August 2012

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

scientific article

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

scientific article published on 25 July 2018

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

scientific article published on 01 February 2019

Automated prediction of CASP-5 structures using the Robetta server.

scientific article

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

scientific article published on April 2014

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

scientific article published on 04 May 2020

BioNetBuilder: automatic integration of biological networks

scientific article published on 30 November 2006

Breaking TADs: insights into hierarchical genome organization.

scientific article published on June 2015

CX₃CR1⁺ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22.

scientific article

Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells

scientific article published on 02 July 2019

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

scientific article published on 17 March 2020

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

scientific article published on 06 February 2020

Chemoselective fragment condensation between peptide and peptidomimetic oligomers ⬇️

scientific article published on July 7, 2013

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

scientific article published on 30 March 2020

Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms

scientific article

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

scientific article published on May 2014

Comparative microbial modules resource: generation and visualization of multi-species biclusters.

scientific article published on December 2011

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

scientific article

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

scientific article

Conformational preferences of peptide-peptoid hybrid oligomers

scientific article published on 01 September 2014

Contact order and ab initio protein structure prediction

scientific article

Coordinated control of neuronal differentiation and wiring by sustained transcription factors

scientific article published on 08 December 2022

Correction to “The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design”

scientific article published on 06 June 2022

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

scientific article published on 6 February 2017

DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

scientific article published on 16 December 2015

DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator

scientific article

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

scientific article

De Novo Prediction of Three-dimensional Structures for Major Protein Families

scientific article published on 01 September 2002

De novo structure prediction and experimental characterization of folded peptoid oligomers.

scientific article

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

scientific article published in Nature Communications

Disrupting Hepatocyte Cyp51 from Cholesterol Synthesis Leads to Progressive Liver Injury in the Developing Mouse and Decreases RORC Signalling

scientific article published on 18 January 2017

Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates

scientific article published on 01 November 2019

Distributions of beta sheets in proteins with application to structure prediction.

scientific article

Diurnally entrained anticipatory behavior in archaea

scientific article published in 2009

Dynamic microRNA gene transcription and processing during T cell development.

scientific article

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

scientific article

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

scientific article published on 29 November 2021

Erratum: Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

scientific article published in Nature

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

scientific article published on 24 June 2021

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

scientific article

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

scientific article

Fungi stabilize connectivity in the lung and skin microbial ecosystems

scientific article published on 15 January 2018

Fused Regression for Multi-source Gene Regulatory Network Inference

scientific article

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

scientific article published on 27 January 2020

General transcription factor specified global gene regulation in archaea

scholarly article

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

scientific article

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

scientific article published on December 2014

Helminth colonization is associated with increased diversity of the gut microbiota.

scientific article

Helminth infection promotes colonization resistance via type 2 immunity.

scientific article

High-definition spatial transcriptomics for in situ tissue profiling

scientific article published on 09 September 2019

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

scientific article

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

scientific article published on 20 July 2016

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

scientific article published on 12 October 2017

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

scientific article published on March 14, 2012

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

scientific article published on 02 June 2020

Inferring causal molecular networks: empirical assessment through a community-based effort

scientific article

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

scientific article published on 09 August 2017

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

scientific article

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

scientific article published on January 2012

Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints

scientific article published on 12 September 2019

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

scientific article

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

scientific article published on 12 March 2020

Interpreting 4C-Seq data: how far can we go?

scientific article

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

scientific article

Learning representations of microbe-metabolite interactions

scientific article published on 04 November 2019

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

Lower airway dysbiosis affects lung cancer progression

scientific article published on 11 November 2020

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

scientific article

Macromolecular modeling and design in Rosetta: recent methods and frameworks

scientific article published on 01 June 2020

Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination

scientific article published on 22 February 2016

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

scientific article published on 15 March 2017

Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions

scientific article

Multi-species integrative biclustering

scientific article

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

article

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

scientific article

N-Naphthyl peptoid foldamers exhibiting atropisomerism

scientific article published on 24 January 2012

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

scientific article published on 24 October 2019

Negative example selection for protein function prediction: the NoGO database

scientific article

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

scientific article

Oligo(N‐alkoxy glycines): Trans substantiating peptoid conformations ⬇️

scientific article published on 01 January 2011

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

scientific article published on 07 January 2021

PPII Helical Peptidomimetics Templated by Cation-π Interactions

scientific article published on 19 August 2016

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

scientific article published on March 19, 2013

Peptoid atropisomers

scientific article published on 22 June 2011

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction ⬇️

scientific article published on September 2, 2011

Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions

scientific article

Retraction Note: DDX5 and its associated lncRNA Rmrp modulate T17 cell effector functions

scientific article published in Nature

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

scientific article

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

scientific article

Rosetta in CASP4: progress in ab initio protein structure prediction

scientific article (publication date: 2001)

Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers

scientific article published on 12 October 2017

Semisynthesis of peptoid-protein hybrids by chemical ligation at serine

scientific article published on 03 January 2014

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

scientific article (publication date: 2013)

Side-Chain Conformational Preferences Govern Protein-Protein Interactions

scientific article published on 2 August 2016

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

scientific article published on 22 February 2012

Sparse and compositionally robust inference of microbial ecological networks ⬇️

scientific article published on 7 May 2015

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

scientific article

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

scientific article published on 13 March 2018

Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology

scientific article

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

scientific article

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

scientific article published on August 31, 2011

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

scientific article published on 19 November 2019

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

scientific article

The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models

scientific article published in January 2009

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

scientific article

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

scientific article published on 10 October 2019

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

scientific article

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

scientific article published on 21 April 2017

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

scientific journal article

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

scientific article published on June 8, 2012

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

scientific article

Translating microbiome futures

scientific article published on 01 November 2018

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

scientific article published on 7 February 2018

sbv IMPROVER Diagnostic Signature Challenge

scientific article published in October 2013

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