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Author: JC Marioni

Rankings

  • All-time downloads: 64,244 (rank: 601 out of 404,161)
  • Categories:
    • bioinformatics: 24,202 (rank: 100 out of 34,272)
    • cell biology: 13,139 (rank: 40 out of 30,511)
    • developmental biology: 7,894 (rank: 60 out of 15,768)
    • evolutionary biology: 1,349 (rank: 3,429 (tie) out of 20,691)
    • genetics: 2,074 (rank: 7,546 (tie) out of 36,792)
    • genomics: 13,324 (rank: 975 out of 42,763)
    • immunology: 2,262 (rank: 1,789 out of 23,479)

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Preprints

The Human Cell Atlas

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

developmental biology more details view paper
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Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours.

bioinformatics more details view paper
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Multi-Omics factor analysis - a framework for unsupervised integration of multi-omic data sets

bioinformatics more details view paper
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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

genomics more details view paper
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iRAP - an integrated RNA-seq Analysis Pipeline

bioinformatics more details view paper
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Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

bioinformatics more details view paper
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Single-cell RNA-seq of differentiating iPS cells reveals dynamic genetic effects on gene expression

genomics more details view paper
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MOFA+: a probabilistic framework for comprehensive integration of structured single-cell data

bioinformatics more details view paper
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    • In bioinformatics: 546 out of 8,837
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Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

genetics more details view paper
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CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets

bioinformatics more details view paper
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    • In bioinformatics: 788 out of 8,837
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Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

genomics more details view paper
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Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

developmental biology more details view paper
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    • In developmental biology: 114 out of 2,812
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Detection and removal of barcode swapping in single-cell RNA-seq data

genomics more details view paper
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    • In genomics: 982 out of 5,955
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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

genomics more details view paper
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    • In genomics: 1,329 out of 5,955
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Assessing The Reliability Of Spike-In Normalization For Analyses Of Single-Cell RNA Sequencing Data

bioinformatics more details view paper
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Beyond comparisons of means: understanding changes in gene expression at the single-cell level

genomics more details view paper
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Investigating higher order interactions in single cell data with scHOT

bioinformatics more details view paper
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    • In bioinformatics: 2,270 out of 8,837
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    • Site-wide: 4,603 out of 94,912

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

cell biology more details view paper
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    • In cell biology: 673 out of 4,894
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Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth

immunology more details view paper
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    • In immunology: 450 out of 2,857
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    • Site-wide: 16,632 out of 94,912

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

bioinformatics more details view paper
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Rora regulates activated T helper cells during inflammation

immunology more details view paper
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    • In immunology: 472 out of 2,857
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Robust expression variability testing reveals heterogeneous T cell responses

bioinformatics more details view paper
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    • Site-wide: 90,289 out of 94,912

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

evolutionary biology more details view paper
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Structure and evolutionary history of a large family of NLR proteins in the zebrafish

evolutionary biology more details view paper
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Ageing compromises mouse thymus function and remodels epithelial cell differentiation

immunology more details view paper
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Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression

genomics more details view paper
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    • Site-wide: 80,247 out of 94,912

Secreted inhibitors drive the loss of regeneration competence in Xenopus limbs

developmental biology more details view paper
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