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Associate Professor Darren Martin PhD (Cape Town)

Computational Biology Group

Darren Martin

Division of Computational Biology, Department of Integrative Biomedical Sciences, & Member of the Institute of Infectious Disease and Molecular Medicine(IDM), Faculty of Health Sciences, University of Cape Town

The Computational Biology (CBIO) Group is the centre of Bioinformatics activities at the University. It aims to perform world-class bioinformatics research and provide high quality bioinformatics education, training and services. The CBIO Division is part of the Department of Integrative Biomedical Sciences and is located within the IDM. Darren Martin’s main research interests lie in studying the role that genetic recombination plays during virus evolution.

As a mechanism that generates virus sequence diversity, recombination participates in the evolution of enhanced pathogenicity, drug resistance, and vaccine escape. Using computational recombination-analysis tools developed at the IDM, his group are searching for recombination hot- and cold-spots within the genomes of all currently described virus families that have sufficient representation in public sequence databases. Using a range of bioinformatic approaches and a novel in vivo recombinant generation and evaluation system we are experimentally testing the hypothesis that obligatory maintenance of the delicate network of intra-genomic interactions that define the biology of virus species, severely limits the types of recombination events that are tolerable in nature. By demarcating the sub-genome modules that are and are not tolerably exchanged between viruses, recombination hot and cold spot maps should be applicable to the rational design of "recombination resistant" vaccines and drugs against viruses such as HIV and Hepatitis C. Such maps should also be applicable to the identification of genome regions that interact with one another.

Contact darrenpatrickmartin@gmail.com if you are interested in customised image analysis software for automated analysis of disease symptoms on plant leaves.

 


Selected publications:

RDP4: Detection and analysis of recombination patterns in virus genomes. DP Martin, B Murrell, M Golden, A Khoosal, B Muhire. Virus Evolution 1 (1), vev003.

Functionally conserved architecture of hepatitis C virus RNA genomes. Mauger DM, Golden M, Yamane D, Williford S, Lemon SM, Martin DP, Weeks KM. Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):3692-7. doi: 10.1073/pnas.1416266112.

Gene-wide identification of episodic selection. Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. Mol Biol Evol. 2015 May;32(5):1365-71. doi: 10.1093/molbev/msv035.

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. Muhire BM, Varsani A, Martin DP. PLoS One. 2014 Sep 26;9(9):e108277. doi: 10.1371/journal.pone.0108277.

High degree of HIV-1 group M genetic diversity within circulating recombinant forms: insight into the early events of HIV-1M evolution. Tongo M, Dorfman JR, Martin DP. J Virol. 2015 Dec 9. pii: JVI.02302-15.

 

The latest publications for Darren can be accessed via Google Scholar citation tracker: http://scholar.google.co.za/citations?user=9OSs25cAAAAJ&hl=en

 


Contact details:

Division of Computational Biology
Room N1.05 Werner Beit North Building
Institute of Infectious Disease and Molecular Medicine
UCT Faculty of Health Sciences
Anzio Road, Observatory 7925
South Africa

Tel:  +27 (83) 2700027

email: darrenpatrickmartin@gmail.com

Alternate site:  www.cbio.uct.ac.za

 


Collaborations:

Pierre Lefeuvre, CIRAD, Reunion

Jean Michel Lett CIRAD, Reunion

Philippe Lemey, University of Leuven, Belgium

Philippe Roumagnac, CIRAD Montpellier, France

Rob Briddon, NIBGE, Pakistan

Alice Nagata EMBRAPA, Brazil

Sunday Oluwafemi, Bowen University, Nigeria

David Posada, University of Vigo, Spain

Ed Rybicki, University of Cape Town, South Africa

Dionne Shepherd, University of Cape Town, South Africa

Arvind Varsani, University of Christchurch, New Zealand

Carolyn Williamson, University of Cape Town, South Africa