Head of Computational Biology

Research Group Home Page: 

Matt joined the Cancer Research UK Cambridge Institute (CRUK CI) in December 2007 as Head of the Bioinformatics Core to provide support to research scientists in data processing, statistics, software development and training.

In addition to managing a team of 11 bioinformaticians, statisticians and software developers, Matt has contributed to various research projects, particularly focusing on analysis of cancer genomes and has developed a number of analysis pipelines and tools for identifying variants in tumour samples and circulating DNA. He has provided bioinformatic support to the UK oesphageal adenocarcinoma cancer genome sequencing project within the International Cancer Genome Consortium (ICGC) and played an active role in an international benchmarking exercise that evaluated the performance of somatic mutation calling approaches used by 17 ICGC project teams from across Europe, the United States, Canada, Japan, China and Australia. He has also gained experience in the analysis of single cell transcriptomic data and quantitative proteomic data from tandem mass tag (TMT) mass spectrometry.

Matt particularly enjoys coding, mostly in R, Java, Python and Ruby. He developed MGA, a contaminant screening QC tool for genomic sequencing data and various utilities for processing sequencing data and analysing genomic variants using the Samtools htsjdk Java API and GATK toolkit. He has developed several interactive web applications in R using the Shiny framework; these include tools for carrying out statistical tests that are used in our training courses, interfaces that provide access to data resources created by CRUK CI research labs (BCaPE), and analysis and visualization applications for low-frequency single nucleotide variant detection, absolute copy number scaling and quantitative proteomics.

Matt oversees the bioinformatics and statistics training programme within the institute, working in partnership with the Bioinformatics Training Facility at the University of Cambridge, and has helped develop and run training courses in data manipulation and visualization in R, cancer genome analysis, introductory statistics, Docker containers, and Shiny web application development, as well as the popular Cancer Research UK Bioinformatics Summer School hosted annually for the past 6 years.

Following a first degree in Chemistry from University of Oxford, Matt completed a D.Phil. in Computational Chemistry also at Oxford. Matt gained over 10 years commerical software development experience in computer-aided drug design and life sciences, consulting for and delivering informatics solutions to several major pharmaceutical and biotechnology companies, prior to joining CRUK CI.

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

NRG1 fusions in breast cancer.

E-pub date: 31 Dec 2020


Genomic copy number predicts esophageal cancer years before transformation.

E-pub date: 31 Aug 2020


ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung.

E-pub date: 31 Jul 2020


The mutREAD method detects mutational signatures from low quantities of cancer DNA.

E-pub date: 31 May 2020


Pan-cancer analysis of whole genomes.

E-pub date: 01 Feb 2020


Identification of Subtypes of Barrett’s Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data.

E-pub date: 31 Jan 2020


Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors.

E-pub date: 31 Jan 2020


Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma.

E-pub date: 01 Jan 2020


GCNA Interacts with Spartan and Topoisomerase II to Regulate Genome Stability.

E-pub date: 31 Dec 2019


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

E-pub date: 30 Nov 2019


Sensitive detection of ctDNA in low burden and ‘challenging’ cancers

E-pub date: 01 Jul 2019


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

E-pub date: 31 Jan 2019


Enhanced detection of circulating tumor DNA by fragment size analysis.

E-pub date: 31 Oct 2018


Copy number signatures and mutational processes in ovarian carcinoma.

E-pub date: 31 Jul 2018


A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes.

E-pub date: 13 Jun 2018


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

E-pub date: 31 Oct 2017


Disseminated Mycobacterium malmoense and Salmonella Infections Associated with a Novel Variant in NFKBIA.

E-pub date: 01 Jul 2017


Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours.

E-pub date: 27 Jun 2017


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

E-pub date: 01 Jun 2017


Impact of mutations in Toll-like receptor pathway genes on esophageal carcinogenesis.

E-pub date: 01 May 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


A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds.

E-pub date: 22 Sep 2016


The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer.

E-pub date: 31 Aug 2016


Whole-genome sequencing of nine esophageal adenocarcinoma cell lines.

E-pub date: 31 Aug 2016


Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples.

E-pub date: 31 Mar 2016


A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

E-pub date: 09 Dec 2015


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

E-pub date: 10 Jul 2015


MOBILE ELEMENT INSERTIONS ARE FREQUENT AND POTENTIALLY MUTAGENIC EVENTS IN OESOPHAGEAL CARCINOGENESIS

E-pub date: 01 Jun 2015


Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

E-pub date: 31 Aug 2014


Multi-genome alignment for quality control and contamination screening of next-generation sequencing data.

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


THE TOLL-LIKE RECEPTOR PATHWAY IS RECURRENTLY MUTATED IN OESOPHAGEAL ADENOCARCINOMA

E-pub date: 01 Jun 2014


THE CANCER RESEARCH UK (CRUK) FUNDED ICGC OESOPHAGEAL ADENOCARCINOMA PROJECT: MRC RESEARCH CENTRE AND CRUK CAMBRIDGE RESEARCH INSTITUTE

E-pub date: 01 Jun 2013


DEFINING THE GENETIC LANDSCAPE OF OESOPHAGEAL ADENOCARCINOMA BY NEXT-GENERATION SEQUENCING

E-pub date: 01 Jul 2012


Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis.

E-pub date: 06 Nov 2011


Cooperative interaction between retinoic acid receptor-alpha and estrogen receptor in breast cancer.

E-pub date: 15 Jan 2010


From molecular activities and processes to biological function.

E-pub date: 01 Mar 2001


Representing and analysing molecular and cellular function using the computer.

E-pub date: 01 Sep 2000


Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model.

E-pub date: 01 Sep 1998


Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

E-pub date: 01 Sep 1997


Stability of the AB crystal for asymmetric binary hard sphere mixtures

E-pub date: 01 Mar 1997


Protein fold recognition by threading: comparison of algorithms and analysis of results.

E-pub date: 01 Dec 1995


BINARY HARD-SPHERE MIXTURES – A COMPARISON BETWEEN COMPUTER-SIMULATION AND EXPERIMENT

E-pub date: 31 Jan 1995


Show all
Research Integrity Conflict of Interest Disclosure: 
Last revised: 
19/10/2018
No items to report
Disclosure guidelines