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Prof. Benjamin Kumwenda

Prof. Benjamin Kumwenda is an Associate Professor of Bioinformatics & Computational Biology at the Kamuzu University of Health Sciences in Malawi. He is the research lead for Bioinformatics and Computational Biology at the University. His research interests are in comparative genomics, bacterial pathogenesis, transcriptomics, next generation sequencing (NGS) and protein modelling. He works on the pathogenesis of Salmonella to understand drug resistance mechanisms using NGS, transcriptomics and protein modelling techniques. He has worked extensively on the Next Generation Sequencing of viral genomes particularly Rotavirus and SARS-CoV-2.

Benjamin Kumwenda holds a BSc Degree in Computer Science from University of Malawi, Chancellor College; a Postgraduate Diploma, Honors and an MSc Degree in Computer Science from the University of the Witwatersrand, Johannesburg, South Africa. He obtained a PhD in Bioinformatics from the University of Pretoria, South Africa in April 2014. He has done Postdoctoral Research Fellowships with the Malawi-Liverpool Wellcome Trust under the H3Africa Bioinformatics Network (H3BioNet). In 2016 he was awarded the prestigious MRC African Research Excellence Fund (AREF) Postdoctoral Fellowship. He is also an awardee of the RISE Graduate Competitive Fund. In 2018, he was awarded the three-years AESA-RISE Postdoctoral Fellowship.

Dr. Kwe Claude Yinda

Dr. Yinda has a Bachelors and Masters degree in Biochemistry from the University of Buea, Cameroon. He obtained his PhD in Viral Metagenomics from the Katholieke Universiteit Leuven, Belgium. Currently, he is a Research Fellow at the Virus Ecology Section of the Rocky Mountains Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health. He uses metagenomics and bioinformatics approaches to identify novel infectious diseases agents, and evaluation of the cross-species transmission, pathogenesis, and outbreak potential of newly identified infectious agents. Over the years Dr. Yinda has developed expertise in next generation sequencing (NGS) and quantitative virome analysis, which have earned him over 45 peer reviewed papers in highly ranked journals such as Nature, Nature Communications, eLife, PLoS Pathogens, and Emerging Infectious Diseases.

Dr. San Emmanuel James

Dr. San is a bioinformatician, molecular biologist and data scientist with specialist expertise in genomics, phylogenetics, statistical genetics and software development. He is currently a postdoctoral researcher at the University of KwaZulu Natal, Durban, South Africa at the KwaZulu Natal Research and Innovation Sequencing Platform (KRISP). He holds a PhD in Medicine and research experience in infectious diseases with a strong track record of combining molecular epidemiology with statistical analysis of pathogen genomic variation and the development of bioinformatics software. He is a member of several professional research bodies and collaborations including the Network for Genomic Surveillance in South Africa (NGS-SA), The Public Health Alliance for Genomic for Genomic Epidemiology (PHA4GE), Africa COVID-19 Genomics consortium, Climate Amplified Diseases and Epidemics (CLIMADE) consortium, Africa Centers for Disease Control and Prevention (CDC) Pathogen Genome Initiative (PGI) Vaccine Preventable Diseases Focus Group (VPD FG), Phylogenetic Analysis for Generalized Epidemics in Africa (PANGEA_HIV) consortium and a fellow of the H3Africa Bioinformatics Network (H3ABionet). Dr. San has published over 40 manuscripts in high-ranking international journals (including Nature, Science, The Lancet, Lancet Infectious Diseases). His work has been cited over 7,000 times. He has an H-index of over 30. His current research interests include the use of phylogenetic models to understand the drivers of infection transmission of SARS-CoV-2, HIV, TB, Arboviruses and vaccine preventable diseases in Africa. He is also interested in the microbiome, transcriptomics and metagenomics to characterize niche viral and bacterial communities and to investigate their impact on host responses and response to treatment.

Dr. Stephanie van Wyk

Dr. Stephanie van Wyk is a research scientist with more than 12 years of research experience in bioinformatics, biochemistry, and genetics. She is based at Stellenbosch University and serves as a bioinformatics researcher at the Centre for Epidemic Response and Innovation (CERI). Here, she generates Next Generation Sequence (NGS) data to support pandemic mitigation, not only locally but across Africa. The work at CERI on molecular epidemiology remained a cornerstone to facilitate timely intervention responses during the COVID-19 pandemic.

She is equally experienced in laboratory and bioinformatic environments, but her true passion lies in comparative genomics. Throughout her postgraduate and postdoctoral career, she served as a supervisor, laboratory manager, and training officer, mentoring a range of audiences. She represents her institute on research committees and forums such as the Africa CDC, the NGS-BRICS consortium (NGS Brazil, Russia, India, China, South Africa) and NGS-South Africa. She is passionate about Python and has strong experience working in Linux environments.

During her years of working as a bioinformatic scientist, she has gained valuable experience in genome assembly, quality control, and working on the evolution of complex traits and phenotypes. A quote from one of her favourite evolutionary biologists John Taylor states: “Genetic variation is the stuff of evolution”. Indeed, investigating the evolutionary potential introduced by large- and small-scale genetic alterations has been the focus of her postgraduate studies that she completed at the Forestry and Agricultural Biotechnology Institute (FABI), at the University of Pretoria. Here, she worked on the magical world of fungal genetics investigating the gain and losses of entire chromosomes, adaptations that resulted from horizontal gene transfer and the manner the accumulation of mutations can drive species divergence and alter host-pathogen interactions.

Prof. Errol Cason

Prof. Errol Duncan Cason is an Associate Professor in the Department of Animal Sciences at the University of the Free State, and his research is focused on quantitative animal breeding. Animal breeding encompasses various aspects of bioinformatics such as genomics studies, variant calling, genomic breeding values, genome wide association studies, among others. In addition, he has a broad background in microbial diversity in niche environments, or biomes and has incorporated this into his animal science research by investigating diversity shifts in rumen biomes due to various treatments. He has also an interest in heritability of rumen biomes and their correlation to production traits in animals. His research publications can be accessed here:

https://scholar.google.com/citations?user=V3fpZ3YAAAAJ&hl=en

His selected presented training include:

16S metagenomics data analysis in Qiime and R. Postgraduate course. University of the Free State (2018-Present).

Introduction to Bioinformatics (IBT). H3ABionet Course. University of the Free State (2019).

Dr. Celeste Donato

Dr. Celeste Donato holds joint Senior Research Fellow positions in the Enteric Diseases research group at the Murdoch Children’s Research Institute, and at the Australian Pathogen Genomics Program at The Peter Doherty Institute for Infection and Immunity. She is also an Honorary Fellow in the Department of Paediatrics at the University of Melbourne as well as an Adjunct Research Fellow and Lecturer in the Department of Microbiology at Monash University.

Dr. Donato is a virologist known for her expertise in rotavirus epidemiology and evolution. In addition to rotavirus, she has extensive experience in RSV, norovirus, enterovirus, astrovirus and influenza research.
Celeste completed her PhD in the Enteric Diseases Group at the Murdoch Children’s Research Institute and Department of Microbiology at La Trobe University in 2015. Her project focussed on the impact of rotavirus vaccine introduction on the diversity and evolution of rotavirus strains in Australia. She then completed a two-year postdoctoral position at Duke-NUS Medical School in Singapore, where she characterised outbreaks of viral infections in several countries within Southeast Asia. Celeste was awarded a prestigious NHMRC Peter Doherty Biomedical Fellowship and joined the Laboratory of Virus Evolution in the Department of Microbiology at Monash University in late 2016. In 2019 Celeste re-joined the Enteric Diseases Group the Murdoch Children’s Research Institute as a Senior Research Officer. She currently leads the genomic characterisation of rotavirus strains within the Australian Rotavirus Surveillance Program and the microbiome and virome exploratory studies within the RV3-BB vaccine clinical trial.

Dr. Donato has extensive laboratory expertise in rotavirus genotyping, full genome sequencing, and NGS methodologies. Dr. Donato is an expert in generation and curation of large genomic datasets, in particular alignments of large, complex genomes of viruses that undergo genomic recombination. She is also an expert in generating and interpreting phylogenetics trees using a variety of programs and Bayesian methods for evolutionary analysis.

Please find a link to the program below:

Workshop Trainers

Prof. Benjamin Kumwenda

Dr. Kwe Claude
Yinda

Dr. San Emmanuel James

Dr. Stephanie van
Wyk

Prof. Errol
Cason

Dr. Celeste
Donato

Prof. Benjamin Kumwenda

Dr. Kwe Claude Yinda

Dr. San Emmanuel James

Dr. Stephanie van Wyk

Prof. Errol Cason

Dr. Celeste Donato

Please find a link to the program below:

Workshop Trainers

Prof. Benjamin Kumwenda

Dr. Kwe ClaudeYinda

Dr. San Emmanuel James

Dr. Stephanie vanWyk

Prof. ErrolCason

Dr. CelesteDonato

Prof. Benjamin Kumwenda

Dr. Kwe Claude Yinda

Dr. San Emmanuel James

Dr. Stephanie van Wyk

Prof. Errol Cason

Dr. Celeste Donato

Dr. Kwe Claude
Yinda

Dr. Stephanie van
Wyk

Prof. Errol
Cason

Dr. Celeste
Donato