References of scientific papers can be found here.
My group and students
- Current postdocs: Dr Ovokeraye Oduaran, Dr Houcemeddine Othman
- Current Postgrad students:
- Claudine Nkera-Gutabara, Division of Human Genetics (PhD topic: Snapshot of the gut microbial diversity of an urban South African population: Impact of diet, lifestyle and socioeconomic status), cosupervised with Drs Robyn Kerr and Jerolen Naidoo.
- Daniel Maina, School of Public Health. (PhD topic: Privacy preserving linkages), cosupervsied with Professor Chodziwadziwa Kabudula.
- Carl Belger, School of Animal, Plant and Environmental Sciences. (MSc topic: Lion microbiome profile), cosupervised with Professor Robyn Hetem
|Those in the group not too shy to be photographed|
Dr Ovokeraye Oduaran
Dr Houcemeddine Othman
Jorge da Rocha
Wits ADME collaboration
Past PhD students: Nechama Brodie (Using mixed-method approaches to provide new insight into media coverage of femicide); Phelelani Mpangase (Bioinformatic analyses of transcriptome
and genetic variation in black South Africans with systemic sclerosis); Andrew Ndhlovu (Comparative metagenomics of a harmful algal
bloom); Laura Cottino (A systematic assessment of the Copy Number Variation (CNV) landscape in ADME genes in Sub-Saharan African populations), cosupervised with Dr Venesa Sahibdeen; David Twesigomwe (Characterisation of CYP2D6 pharmacogenomic variation in African populations: an integrative bioinformatics approach), cosupervised with Professor Zane Lombard. Emma Wiener cosupervised with Professor Zane Lombard. Liron Pantanowitz, Digital Pathology and Artificial Intelligence: Feasibility for Clinical Practice), cosupervised with Professor Pamela Michelow. Jorge da Rocha Characterisation of key ADME gene variants in African populations through functional annotation and structural bioinformatics approache, cosupervised with Michele Ramsay and and Houcemeddine Othman.
Past MSc Students: Craig Faasen (Implementing tuple space on transputer meshes); Vashti Galpin (Equivalence semantics for concurrency : comparison and application); Philip Green (Partially ordered logical clocks for monitoring concurrent programs); Shane Morton (Software verification with symbolic trajectory evaluation); Gloria Aikhorin (Using FPGAs for the comparison of protein sequences); Ndellie Mwanangulu-Massey (An extensible architecture for a Java electronic purse system); Raymond Sinnappan (A reconfigurable approach to TCP/IP packet filtering); Adi Attar (Performance characteristics of BDD-based packet filters); Robin Phillips (Digital signatures -- a legal alternative to handwritten signatures); Pravesh Ranchod (Parallelisation of EST clustering); Seare Araya (Support vector machine prediction of HIV-1 drug resistance using the viral nucleotide patterns); Benjamin Kumwenda (A tree-structured index algorithm for expressed sequence tags clustering); Dane Kennedy (Using Manhattan distance and standard deviation for expressed sequence tag clustering); Charl van Deventer (Expressed sequence tag clustering using commercial gaming hardware); Simeon Miteff (An SDN-based firewall shunt for data-intensive science applications); Edward
Steere (Massive parallelism for combinatorial problems by hardware acceleration with an application to the label switching problem); Delia Kench (Evaluating the development and effectiveness of grit and growth mindset among high school students in a computer programming project ), Joshua Selvan (GPU-based algorithms for PDB structure searching), Blessing Sitabule (Structural Bioinformatics Analysis of CYP2D6 Pharmacogenetic Variation Relevant to Sub-Saharan African Populations) cosupervised with Dr Houcemeddine Othman, Yaniv Swiel, (FPGA acceleration of GWAS permutation testing), cosupervised with Dr Mitchell Cox. Irma Maré, (Support strategies for the adoption of electronic data capture systems for biomedical research and clinical service deliver records in a heterogeneous, research intensive organization in resource constrained environments), cosupervised with Dr Mike Klipin.
Samantha Schnell, (Exploring the Interaction of Host Genetics and the Gut Microbiome in Obesity), cosupervised with Dr Ovokeraye Oduaran. Ross Booyse, (Characterisation of variation in the CYP2C gene cluster in African populations), cosupervised with David Twesigomwe.
Past honours students and fourth-year projects: students: Gavin Sinai, Keitu
Motlhaga, Michael Berry, Jin Wang, Nitesh
Vallabh, Rogers Sithole, Kirsten Leong, Marko Divac, Anton
Fatti, Andrew Henwood, Saul Tombuk, Christian Gotschi, George
Christelis, Josh Adler, Mpiti Matsoso, Charmaine Venter, John
Deneys, Asher Lipson, Moshe Waisberg, Sefako Tholo, Sibongile Eland, Burcak
Birinci, Greg Kempe, Sascha Mohr, Sam Hutchinson, Opeyemi
Ono, Yatin Narsai, Anastasia Soseilos, Craig Sizer, Tal Even-Tov, Jarryd Chengalroyen, Stuart
Venter, Victor Neiman, Louis du Plessis, Yestin Johnson, Yair Mark,
Melissa Wu, Sonali Parboo, Kershia Perumal, Mokgadi Rasekgala,
Lazarus Baloyi, Mcebisi Mdlozini, Jan-Willem Steeb, Catherine Pavard, Sasha
Naidoo, Rob Clucas, Tapiwa Chimana, Noel Moyo, James Allingham, Paul Cresswell, Tyron Amoretti,
Matthew Bezuidenhout, Joseph Gage, Julian Zeegers, Gary Bezuidenhout,
Evan Rubin, Kashann Wright, David Golach, Ross Pearse, Tshembani Mbuyi, Robin Joncker, Tristan Lilford, Gia Croock, Rael Ware.
Some interesting links
- The Pan African Bioinformatics Network for H3Africa GWAS Pipline
- Some scripts for helping use the eigenstrat, admixture, CLUMPP and distruct tools.
- Our Genesis
tool for displaying PCA and admixture charts.
- You can download wcd
EST Clustering system. This is an open source software package for clustering
expressed sequence tags. This tool is free for download. The latest
version is here.
- The ESTSim package, a package for generating simulated ESTs, has been
moved and can be found here here.
- The Voss System is a hardware verification system including an
efficient implementation of BDDs, a lazy functional language and
an accurate simulator.
- The Voss manual: Carl Seger. Voss --- A Formal Hardware
Verification System User's Guide,
Technical Report 93-45, Department of Computer Science,
University of British Columbia,
Available by anonymous
- Some introductory
tutorial (a gzipped, tarred directory including some PostScript
files and some programs)
- Update 2021! New version available from @cjhseger https://github.com/TeamVoss/
Varsity Kudus Running Club
Lenn Smith race
Very out of date: