Associate Professor Darren Martin

Computational Biology Group

Associate Professor Darren Martin PhD (Cape Town)

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. With a focus on combining computational and wet-lab experimental approaches Darren’s group tests hypothesis relating to genetic recombination, the evolution of genome-scale secondary structures and fitness trad-offs. For example, the group has shown that obligatory maintenance of the delicate network of co-evolved 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.

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.

Pervasive tertiary structure in the dengue virus RNA genome. Dethoff EA, Boerneke MA, Gokhale NS, Muhire BM, Martin DP, Sacco MT, McFadden MJ, Weinstein JB, Messer WB, Horner SM, Weeks KM. Proc Natl Acad Sci U S A. 2018 115(45):11513-11518.

Integrative landscape of dysregulated signaling pathways of clinically distinct pancreatic cancer subtypes. Sinkala M, Mulder N, Martin DP. 2018. Oncotarget 26;9(49):29123. (JIF 5,168).

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.

Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptation. Tongo M, de Oliveira T, Martin DP.  Virus Evolution 2018 11;4(1):vey015.

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

Alternate site:


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