Director of the CRI

Research Group Home Page: 

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

Transcriptomic profiling reveals three molecular phenotypes of adenocarcinoma at the gastroesophageal junction.

E-pub date: 30 Nov 2019

Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma.

E-pub date: 30 Jun 2019

Loss of the interleukin-6 receptor causes immunodeficiency, atopy, and abnormal inflammatory responses.

E-pub date: 31 May 2019

The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic.

E-pub date: 31 Jan 2019

Author Correction: Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1.

E-pub date: 31 Dec 2018

Identification of Prognostic Phenotypes of Esophageal Adenocarcinoma in 2 Independent Cohorts.

E-pub date: 01 Dec 2018

Introduction to the Paul Joyce special issue.

E-pub date: 01 Jul 2018

Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium.

E-pub date: 01 Jun 2018

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

E-pub date: 31 May 2018

Ancestral inference from haplotypes and mutations.

E-pub date: 25 Apr 2018

Division-independent differentiation mandates proliferative competition among stem cells.

E-pub date: 03 Apr 2018

Simulating the component counts of combinatorial structures.

E-pub date: 09 Feb 2018

Multicentre cohort study to define and validate pathological assessment of response to neoadjuvant therapy in oesophagogastric adenocarcinoma.

E-pub date: 31 Dec 2017

Corrigendum: A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.

E-pub date: 31 Oct 2017

Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer.

E-pub date: 29 Aug 2017

New Model for Estimating Glomerular Filtration Rate in Patients With Cancer.

E-pub date: 20 Aug 2017

A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.

E-pub date: 01 Jun 2017

Corrigendum: Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

E-pub date: 31 Jan 2017

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

E-pub date: 31 Oct 2016

Mutational signatures of ionizing radiation in second malignancies.

E-pub date: 12 Sep 2016

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1.

E-pub date: 07 Sep 2016

HDTD: analyzing multi-tissue gene expression data.

E-pub date: 15 Jul 2016

Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target.

E-pub date: 31 May 2016

Erratum to: Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes.

E-pub date: 06 May 2016

Whole-genome sequencing provides new insights into the clonal architecture of Barrett’s esophagus and esophageal adenocarcinoma.

E-pub date: 01 Sep 2015

Metabolomic changes during cellular transformation monitored by metabolite-metabolite correlation analysis and correlated with gene expression.

E-pub date: 31 Aug 2015

Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis.

E-pub date: 10 Jul 2015

multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples.

E-pub date: 19 May 2015

HES5 silencing is an early and recurrent change in prostate tumourigenesis.

E-pub date: 01 Apr 2015

Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.

E-pub date: 31 Mar 2015

Epigenetic profile of human adventitial progenitor cells correlates with therapeutic outcomes in a mouse model of limb ischemia.

E-pub date: 31 Mar 2015

Testing the mean matrix in high-dimensional transposable data.

E-pub date: 31 Mar 2015

Genetic mapping of natural variation in schooling tendency in the threespine stickleback.

E-pub date: 25 Feb 2015

A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.

E-pub date: 31 Jan 2015

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

E-pub date: 01 Jan 2015

Boosting Wnt activity during colorectal cancer progression through selective hypermethylation of Wnt signaling antagonists.

E-pub date: 29 Nov 2014

Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

E-pub date: 31 Aug 2014

Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data.

E-pub date: 31 Aug 2014

Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics.

E-pub date: 31 Aug 2014

Normalization of metabolomics data with applications to correlation maps.

E-pub date: 01 Aug 2014

PTU-153 The Timing Of Oncogenic Events In The Evolution Of The Oesophageal Adenocarcinoma Genome And Implications For Clinical Diagnostics.

E-pub date: 01 Jun 2014

Flexible analysis of RNA-seq data using mixed effects models.

E-pub date: 15 Jan 2014

Defining stem cell dynamics in models of intestinal tumor initiation.

E-pub date: 22 Nov 2013

Continuous clonal labeling reveals small numbers of functional stem cells in intestinal crypts and adenomas.

E-pub date: 07 Nov 2013

Transcriptional dynamics elicited by a short pulse of notch activation involves feed-forward regulation by E(spl)/Hes genes.

E-pub date: 31 Aug 2013

Assessing senescence in Drosophila using video tracking.

E-pub date: 31 Aug 2013

The relative timing of mutations in a breast cancer genome.

E-pub date: 31 Aug 2013

The level of origin firing inversely affects the rate of replication fork progression.

E-pub date: 29 Apr 2013

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

E-pub date: 05 Mar 2013

Three-dimensional tracking and behaviour monitoring of multiple fruit flies.

E-pub date: 06 Jan 2013

Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization.

E-pub date: 01 Jan 2013

Calling sample mix-ups in cancer population studies.

E-pub date: 31 Aug 2012

Using GFP video to track 3D movement and conditional gene expression in free-moving flies.

E-pub date: 31 Aug 2012

Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation.

E-pub date: 27 Jul 2012

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

E-pub date: 18 Apr 2012

Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae.

E-pub date: 20 Jan 2012

A Bayesian approach to phylogeographic clustering.

E-pub date: 06 Dec 2011

High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers.

E-pub date: 31 Aug 2011

Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

E-pub date: 31 May 2011

Spatial coupling of mTOR and autophagy augments secretory phenotypes.

E-pub date: 20 May 2011

Sequential DNA methylation changes are associated with DNMT3B overexpression in colorectal neoplastic progression.

E-pub date: 01 Apr 2011

BayesPeak–an R package for analysing ChIP-seq data.

E-pub date: 01 Mar 2011

Dating primate divergences through an integrated analysis of palaeontological and molecular data.

E-pub date: 31 Jan 2011

CNAseg–a novel framework for identification of copy number changes in cancer from second-generation sequencing data.

E-pub date: 15 Dec 2010

The cost of reducing starting RNA quantity for Illumina BeadArrays: a bead-level dilution experiment.

E-pub date: 06 Oct 2010

The importance of platform annotation in interpreting microarray data.

E-pub date: 31 Aug 2010

The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans.

E-pub date: 01 Jun 2010

CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data.

E-pub date: 01 Jun 2010

Data analysis issues for allele-specific expression using Illumina’s GoldenGate assay.

E-pub date: 26 May 2010

Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data.

E-pub date: 27 Apr 2010

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.

E-pub date: 19 Apr 2010

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

E-pub date: 31 Jan 2010

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

E-pub date: 08 Dec 2009

Characterisation of microRNA expression in post-natal mouse mammary gland development.

E-pub date: 20 Nov 2009

Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression.

E-pub date: 01 Nov 2009

Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster.

E-pub date: 28 Oct 2009

Drosophila melanogaster p53 has developmental stage-specific and sex-specific effects on adult life span indicative of sexual antagonistic pleiotropy.

E-pub date: 27 Oct 2009

R/Bioconductor software for Illumina’s Infinium whole-genome genotyping BeadChips.

E-pub date: 01 Oct 2009

Strategies for analyzing highly enriched IP-chip datasets.

E-pub date: 22 Sep 2009

BayesPeak: Bayesian analysis of ChIP-seq data.

E-pub date: 21 Sep 2009

Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel.

E-pub date: 15 Jul 2009

Many colorectal cancers are “flat” clonal expansions.

E-pub date: 15 Jul 2009

Estimating primate divergence times by using conditioned birth-and-death processes.

E-pub date: 01 Jun 2009

Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae.

E-pub date: 01 May 2009

Simultaneous tracking of movement and gene expression in multiple Drosophila melanogaster flies using GFP and DsRED fluorescent reporter transgenes.

E-pub date: 17 Apr 2009

Autophagy mediates the mitotic senescence transition.

E-pub date: 01 Apr 2009

Older individuals appear to acquire mitotically older colorectal cancers.

E-pub date: 31 Mar 2009

Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers.

E-pub date: 24 Mar 2009

Population genetic inference from resequencing data.

E-pub date: 31 Jan 2009

A screen of apoptosis and senescence regulatory genes for life span effects when over-expressed in Drosophila.

E-pub date: 30 Jan 2009

Simultaneous tracking of fly movement and gene expression using GFP.

E-pub date: 16 Dec 2008

Modifier effects between regulatory and protein-coding variation.

E-pub date: 31 Oct 2008

Species-specific transcription in mice carrying human chromosome 21.

E-pub date: 17 Oct 2008

O fly, where art thou?

E-pub date: 06 Oct 2008

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

E-pub date: 01 Sep 2008

Endometrial-peritoneal interactions during endometriotic lesion establishment.

E-pub date: 01 Sep 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

Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae.

E-pub date: 15 Jul 2008

Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline.

E-pub date: 11 Jul 2008

Spike-in validation of an Illumina-specific variance-stabilizing transformation.

E-pub date: 04 Jun 2008

Inferring relative numbers of human leucocyte genome replications.

E-pub date: 01 Jun 2008

Pediatric malignant germ cell tumors show characteristic transcriptome profiles.

E-pub date: 01 Jun 2008

Statistical issues in the analysis of Illumina data.

E-pub date: 06 Feb 2008

Population genomics of human gene expression.

E-pub date: 31 Oct 2007

Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor.

E-pub date: 24 Oct 2007

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

MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype.

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

Explaining differences in saturation levels for Affymetrix GeneChip arrays.

E-pub date: 31 Aug 2007

Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes.

E-pub date: 31 Aug 2007

Primate origins: implications of a cretaceous ancestry.

E-pub date: 31 Aug 2007

beadarray: R classes and methods for Illumina bead-based data.

E-pub date: 15 Aug 2007

Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging.

E-pub date: 31 Jul 2007

Using expression arrays for copy number detection: an example from E. coli.

E-pub date: 14 Jun 2007

Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers.

E-pub date: 22 Mar 2007

The stem cell population of the human colon crypt: analysis via methylation patterns.

E-pub date: 02 Mar 2007

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

E-pub date: 09 Feb 2007

Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States.

E-pub date: 01 Apr 2004

Linkage disequilibrium: what history has to tell us.

E-pub date: 01 Feb 2002

A model for phylogenetic inference using structural and chemical covariates.

E-pub date: 01 Aug 2001

Genetic reconstruction of individual colorectal tumor histories.

E-pub date: 31 Jan 2000

Polymorphisms in the human DNA repair gene XPF.

E-pub date: 31 Aug 1999

Analysis of germline mutation spectra at the Huntington’s disease locus supports a mitotic mutation mechanism.

E-pub date: 01 Feb 1999

Estimating the age of the common ancestor of men from the ZFY intron.

E-pub date: 30 Apr 1996

Estimating the age of the common ancestor of men from the ZFY intron.

E-pub date: 30 Apr 1996

Single sperm analysis of the trinucleotide repeats in the Huntington’s disease gene: quantification of the mutation frequency spectrum.

E-pub date: 01 Sep 1995

The distribution of rare alleles.

E-pub date: 01 Aug 1995

Unrooted genealogical tree probabilities in the infinitely-many-sites model.

E-pub date: 01 May 1995

Modeling the evolution of the human mitochondrial genome.

E-pub date: 01 Dec 1992

Estimating substitution rates from molecular data using the coalescent.

E-pub date: 30 Jun 1992

Genomic mapping by anchoring random clones: a mathematical analysis.

E-pub date: 01 Dec 1991

Codon preference and primary sequence structure in protein-coding regions.

E-pub date: 01 Aug 1989

The population genealogy of the infinitely–many neutral alleles model.

E-pub date: 01 Aug 1987

The birth process with immigration, and the genealogical structure of large populations.

E-pub date: 01 Aug 1987

Line-of-descent and genealogical processes, and their applications in population genetics models.

E-pub date: 01 Oct 1984

New approaches for computer analysis of nucleic acid sequences.

E-pub date: 01 Sep 1983

Some stochastic models for plasmid copy number.

E-pub date: 01 Apr 1983

The detection of particular genotypes in finite populations. I. Natural selection effects.

E-pub date: 01 Apr 1981

The detection of particular genotypes in finite populations. II. The effects of partial penetrance and family structure.

E-pub date: 01 Apr 1981

Dual diffusions, killed diffusions, and the age distribution problem in population genetics.

E-pub date: 01 Dec 1979

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