Alan Christoffels is a bioinformatics scientist, academic, and an author. He is Professor of Bioinformatics, and the director of the South African National Bioinformatics Institute at the University of the Western Cape. He has been serving as a senior advisor to the Africa Centres for Disease Control and Prevention Pathogen genomics & Partnerships and DSI/NRF Research Chair in Bioinformatics and Public Health Genomics.
Christoffels’ primary contributions and research work are in the areas of host-pathogen interaction, genome evolution, pathogen genomics, and biobank LIMS.
Christoffels is a founding member of Global Emerging Pathogens Consortium, elected member of the Academy of Science of South Africa, and President of the African Society for Bioinformatics and Computational Biology from 2020 until 2022. He was elected as a fellow of the Royal Society of South Africa in 2022.
Education
Christoffels graduated with BSc. in Microbiology and Biochemistry in 1992 and BSc (Hons.) in Pharmacology from the University of Cape Town in 1993. Between 1995 and 1997, he enrolled at the Stellenbosch University for a MSc. in Genetics. His research centered upon identification of novel markers in the fine mapping of a locally prevalent cardiac disease (PFHB1). He proceeded with a Ph.D. in bioinformatics at the South African National Bioinformatics Institute University of the Western Cape. His thesis was titled, "Generation of a human gene index and its application to disease candidacy".
Career
Christoffels started his academic career in 1994 as a Genetics Technician in medical Biochemistry at the Stellenbosch University. Between 2001 and 2004, he held the postdoctoral fellowship at the Institute of Molecular & Cell Biology in Singapore. Followed by this appointment, he served as an Adjunct Assistant Professor at the Nanyang Technological University based in Singapore. Later on, he held the appointment of associate professor from 2007 to 2012 in the South African National Bioinformatics Institute at the University of the Western Cape. He was promoted to the position of Professor in 2013 and currently holds this appointment.
From 2009, Christoffels serves as the Director of South African National Bioinformatics Institute at the University of the Western Cape. For the next five years, he served on the board of directors for International Society for Computational Biology (ISCB). He has been holding the appointment of SA Medical Research Council Unit Director at the Bioinformatics Capacity Development Unit since 2012. Later on, he held a brief appointment as vice president for the South African Society for Bioinformatics. He was appointed as President of African Society of Bioinformatics & Computational Biology in 2020 for a two-year term.
Followed by stakeholder meeting convened by Bill & Melinda Gates Foundation, Christoffels and his international partners launched a global initiative called Public Health Alliance for Genomic Epidemiology in October 2019 at the GrandChallenges meeting in Ethiopia. He serves as the principal investigator of this initiative. The research prototypes generated in the lab are integrated into the working groups within the alliance.
Research
Christoffels has more than 400 publications under his name. His research spans host-pathogen interaction, pathogen genomics, genome evolution with a particular focus on the genome annotation and sequence data analysis.
Public health bioinformatics
Christoffels and a team of scientists at his lab based in South African National Bioinformatics Institute presented the first genome sequence of SARS-CoV-2, the virus that causes COVID-19, found in South Africa. His recent work features conducting research on scaling up disease surveillance systems on the African continent.
Christoffels has developed technologies for application of bioinformatics in public health. He has developed an analysis platform for Tuberculosis sequencing data called COMBAT-TB. This tool can be deployed in resource limited settings.
Biobank LIMS
With a group of researchers, Christoffels developed a management system for biobanking, Laboratory Information Management System (LIMS) at the South African National Bioinformatics Institute. The purpose of the management system is to collect, store, process and, manage the bio samples appropriately. This human biobanking system is based upon the Plone web-content management framework.