H3ABioNet

Pan African Bioinformatics Network for H3Africa

The University of Witwatersrand (Wits)

The Wits H3ABioNet node is based in the Wits Bioinformatics department, which is a joint project of the Faculties of Health Science and Science, and a division of the Sydney Brenner Institute for Molecular Bioscience. Currently, Wits Bioinformatics has four staff members, three postdoctoral fellows and several postgraduate students, but they work closely with several other staff at Wits. The Wits node is very active in H3ABioNet and other H3Africa projects. This node is involved in training and is part of several H3ABioNet and H3Africa working groups. In addition, this node will be actively involved in the bioinformatics analysis of the H3A AWIGEN project. Outside of H3A the node members teach, research and provide bioinformatics services.

This node is improving its expertise in genome wide association studies, population structure and computing. For more information visit: http://www.bioinf.wits.ac.za


Members


Associate Professor Scott Hazelhurst

 scott website

Principal Investigator: Scott is an Associate Professor in the School of Electrical and Information Engineering at Wits and has been an active member of Wits Bioinformatics since it was set up in 2004. His research interests are algorithms, high performance computing and bioinformatics. He is co-chair of the Bionet Infrastructure Working Group. Besides involvement in Bionet, he is also an active collaborator on the H3Africa AWIGEN Project. Scott completed his MSc at Wits and his PhD at the University of British Columbia.


 Dr Zane Lombard 

 zane website

Senior Lecturer: Zané joined the Wits Bioinformatics staff in 2012 as a Lecturer, but was priorly associated with Wits Bioinformatics as a student when she enrolled for a PhD in Bioinformatics/Human Genetics in 2004. She completed her PhD in 2008 on the topic of Computational Prediction of Gene Targets for Fetal Alcohol Spectrum Disorders. Subsequently she spent 4 years working as a Medical Scientist/Researcher at the Division of Human Genetics (NHLS & Wits University) where she was lab manager of the Genotyping Facility and Biorepository. Her current research focus is on genetic epidemiology, specifically genome-wide association studies of complex traits, and computational epigenetics. She is co-chair of the H3A Genome Analysis working group and a collaborator on the H3Africa AWI-GEN project. 


Dr Liam Thompson

Part-time developer: Liam is a molecular biologist by training with an active interest in computing, electronics and open source solutions. After graduating with a PhD in 2012, he interned at the Joburg Centre for Software Engineering where he got his first taste of C#. Since March 2013, he has been working part-time with Wits Bioinformatics to develop a data storage system for Wits researchers involved in the H3Africa project. This project aims to make resources available at the South African Grid easier to access for researchers. His interests involve open source hardware and software, the Maker movement and very strong coffee.


Dr Nadia Carstens  

Postdoctoral Fellow: Nadia Carstens joined Wits Bioinformatics in June 2012 as a postdoctoral fellow in the NIH/Fogarty Non-communicable Disease Leadership Program. She obtained her PhD in Human Genetics from Stellenbosch University in 2012 on the topic of the complex hypertrophic phenotype of hypertrophic cardiomyopathy, a Mendelian disorder where a multitude of modifiers work together to shape the eventual disease phenotype. She is currently interested in the use of next-generation sequencing (NGS) technology to generate novel molecular insights into non-communicable diseases that are prevalent among African populations. Two of her current projects are on the use of NGS data to identify the cause(s) of rare Mendelian eye diseases in South African families. She represents AWI-Gen on the H3Africa Biorepository Users working group as well as a writing subgroup within the working group, which is aimed at developing policies and guidelines to govern H3Africa Biorepositories.


Dr Ananyo Choudhury 

Post-doctoral Fellow: Ananyo Choudhury joined Wits Bioinformatics as a Postdoctoral Fellow in December 2010 (funded by the University of Witwatersrand, SPARC Fellowship and NRF Postdoctoral Research Fellowship programs) after obtaining his PhD from the University of Calcutta, Kolkata, India. His doctoral research work involved computational analysis of genome wide transcription regulation by Abscisic acid (ABA) -a key phytohormone. He conceptualized, designed and implemented a database for storage and analysis of ABA signaling related transcriptomic data and a web server for identification and evaluation of transcription regulatory networks using statistical and comparative genomic approaches. His postdoctoral research has been a collection of four different projects with the overarching theme of characterizing genetic variations in African populations and studying their association to different traits as well as to the incidence of different non communicable diseases in these populations. He has also been a visiting member of the African Genome Variation Project analyst group at Wellcome Trust Sanger Institute, Cambridge, UK, since Nov 2012.


Shaun Aron

Shaun website

Consultant/Trainer: Shaun Aron has been a member of Wits Bioinformatics since 2007 when he joined as an MSc student in Human Genetics/Bioinformatics. After completing an Honours degree in Human Genetics, he was intrigued by the computational approaches being developed to address complex biological questions and decided to hang up the pipette and pick up a computer instead. His MSc aimed to apply relevant bioinformatic techniques to characterise and identify the molecular cause for a rare genetic skin disorder called Keratolytic Winter Erythema. While completing his MSc he joined Wits Bioinformatics as an Associate Lecturer/Consultant in 2009 and has been involved in various teaching, training and consulting activities within the university. In 2013 he took up the position of H3ABioNet Bioinformatics Consultant/Trainer at the Wits Node of H3ABioNet. Shaun has a keen interest in the genetic basis of rare genetic disorders, population genetics and the practical application of bioinformatics for biologists. He is also actively involved in the education and training endeavours of the H3ABioNet and H3Africa AWIGEN project.


 Phelelani Mpangase

phelalani website

Lecturer: Phelelani Mpangase obtained his BSc in Biochemistry/Genetics and BSc Honours in Biochemistry at the University of Kwa-Zulu Natal. He then pursued a Masters degree in Bioinformatics at the University of Pretoria, where he worked on a project aimed at designing a web resource for integrating protein annotations in order to identify potential drug targets in malaria. After completing his Masters degree, he joined Wits Bioinformatics as a Bioinformatics consultant, working on projects involving protein structure and function. His main research interests are protein bioinformatics, drug target discovery, data-mining/database design and data curation. Apart from doing research, he is also involved in teaching an introductory Bioinformatics course to Molecular Biology and Human Genetics honours students. He is also responsible for giving Bioinformatics support, not only to the students, but to other researchers in the University community that require Bioinformatics support.