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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 67,545 bioRxiv papers from 297,698 authors.

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: 44,084 (rank: 342 out of 298,105)
  • Categories:
    • bioengineering: 928 (rank: 1,312 (tie) out of 7,550)
    • bioinformatics: 13,062 (rank: 192 out of 25,906)
    • biophysics: 4,271 (rank: 157 out of 11,764)
    • ecology: 768 (rank: 2,303 (tie) out of 11,798)
    • genomics: 11,429 (rank: 897 out of 33,782)
    • immunology: 3,054 (rank: 298 out of 13,971)
    • microbiology: 1,695 (rank: 1,653 (tie) out of 30,682)
    • neuroscience: 2,173 (rank: 4,426 (tie) out of 49,741)
    • systems biology: 6,704 (rank: 52 out of 8,948)

Downloads per author, site-wide

Preprints

High-density spatial transcriptomics arrays for in situ tissue profiling

genomics more details view paper
  • Downloaded 5,339 times
  • Download rankings, all-time:
    • Site-wide: 393 out of 67,553
    • In genomics: 101 out of 4,580
  • Year to date:
    • Site-wide: 82 out of 67,553
  • Since beginning of last month:
    • Site-wide: 1,036 out of 67,553

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

biophysics more details view paper
  • Downloaded 2,733 times
  • Download rankings, all-time:
    • Site-wide: 1,403 out of 67,553
    • In biophysics: 34 out of 2,865
  • Year to date:
    • Site-wide: 17,043 out of 67,553
  • Since beginning of last month:
    • Site-wide: 23,365 out of 67,553

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

genomics more details view paper
  • Downloaded 2,462 times
  • Download rankings, all-time:
    • Site-wide: 1,692 out of 67,553
    • In genomics: 375 out of 4,580
  • Year to date:
    • Site-wide: 367 out of 67,553
  • Since beginning of last month:
    • Site-wide: 940 out of 67,553

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 2,382 times
  • Download rankings, all-time:
    • Site-wide: 1,804 out of 67,553
    • In systems biology: 44 out of 1,871
  • Year to date:
    • Site-wide: 13,613 out of 67,553
  • Since beginning of last month:
    • Site-wide: 20,266 out of 67,553

Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis

neuroscience more details view paper
  • Downloaded 2,173 times
  • Download rankings, all-time:
    • Site-wide: 2,128 out of 67,553
    • In neuroscience: 310 out of 12,107
  • Year to date:
    • Site-wide: 1,333 out of 67,553
  • Since beginning of last month:
    • Site-wide: 9,864 out of 67,553

Normalization methods for microbial abundance data strongly affect correlation estimates

bioinformatics more details view paper
  • Downloaded 2,170 times
  • Download rankings, all-time:
    • Site-wide: 2,131 out of 67,553
    • In bioinformatics: 433 out of 6,650
  • Year to date:
    • Site-wide: 762 out of 67,553
  • Since beginning of last month:
    • Site-wide: 702 out of 67,553

The impact of endogenous retroviruses on nuclear organization and gene expression

genomics more details view paper
  • Downloaded 1,820 times
  • Download rankings, all-time:
    • Site-wide: 2,866 out of 67,553
    • In genomics: 571 out of 4,580
  • Year to date:
    • Site-wide: 12,301 out of 67,553
  • Since beginning of last month:
    • Site-wide: 9,641 out of 67,553

deepNF: Deep network fusion for protein function prediction

systems biology more details view paper
  • Downloaded 1,709 times
  • Download rankings, all-time:
    • Site-wide: 3,195 out of 67,553
    • In systems biology: 76 out of 1,871
  • Year to date:
    • Site-wide: 21,107 out of 67,553
  • Since beginning of last month:
    • Site-wide: 53,860 out of 67,553

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

bioinformatics more details view paper
  • Downloaded 1,579 times
  • Download rankings, all-time:
    • Site-wide: 3,648 out of 67,553
    • In bioinformatics: 728 out of 6,650
  • Year to date:
    • Site-wide: 862 out of 67,553
  • Since beginning of last month:
    • Site-wide: 2,405 out of 67,553

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

bioinformatics more details view paper
  • Downloaded 1,543 times
  • Download rankings, all-time:
    • Site-wide: 3,797 out of 67,553
    • In bioinformatics: 757 out of 6,650
  • Year to date:
    • Site-wide: 8,688 out of 67,553
  • Since beginning of last month:
    • Site-wide: 6,622 out of 67,553

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

systems biology more details view paper
  • Downloaded 1,465 times
  • Download rankings, all-time:
    • Site-wide: 4,157 out of 67,553
    • In systems biology: 103 out of 1,871
  • Year to date:
    • Site-wide: 8,435 out of 67,553
  • Since beginning of last month:
    • Site-wide: 24,859 out of 67,553

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

immunology more details view paper
  • Downloaded 1,457 times
  • Download rankings, all-time:
    • Site-wide: 4,197 out of 67,553
    • In immunology: 64 out of 1,721
  • Year to date:
    • Site-wide: 20,511 out of 67,553
  • Since beginning of last month:
    • Site-wide: 40,875 out of 67,553

Structure-Based Function Prediction using Graph Convolutional Networks

bioinformatics more details view paper
  • Downloaded 1,446 times
  • Download rankings, all-time:
    • Site-wide: 4,253 out of 67,553
    • In bioinformatics: 832 out of 6,650
  • Year to date:
    • Site-wide: 1,018 out of 67,553
  • Since beginning of last month:
    • Site-wide: 414 out of 67,553

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

microbiology more details view paper
  • Downloaded 1,323 times
  • Download rankings, all-time:
    • Site-wide: 4,926 out of 67,553
    • In microbiology: 165 out of 5,460
  • Year to date:
    • Site-wide: 1,228 out of 67,553
  • Since beginning of last month:
    • Site-wide: 5,192 out of 67,553

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

immunology more details view paper
  • Downloaded 1,135 times
  • Download rankings, all-time:
    • Site-wide: 6,330 out of 67,553
    • In immunology: 100 out of 1,721
  • Year to date:
    • Site-wide: 2,559 out of 67,553
  • Since beginning of last month:
    • Site-wide: 5,867 out of 67,553

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

bioinformatics more details view paper
  • Downloaded 1,050 times
  • Download rankings, all-time:
    • Site-wide: 7,216 out of 67,553
    • In bioinformatics: 1,285 out of 6,650
  • Year to date:
    • Site-wide: 1,810 out of 67,553
  • Since beginning of last month:
    • Site-wide: 1,520 out of 67,553

Fused regression for multi-source gene regulatory network inference

bioinformatics more details view paper
  • Downloaded 1,026 times
  • Download rankings, all-time:
    • Site-wide: 7,480 out of 67,553
    • In bioinformatics: 1,325 out of 6,650
  • Year to date:
    • Site-wide: 34,448 out of 67,553
  • Since beginning of last month:
    • Site-wide: 43,869 out of 67,553

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

bioinformatics more details view paper
  • Downloaded 942 times
  • Download rankings, all-time:
    • Site-wide: 8,618 out of 67,553
    • In bioinformatics: 1,503 out of 6,650
  • Year to date:
    • Site-wide: 58,435 out of 67,553
  • Since beginning of last month:
    • Site-wide: 64,754 out of 67,553

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

systems biology more details view paper
  • Downloaded 938 times
  • Download rankings, all-time:
    • Site-wide: 8,698 out of 67,553
    • In systems biology: 244 out of 1,871
  • Year to date:
    • Site-wide: 18,308 out of 67,553
  • Since beginning of last month:
    • Site-wide: 30,195 out of 67,553

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

genomics more details view paper
  • Downloaded 904 times
  • Download rankings, all-time:
    • Site-wide: 9,171 out of 67,553
    • In genomics: 1,388 out of 4,580
  • Year to date:
    • Site-wide: 2,361 out of 67,553
  • Since beginning of last month:
    • Site-wide: 7,628 out of 67,553

Biophysically motivated regulatory network inference: progress and prospects

bioinformatics more details view paper
  • Downloaded 831 times
  • Download rankings, all-time:
    • Site-wide: 10,483 out of 67,553
    • In bioinformatics: 1,779 out of 6,650
  • Year to date:
    • Site-wide: 63,304 out of 67,553
  • Since beginning of last month:
    • Site-wide: 60,102 out of 67,553

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

bioinformatics more details view paper
  • Downloaded 795 times
  • Download rankings, all-time:
    • Site-wide: 11,195 out of 67,553
    • In bioinformatics: 1,886 out of 6,650
  • Year to date:
    • Site-wide: 24,820 out of 67,553
  • Since beginning of last month:
    • Site-wide: 13,594 out of 67,553

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

ecology more details view paper
  • Downloaded 768 times
  • Download rankings, all-time:
    • Site-wide: 11,792 out of 67,553
    • In ecology: 297 out of 2,880
  • Year to date:
    • Site-wide: 41,613 out of 67,553
  • Since beginning of last month:
    • Site-wide: 60,000 out of 67,553

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

bioinformatics more details view paper
  • Downloaded 700 times
  • Download rankings, all-time:
    • Site-wide: 13,482 out of 67,553
    • In bioinformatics: 2,186 out of 6,650
  • Year to date:
    • Site-wide: 52,546 out of 67,553
  • Since beginning of last month:
    • Site-wide: 47,316 out of 67,553

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

genomics more details view paper
  • Downloaded 687 times
  • Download rankings, all-time:
    • Site-wide: 13,838 out of 67,553
    • In genomics: 1,847 out of 4,580
  • Year to date:
    • Site-wide: 58,530 out of 67,553
  • Since beginning of last month:
    • Site-wide: 58,569 out of 67,553

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

biophysics more details view paper
  • Downloaded 629 times
  • Download rankings, all-time:
    • Site-wide: 15,705 out of 67,553
    • In biophysics: 521 out of 2,865
  • Year to date:
    • Site-wide: 44,781 out of 67,553
  • Since beginning of last month:
    • Site-wide: 44,803 out of 67,553

Designing Peptides on a Quantum Computer

bioengineering more details view paper
  • Downloaded 629 times
  • Download rankings, all-time:
    • Site-wide: 15,692 out of 67,553
    • In bioengineering: 273 out of 1,363
  • Year to date:
    • Site-wide: 4,450 out of 67,553
  • Since beginning of last month:
    • Site-wide: 2,534 out of 67,553

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

bioinformatics more details view paper
  • Downloaded 607 times
  • Download rankings, all-time:
    • Site-wide: 16,475 out of 67,553
    • In bioinformatics: 2,552 out of 6,650
  • Year to date:
    • Site-wide: 4,718 out of 67,553
  • Since beginning of last month:
    • Site-wide: 1,503 out of 67,553

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

biophysics more details view paper
  • Downloaded 464 times
  • Download rankings, all-time:
    • Site-wide: 23,331 out of 67,553
    • In biophysics: 866 out of 2,865
  • Year to date:
    • Site-wide: 62,691 out of 67,553
  • Since beginning of last month:
    • Site-wide: 44,244 out of 67,553

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

immunology more details view paper
  • Downloaded 462 times
  • Download rankings, all-time:
    • Site-wide: 23,446 out of 67,553
    • In immunology: 441 out of 1,721
  • Year to date:
    • Site-wide: 7,497 out of 67,553
  • Since beginning of last month:
    • Site-wide: 7,034 out of 67,553

Towards region-specific propagation of protein functions

bioinformatics more details view paper
  • Downloaded 373 times
  • Download rankings, all-time:
    • Site-wide: 29,629 out of 67,553
    • In bioinformatics: 3,895 out of 6,650
  • Year to date:
    • Site-wide: 45,796 out of 67,553
  • Since beginning of last month:
    • Site-wide: 23,627 out of 67,553

Distinct polysaccharide growth profiles of human intestinal Prevotella copri isolates

microbiology more details view paper
  • Downloaded 372 times
  • Download rankings, all-time:
    • Site-wide: 29,765 out of 67,553
    • In microbiology: 1,782 out of 5,460
  • Year to date:
    • Site-wide: 10,750 out of 67,553
  • Since beginning of last month:
    • Site-wide: 2,811 out of 67,553

An Adaptive Geometric Search Algorithm for Macromolecular Scaffold Selection

bioengineering more details view paper
  • Downloaded 299 times
  • Download rankings, all-time:
    • Site-wide: 36,580 out of 67,553
    • In bioengineering: 680 out of 1,363
  • Year to date:
    • Site-wide: 56,287 out of 67,553
  • Since beginning of last month:
    • Site-wide: 43,561 out of 67,553

Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints

biophysics more details view paper
  • Downloaded 237 times
  • Download rankings, all-time:
    • Site-wide: 43,892 out of 67,553
    • In biophysics: 1,837 out of 2,865
  • Year to date:
    • Site-wide: 20,858 out of 67,553
  • Since beginning of last month:
    • Site-wide: 11,175 out of 67,553

A B-cell acute lymphoblastic leukemia regulatory network defines novel therapeutic targets in IGH-CRLF2 patients

genomics more details view paper
  • Downloaded 217 times
  • Download rankings, all-time:
    • Site-wide: 46,359 out of 67,553
    • In genomics: 3,837 out of 4,580
  • Year to date:
    • Site-wide: 23,266 out of 67,553
  • Since beginning of last month:
    • Site-wide: 56,675 out of 67,553

Inference of bacterial small RNA regulatory networks and integration with transcription factor driven regulatory networks

systems biology more details view paper
  • Downloaded 210 times
  • Download rankings, all-time:
    • Site-wide: 47,342 out of 67,553
    • In systems biology: 1,451 out of 1,871
  • Year to date:
    • Site-wide: 24,338 out of 67,553
  • Since beginning of last month:
    • Site-wide: 41,909 out of 67,553

A novel domain assembly routine for creating full-length models of membrane proteins from known domain structures

biophysics more details view paper
  • Downloaded 208 times
  • Download rankings, all-time:
    • Site-wide: 47,600 out of 67,553
    • In biophysics: 2,025 out of 2,865
  • Year to date:
    • Site-wide: 56,816 out of 67,553
  • Since beginning of last month:
    • Site-wide: 55,432 out of 67,553

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