Head of Computational Biology
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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 8 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 enjoys coding, mostly in R, Java, Python and, more recently, Rust. He developed MGA, a contaminant screening QC tool for genomic sequencing data, ampliconseq, a variant calling pipeline for amplicon 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 (rascal) 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 R for Cancer Scientists, cancer genome analysis, introductory statistics, analysis worfklow development using Nextflow, Docker containers, and Shiny web application development, as well as the popular Cancer Research UK Bioinformatics Summer School hosted annually from 2015 to 2021.
Following a first degree in Chemistry from University of Oxford, Matt completed a D.Phil. in Computational Chemistry also at Oxford. Prior to joining CRUK CI, 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.
- Work address:
- Cancer Research UK Cambridge Institute University of Cambridge Li Ka Shing Centre Robinson Way Cambridge CB2 0RE
Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significantE-pub date: 8 Jun 2022Journal name: NPJ Breast Cancer
Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas.E-pub date: 8 Apr 2022Journal name: Commun Biol
Fragmentation patterns and personalized sequencing of cell‐free DNA in urine and plasma of glioma patientsE-pub date: 9 Aug 2021Journal name: EMBO Mol Med
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