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

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

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