Richard Bonneau

发表

QS437. Integrated Biological and Computational Analysis of Important But Largely Under-Studied Organisms

Michael H. Johnson, Marc T. Facciotti, David J. Reiss, 2008 .

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

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

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..

SCORCh.R: Clustering and visualization of sequencing derived multiple transcription factor loci

Richard Bonneau, Dan R. Littman, Kieran Mace, 2005 .

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

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

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

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

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

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

Macromolecular modeling and design in Rosetta: recent methods and frameworks

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

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

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

Generative Models for Quantification of DNA Modifications.

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

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

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

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

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

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.

Shrinkage improves estimation of microbial associations under different normalization methods

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

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

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

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

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

An adaptive geometric search algorithm for macromolecular scaffold selection

Richard Bonneau, Tian Jiang, Kevin Drew, 2018, Protein engineering, design & selection : PEDS.

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

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

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

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

Detecting Bots on Russian Political Twitter

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

Specificities of modeling membrane proteins using multi-template homology modeling

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

Masked graph modeling for molecule generation

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

A Summary Statistic for Political Ideology of Web Domains Using Differentially Private Engagement Data with Applications to Social Science One

Cody Buntain, Richard Bonneau, Jonathan Nagler, 2021, SSRN Electronic Journal.

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

Kyunghyun Cho, Richard Bonneau, Vladimir Gligorijević, 2021, Bioinform..

YouTube Recommendations and Effects on Sharing Across Online Social Platforms

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

Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota

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

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.

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

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

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

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

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

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

High-density spatial transcriptomics arrays for in situ tissue profiling

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

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.

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

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

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

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

High-definition spatial transcriptomics for in situ tissue profiling

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

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.

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

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

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

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

Ab initio methods.

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

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

Richard Bonneau, Tarmo Äijö, Christian L. Mueller, 2016 .

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

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

Multi-species integrative biclustering

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

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

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

Biophysically motivated regulatory network inference: progress and prospects

Richard Bonneau, Tarmo Äijö, Richard Bonneau, 2016 .

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

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

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.

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

Richard Bonneau, Julia Koehler Leman, Martin B Ulmschneider, 2018, Scientific Reports.

A preliminary survey of the peptoid folding landscape.

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

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.

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.

Diurnally Entrained Anticipatory Behavior in Archaea

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

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.

Biophysically motivated regulatory network inference: progress and prospects

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

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.

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction

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

Fused regression for multi-source gene regulatory network inference

Richard Bonneau, Lionel Christiaen, Kari Y. Lam, 2016 .

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

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

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

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

Fungi stabilize connectivity in the lung and skin microbial ecosystems

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

Translating microbiome futures

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

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

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

Conformational preferences of peptide–peptoid hybrid oligomers

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

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.

Measuring the prevalence of online hate speech , with an application to the 2016 U . S . election

Richard Bonneau, Jonathan Nagler, Joshua A. Tucker, 2018 .

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

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

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

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

Protest in the age of social media

Richard Bonneau, Jonathan Nagler, John T. Jost, 2015 .

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

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

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

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