- Director & DST/NRF Research Chair in Bioinformatics and Health Genomics
- Telephone: +27-(0)21-9592969
- Fax: +27-(0)21-9592512
- Email: alan_at_sanbi ac za
- Skype: alan.christoffels
My bioinformatics laboratory focuses on host-pathogen interactions where we are developing high throughput genomics methods including next generation sequencing data analysis approaches to study communicable diseases such as tuberculosis, malaria and sleeping sickness [see database tools link below]. This work includes analyzing illumina and PacBio sequencing data for multiple Mycobacterial strains to answer questions about virulence and the application of machine learning tools to identify interaction networks.
During the past three years, we have expanded our methods in collaboration with the Agricultural Research Council of South Africa to analyze the first genome sequence for the fungal pathogen, Venturia inaequalis
Metazoan Genome Complexity
During 2004/5, we published the whole genome scale data for whole genome duplication specifically in teleosts (Christoffels et al., 2004, 2005) and the first HOX analysis for the Coelacanth. Recently my group was invited to be part of the consortium to analyze the Coelacanth genome assembly where focused on gene families that were expanded or duplicated specifically in the Coelacanth. This work was recently published (Amemiya et al., Nature 496: 311-316, 2013; Picone et al., J Exp Zool in press) and shows clear evidence that the chemoreceptors in Coelacanth represent a gene repertoire in transition.
Glossina Functional Genomics Network: As of 2009 I have coordinated genomics training on the African continent for the WHO-tropical disease research programme – the Glossina Functional Genomics Network (GFGN) as part of the International Glossina Genome Initiative.
Human, Heredity and Health in Africa: In 2010 I was elected to be part of an international working group developing policy guidelines for the National Institutes of Health “Human, Heredity and Health in Africa” Programme. In 2012, my group was funded to support the development of a Biobank for Africa at Tygerberg Medical School, Stellenbosch.
Southern African Human Genome Programme: The SAHGP was established in 2011 by the South African Genetics community. In March 2012, we were able to leverage funds from the Department of Science and Technology to initiate the sequencing of 25 Southern African human genomes. My group will be providing bioinformatics research support to the SAHGP.
Lab Members List
- Genomics, genome visualization, next generation sequencing methods