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 Prof. Alan Christoffels

Position: Director of SANBI
Department: South African National Bioinformatics Institute (SANBI)
Faculty: Faculty of Natural Science
Qualifications: BSc (Microbiology, Biochemistry) UCT, BSc Hons (Pharmacology) UCT, MedMSc (Genetics) Stellenbosh University, PhD (Bioinformatics) UWC
Tel: 021 959 2969
Fax: 021 959 2512
Email: alan@sanbi.ac.za
Research:
 
 
 
 

Biography

 Alan Christoffels hold a Ph.D. in bioinformatics from the University of the Western Cape, South Africa. Subsequently, completed a 3-year postdoctoral study in Singapore in the laboratory of the Dr Byrappa Venkatesh and Novel Laureate Dr Sydney Brenner and then established a research lab at Temasek LifeSciences Laboratories (TLL) in Singapore, for 3 years before returning to South Africa. He is the director of the South African National Bioinformatics Institute and director of the Medical Research Council Bioinformatics Capacity Development Research Unit. In 2009 he received the Department of Science and Technology/National Research Foundation Research Chair in Bioinformatics and Public Health Genomics. . As of 2009 I have coordinatored genomics trainin 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.
My bioinformatics laboratory studies host-pathogen interactions with a view to understand the regulatory networks that control immune responses to pathogen challenge. Machine learning approaches are being implemented in an attempt to identify novel protein-protein interactions that can be tested experimentally. These studies are complemented by next generation sequencing data that allows us to get a glimpse of the host and pathogenic genes that are triggered during an infection. In this regard, we have been developing methods to analyze this rich source of genomic and transcriptomic data.

Publications

  • Ruben Cloete, Ekow Oppon, Marc Marti-Renom, Edwin Murungi, Wolf-Dieter Shubert and Alan Christoffels. Novel drug target selection strategies and in silico 3-D structure prediction of two potential drug targets in Mycobacterium tuberculosis. In prep.

  • Murungi, E., Adunga, V., Amanda J. O’Reilly, A.J., Field, M.C., and Christoffels, A. Phylogenetic analysis of Trypanosoma brucei SNAREs and sub-cellular localization of a Golgi complex member In prep

  • Musa Nur Gabere, Alan Christoffels, William Stafford Noble, Mushal Allam, Ashley Pretorius, Saleem Adam, Vijayaraghava Sundararajan, Minna Lehvaslaiho and Vladimir Bajic. Prediction of antimicrobial peptides using optimization of support vector machines. Submitted 

  • Adam Dawe, Aleksandar Radovanovic, Mandeep Kaur, Sunil Sagar, Sundarararajan Seshadri, Ulf Schaefer, Allan Kamau, Alan Christoffels and Vladimir Bajic (2012) DESTAF: A Database of Text-Mined Associations for Reproductive Toxins Potentially Affecting Human Fertility. Reproductive Toxicology 33 (2012) 99– 105.

  • Vijayaraghava Sundararajan, Musa Nur Gabere, Ashley Pretorius, Saleem Adam, Alan Christoffels, Minna Lehvaslaiho and Vladimir Bajic (2012). DAMPD: A manually curated antimicrobial peptide database. Nucleic Acids Research. 40(Database issue): D1108-12 

  • Samuel Kwofie, Ulf Schaefer, Vijayaraghava Sundararajan, Vladimir Bajic, Alan Christoffels (2011). HCVpro: Hepatitis C virus protein interaction database (2011). Infection, Genetics and Evolution. 11:1971-1977

  • Samuel K Kwofie, Aleksandar Radovanovic, Vijayaraghava S Sundararajan, Monique Maqungo, Alan Christoffels and Vladimir B Bajic (2011). Dragon Exploratory System on Hepatitis C Virus (DESHCV). Infection, Genetics and Evolution. 11(4):734-9

  • Sarah Mwangi, Edwin Murungi, Mario Jonas and Alan Christoffels (2011) Evolutionary Genomics of Glossina morsitans immune-related Serine proteases and Serine Protease inhibitors. Infection, Genetics and Evolution. 11: 740-745.

  • Vladimir Shulaev, Daniel J Sargent, Ross N Crowhurst, Todd C Mockler, Otto Folkerts, Arthur L Delcher, Pankaj Jaiswal, Keithanne Mockaotis, Aaron Liston, Shrinivasrao P Mane, Paul Burns, Thomas M Davis, Janet P Slovin, Nahla Bassil, Roger P Hellens, Clive Evans, Tim Harkins, Chinnappa Kodira, Brian Desany, Oswald R Crastam Roderick V Jensen, Andrew C Allan, Todd P Michael, Joao Carlos Setubal, Jean-Marc Celton, D Jasper G Rees, Kelly P Williams, Sarah H Holt, Juan Jairo Ruiz Rojas, Mithu Chatterjee, Bo Liu, Herman Silva, Lee Meisel, Avital Adato, Sergei A Filichkin, Michela Troggio, Roberto Viola, Tia-Lynn Ashman, Hao Wang, Palitha Dharmawardhana, Justin Elser, Rajani Raja, Henry D Priet, Douglas W Bruant Jr, Samuel E Fox, Scott A Givan, Larry J Wilhelm, Sushma Naithani, Alan Christoffels et al (2011) The genome of woodland strawberry (Fragaria vesca). Nature Genetics. 43: 109-116. Doi:10.1038/ng.740

  • Jean-Marc Celton, Alan Christoffels, Daniel J Sargent, Xiangming X and David J.G Rees (2010) Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map. BMC Biology. 8:155-8

  • Monique Maqungo; Mandeep Kaur; Samuel K. Kwofie; Aleksandar Radovanovic; Ulf Schaefer; Sebastian Schmeier; Ekow Oppon; Alan Christoffels; Vladimir B. Bajic (2011)
 DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Research 39: D980-D985; doi: 10.1093/nar/gkq849.

  • Shu-Ye Jiang, Alan Christoffels, Rengasamy Ramamoorthy and Srinivasan Ramachandran

  • Expansion mechanisms and functional annotations of hypothetical genes in the rice genome (2009). Plant Physiology. 150: 1997-2008.

  • Magbubah Essack, Aleksandar Radovanovic, Ulf Schaefer, Sebastian Schmeier, Sundararajan V Seshadri, Alan Christoffels, Mandeep Kaur and Vladimir B Bajic (2009) DDEC: Dragon Database of Genes Implicated in Esophageal Cancer. BMC Cancer 9: 219-226. 

  • Sunil Sagar, Mandeep Kaur, Adam Dawe, Sundararajan V Seshadri, Alan Christoffels, Ulf Schaefer, Aleksandar Radovanovic and Vladimir B Bajic (2008). DDESC: Dragon Database for exploration of sodium channels in human. BMC Genomics 9: 622-9

  • Mandeep Kaur, Aleksandar Radovanovic, Magbubah Essack, Ulf Schaefer, Monique Maqungo, Tracey Kibler, Sebastian Schmeier, Alan Christoffels, Kothandaraman Narasimhan, Mahesh Choolani and Vladimir Bajic (2009). Database for exploration of functional context of genes implicated in ovarian cancer. Nucleic Acids Res. 37 (Database issue) D820-D823. Doi: 10.1093/nar/gkn593.

  • Rajini Sreenivasan, Minnie Cai, Richard Bartfai, Xingang Wang, Alan Christoffels and Laszlo Orban (2008). Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. PloSONE 3(3) e1791.


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Networks

 2012 - Web Project Steering Committee
2012 - Institute for Molecular Biology and Metagenomics Institute Management Board
2011 - HIV Research Centre Management Board
2012 Enterprise Architecture and Information Systems Committee
2012 - Intellectual Property Advisory Committee
2011 SASHMI Review Panel
2011 Chairperson, Research Office Review Panel
2009 - 2012 Senate
2009-2012 Science Faculty Management Committee
2009-2011 Science Faculty Planning Committee
2009-2010 Science Faculty Postgraduate Committee
Science Faculty International Relations and Research Committee

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