John Marioni

Group Leader

Research Group Home Page:: Marioni Group

Work address:: Cancer Research UK Cambridge Institute University of Cambridge Li Ka Shing Centre Robinson Way Cambridge CB2 0RE

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

E-pub date: 30 Sep 2019; Expression Atlas update: from tissues to single cells.

E-pub date: 30 Sep 2019; Resolving the fibrotic niche of human liver cirrhosis at single-cell level.

E-pub date: 30 Sep 2019; A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans.

E-pub date: 01 Jul 2019; IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response.

E-pub date: 30 Jun 2019; Author Correction: Challenges in measuring and understanding biological noise.

E-pub date: 31 May 2019; Identification of a regeneration-organizing cell in the Xenopus tail.

E-pub date: 30 Apr 2019; Challenges in measuring and understanding biological noise.

E-pub date: 30 Apr 2019; Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.

E-pub date: 28 Feb 2019; EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.

E-pub date: 28 Feb 2019; A single-cell molecular map of mouse gastrulation and early organogenesis.

E-pub date: 31 Jan 2019; Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.

E-pub date: 31 Dec 2018; SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4.

E-pub date: 30 Nov 2018; Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias.

E-pub date: 30 Sep 2018; COMRADES determines in vivo RNA structures and interactions.

E-pub date: 31 Aug 2018; T cell cytolytic capacity is independent of initial stimulation strength.

E-pub date: 31 Aug 2018; Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens.

E-pub date: 01 Aug 2018; CTCF maintains regulatory homeostasis of cancer pathways.

E-pub date: 31 Jul 2018; Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.

E-pub date: 31 Jul 2018; Detection and removal of barcode swapping in single-cell RNA-seq data.

E-pub date: 10 Jul 2018; Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

E-pub date: 01 Jun 2018; Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.

E-pub date: 01 Jun 2018; CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

E-pub date: 31 May 2018; Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

E-pub date: 31 May 2018; Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body.

E-pub date: 01 May 2018; Using single-cell genomics to understand developmental processes and cell fate decisions.

E-pub date: 31 Mar 2018; Erratum: Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.

E-pub date: 28 Feb 2018; scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.

E-pub date: 22 Feb 2018; Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

E-pub date: 01 Feb 2018; SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.

E-pub date: 01 Jan 2018; Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.

E-pub date: 14 Dec 2017; Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.

E-pub date: 12 Dec 2017; Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.

E-pub date: 11 Dec 2017; The Human Cell Atlas.

E-pub date: 05 Dec 2017; Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.

E-pub date: 25 Nov 2017; f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

E-pub date: 07 Nov 2017; Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data.

E-pub date: 01 Nov 2017; Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.

E-pub date: 23 Oct 2017; How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.

E-pub date: 06 Oct 2017; Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.

E-pub date: 01 Aug 2017; Impact of Alternative Splicing on the Human Proteome.

E-pub date: 01 Aug 2017; Testing for differential abundance in mass cytometry data.

E-pub date: 31 Jul 2017; Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.

E-pub date: 01 Jul 2017; Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

E-pub date: 26 Jun 2017; Normalizing single-cell RNA sequencing data: challenges and opportunities.

E-pub date: 01 Jun 2017; Aging increases cell-to-cell transcriptional variability upon immune stimulation.

E-pub date: 31 Mar 2017; Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.

E-pub date: 21 Mar 2017; A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

E-pub date: 31 Aug 2016; HDTD: analyzing multi-tissue gene expression data.

E-pub date: 15 Jul 2016; Resolving early mesoderm diversification through single-cell expression profiling.

E-pub date: 14 Jul 2016; Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.

E-pub date: 31 May 2016; Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

E-pub date: 27 Apr 2016; Beyond comparisons of means: understanding changes in gene expression at the single-cell level.

E-pub date: 15 Apr 2016; Structure and evolutionary history of a large family of NLR proteins in the zebrafish.

E-pub date: 01 Apr 2016; Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

E-pub date: 24 Mar 2016; Classification of low quality cells from single-cell RNA-seq data.

E-pub date: 17 Feb 2016; Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.

E-pub date: 16 Dec 2015; Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

E-pub date: 22 Oct 2015; Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.

E-pub date: 01 Oct 2015; Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength.

E-pub date: 21 Sep 2015; Computational assignment of cell-cycle stage from single-cell transcriptome data.

E-pub date: 01 Sep 2015; Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

E-pub date: 31 Aug 2015; Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.

E-pub date: 25 Jun 2015; BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.

E-pub date: 01 Jun 2015; High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.

E-pub date: 31 May 2015; The technology and biology of single-cell RNA sequencing.

E-pub date: 21 May 2015; Computational and analytical challenges in single-cell transcriptomics.

E-pub date: 31 Mar 2015; Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

E-pub date: 01 Feb 2015; Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone.

E-pub date: 01 Jan 2015; Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

E-pub date: 24 Dec 2014; High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

E-pub date: 01 Nov 2014; Single Cell Genomics meeting in Stockholm: from single cells to cell types.

E-pub date: 18 Oct 2014; Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.

E-pub date: 03 Oct 2014; Identifying cell types from spatially referenced single-cell expression datasets.

E-pub date: 01 Sep 2014; RNA-Seq gene profiling–a systematic empirical comparison.

E-pub date: 31 Aug 2014; Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.

E-pub date: 31 Jul 2014; Random monoallelic gene expression increases upon embryonic stem cell differentiation.

E-pub date: 24 Feb 2014; Expression Atlas update–a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

E-pub date: 31 Jan 2014; Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.

E-pub date: 01 Aug 2013; bioWeb3D: an online webGL 3D data visualisation tool.

E-pub date: 07 Jun 2013; Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

E-pub date: 05 Mar 2013; Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.

E-pub date: 28 Jan 2013; Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

E-pub date: 31 Dec 2012; Tools for mapping high-throughput sequencing data.

E-pub date: 15 Dec 2012; Comparative RNA sequencing reveals substantial genetic variation in endangered primates.

E-pub date: 01 Apr 2012; Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.

E-pub date: 24 Jan 2012; The variant call format and VCFtools.

E-pub date: 01 Aug 2011; Gene expression differences among primates are associated with changes in a histone epigenetic modification.

E-pub date: 01 Apr 2011; A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

E-pub date: 01 Feb 2011; Genomic-scale capture and sequencing of endogenous DNA from feces.

E-pub date: 31 Dec 2010; Functional comparison of innate immune signaling pathways in primates.

E-pub date: 16 Dec 2010; Understanding mechanisms underlying human gene expression variation with RNA sequencing.

E-pub date: 01 Apr 2010; Sex-specific and lineage-specific alternative splicing in primates.

E-pub date: 01 Feb 2010; Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

E-pub date: 15 Dec 2009; The pitfalls of platform comparison: DNA copy number array technologies assessed.

E-pub date: 08 Dec 2009; An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).

E-pub date: 01 Sep 2008; RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.

E-pub date: 01 Sep 2008; ESR1 gene amplification in breast cancer: a common phenomenon?

E-pub date: 31 Jul 2008; A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

E-pub date: 31 Jul 2008; Hidden copy number variation in the HapMap population.

E-pub date: 22 Jul 2008; Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

E-pub date: 31 Aug 2007; Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments.

E-pub date: 31 Aug 2007; High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

E-pub date: 31 Aug 2007; Show all Hide all

Research Integrity Conflict of Interest Disclosure:

Last revised:: 26/11/2018

No items to report

Disclosure guidelines

John Marioni

Group Leader

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

Expression Atlas update: from tissues to single cells.

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

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

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

Author Correction: Challenges in measuring and understanding biological noise.

Identification of a regeneration-organizing cell in the Xenopus tail.

Challenges in measuring and understanding biological noise.

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.

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

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

Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.

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

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

COMRADES determines in vivo RNA structures and interactions.

T cell cytolytic capacity is independent of initial stimulation strength.

Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens.

CTCF maintains regulatory homeostasis of cancer pathways.

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

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

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

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

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

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

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

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

Erratum: Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.

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

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

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

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.

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

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

The Human Cell Atlas.

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.

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

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

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

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.

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

Impact of Alternative Splicing on the Human Proteome.

Testing for differential abundance in mass cytometry data.

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

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

Normalizing single-cell RNA sequencing data: challenges and opportunities.

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

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

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

HDTD: analyzing multi-tissue gene expression data.

Resolving early mesoderm diversification through single-cell expression profiling.

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

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

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

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

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

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

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

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

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

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

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

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

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

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.

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

The technology and biology of single-cell RNA sequencing.

Computational and analytical challenges in single-cell transcriptomics.

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

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

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

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

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

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

Identifying cell types from spatially referenced single-cell expression datasets.

RNA-Seq gene profiling–a systematic empirical comparison.

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

Random monoallelic gene expression increases upon embryonic stem cell differentiation.

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