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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: 51,454 (rank: 482 out of 338,526)
  • Categories:
    • bioengineering: 1,465 (rank: 954 (tie) out of 9,205)
    • bioinformatics: 16,630 (rank: 157 out of 29,070)
    • biophysics: 4,456 (rank: 184 out of 13,577)
    • ecology: 795 (rank: 2,841 (tie) out of 14,104)
    • genomics: 12,742 (rank: 863 out of 37,144)
    • immunology: 3,440 (rank: 375 out of 16,878)
    • microbiology: 1,960 (rank: 2,292 (tie) out of 36,021)
    • neuroscience: 2,397 (rank: 5,190 (tie) out of 56,993)
    • systems biology: 7,569 (rank: 184 out of 10,196)

Downloads per author, site-wide

Preprints

High-density spatial transcriptomics arrays for in situ tissue profiling

genomics more details view paper
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    • In genomics: 95 out of 5,109
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    • Site-wide: 884 out of 78,182
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    • Site-wide: 857 out of 78,182

Shrinkage improves estimation of microbial associations under different normalization methods

bioinformatics more details view paper
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    • In bioinformatics: 269 out of 7,541
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    • Site-wide: 534 out of 78,182

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

genomics more details view paper
  • Downloaded 2,796 times
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The Rosetta all-atom energy function for macromolecular modeling and design

biophysics more details view paper
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    • In biophysics: 36 out of 3,324
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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
  • Downloaded 2,492 times
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    • In systems biology: 52 out of 2,105
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    • Site-wide: 15,987 out of 78,182
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    • Site-wide: 22,689 out of 78,182

Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis

neuroscience more details view paper
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    • In neuroscience: 322 out of 13,996
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    • Site-wide: 5,150 out of 78,182
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    • Site-wide: 4,717 out of 78,182

Structure-Based Function Prediction using Graph Convolutional Networks

bioinformatics more details view paper
  • Downloaded 2,127 times
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    • In bioinformatics: 520 out of 7,541
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The impact of endogenous retroviruses on nuclear organization and gene expression

genomics more details view paper
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    • In genomics: 618 out of 5,109
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    • Site-wide: 22,784 out of 78,182

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

bioinformatics more details view paper
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    • In bioinformatics: 660 out of 7,541
  • Year to date:
    • Site-wide: 3,684 out of 78,182
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    • Site-wide: 4,030 out of 78,182

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

bioinformatics more details view paper
  • Downloaded 1,781 times
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    • Site-wide: 3,633 out of 78,182
    • In bioinformatics: 698 out of 7,541
  • Year to date:
    • Site-wide: 7,183 out of 78,182
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    • Site-wide: 9,216 out of 78,182

deepNF: Deep network fusion for protein function prediction

systems biology more details view paper
  • Downloaded 1,772 times
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    • In systems biology: 93 out of 2,105
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    • Site-wide: 21,237 out of 78,182

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

systems biology more details view paper
  • Downloaded 1,536 times
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    • In systems biology: 116 out of 2,105
  • Year to date:
    • Site-wide: 29,182 out of 78,182
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    • Site-wide: 22,988 out of 78,182

c-Maf-dependent regulatory T cells mediate immunological tolerance to intestinal microbiota

immunology more details view paper
  • Downloaded 1,522 times
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    • In immunology: 90 out of 2,106
  • Year to date:
    • Site-wide: 27,354 out of 78,182
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    • Site-wide: 63,040 out of 78,182

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

systems biology more details view paper
  • Downloaded 1,475 times
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    • Site-wide: 4,987 out of 78,182
    • In systems biology: 128 out of 2,105
  • Year to date:
    • Site-wide: 1,069 out of 78,182
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    • Site-wide: 321 out of 78,182

The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations

microbiology more details view paper
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    • In microbiology: 240 out of 6,486
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    • Site-wide: 21,614 out of 78,182
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    • Site-wide: 19,814 out of 78,182

Transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells

immunology more details view paper
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    • In immunology: 111 out of 2,106
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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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    • In bioinformatics: 1,227 out of 7,541
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    • Site-wide: 25,818 out of 78,182

Designing Peptides on a Quantum Computer

bioengineering more details view paper
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    • Site-wide: 7,621 out of 78,182
    • In bioengineering: 136 out of 1,662
  • Year to date:
    • Site-wide: 1,289 out of 78,182
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    • Site-wide: 750 out of 78,182

Fused regression for multi-source gene regulatory network inference

bioinformatics more details view paper
  • Downloaded 1,072 times
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    • Site-wide: 8,491 out of 78,182
    • In bioinformatics: 1,466 out of 7,541
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    • Site-wide: 47,368 out of 78,182
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    • Site-wide: 52,735 out of 78,182

Splotch: Robust estimation of aligned spatial temporal gene expression data.

bioinformatics more details view paper
  • Downloaded 984 times
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    • Site-wide: 9,778 out of 78,182
    • In bioinformatics: 1,651 out of 7,541
  • Year to date:
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    • Site-wide: 2,354 out of 78,182

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

genomics more details view paper
  • Downloaded 978 times
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    • Site-wide: 9,873 out of 78,182
    • In genomics: 1,457 out of 5,109
  • Year to date:
    • Site-wide: 22,744 out of 78,182
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    • Site-wide: 22,037 out of 78,182

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

bioinformatics more details view paper
  • Downloaded 967 times
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    • Site-wide: 10,044 out of 78,182
    • In bioinformatics: 1,689 out of 7,541
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    • Site-wide: 72,431 out of 78,182

Biophysically motivated regulatory network inference: progress and prospects

bioinformatics more details view paper
  • Downloaded 850 times
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    • In bioinformatics: 2,013 out of 7,541
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    • Site-wide: 75,924 out of 78,182

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

bioinformatics more details view paper
  • Downloaded 833 times
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    • In bioinformatics: 2,065 out of 7,541
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    • Site-wide: 56,665 out of 78,182

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

ecology more details view paper
  • Downloaded 795 times
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    • In ecology: 348 out of 3,418
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    • Site-wide: 59,859 out of 78,182

4C-ker: A method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments

bioinformatics more details view paper
  • Downloaded 728 times
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    • In bioinformatics: 2,424 out of 7,541
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    • Site-wide: 60,257 out of 78,182

The interdependent nature of multi-loci associations can be revealed by 4C-Seq

genomics more details view paper
  • Downloaded 726 times
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    • In genomics: 1,997 out of 5,109
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    • Site-wide: 46,205 out of 78,182

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

biophysics more details view paper
  • Downloaded 657 times
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    • Site-wide: 18,030 out of 78,182
    • In biophysics: 606 out of 3,324
  • Year to date:
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    • Site-wide: 53,008 out of 78,182

A comprehensive map of the dendritic cell transcriptional network engaged upon innate sensing of HIV

immunology more details view paper
  • Downloaded 613 times
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    • In immunology: 407 out of 2,106
  • Year to date:
    • Site-wide: 8,979 out of 78,182
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    • Site-wide: 34,250 out of 78,182

Distinct polysaccharide growth profiles of human intestinal Prevotella copri isolates

microbiology more details view paper
  • Downloaded 544 times
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    • Site-wide: 23,446 out of 78,182
    • In microbiology: 1,340 out of 6,486
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    • Site-wide: 8,655 out of 78,182

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

biophysics more details view paper
  • Downloaded 491 times
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    • Site-wide: 26,651 out of 78,182
    • In biophysics: 1,017 out of 3,324
  • Year to date:
    • Site-wide: 70,639 out of 78,182
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    • Site-wide: 69,084 out of 78,182

Towards region-specific propagation of protein functions

bioinformatics more details view paper
  • Downloaded 411 times
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    • Site-wide: 32,828 out of 78,182
    • In bioinformatics: 4,197 out of 7,541
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    • Site-wide: 55,491 out of 78,182
  • Since beginning of last month:
    • Site-wide: 53,934 out of 78,182

Revisiting microbe-metabolite interactions: doing better than random

bioinformatics more details view paper
  • Downloaded 393 times
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    • In bioinformatics: 4,328 out of 7,541
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    • Site-wide: 10,849 out of 78,182

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

bioinformatics more details view paper
  • Downloaded 351 times
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    • In bioinformatics: 4,691 out of 7,541
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    • Site-wide: 14,952 out of 78,182

An Adaptive Geometric Search Algorithm for Macromolecular Scaffold Selection

bioengineering more details view paper
  • Downloaded 321 times
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    • In bioengineering: 780 out of 1,662
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    • Site-wide: 66,838 out of 78,182

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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    • Site-wide: 30,656 out of 78,182

Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints

biophysics more details view paper
  • Downloaded 289 times
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    • Site-wide: 51,062 out of 78,182

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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    • In genomics: 4,040 out of 5,109
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    • Site-wide: 41,630 out of 78,182

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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    • Site-wide: 54,250 out of 78,182
    • In biophysics: 2,306 out of 3,324
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  • Since beginning of last month:
    • Site-wide: 65,877 out of 78,182

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