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Author: John C Marioni

Rankings

  • All-time downloads: 73,024 (rank: 1,760 )
  • Categories:
    • bioinformatics: 26,911 (rank: 100 )
    • cell biology: 13,398 (rank: 46 )
    • developmental biology: 11,179 (rank: 33 )
    • evolutionary biology: 1,428 (rank: 3,723 )
    • genetics: 2,653 (rank: 6,449 (tie) )
    • genomics: 13,730 (rank: 1,046 )
    • immunology: 2,753 (rank: 2,293 )
    • molecular biology: 972 (rank: 5,127 (tie) )

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Preprints

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

infectious diseases more details view paper

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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

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The Human Cell Atlas

cell biology more details view paper
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    • Site-wide: 510
    • In cell biology: 4
  • Year to date:
    • Site-wide: 27,180
  • Since beginning of last month:
    • Site-wide: 15,873

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

developmental biology more details view paper
  • Downloaded 6,108 times
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    • Site-wide: 1,313
    • In developmental biology: 7
  • Year to date:
    • Site-wide: 26,224
  • Since beginning of last month:
    • Site-wide: 16,946

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

bioinformatics more details view paper
  • Downloaded 5,140 times
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    • Site-wide: 1,673
    • In bioinformatics: 142
  • Year to date:
    • Site-wide: 62,616
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    • Site-wide: 56,976

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

bioinformatics more details view paper
  • Downloaded 4,958 times
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    • Site-wide: 1,761
    • In bioinformatics: 161
  • Year to date:
    • Site-wide: 56,822
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    • Site-wide: 17,347

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

genomics more details view paper
  • Downloaded 4,841 times
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    • Site-wide: 1,816
    • In genomics: 200
  • Year to date:
    • Site-wide: 47,487
  • Since beginning of last month:
    • Site-wide: 40,299

iRAP - an integrated RNA-seq Analysis Pipeline

bioinformatics more details view paper
  • Downloaded 3,641 times
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    • Site-wide: 2,728
    • In bioinformatics: 277
  • Year to date:
    • Site-wide: 57,311
  • Since beginning of last month:
    • Site-wide: 64,031

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

bioinformatics more details view paper
  • Downloaded 3,208 times
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    • Site-wide: 3,314
    • In bioinformatics: 362
  • Year to date:
    • Site-wide: 59,403
  • Since beginning of last month:
    • Site-wide: 59,527

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

genetics more details view paper
  • Downloaded 2,653 times
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    • Site-wide: 4,331
    • In genetics: 210
  • Year to date:
    • Site-wide: 5,505
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    • Site-wide: 5,763

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

developmental biology more details view paper
  • Downloaded 2,559 times
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    • Site-wide: 4,562
    • In developmental biology: 49
  • Year to date:
    • Site-wide: 5,771
  • Since beginning of last month:
    • Site-wide: 572

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

bioinformatics more details view paper
  • Downloaded 2,555 times
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    • Site-wide: 4,580
    • In bioinformatics: 530
  • Year to date:
    • Site-wide: 3,342
  • Since beginning of last month:
    • Site-wide: 4,327

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

genomics more details view paper
  • Downloaded 2,500 times
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    • Site-wide: 4,715
    • In genomics: 568
  • Year to date:
    • Site-wide: 71,813
  • Since beginning of last month:
    • Site-wide: 82,747

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

bioinformatics more details view paper
  • Downloaded 2,499 times
  • Download rankings, all-time:
    • Site-wide: 4,720
    • In bioinformatics: 553
  • Year to date:
    • Site-wide: 17,409
  • Since beginning of last month:
    • Site-wide: 26,611

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

genomics more details view paper
  • Downloaded 1,843 times
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    • Site-wide: 7,418
    • In genomics: 841
  • Year to date:
    • Site-wide: 109,258
  • Since beginning of last month:
    • Site-wide: 113,206

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

developmental biology more details view paper
  • Downloaded 1,604 times
  • Download rankings, all-time:
    • Site-wide: 9,166
    • In developmental biology: 124
  • Year to date:
    • Site-wide: 100,458
  • Since beginning of last month:
    • Site-wide: 68,088

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

genomics more details view paper
  • Downloaded 1,571 times
  • Download rankings, all-time:
    • Site-wide: 9,458
    • In genomics: 1,073
  • Year to date:
    • Site-wide: 76,578
  • Since beginning of last month:
    • Site-wide: 92,394

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

genomics more details view paper
  • Downloaded 1,258 times
  • Download rankings, all-time:
    • Site-wide: 13,169
    • In genomics: 1,450
  • Year to date:
    • Site-wide: 56,116
  • Since beginning of last month:
    • Site-wide: 51,413

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

bioinformatics more details view paper
  • Downloaded 1,231 times
  • Download rankings, all-time:
    • Site-wide: 13,607
    • In bioinformatics: 1,705
  • Year to date:
    • Site-wide: 2,488
  • Since beginning of last month:
    • Site-wide: 1,132

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

bioinformatics more details view paper
  • Downloaded 1,141 times
  • Download rankings, all-time:
    • Site-wide: 15,227
    • In bioinformatics: 1,913
  • Year to date:
    • Site-wide: 93,849
  • Since beginning of last month:
    • Site-wide: 50,270

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

genomics more details view paper
  • Downloaded 1,088 times
  • Download rankings, all-time:
    • Site-wide: 16,415
    • In genomics: 1,742
  • Year to date:
    • Site-wide: 109,596
  • Since beginning of last month:
    • Site-wide: 92,530

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

molecular biology more details view paper
  • Downloaded 972 times
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    • Site-wide: 19,387
    • In molecular biology: 525
  • Year to date:
    • Site-wide: 13,466
  • Since beginning of last month:
    • Site-wide: 4,963

Investigating higher order interactions in single cell data with scHOT

bioinformatics more details view paper
  • Downloaded 971 times
  • Download rankings, all-time:
    • Site-wide: 19,439
    • In bioinformatics: 2,388
  • Year to date:
    • Site-wide: 95,383
  • Since beginning of last month:
    • Site-wide: 55,046

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

immunology more details view paper
  • Downloaded 965 times
  • Download rankings, all-time:
    • Site-wide: 19,592
    • In immunology: 528
  • Year to date:
    • Site-wide: 18,688
  • Since beginning of last month:
    • Site-wide: 25,581

Rora regulates activated T helper cells during inflammation

immunology more details view paper
  • Downloaded 964 times
  • Download rankings, all-time:
    • Site-wide: 19,626
    • In immunology: 529
  • Year to date:
    • Site-wide: 19,358
  • Since beginning of last month:
    • Site-wide: 29,996

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

cell biology more details view paper
  • Downloaded 894 times
  • Download rankings, all-time:
    • Site-wide: 21,897
    • In cell biology: 785
  • Year to date:
    • Site-wide: 119,191
  • Since beginning of last month:
    • Site-wide: 52,968

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

bioinformatics more details view paper
  • Downloaded 843 times
  • Download rankings, all-time:
    • Site-wide: 23,818
    • In bioinformatics: 2,892
  • Year to date:
    • Site-wide: 104,285
  • Since beginning of last month:
    • Site-wide: 96,657

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

immunology more details view paper
  • Downloaded 824 times
  • Download rankings, all-time:
    • Site-wide: 24,594
    • In immunology: 668
  • Year to date:
    • Site-wide: 39,163
  • Since beginning of last month:
    • Site-wide: 20,663

Robust expression variability testing reveals heterogeneous T cell responses

bioinformatics more details view paper
  • Downloaded 724 times
  • Download rankings, all-time:
    • Site-wide: 29,427
    • In bioinformatics: 3,415
  • Year to date:
    • Site-wide: 87,318
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    • Site-wide: 105,701

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

evolutionary biology more details view paper
  • Downloaded 723 times
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    • Site-wide: 29,490
    • In evolutionary biology: 1,500
  • Year to date:
    • Site-wide: 108,184
  • Since beginning of last month:
    • Site-wide: 101,894

Secreted inhibitors drive the loss of regeneration competence in Xenopus limbs

developmental biology more details view paper
  • Downloaded 721 times
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    • Site-wide: 29,631
    • In developmental biology: 625
  • Year to date:
    • Site-wide: 13,053
  • Since beginning of last month:
    • Site-wide: 45,778

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 705 times
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    • Site-wide: 30,491
    • In evolutionary biology: 1,559
  • Year to date:
    • Site-wide: 83,916
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    • Site-wide: 115,594

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

genomics more details view paper
  • Downloaded 629 times
  • Download rankings, all-time:
    • Site-wide: 35,527
    • In genomics: 3,093
  • Year to date:
    • Site-wide: 121,238
  • Since beginning of last month:
    • Site-wide: 90,494

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

developmental biology more details view paper
  • Downloaded 187 times
  • Download rankings, all-time:
    • Site-wide: 100,593
    • In developmental biology: 2,731
  • Year to date:
    • Site-wide: 3,396
  • Since beginning of last month:
    • Site-wide: 4,674

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