List of works - John Marioni

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

scientific article

A comparison of dermatologists', surgeons' and general practitioners' surgical management of cutaneous melanoma

scientific article published in September 2004

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

scientific article

A single-cell molecular map of mouse gastrulation and early organogenesis

scientific article published on 20 February 2019

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

scientific article

A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans

scientific article published on 31 July 2019

Accounting for technical noise in single-cell RNA-seq experiments.

scientific article published on 22 September 2013

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

scientific article published on 25 August 2020

Aging increases cell-to-cell transcriptional variability upon immune stimulation

scientific article published on March 2017

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

article

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

scientific article

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data ⬇️

scientific article published on 13 October 2017

Author Correction: Challenges in measuring and understanding biological noise

scientific article published on 01 September 2019

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

scientific article

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

scientific article published on 02 April 2018

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

scientific article

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

article

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

scientific article

COMRADES determines in vivo RNA structures and interactions

scientific article published on 10 September 2018

CTCF maintains regulatory homeostasis of cancer pathways

scientific article published on 07 August 2018

Cells of the human intestinal tract mapped across space and time

Challenges in measuring and understanding biological noise

scientific article published on 01 September 2019

Characterization of a common progenitor pool of the epicardium and myocardium

scientific article published on 07 January 2021

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

scientific article

Classification of low quality cells from single-cell RNA-seq data

scientific article published on 17 February 2016

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.

scientific article

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

scientific article (publication date: April 2012)

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

scientific article

Computational and analytical challenges in single-cell transcriptomics

scientific article

Computational assignment of cell-cycle stage from single-cell transcriptome data

scientific article

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone

scientific article

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals

scientific article

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

scientific article published on 29 August 2018

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

scientific article published on 01 October 2019

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

scientific article published on 11 January 2016

CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

scientific article

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

scientific article published on 10 January 2012

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

scientific article published on 8 January 2018

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

scientific article published in Nature Communications

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing

scientific article published on 11 December 2017

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

ESR1 gene amplification in breast cancer: a common phenomenon?

scientific article published on July 2008

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

scientific article

Effects of a brief course of azithromycin on soluble cell adhesion molecules and markers of inflammation in survivors of an acute coronary syndrome: A double-blind, randomized, placebo-controlled study

scientific article published on July 2004

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

article by Aaron T L Lun et al published 22 March 2019 in Genome Biology

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

scientific article

Expression Atlas update: gene and protein expression in multiple species

scientific article published on 19 November 2021

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

scientific article

Functional comparison of innate immune signaling pathways in primates

scientific article

Gene expression differences among primates are associated with changes in a histone epigenetic modification

scientific article

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

scientific article

Genomic-scale capture and sequencing of endogenous DNA from feces

scientific article

Guidelines for reporting single-cell RNA-seq experiments

scientific article published on 13 November 2020

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

scientific article

Hidden copy number variation in the HapMap population.

scholarly article

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq

scientific article

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

scientific article

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface

scientific article

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

scientific article

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology

scientific article

IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response

scientific article published on 08 July 2019

Identification of a regeneration-organizing cell in the Xenopus tail

scientific article published on 01 May 2019

Identifying cell types from spatially referenced single-cell expression datasets

scientific article

Impact of Alternative Splicing on the Human Proteome

scientific article

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data ⬇️

scientific article published on January 28, 2013

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

scientific article

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

scientific article published on 14 February 2013

Investigating higher-order interactions in single-cell data with scHOT

scientific article published on 13 July 2020

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells

scientific article

LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 07 September 2020

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

scientific article published on 25 May 2014

Mapping Rora expression in resting and activated CD4+ T cells

scientific article published on 18 May 2021

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse

scientific article

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data

scientific article published on 25 November 2017

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

scientific article published on 20 June 2018

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

scientific article

Normalizing single-cell RNA sequencing data: challenges and opportunities

scientific article

Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments

scientific article published on August 2007

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

scientific article

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

scholarly article published 8 September 2016

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos

scientific article published on 29 November 2017

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

scientific article

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

scientific article published on 04 March 2021

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 17 March 2021

Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

scientific article published on 23 March 2020

Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels

scientific article published on 13 March 2020

RNA-Seq gene profiling--a systematic empirical comparison

scientific article

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

scientific article

Random monoallelic gene expression increases upon embryonic stem cell differentiation

scientific article

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength

scientific article published on 21 September 2015

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System

scientific article published on 4 September 2015

Resolving early mesoderm diversification through single-cell expression profiling

scientific article published on 6 July 2016

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

scientific article published on 09 October 2019

SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4

scientific article published in Nature Communications

SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.

scientific article

Sex-specific and lineage-specific alternative splicing in primates

scientific article

Single Cell Genomics meeting in Stockholm: from single cells to cell types

scientific article

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

scientific article

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

scientific article published on August 2017

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

scientific article published on 10 February 2020

Single-cell multi-omics analysis of the immune response in COVID-19

scientific article published on 20 April 2021

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

scientific article published on 01 July 2018

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

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

scientific article published on 19 March 2019

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.

scientific article

Stimulation strength controls the rate of initiation but not the molecular organization of TCR-induced signalling

scientific article published on 15 May 2020

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

scientific article

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

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

article

T cell cytolytic capacity is independent of initial stimulation strength

scholarly article by Arianne C Richard et al published 16 July 2018 in Nature Immunology

Testing for differential abundance in mass cytometry data

scientific article

Testing the mean matrix in high-dimensional transposable data ⬇️

scientific article published on 23 January 2015

The Human Cell Atlas

scientific article

The Human Cell Atlas White Paper ⬇️

journal article from 'arXiv:1810.05192 [q-bio]' published in 2018

The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors

scientific article published on 08 January 2021

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

scientific article published on 15 January 2021

The pitfalls of platform comparison: DNA copy number array technologies assessed

scientific article

The technology and biology of single-cell RNA sequencing

scientific article

Tools for mapping high-throughput sequencing data

scientific article

Toward a Common Coordinate Framework for the Human Body

scientific article published on 01 December 2019

Using single-cell genomics to understand developmental processes and cell fate decisions.

scientific article

Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body

scientific article

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

Yolk sac cell atlas reveals multiorgan functions during human early development

scientific article published on 17 August 2023

bioWeb3D: an online webGL 3D data visualisation tool

scientific article

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

scientific article

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

scientific article published on 22 February 2018

List of works by John Marioni

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

A comparison of dermatologists', surgeons' and general practitioners' surgical management of cutaneous melanoma

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

A single-cell molecular map of mouse gastrulation and early organogenesis

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans

Accounting for technical noise in single-cell RNA-seq experiments.

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

Aging increases cell-to-cell transcriptional variability upon immune stimulation

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

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data ⬇️

Author Correction: Challenges in measuring and understanding biological noise

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

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

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

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

COMRADES determines in vivo RNA structures and interactions

CTCF maintains regulatory homeostasis of cancer pathways

Cells of the human intestinal tract mapped across space and time

Challenges in measuring and understanding biological noise

Characterization of a common progenitor pool of the epicardium and myocardium

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

Classification of low quality cells from single-cell RNA-seq data

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Computational and analytical challenges in single-cell transcriptomics

Computational assignment of cell-cycle stage from single-cell transcriptome data

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

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

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing

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

ESR1 gene amplification in breast cancer: a common phenomenon?

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

Effects of a brief course of azithromycin on soluble cell adhesion molecules and markers of inflammation in survivors of an acute coronary syndrome: A double-blind, randomized, placebo-controlled study

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Expression Atlas update: gene and protein expression in multiple species

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

Functional comparison of innate immune signaling pathways in primates

Gene expression differences among primates are associated with changes in a histone epigenetic modification

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

Genomic-scale capture and sequencing of endogenous DNA from feces

Guidelines for reporting single-cell RNA-seq experiments

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

Hidden copy number variation in the HapMap population.

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology

IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response

Identification of a regeneration-organizing cell in the Xenopus tail

Identifying cell types from spatially referenced single-cell expression datasets

Impact of Alternative Splicing on the Human Proteome

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data ⬇️

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

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

Investigating higher-order interactions in single-cell data with scHOT

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells

LifeTime and improving European healthcare through cell-based interceptive medicine

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

Mapping Rora expression in resting and activated CD4+ T cells

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

Normalizing single-cell RNA sequencing data: challenges and opportunities

Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments

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