H3ABioNet

Pan African Bioinformatics Network for H3Africa

The Computational and Biology Group (CBIO)

The University of Cape Town (UCT) Computational Biology Group (CBIO)  (http://www.cbio.uct.ac.za/) is the centre of bioinformatics activities at the university.  It was originally set up as a Node of the National Bioinformatics Network, which aimed to develop capacity in bioinformatics in South Africa, and to perform world-class bioinformatics research. CBIO is located within the Institute for Infectious Disease and Molecular Medicine (IDM) in the Health Science Faculty, and integrates researchers interested in bioinformatics at the university. The group performs bioinformatics research and provides training and services in the discipline.

CBIO  has over 20 people and is headed by Professor (Prof) Nicola Mulder. CBIO consists of two senior academics, an administrator, five staff members, several Postdocs, PhD and Masters students. The academics teach bioinformatics  at the undergraduate and postgraduate levels and convene an Honours Programme in Bioinformatics. The technical staff members provide bioinformatics support to researchers at the university and other universities in the area, and the group provides short training courses in specialised topics.

Prof Mulder’s research focuses on infectious diseases from both the host and pathogen perspectives and she has a number of collaborations with researchers at UCT, the University of Stellenbosch, and with the Swiss Institute of Bioinformatics in Switzerland. Dr Darren Martin, a Senior Lecturer in the group does research on viral evolution, focusing on the development of computational tools for analysing genetic recombination, phylogeography, and the biological relevance of nucleic acid secondary structures.

The CBIO group is playing a leading role in H3ABioNet, the NIH funded Pan African Bioinformatics Network for Human Heredity and Health in Africa.

 

 Members


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Professor Nicola Mulder - Principal Investigator

Professor Mulder heads CBIO. She graduated with a BSc degree (cum laude) in Chemistry and Microbiology, and a first class Honours degree in Microbiology, followed by a PhD in Medical Microbiology. She then spent over 8 years at the European Bioinformatics Institute (EBI) in Cambridge, moving into the area of bioinformatics. At the EBI she was a Team Leader, responsible for the development of InterPro and the Gene Ontology Annotation Project. InterPro was one of the most heavily used Bioinformatics resources at the Institute. At UCT, Prof Mulder works in the area of bioinformatics of infectious diseases, including pathogen and host genomics and biological networks, human variation and disease association studies. She heads the CBIO group, which consists of over 20 staff and students. The group provides bioinformatics support and training for postgraduate students and local researchers, and Prof Mulder convenes an Honours programme in Bioinformatics, and organises a South African national bioinformatics training course for postgraduate students.

Internationally, she is involved in capacity development in Africa, as leader of a large NIH-funded consortium, H3ABioNet, to build a Pan-African Bioinformatics network for H3Africa, and through her position as President of the African Society for Bioinformatics and Computational Biology. Prof Mulder is also a member of the ELIXIR Scientific Advisory Board, which forms part of a major EU funded European initiative involving all the bioinformatics stakeholders in Europe and many others world-wide, and a founding member of the Global Organisation for Bioinformatics Learning, Education & Training (GOBLET). She is on the executive committee of the African Institute for Mathematical Sciences, as well as a number of review and advisory boards.


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Dr Darren Martin - Senior Lecturer

Dr. Darren obtained his PhD from the University of Cape Town in 2001. He is  a senior lecturer at CBIO and his research group consists of 2 MSc students, 2 PhD students, and 1 Post-Doctoral student. He is the lead developer of the computer program RDP4 that is widely used for analyzing genetic recombination and has been actively pursuing both computational and wet-lab based research aimed at defining the adaptive value of recombination and the evolutionary constraints under which it operates.


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Dr Sumir Panji - H3ABioNet Network Manager

Sumir obtained his PhD in Bioinformatics from the University of the Western Cape as part of the Stanford South Africa Biomedical Informatics (SSABMI) programme where he developed computational and analyses pipelines to determine the intersection between bacterial virulence and positive selection in Professor Winston Hide's laboratory. He completed his postdoctoral studies in Professor Alan Christoffels' laboratory at the South African National Bioinformatics Institute (SANBI) where his focus was on genome assembly, annotation, data mining, large scale statistical analysis of genomics data and development of various computational pipelines and analyses workflows for a myriad of genomics' data types. Dr Panji's main interests are in creating and implementing computational and analyses workflows, statistical analysis of biomedical data, biological algorithms, high performance computing and the overall application of bioinformatics and genomics methods to better understand complex biological systems. Sumir is currently a bioinformatician within the H3ABioNet consortium who is interested in genome science, data analysis workflows, statistical analyses of large 'omics datasets, implementation and interpretation of bioinformatics solutions to diverse biological problems and providing bioinformatics support to the H3Africa projects.


Ayton Meintjes - Software Developer

Ayton Meintjes is a Bioinformatics software engineer at CBIO. He completed a BSc in Computer Science at the University of Pretoria, and after a period of development in the commercial field, returned to do a BSc (Hons) with specialisation in Bioinformatics. In 2008, he joined the CBIO Group at UCT and has collaborated on projects mostly focusing on human population genetics and genome wide association studies. He is currently part of the H3ABioNet Central Node, taking active part in the Infrastructure, Research, Node Assessment and User Support groups. His current research interests are in visualisation of complex biological datasets, workflow integration and computational challenges posed by the large databases produced by modern sequencing technologies.


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Gerrit Botha - Software Developer

Gerrit Botha is a Bioinformatics engineer at CBIO. He received his bachelors degree in Computer Engineering from the University of Pretoria in 2004. From 2006 to 2008 he was part of the of the Human Language Technologies group at the Meraka Insititute (CSIR) where his research focused on natural language processing, speech synthesis and text-based language identification. In 2008 he completed his masters degree in Electronic Engineering and joined the Computational Biology group the same year. He is responsible for providing bioinformatics support and works on a variety of projects such as functional annotation pipelines, whole-genome and exome sequencing analysis and bacterial diversity studies.


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Suresh Maslamoney - System Administrator

Suresh Maslamoney is a techie at heart and has experience in system and network administration as well as in designing and developing ICT infrastructure. Suresh joined CBIO in February 2013 as a systems administrator and is tasked with developing and providing support on the core computational infrastructure for the CBIO and the H3ABioNet consortium. Prior to joining CBIO, Suresh spent 3 years in the UK working in various ICT posts before returning to RSA where he joined the South African Tuberculosis Vaccine Initiative (SATVI). At SATVI Suresh was responsible for managing the IT section and all ICT related technical matters.


 Cashifa Karrien - Administrator

 


  

 

Dr Vicky Nembaware- H3Africa/H3ABioNet Trainining Coordinator

Vicky is the training coordinator and a bioinformatician for the H3Africa and H3ABioNet consortiums. She is involved in several H3Africa working groups and is Chair of the Ontology Task Force. Vicky earned her PhD in Bioinformatics in 2008 from the University of Cape Town under the Supervision of Prof. Cathal Seoighe. In addition, she was also awarded an MPhil in Monitoring and Evaluation in 2012. She has experience in Bioinformatics and in the Public Health field in designing, monitoring and evaluating of programs/research studies particularly in the Information Communication Technologies field. Her broadbase of training and experience is reflected in a her research interests which include creating standards in the genomics and bioinformatics field and in using next generation sequencing technologies to advance translational research in Africa. She is passionate about training and mentoring the next generation of African scientists.