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Author Details

Richard Bonneau
Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation
1983
212
69
PMIDPaper TitleJournal TitlePublished Year
36600182Alterations in the cutaneous microbiome of patients with psoriasis and psoriatic arthritis reveal similarities between non-lesional and lesional skin.Ann Rheum Dis2023
37010293Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method.mSystems2023
37365313Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles.Nat Neurosci2023
37330554CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection.Microbiome2023
36959446Specificities of Modeling of Membrane Proteins Using Multi-Template Homology Modeling.Methods Mol Biol2023
36624094Exposure to the Russian Internet Research Agency foreign influence campaign on Twitter in the 2016 US election and its relationship to attitudes and voting behavior.Nat Commun2023
36477794TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs.Bioinformatics2023
36778259Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference.bioRxiv2023
34534872SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases.Sci Total Environ2022
35667008Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design".J Chem Theory Comput2022
35820178Evaluating the Conformations and Dynamics of Peptoid Macrocycles.J Phys Chem B2022
35522751News credibility labels have limited average effects on news diet quality and fail to reduce misperceptions.Sci Adv2022
36480601Coordinated control of neuronal differentiation and wiring by sustained transcription factors.Science2022
36034180Engineered multivalent self-assembled binder protein against SARS-CoV-2 RBD.Biochem Eng J2022
36227640Supramolecular Assembly and Small-Molecule Binding by Protein-Engineered Coiled-Coil Fibers.Biomacromolecules2022
35188184High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0.Bioinformatics2022
33411784Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data.PLoS Comput Biol2021
33576802NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity.Bioinformatics2021
33826625Correction: Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota.PLoS Negl Trop Dis2021
33723038Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1.Proc Natl Acad Sci U S A2021
34552240Genetic and epigenetic coordination of cortical interneuron development.Nature2021
34715023GABA-receptive microglia selectively sculpt developing inhibitory circuits.Cell2021
34131075Testing the effects of Facebook usage in an ethnically polarized setting.Proc Natl Acad Sci U S A2021
34128955A convolutional neural network for common coordinate registration of high-resolution histology images.Bioinformatics2021
34039973Masked graph modeling for molecule generation.Nat Commun2021
34039967Structure-based protein function prediction using graph convolutional networks.Nat Commun2021
34289377Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice.Cell Host Microbe2021
34288913Viewing the US presidential electoral map through the lens of public health.PLoS One2021
34166363Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.PLoS Comput Biol2021
33398188Reply to: Examining microbe-metabolite correlations by linear methods.Nat Methods2021
33177060Lower Airway Dysbiosis Affects Lung Cancer Progression.Cancer Discov2021
32483333Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nat Methods2020
33575644Shrinkage improves estimation of microbial associations under different normalization methods.NAR Genom Bioinform2020
32029740Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling.Nat Commun2020
31968263A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV.Cell Rep2020
31729183Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25-Driven Intestinal Inflammation.Arthritis Rheumatol2020
31985403Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments.Elife2020
31916812Political psycholinguistics: A comprehensive analysis of the language habits of liberal and conservative social media users.J Pers Soc Psychol2020
31883968CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer.Cancer Cell2020
32607521SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases.medRxiv2020
32661179Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs.J Immunol2020
32811842Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality.Sci Rep2020
32365137Better together: Elements of successful scientific software development in a distributed collaborative community.PLoS Comput Biol2020
32178738Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection.Microbiome2020
32546676Initial Mapping of the New York City Wastewater Virome.mSystems2020
32207963Classification of the Molecular Defects Associated with Pathogenic Variants of the <i>SLC6A8</i> Creatine Transporter.Biochemistry2020
32321967OutPredict: multiple datasets can improve prediction of expression and inference of causality.Sci Rep2020
32487739Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks.mSystems2020
30696696Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.Genome Res2019
31726030Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates.Cell Host Microbe2019
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Alan Aderem
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Yuval Kluger
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Pieter C Dorrestein
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Release 1.2