Computational Modelling Group

RStudio

For queries about this topic, contact Marcin Knut.

Projects

Application of RNA-Seq for gene fusion identification in blood cancers

William Tapper (Investigator), Marcin Knut

Gene fusions are often the cause of different blood cancers. As such, accurate identification of them provides information on the underlying cause of a cancer, ensuring appropriate choice of treatment. However, due to shortcomings of the currently applied methods for gene fusion identification, some of them escape undetected. We are employing RNA-Seq, a cutting-edge method for sequencing RNA, the messenger of genetic information, to investigate gene fusions.

E ffects of Sample Contamination on Alternate Allele Frequency

Jane Gibson (Investigator), Roshan Sood

Accurate calling of genetic variants is reliant on the purity of samples, contamination will reduce the accuracy of results. Currently there are few programs able to identify contamination in samples, potentially misinforming a researcher or clinician. To better understand the changes caused by sample contamination in
silico simulations were performed where a known percentage of DNA sequence reads from a contaminating
fi le were added. Understanding the changes will assist the development of a new method and program to
detect sample contamination.

SAVE: Solent Achieving Value through Efficiency

Patrick James, Ben Anderson (Investigators), Luke Blunden

Analysis of 15 minute electricity consumption and 10 second instantaneous power data from 4,000+ households in the Solent region collected over 3 years of a randomised control trial study.

Studying microevolution in clinical isolates of Neisseria lactamica

Robert Read (Investigator), Jay Laver, Anish Pandey

We intranasally infected and successfully colonised six volunteers with Neisseria lactamica, a commensal species genetically similar to Neisseria meningitidis. A bioinformatics approach was then used to understand the microevolution of this bacterium and its adaptations to the nasopharynx.

People

Robert Read
Professor, Medicine (FM)
Patrick James
Senior Lecturer, Civil Engineering & the Environment (FEE)
Jane Gibson
Lecturer, Biological Sciences (FNES)
Ben Anderson
Senior Research Fellow, Civil Engineering & the Environment (FEE)
Jay Laver
Senior Research Fellow, Medicine (FM)
Luke Blunden
Research Fellow, Civil Engineering & the Environment (FEE)
Graham Elliott
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Marcin Knut
Postgraduate Research Student, Medicine (FM)
Anish Pandey
Postgraduate Research Student, Medicine (FM)
Roshan Sood
None, None
William Tapper
None, None