Computational Modelling Group

Perl

Perl is a general-purpose programming language originally developed for text manipulation and now used for a wide range of tasks including system administration, web development, network programming, GUI development, and more. The language is intended to be practical which means easy to use, efficient and complete. It supports both procedural and object-oriented (OO) programming and has powerful built-in support for text processing (http://www.perl.org).

For queries about this topic, contact Gaia Andreoletti.

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.

Identification of Gene-Modules Associated to a Predisposition of Post-Traumatic Stress Disorder

Christopher Woelk (Investigator), Michael Breen

The predisposing genetic factors associated to Post-Traumatic Stress Disorder (PTSD) are altogether unknown. Since not all trauma-survivors later develop the PTSD, it has been hypothesized that transcript differentiation prior–to-trauma exposure could be associated to the risk and resilience of PTSD. We apply a systems-level approach to investigate changes in transcript abundance (gene expression profiles) in whole blood of U.S. Marines sampled prior-to-deployment to the battlefield and followed through-out a seven month deployment to obtain disorder related outcomes.

Identifying variants in next generation sequencing data of 61 paediatric Inflammatory Bowel Disease patients

Sarah Ennis (Investigator), Gaia Andreoletti

This study aims to characterise the mutations of genes known to predispose Inflammatory bowel disease in 61 paediatric patients using next generation sequencing analysis. Our aim is to identify the relative impact of known genes in individual case presentations of disease and correlate matches with clinical manifestation.

Sample tracking in whole-exome sequencing projects

Andrew Collins, Sarah Ennis (Investigators), Reuben Pengelly

Whole-exome sequencing is entering clinical use for genetic investigations, and it is therefore essential that robust quality control is utilised. As such we designed and validated a tool to allow for unambiguous tying of patient data to a patient, to identify, and thus prevent errors such as the switching of samples during processing.

THE NORM MATE TRANSPORTER FROM N. GONORRHEAE: INSIGHTS INTO DRUG & ION BINDING FROM ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS

Syma Khalid (Investigator), Daniel Holdbrook, Thomas Piggot, Yuk Leung

The multidrug and toxic compound extrusion (MATE) transporters extrude a wide variety of substrates out of both mammalian and bacterial cells via the electrochemical gradient of protons and cations across the membrane. Multiple atomistic simulation are performed on a MATE transporter, NorM from Neisseria gonorrheae (NorM_NG) and NorM from Vibrio cholera (NorM_VC). These simulations have allowed us to identify the nature of the drug-protein/ion-protein interactions, and secondly determine how these interactions contribute to the conformational rearrangements of the protein.

Whole exome sequencing identifies novel FLNA mutation in familial Ebstein's anomaly

Jane Gibson, Andrew Collins, Sarah Ennis (Investigators), Gaia Andreoletti

We describe the application of whole-exome sequencing in a family in which eight people in three generations presented Ebstein's anomaly.

People

Andrew Collins
Professor, Medicine (FM)
Sarah Ennis
Professor, Medicine (FM)
Robert Ewing
Senior Lecturer, Biological Sciences (FNES)
Jane Gibson
Lecturer, Biological Sciences (FNES)
Syma Khalid
Principal Research Fellow, Chemistry (FNES)
Reuben Pengelly
Research Fellow, Medicine (FM)
Gaia Andreoletti
Postgraduate Research Student, Medicine (FM)
Michael Breen
Postgraduate Research Student, Medicine (FM)
Marcin Knut
Postgraduate Research Student, Medicine (FM)
Andrew Lawson
Postgraduate Research Student, Physics & Astronomy (FPAS)
Yuk Leung
Postgraduate Research Student, Chemistry (FNES)
Jess Jones
Technical Staff, iSolutions
Daniel Holdbrook
None, None
Thomas Piggot
None, None
Roshan Sood
None, None
William Tapper
None, None
Christopher Woelk
None, None
Sheng Yang
None, None