Author: John C Marioni

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Preprints

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

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

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The Human Cell Atlas

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

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

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

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

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iRAP - an integrated RNA-seq Analysis Pipeline

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

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

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Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

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

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

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

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

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Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

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

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

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

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

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

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

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Investigating higher order interactions in single cell data with scHOT

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

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Rora regulates activated T helper cells during inflammation

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

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

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Ageing compromises mouse thymus function and remodels epithelial cell differentiation

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Robust expression variability testing reveals heterogeneous T cell responses

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

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Secreted inhibitors drive the loss of regeneration competence in Xenopus limbs

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

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

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

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