Bioinformatics & Data Science

Introduction

The Computational Biology and Bioinformatics team, headed by Prof Crispin Miller, provides support to scientists at the Institute, covering a range of research projects that require large-scale exploratory data analysis, advanced statistics and mathematical modelling. We aim to provide insights that advance our understanding of cancer biology; specifically, we offer our expertise in:

  • Analysis of large datasets from high-throughput technologies (next generation sequencing, microarrays, metabolomics and RNAi screening).
  • Functional and pathway analyses using Ingenuity Pathway Analysis and GeneGo Metacore.
  • Data-mining with Oncomine Research Premium Edition and Oncomine Gene Browser.
  • Complex statistical analyses (mixed modelling, Bayesian and multivariate analyses), machine learning, and graph and network theory-based analyses.
  • Power and sample size estimation, experimental design, data presentation and visualisation.
  • Mathematical modelling and simulation of biological processes (such as cell migration, chemotaxis and cell-cell interactions).
  • Computer programming in R (including Bioconductor), Matlab, Fortran, Perl, Python, PHP and Bash.

Recent Publications

2020

Casciano JC, Perry C, Cohen-Nowak AJ, Miller KD, Vande Voorde J, Zhang Q, Chalmers S, Sandison ME, Liu Q, Hedley A, McBryan T, Tang HY, Gorman N, Beer T, Speicher DW, Adams PD, Liu X, Schlegel R, McCarron JG, Wakelam MJO, Gottlieb E, Kossenkov AV, Schug ZT. MYC regulates fatty acid metabolism through a multigenic program in claudin-low triple negative breast cancer. British journal of cancer. 2020;10.1038/s41416-019-0711-3.

Muthalagu N, Monteverde T, Raffo-Iraolagoitia X, Wiesheu R, Whyte D, Hedley A, Laing S, Kruspig B, Upstill-Goddard R, Shaw R, Neidler S, Rink C, Karim SA, Gyuraszova K, Nixon C, Clark W, Biankin AV, Carlin LM, Coffelt SB, Sansom OJ, Morton JP, Murphy DJ. Repression of the Type I Interferon pathway underlies MYC & KRAS-dependent evasion of NK & B cells in Pancreatic Ductal Adenocarcinoma. Cancer discovery. 2020;

Rooney N, Mason SM, McDonald L, Däbritz JHM, Campbell KJ, Hedley A, Howard S, Athineos D, Nixon C, Clark W, Leach JDG, Sansom OJ, Edwards J, Cameron ER, Blyth K RUNX1 is a driver of renal cell carcinoma correlating with clinical outcome Cancer Res. 2020;

Rudzka DA, Mason S, Neilson M, McGarry L, Kalna G, Hedley A, Blyth K, Olson MF. Selection of established tumour cells through narrow diameter micropores enriches for elevated Ras/Raf/MEK/ERK MAPK signalling and enhanced tumour growth. Small GTPases. 2020;10.1080/21541248.2020.1780108:1-17.

2019

Jackstadt R, van Hooff SR, Leach JD, Cortes-Lavaud X, Lohuis JO, Ridgway RA, Wouters VM, Roper J, Kendall TJ, Roxburgh CS, Horgan PG, Nixon C, Nourse C, Gunzer M, Clark W, Hedley A, Yilmaz OH, Rashid M, Bailey P, Biankin AV, Campbell AD, Adams DJ, Barry ST, Steele CW, Medema JP, Sansom OJ. Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis. Cancer cell. 2019;36:319-336.e317.

Loveridge CJ, Slater S, Campbell KJ, Nam NA, Knight J, Ahmad I, Hedley A, Lilla S, Repiscak P, Patel R, Salji M, Fleming J, Mitchell L, Nixon C, Strathdee D, Neilson M, Ntala C, Bryson S, Zanivan S, Edwards J, Robson CN, Goodyear CS, Blyth K, Leung HY. BRF1 accelerates prostate tumourigenesis and perturbs immune infiltration. Oncogene. 2019;10.1038/s41388-019-1106-x.

Neidler S, Kruspig B, Hewit K, Monteverde T, Gyuraszova K, Braun A, Clark W, James D, Hedley A, Nieswandt B, Shanks E, Dick C, Murphy DJ. Identification of a Clinically Relevant Signature for Early Progression in KRAS-Driven Lung Adenocarcinoma. Cancers 2019; 11: 600.

Patel R, Brzezinska EA, Repiscak P, Ahmad I, Mui E, Gao M, Blomme A, Harle V, Tan EH, Malviya G, Mrowinska A, Loveridge CJ, Rushworth LK, Edwards J, Ntala C, Nixon C, Hedley A, Mackay G, Tardito S, Sansom OJ, Leung HY. Activation of beta-catenin cooperates with loss of Pten to drive AR-independent castration-resistant prostate cancer. Cancer research. 2019;10.1158/0008-5472.Can-19-1684

Rudzka DA, Spennati G, McGarry DJ, Chim YH, Neilson M, Ptak A, Munro J, Kalna G, Hedley A, Moralli D, Green C, Mason S, Blyth K, Mullin M, Yin H, Olson MF. Migration through physical constraints is enabled by MAPK-induced cell softening via actin cytoskeleton re-organization. Journal of cell science. 2019;132.

2016

Birch J, Clarke CJ, Campbell AD, Campbell K, Mitchell L, Liko D, Kalna G, Strathdee D, Sansom OJ, Neilson M, Blyth K, Norman JC. The initiator methionine tRNA drives cell migration and invasion leading to increased metastatic potential in melanoma. Biol Open.

Group Members

Head

Crispin Miller

Bioinformaticians

Ann Hedley
Matthew Neilson
Robin Shaw

Research

At the bench 3 160

Read more about the Research Groups working at the Beatson Institute.

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Seminars

Running a gel 154

Find out more about our seminars including our Distinguished Seminar Programme.

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