Rxivist logo

Author: John Marioni

Rankings

  • All-time downloads: 94,457 (rank: 1,782 )
  • Categories:
    • bioinformatics: 35,031 (rank: 93 )
    • cell biology: 15,981 (rank: 95 )
    • developmental biology: 15,067 (rank: 35 )
    • evolutionary biology: 1,582 (rank: 4,689 (tie) )
    • genetics: 4,443 (rank: 4,446 (tie) )
    • genomics: 14,479 (rank: 1,291 )
    • immunology: 3,614 (rank: 3,437 (tie) )
    • infectious diseases: 2,741 (rank: 16,359 (tie) )
    • molecular biology: 1,519 (rank: 4,573 (tie) )

Downloads per author, site-wide

Preprints

The Human Cell Atlas

cell biology more details view paper
  • Downloaded 12,890 times
  • Download rankings, all-time:
    • Site-wide: 773
    • In cell biology: 6
  • Year to date:
    • Site-wide: 22,225
  • Since beginning of last month:
    • Site-wide: 29,450

Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification

developmental biology more details view paper
  • Downloaded 6,409 times
  • Download rankings, all-time:
    • Site-wide: 1,902
    • In developmental biology: 13
  • Year to date:
    • Site-wide: 31,732
  • Since beginning of last month:
    • Site-wide: 29,284

Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours.

bioinformatics more details view paper
  • Downloaded 5,309 times
  • Download rankings, all-time:
    • Site-wide: 2,437
    • In bioinformatics: 182
  • Year to date:
    • Site-wide: 67,261
  • Since beginning of last month:
    • Site-wide: 98,511

Multi-Omics factor analysis - a framework for unsupervised integration of multi-omic data sets

bioinformatics more details view paper
  • Downloaded 5,271 times
  • Download rankings, all-time:
    • Site-wide: 2,467
    • In bioinformatics: 185
  • Year to date:
    • Site-wide: 30,925
  • Since beginning of last month:
    • Site-wide: 22,160

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

genomics more details view paper
  • Downloaded 5,083 times
  • Download rankings, all-time:
    • Site-wide: 2,610
    • In genomics: 239
  • Year to date:
    • Site-wide: 43,342
  • Since beginning of last month:
    • Site-wide: 64,279

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

developmental biology more details view paper
  • Downloaded 4,599 times
  • Download rankings, all-time:
    • Site-wide: 2,983
    • In developmental biology: 22
  • Year to date:
    • Site-wide: 1,836
  • Since beginning of last month:
    • Site-wide: 9,136

CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets

bioinformatics more details view paper
  • Downloaded 4,424 times
  • Download rankings, all-time:
    • Site-wide: 3,163
    • In bioinformatics: 249
  • Year to date:
    • Site-wide: 2,021
  • Since beginning of last month:
    • Site-wide: 1,815

Milo: differential abundance testing on single-cell data using k-NN graphs

bioinformatics more details view paper
  • Downloaded 4,309 times
  • Download rankings, all-time:
    • Site-wide: 3,285
    • In bioinformatics: 268
  • Year to date:
    • Site-wide: 1,059
  • Since beginning of last month:
    • Site-wide: 1,110

iRAP - an integrated RNA-seq Analysis Pipeline

bioinformatics more details view paper
  • Downloaded 3,783 times
  • Download rankings, all-time:
    • Site-wide: 3,929
    • In bioinformatics: 351
  • Year to date:
    • Site-wide: 79,730
  • Since beginning of last month:
    • Site-wide: 87,768

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

genetics more details view paper
  • Downloaded 3,526 times
  • Download rankings, all-time:
    • Site-wide: 4,330
    • In genetics: 150
  • Year to date:
    • Site-wide: 6,007
  • Since beginning of last month:
    • Site-wide: 21,106

Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

bioinformatics more details view paper
  • Downloaded 3,369 times
  • Download rankings, all-time:
    • Site-wide: 4,638
    • In bioinformatics: 431
  • Year to date:
    • Site-wide: 70,641
  • Since beginning of last month:
    • Site-wide: 34,864

MOFA+: a probabilistic framework for comprehensive integration of structured single-cell data

bioinformatics more details view paper
  • Downloaded 2,759 times
  • Download rankings, all-time:
    • Site-wide: 6,175
    • In bioinformatics: 616
  • Year to date:
    • Site-wide: 37,225
  • Since beginning of last month:
    • Site-wide: 37,992

Single-cell RNA-seq of differentiating iPS cells reveals dynamic genetic effects on gene expression

genomics more details view paper
  • Downloaded 2,627 times
  • Download rankings, all-time:
    • Site-wide: 6,630
    • In genomics: 670
  • Year to date:
    • Site-wide: 90,101
  • Since beginning of last month:
    • Site-wide: 130,765

The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres

infectious diseases more details view paper
  • Downloaded 2,366 times
  • Download rankings, all-time:
    • Site-wide: 7,770
    • In infectious diseases: 1,254
  • Year to date:
    • Site-wide: 1,565
  • Since beginning of last month:
    • Site-wide: 12,187

Cells of the human intestinal tract mapped across space and time

cell biology more details view paper
  • Downloaded 2,136 times
  • Download rankings, all-time:
    • Site-wide: 9,012
    • In cell biology: 196
  • Year to date:
    • Site-wide: 1,783
  • Since beginning of last month:
    • Site-wide: 3,182

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

genomics more details view paper
  • Downloaded 1,913 times
  • Download rankings, all-time:
    • Site-wide: 10,621
    • In genomics: 1,049
  • Year to date:
    • Site-wide: 138,723
  • Since beginning of last month:
    • Site-wide: 139,495

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

developmental biology more details view paper
  • Downloaded 1,702 times
  • Download rankings, all-time:
    • Site-wide: 12,644
    • In developmental biology: 178
  • Year to date:
    • Site-wide: 113,737
  • Since beginning of last month:
    • Site-wide: 125,899

Detection and removal of barcode swapping in single-cell RNA-seq data

genomics more details view paper
  • Downloaded 1,661 times
  • Download rankings, all-time:
    • Site-wide: 13,103
    • In genomics: 1,309
  • Year to date:
    • Site-wide: 117,686
  • Since beginning of last month:
    • Site-wide: 137,555

Transposable element expression at unique loci in single cells with CELLO-seq

molecular biology more details view paper
  • Downloaded 1,519 times
  • Download rankings, all-time:
    • Site-wide: 15,074
    • In molecular biology: 407
  • Year to date:
    • Site-wide: 12,784
  • Since beginning of last month:
    • Site-wide: 6,643

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

genomics more details view paper
  • Downloaded 1,352 times
  • Download rankings, all-time:
    • Site-wide: 18,037
    • In genomics: 1,724
  • Year to date:
    • Site-wide: 112,459
  • Since beginning of last month:
    • Site-wide: 137,614

Rora regulates activated T helper cells during inflammation

immunology more details view paper
  • Downloaded 1,333 times
  • Download rankings, all-time:
    • Site-wide: 18,433
    • In immunology: 643
  • Year to date:
    • Site-wide: 23,441
  • Since beginning of last month:
    • Site-wide: 36,595

Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth

immunology more details view paper
  • Downloaded 1,271 times
  • Download rankings, all-time:
    • Site-wide: 19,794
    • In immunology: 691
  • Year to date:
    • Site-wide: 30,314
  • Since beginning of last month:
    • Site-wide: 31,908

Assessing The Reliability Of Spike-In Normalization For Analyses Of Single-Cell RNA Sequencing Data

bioinformatics more details view paper
  • Downloaded 1,238 times
  • Download rankings, all-time:
    • Site-wide: 20,579
    • In bioinformatics: 2,323
  • Year to date:
    • Site-wide: 113,810
  • Since beginning of last month:
    • Site-wide: 147,556

Investigating higher order interactions in single cell data with scHOT

bioinformatics more details view paper
  • Downloaded 1,177 times
  • Download rankings, all-time:
    • Site-wide: 22,236
    • In bioinformatics: 2,511
  • Year to date:
    • Site-wide: 54,533
  • Since beginning of last month:
    • Site-wide: 57,245

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

genomics more details view paper
  • Downloaded 1,142 times
  • Download rankings, all-time:
    • Site-wide: 23,249
    • In genomics: 2,155
  • Year to date:
    • Site-wide: 150,364
  • Since beginning of last month:
    • Site-wide: 160,377

Secreted inhibitors drive the loss of regeneration competence in Xenopus limbs

developmental biology more details view paper
  • Downloaded 1,130 times
  • Download rankings, all-time:
    • Site-wide: 23,608
    • In developmental biology: 405
  • Year to date:
    • Site-wide: 19,541
  • Since beginning of last month:
    • Site-wide: 73,511

CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq

bioinformatics more details view paper
  • Downloaded 1,082 times
  • Download rankings, all-time:
    • Site-wide: 25,280
    • In bioinformatics: 2,834
  • Year to date:
    • Site-wide: 4,716
  • Since beginning of last month:
    • Site-wide: 3,524

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

immunology more details view paper
  • Downloaded 1,010 times
  • Download rankings, all-time:
    • Site-wide: 28,034
    • In immunology: 949
  • Year to date:
    • Site-wide: 58,739
  • Since beginning of last month:
    • Site-wide: 77,612

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

cell biology more details view paper
  • Downloaded 955 times
  • Download rankings, all-time:
    • Site-wide: 30,392
    • In cell biology: 1,149
  • Year to date:
    • Site-wide: 146,587
  • Since beginning of last month:
    • Site-wide: 148,811

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data

bioinformatics more details view paper
  • Downloaded 936 times
  • Download rankings, all-time:
    • Site-wide: 31,341
    • In bioinformatics: 3,443
  • Year to date:
    • Site-wide: 117,742
  • Since beginning of last month:
    • Site-wide: 162,785

Mapping interindividual dynamics of innate immune response at single-cell resolution

genetics more details view paper
  • Downloaded 917 times
  • Download rankings, all-time:
    • Site-wide: 32,308
    • In genetics: 1,418
  • Year to date:
    • Site-wide: 6,073
  • Since beginning of last month:
    • Site-wide: 4,345

Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues

evolutionary biology more details view paper
  • Downloaded 794 times
  • Download rankings, all-time:
    • Site-wide: 39,769
    • In evolutionary biology: 1,785
  • Year to date:
    • Site-wide: 119,982
  • Since beginning of last month:
    • Site-wide: 88,518

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

evolutionary biology more details view paper
  • Downloaded 788 times
  • Download rankings, all-time:
    • Site-wide: 40,210
    • In evolutionary biology: 1,811
  • Year to date:
    • Site-wide: 142,550
  • Since beginning of last month:
    • Site-wide: 151,789

Robust expression variability testing reveals heterogeneous T cell responses

bioinformatics more details view paper
  • Downloaded 762 times
  • Download rankings, all-time:
    • Site-wide: 42,282
    • In bioinformatics: 4,429
  • Year to date:
    • Site-wide: 159,150
  • Since beginning of last month:
    • Site-wide: 150,816

Coordinated Changes in Gene Expression Kinetics Underlie both Mouse and Human Erythroid Maturation

developmental biology more details view paper
  • Downloaded 719 times
  • Download rankings, all-time:
    • Site-wide: 45,818
    • In developmental biology: 1,014
  • Year to date:
    • Site-wide: 11,717
  • Since beginning of last month:
    • Site-wide: 25,467

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression

genomics more details view paper
  • Downloaded 701 times
  • Download rankings, all-time:
    • Site-wide: 47,516
    • In genomics: 3,652
  • Year to date:
    • Site-wide: 138,773
  • Since beginning of last month:
    • Site-wide: 141,134

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

bioinformatics more details view paper
  • Downloaded 612 times
  • Download rankings, all-time:
    • Site-wide: 57,110
    • In bioinformatics: 5,648
  • Year to date:
    • Site-wide: 11,516
  • Since beginning of last month:
    • Site-wide: 9,437

Acquisition of alveolar fate and differentiation competence by human fetal lung epithelial progenitor cells

developmental biology more details view paper
  • Downloaded 508 times
  • Download rankings, all-time:
    • Site-wide: 71,540
    • In developmental biology: 1,802
  • Year to date:
    • Site-wide: 15,355
  • Since beginning of last month:
    • Site-wide: 11,720

Factor V is an immune inhibitor that is expressed at increased levels in leukocytes of patients with severe Covid-19

infectious diseases more details view paper
  • Downloaded 375 times
  • Download rankings, all-time:
    • Site-wide: 97,677
    • In infectious diseases: 4,623
  • Year to date:
    • Site-wide: 24,522
  • Since beginning of last month:
    • Site-wide: 85,335

PanLingua

News