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Author: Richard Bonneau

  • ORCiD: http://orcid.org/0000-0003-4354-7906
  • Most recently observed institution: Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA, Center for Data Science, New York University, New York, NY, USA

Rankings

  • All-time downloads: 62,422 (rank: 618 out of 397,591)
  • Categories:
    • bioengineering: 2,298 (rank: 587 (tie) out of 11,778)
    • bioinformatics: 20,463 (rank: 124 out of 33,899)
    • biophysics: 4,671 (rank: 254 out of 16,544)
    • ecology: 822 (rank: 3,580 (tie) out of 17,222)
    • genomics: 13,679 (rank: 900 out of 42,208)
    • immunology: 3,756 (rank: 1,016 out of 22,509)
    • microbiology: 2,313 (rank: 3,558 (tie) out of 45,699)
    • neuroscience: 2,538 (rank: 6,104 (tie) out of 66,498)
    • systems biology: 11,882 (rank: 165 out of 11,641)

Downloads per author, site-wide

Preprints

NetQuilt: Deep Multispecies Network-based Protein Function Prediction using Homology-informed Network Similarity

bioinformatics more details view paper

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High-density spatial transcriptomics arrays for in situ tissue profiling

genomics more details view paper
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Multi-study inference of regulatory networks for more accurate models of gene regulation

systems biology more details view paper
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    • In systems biology: 18 out of 2,380
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Shrinkage improves estimation of microbial associations under different normalization methods

bioinformatics more details view paper
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Structure-Based Function Prediction using Graph Convolutional Networks

bioinformatics more details view paper
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Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

genomics more details view paper
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The Rosetta all-atom energy function for macromolecular modeling and design

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

systems biology more details view paper
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Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis

neuroscience more details view paper
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    • Site-wide: 9,071 out of 93,146
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The impact of endogenous retroviruses on nuclear organization and gene expression

genomics more details view paper
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Designing Peptides on a Quantum Computer

bioengineering more details view paper
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    • In bioengineering: 76 out of 2,111
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Characterizing the epigenetic landscape of cellular populations from bulk and single-cell ATAC-seq information.

bioinformatics more details view paper
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    • In bioinformatics: 740 out of 8,711
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Robust Classification of Protein Variation Using Structural Modeling and Large-Scale Data Integration

bioinformatics more details view paper
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    • In bioinformatics: 754 out of 8,711
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deepNF: Deep network fusion for protein function prediction

systems biology more details view paper
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    • In systems biology: 116 out of 2,380
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Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

systems biology more details view paper
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    • In systems biology: 138 out of 2,380
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c-Maf-dependent regulatory T cells mediate immunological tolerance to intestinal microbiota

immunology more details view paper
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    • In immunology: 150 out of 2,760
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The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations

microbiology more details view paper
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Transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells

immunology more details view paper
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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

bioinformatics more details view paper
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Splotch: Robust estimation of aligned spatial temporal gene expression data.

bioinformatics more details view paper
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    • Site-wide: 8,620 out of 93,146

Fused regression for multi-source gene regulatory network inference

bioinformatics more details view paper
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NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

genomics more details view paper
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Mocap: Large-scale inference of transcription factor binding sites from chromatin accessibility

bioinformatics more details view paper
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Rotamer libraries for the high-resolution design of beta-amino acid foldamers

bioinformatics more details view paper
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Biophysically motivated regulatory network inference: progress and prospects

bioinformatics more details view paper
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Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing

ecology more details view paper
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    • In ecology: 396 out of 4,104
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4C-ker: A method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments

bioinformatics more details view paper
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The interdependent nature of multi-loci associations can be revealed by 4C-Seq

genomics more details view paper
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Distinct polysaccharide growth profiles of human intestinal Prevotella copri isolates

microbiology more details view paper
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    • In microbiology: 1,191 out of 8,109
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Explicit Modeling of RNA Stability Improves Large-Scale Inference of Transcription Regulation

biophysics more details view paper
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A comprehensive map of the dendritic cell transcriptional network engaged upon innate sensing of HIV

immunology more details view paper
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    • In immunology: 536 out of 2,760
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Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP

biophysics more details view paper
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    • Site-wide: 71,913 out of 93,146

Revisiting microbe-metabolite interactions: doing better than random

bioinformatics more details view paper
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    • Site-wide: 24,259 out of 93,146

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

bioinformatics more details view paper
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Towards region-specific propagation of protein functions

bioinformatics more details view paper
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Inference of bacterial small RNA regulatory networks and integration with transcription factor driven regulatory networks

systems biology more details view paper
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An Adaptive Geometric Search Algorithm for Macromolecular Scaffold Selection

bioengineering more details view paper
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Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints

biophysics more details view paper
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A B-cell acute lymphoblastic leukemia regulatory network defines novel therapeutic targets in IGH-CRLF2 patients

genomics more details view paper
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A novel domain assembly routine for creating full-length models of membrane proteins from known domain structures

biophysics more details view paper
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