Research Associate

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: 

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

E-pub date: 28 Feb 2019


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

E-pub date: 31 Dec 2018


Transcription-factor-mediated supervision of global genome architecture maintains B cell identity.

E-pub date: 01 Nov 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


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


Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development.

E-pub date: 01 Jun 2018


beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.

E-pub date: 31 May 2018


iSEE: Interactive SummarizedExperiment Explorer.

E-pub date: 01 Jan 2018


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

E-pub date: 12 Dec 2017


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

E-pub date: 01 Nov 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


No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data.

E-pub date: 25 Apr 2017


Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.

E-pub date: 15 Apr 2017


A non-canonical function of Ezh2 preserves immune homeostasis.

E-pub date: 01 Apr 2017


Acetylation of the Cd8 Locus by KAT6A Determines Memory T Cell Diversity.

E-pub date: 20 Sep 2016


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

E-pub date: 31 Aug 2016


From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.

E-pub date: 31 Aug 2016


Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments.

E-pub date: 31 Aug 2016


It’s DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR.

E-pub date: 31 Aug 2016


Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.

E-pub date: 01 Jun 2016


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

E-pub date: 27 Apr 2016


RUNX2 Mediates Plasmacytoid Dendritic Cell Egress from the Bone Marrow and Controls Viral Immunity.

E-pub date: 26 Apr 2016


csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows.

E-pub date: 18 Mar 2016


Transcriptome and H3K27 tri-methylation profiling of Ezh2-deficient lung epithelium.

E-pub date: 01 Sep 2015


From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data.

E-pub date: 31 Aug 2015


diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data.

E-pub date: 19 Aug 2015


[Eagle’s syndrome].

E-pub date: 31 May 2015


Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung.

E-pub date: 15 Apr 2015


EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival.

E-pub date: 01 Apr 2015


De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly.

E-pub date: 01 Jun 2014


Polycomb repressive complex 2 (PRC2) suppresses Eμ-myc lymphoma.

E-pub date: 10 Oct 2013


Mass trees: a new phylogenetic approach and algorithm to chart evolutionary history with mass spectrometry.

E-pub date: 04 Jun 2013


FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry.

E-pub date: 20 Aug 2012


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