Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 71,037 bioRxiv papers from 309,945 authors.

Author: John Marioni

Rankings

  • All-time downloads: 64,149 (rank: 202 out of 309,498)
  • Categories:
    • bioinformatics: 27,340 (rank: 66 out of 26,887)
    • cell biology: 12,500 (rank: 55 out of 21,502)
    • developmental biology: 6,840 (rank: 38 out of 11,891)
    • evolutionary biology: 1,221 (rank: 2,769 (tie) out of 16,620)
    • genomics: 13,092 (rank: 745 out of 34,893)
    • immunology: 1,107 (rank: 1,759 (tie) out of 14,846)
    • zoology: 2,049 (rank: 13 (tie) out of 1,736)

Downloads per author, site-wide

Preprints

The Human Cell Atlas

cell biology more details view paper
  • Downloaded 11,841 times
  • Download rankings, all-time:
    • Site-wide: 91 out of 70,927
    • In cell biology: 3 out of 3,477
  • Year to date:
    • Site-wide: 21,220 out of 70,927
  • Since beginning of last month:
    • Site-wide: 8,300 out of 70,927

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

developmental biology more details view paper
  • Downloaded 5,429 times
  • Download rankings, all-time:
    • Site-wide: 400 out of 70,927
    • In developmental biology: 6 out of 2,118
  • Year to date:
    • Site-wide: 1,870 out of 70,927
  • Since beginning of last month:
    • Site-wide: 655 out of 70,927

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

bioinformatics more details view paper
  • Downloaded 4,860 times
  • Download rankings, all-time:
    • Site-wide: 486 out of 70,927
    • In bioinformatics: 99 out of 6,940
  • Year to date:
    • Site-wide: 9,926 out of 70,927
  • Since beginning of last month:
    • Site-wide: 23,377 out of 70,927

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

bioinformatics more details view paper
  • Downloaded 4,589 times
  • Download rankings, all-time:
    • Site-wide: 552 out of 70,927
    • In bioinformatics: 110 out of 6,940
  • Year to date:
    • Site-wide: 37,841 out of 70,927
  • Since beginning of last month:
    • Site-wide: 15,677 out of 70,927

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

genomics more details view paper
  • Downloaded 4,574 times
  • Download rankings, all-time:
    • Site-wide: 554 out of 70,927
    • In genomics: 142 out of 4,728
  • Year to date:
    • Site-wide: 21,024 out of 70,927
  • Since beginning of last month:
    • Site-wide: 22,079 out of 70,927

RNA-seq gene profiling - a systematic empirical comparison

bioinformatics more details view paper
  • Downloaded 3,866 times
  • Download rankings, all-time:
    • Site-wide: 777 out of 70,927
    • In bioinformatics: 150 out of 6,940
  • Year to date:
    • Site-wide: 18,688 out of 70,927
  • Since beginning of last month:
    • Site-wide: 30,428 out of 70,927

iRAP - an integrated RNA-seq Analysis Pipeline

bioinformatics more details view paper
  • Downloaded 3,487 times
  • Download rankings, all-time:
    • Site-wide: 951 out of 70,927
    • In bioinformatics: 187 out of 6,940
  • Year to date:
    • Site-wide: 19,489 out of 70,927
  • Since beginning of last month:
    • Site-wide: 15,931 out of 70,927

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

bioinformatics more details view paper
  • Downloaded 3,003 times
  • Download rankings, all-time:
    • Site-wide: 1,255 out of 70,927
    • In bioinformatics: 247 out of 6,940
  • Year to date:
    • Site-wide: 36,498 out of 70,927
  • Since beginning of last month:
    • Site-wide: 16,434 out of 70,927

Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects

bioinformatics more details view paper
  • Downloaded 2,793 times
  • Download rankings, all-time:
    • Site-wide: 1,428 out of 70,927
    • In bioinformatics: 283 out of 6,940
  • Year to date:
    • Site-wide: 44,090 out of 70,927
  • Since beginning of last month:
    • Site-wide: 54,847 out of 70,927

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

genomics more details view paper
  • Downloaded 2,094 times
  • Download rankings, all-time:
    • Site-wide: 2,389 out of 70,927
    • In genomics: 497 out of 4,728
  • Year to date:
    • Site-wide: 2,924 out of 70,927
  • Since beginning of last month:
    • Site-wide: 3,764 out of 70,927

Placozoa and Cnidaria are sister taxa

zoology more details view paper
  • Downloaded 2,049 times
  • Download rankings, all-time:
    • Site-wide: 2,491 out of 70,927
    • In zoology: 3 out of 365
  • Year to date:
    • Site-wide: 11,363 out of 70,927
  • Since beginning of last month:
    • Site-wide: 23,280 out of 70,927

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

genomics more details view paper
  • Downloaded 1,752 times
  • Download rankings, all-time:
    • Site-wide: 3,235 out of 70,927
    • In genomics: 626 out of 4,728
  • Year to date:
    • Site-wide: 47,706 out of 70,927
  • Since beginning of last month:
    • Site-wide: 40,878 out of 70,927

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

developmental biology more details view paper
  • Downloaded 1,411 times
  • Download rankings, all-time:
    • Site-wide: 4,708 out of 70,927
    • In developmental biology: 92 out of 2,118
  • Year to date:
    • Site-wide: 24,189 out of 70,927
  • Since beginning of last month:
    • Site-wide: 9,954 out of 70,927

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

genomics more details view paper
  • Downloaded 1,406 times
  • Download rankings, all-time:
    • Site-wide: 4,731 out of 70,927
    • In genomics: 841 out of 4,728
  • Year to date:
    • Site-wide: 14,854 out of 70,927
  • Since beginning of last month:
    • Site-wide: 12,848 out of 70,927

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

genomics more details view paper
  • Downloaded 1,128 times
  • Download rankings, all-time:
    • Site-wide: 6,833 out of 70,927
    • In genomics: 1,108 out of 4,728
  • Year to date:
    • Site-wide: 33,759 out of 70,927
  • Since beginning of last month:
    • Site-wide: 45,102 out of 70,927

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

bioinformatics more details view paper
  • Downloaded 1,031 times
  • Download rankings, all-time:
    • Site-wide: 7,895 out of 70,927
    • In bioinformatics: 1,394 out of 6,940
  • Year to date:
    • Site-wide: 787 out of 70,927
  • Since beginning of last month:
    • Site-wide: 495 out of 70,927

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

genomics more details view paper
  • Downloaded 1,014 times
  • Download rankings, all-time:
    • Site-wide: 8,110 out of 70,927
    • In genomics: 1,274 out of 4,728
  • Year to date:
    • Site-wide: 63,657 out of 70,927
  • Since beginning of last month:
    • Site-wide: 51,975 out of 70,927

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

bioinformatics more details view paper
  • Downloaded 928 times
  • Download rankings, all-time:
    • Site-wide: 9,402 out of 70,927
    • In bioinformatics: 1,615 out of 6,940
  • Year to date:
    • Site-wide: 12,289 out of 70,927
  • Since beginning of last month:
    • Site-wide: 30,539 out of 70,927

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

bioinformatics more details view paper
  • Downloaded 879 times
  • Download rankings, all-time:
    • Site-wide: 10,221 out of 70,927
    • In bioinformatics: 1,740 out of 6,940
  • Year to date:
    • Site-wide: 999 out of 70,927
  • Since beginning of last month:
    • Site-wide: 1,504 out of 70,927

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

bioinformatics more details view paper
  • Downloaded 722 times
  • Download rankings, all-time:
    • Site-wide: 13,773 out of 70,927
    • In bioinformatics: 2,217 out of 6,940
  • Year to date:
    • Site-wide: 64,414 out of 70,927
  • Since beginning of last month:
    • Site-wide: 62,261 out of 70,927

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

cell biology more details view paper
  • Downloaded 659 times
  • Download rankings, all-time:
    • Site-wide: 15,679 out of 70,927
    • In cell biology: 642 out of 3,477
  • Year to date:
    • Site-wide: 12,371 out of 70,927
  • Since beginning of last month:
    • Site-wide: 12,693 out of 70,927

Robust expression variability testing reveals heterogeneous T cell responses

bioinformatics more details view paper
  • Downloaded 639 times
  • Download rankings, all-time:
    • Site-wide: 16,405 out of 70,927
    • In bioinformatics: 2,523 out of 6,940
  • Year to date:
    • Site-wide: 48,656 out of 70,927
  • Since beginning of last month:
    • Site-wide: 64,530 out of 70,927

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

evolutionary biology more details view paper
  • Downloaded 611 times
  • Download rankings, all-time:
    • Site-wide: 17,492 out of 70,927
    • In evolutionary biology: 1,215 out of 4,638
  • Year to date:
    • Site-wide: 49,253 out of 70,927
  • Since beginning of last month:
    • Site-wide: 48,856 out of 70,927

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 610 times
  • Download rankings, all-time:
    • Site-wide: 17,519 out of 70,927
    • In evolutionary biology: 1,220 out of 4,638
  • Year to date:
    • Site-wide: 68,594 out of 70,927
  • Since beginning of last month:
    • Site-wide: 41,756 out of 70,927

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

immunology more details view paper
  • Downloaded 588 times
  • Download rankings, all-time:
    • Site-wide: 18,449 out of 70,927
    • In immunology: 344 out of 1,828
  • Year to date:
    • Site-wide: 6,198 out of 70,927
  • Since beginning of last month:
    • Site-wide: 23,509 out of 70,927

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

genomics more details view paper
  • Downloaded 567 times
  • Download rankings, all-time:
    • Site-wide: 19,383 out of 70,927
    • In genomics: 2,300 out of 4,728
  • Year to date:
    • Site-wide: 59,607 out of 70,927
  • Since beginning of last month:
    • Site-wide: 47,207 out of 70,927

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

genomics more details view paper
  • Downloaded 557 times
  • Download rankings, all-time:
    • Site-wide: 19,839 out of 70,927
    • In genomics: 2,333 out of 4,728
  • Year to date:
    • Site-wide: 59,906 out of 70,927
  • Since beginning of last month:
    • Site-wide: 45,091 out of 70,927

Investigating higher order interactions in single cell data with scHOT

bioinformatics more details view paper
  • Downloaded 543 times
  • Download rankings, all-time:
    • Site-wide: 20,536 out of 70,927
    • In bioinformatics: 2,999 out of 6,940
  • Year to date:
    • Site-wide: 2,452 out of 70,927
  • Since beginning of last month:
    • Site-wide: 1,049 out of 70,927

Rora regulates activated T helper cells during inflammation

immunology more details view paper
  • Downloaded 519 times
  • Download rankings, all-time:
    • Site-wide: 21,734 out of 70,927
    • In immunology: 417 out of 1,828
  • Year to date:
    • Site-wide: 9,112 out of 70,927
  • Since beginning of last month:
    • Site-wide: 21,674 out of 70,927

PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News