Scott Hazelhurst home page

Scott Hazelhurst

BScHons MSc (Wits) PhD (British Columbia)
Professor of Bioinformatics in the School of Electrical and Information Engineering;
Senior Scientist, Sydney Brenner Institute for Molecular Bioscience

E-mail: Scott.Hazelhurst@wits.ac.za

School of Electrical and Information Engineering
University of the Witwatersrand, Johannesburg
Private Bag 3, 2050 Wits, South Africa
Tel: +27 11 717-6181

Research

Much of my research is collaborative. My areas of interest are:

algorithms, and data structures, particularly parallelism..

I am PI of the MADIVA Research Hub The Multimorbidity in Africa Digital Innovation, Visualisation and Application Research Hub is a research hub of the Data Science Innovation for Health in Africa Initiative of the US National Institutes of Health/Fogarty, Grant U54TW012077. .
Bioinformatics
- Tool and algorithm development
- I have an interest in GWAS and population structure
- I am the PI for the Wits node of H3A Bionet
- A collaborator on the H3A AWI-Gen project exploring genetic and environmental risk factors for cardio-metabolic disorders in African populations. I am coordinating a pilot microbiome project for AWI-Gen.
In past lives, I was interested in formal methods, Fault-tolerant and distributed systems, and network firewalls . I still have an interest in network and am supervising an MSc student exploring software defined networks for large-scale transfer of data for science.
Formal methods, verification and concurrency -- in particular symbolic trajectory evaluation.

Possible research topics

I am currently not able to supervise more students in the 2026 year.

Publications

References of scientific papers can be found here.

My group and students

Current postdocs: Dr Kayode Adetunji, Luicer Olubayo
Current PhDstudents:
- Aaron Berkman, Division of Human Genetics, cosupervised with Dr Luicer Olubayo
- Daniel Maina, School of Public Health. (PhD topic: Privacy preserving linkages), cosupervsied with Dr Chodziwadziwa Kabudula.
- Phophi Mmbi, Division of Human Genetics, cosupervised with Drs Carl Chen and Phelelani Mpangase.
- Yumna Dadi Patel, Division of Human Genetics, cosupervised with Dr Zané Lombard.
- Yonatan Wolberg, Division of Human Genetics, cosupervised with Dr Zane Lombard

Those in the group not too shy to be photographed
Shaun Aron, H3ABioNet Bioinformatics Consultant	Phelelani Mpangase Bioinformaticist	Dr Ovokeraye Oduaran Postdoctoral Fellow	Dr Houcemeddine Othman Postdoctoral Fellow
David Twesigomwe PhD student	Jorge da Rocha PhD student	Laura Cottino PhD student	Wits ADME collaboration

Past members

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. Claudine Nkera-Gutabara, Daniel Ohene-Kwofie

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. Carl Belger, (MSc topic: Lion microbiome profile), cosupervised with Professor Robyn Hetem

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 ftp.
- 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/

Other...

Some LaTeX sources
Archival material from the 1980s at Wits
Cities I have lived: Johannesburg , Vancouver, Toulouse.
University of the Witwatersrand, Johannesburg
University of British Columbia
Computer Science, ISD Lab)
Green College soc.culture.african FAQ and soc.culture.african FAQ
Varsity Kudus Running Club
Lenn Smith race
Very out of date: soc.culture.south-africa FAQ, soc.culture.south-africa FAQ