Group Leader: Simon Travers

Simon Travers is the principal investigator of the HIV molecular evolution research group.  He graduated from his undergraduate degree in Biotechnology at the National University of Ireland, Maynooth in 2001 and completed his PhD (Bioinformatics) in 2004 also at NUI Maynooth.  Following his PhD he undertook post-doctoral research with Dr Mario Fares in NUI Maynooth and Trinity College, Dublin.  In late 2006 he received funding from the Irish Health Research Board (HRB) and established his research group initially in NUI Maynooth before moving to NUI Galway.  He is currently employed as an Associate Professor at the South African National Bioinformatics Institute (SANBI) where he has been since April 2010.

 

Current Group Members

Dr Natasha Wood (Postdoctoral Researcher)

Natasha is using computational approaches to model the structural properties of the 'glycan shield' that protects the surface of the HIV gp120 protein.  This shield comprises carbohydrates that are added to gp120 by the host glycosylation system.  Natasha is attempting to model the biological characteristics of the glycan shield by investigating the interactions between various N-linked glycans and comprehensively describing the full extent of the flexibility of the glycan shield.  This modelling is performed using cutting edge software developed by our collaborators in NUI Galway, Ireland.      

 

Ram Krishna Shrestha (PhD student)

Ram is working on a project focused on the management and analysis of HIV-1 ultra-deep sequencing data.  He is developing methods to process and analyse HIV sequence data generated using 454 sequencing technology for the detection of drug resistance.  His project also focuses on analysis of 454 sequence data from individuals infected with HIV-1 subtype C produced as part of a collaboration with Dr Grace McCormack (NUI Galway) and the members of the Karonga Prevention Study (KPS) in Malawi.  This data is being used to examine the effect of minor variant drug resistant viruses on the treatment outcome of individuals infected with HIV-1 subtype C.     

 

Imogen Wright (PhD student)

Imogen's previous training is as a theoretical physicist and she has significant experience in harnessing the power of the graphics processing units (GPUs) of computers.  In her project she is using this experience to develop algorithms and methods for the analysis of next generation sequence data.  Specifically, she is harnessing the power of GPUs to develop a novel (and fast) approach for mapping next generation sequence reads to reference sequences.  Initially she is focusing on fast mapping of amplicon based sequencing but the long-term focus is to develop a fast and efficient approach for genome assembly.

 

 

Saleema Crous (MSc student)

Saleema is working on coreceptor usage in HIV-1 subtype C.  Transmitted viruses mostly use the CCR5 chemokine receptor as a coreceptor for host cell entry.  Using sequence data from viruses whose coreceptor preference is known this project aims to better understand the molecular mechanisms that lead to the change of coreceptor usage in HIV-1 subtype C.    

 

 

 

 

Former Group Members

 

Dr Conor Meehan

Conor graduated in March 2010 from National University of Ireland, Galway.  He studied the molecular mechanisms of coreceptor switching in HIV specifically characterising the modes of resistance to CCR5 antagonists.  

He is currently working as a postdoc in Dalhousie University, Halifax, Canada.

 

 

Dr Vijay Bansode 

Dr Bansode was a PhD student cosupervised with Dr Grace McCormack (NUI Galway, Ireland).  He worked as part of a collaborative project with the Karonga Prevention Study (KPS), Malawi.  He investigated the prevalence and possible transmission of drug resistant viruses in a treatment naive population of individuals infected with HIV-1 subtype C.  He used ultra-deep sequencing approaches to study drug resistant minor variants present within individuals prior to ART initiation and to monitor the subsequent emergence of these variants in response to therapy.  

He is currently working as a posdoctoral researcher at CNRS Strasbourg, France with Dr Matteo Negroni.

 

Dr Ishla Seager 

Dr Seager was a PhD student cosupervised with Dr Grac McCormack in NUI Galway, Ireland.  She worked on a project using data from the Karonga Prevention Study in Malawi.  The main focus of her project was examining the role of viral factor in long term survivors (individuals infected with HIV for long periods who do not progress to AIDS in the absence of ARTs).  She used sequential samples collected from long term survivors at regular intervals from the early 1980s through to the present time.  As well as sequencing and analysing a number of genes from each timepoint she performed fitness assays to compare the relative fitness of the viruses infecting long term survivors to those with archetypal disease progression.

She is currently working in the Veterinary School at the University of Cambridge. 

Fredrick Nindo (MSc student)

Fred completed a MSc in 2012 using a molecular phylodynamic approach to study the extent of transmission networks of HIV within a population of HIV infected individuals in Karonga District, Malawi.  He is currently working towards his PhD with Dr Darren Martin at the University of Cape Town.

 

 

 

 

Dr Hannah Ajoge (postdoctoral researcher)

Hannah was part of the research group as a postdoctoral research fellow from June 2012 - December 2013.