Home » People » Faculty » Alan Christoffels

Alan Christoffels

Alan Christoffels

  • Role: DST/NRF Research Chair in Bioinformatics and Health Genomics
  • Contact Details
    • Telephone: +27-(0)21-9592969
    • Fax: +27-(0)21-9592512
    • Email: alan_at_sanbi ac za
    • Skype: alan.christoffels
  • Research Areas
    • Microbial Comparative Genomics
    • Genome Annotation and Evolution
    • Web-based Bioinformatics support services
    • Analysis of high-throughput sequencing data
  • Current Projects
    Lab Members
    • MSc students
      • Wisdom Akurugu
      • Oreetseng Moncho
      • Mmakamohelo Direko
      • James Mathews (co-supervision)
    • PhD Students
      • Ibrahim Ahmed
      • Mushal Allam
      • Ruben Cloete
      • Zahra Jalali
      • Mbandi Kimbung
      • Sarah Mwangi
      • Edwin Murungi
      • Alecia Naidu
      • Kavisha Ramdayal (co-supervision)
      • Adugna Woldesemayat
      • Mahjoubeh Jalali (co-supervision)
    • Post Doctoral Fellows
      • Uljana Hesse
      • Monique Maqungo
      • Samson Muyanga
      • Sumir Panji
      • Barbara Picone
    • Alumni
      • Musa Nur Gabere (PhD)
      • Samuel Kwofie (PhD)
      • Sarah Mwangi (MSc)
      • Feziwe Mpondo (MSc)
      • Ashley Pretorius (Post-Doc)
      • Mark Wamalwa (PhD)

Publications: Journals, Book Chapters, Conference Proceedings

  1. Samuel Kwofie, Ulf Schaefer, Vijayaraghava Sundararajan, Vladimir Bajic, Alan Christoffels. HCVpro: Hepatitis C virus protein interaction database (2011). Infection, Genetics and Evolution. Accepted.
  2. Samuel K Kwofie, Aleksandar Radovanovic, Vijayaraghava S Sundararajan, Monique Maqungo, Alan Christoffels and Vladimir B Bajic. Hepatitis C Virus discovery database (HCVdd): Dragon Exploratory System on Hepatitis C Virus (DESHCV) 2010. Journal, Genetics and Evolution.  Accepted.
  3. Sarah Mwangi, Edwin Murungi, Mario Jonas and Alan Christoffels (2010) Evolutionary Genomics of Glossina morsitans immune-related Serine proteases and Serine Protease inhibitors. Infection, Genetics and Evolution. Accepted.
  4. 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 (2010) The genome of woodland strawberry (Fragaria vesca). Nature Genetics accepted. Doi:10.1038/ng.740
  5. 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
  6. Monique Maqungo; Mandeep Kaur; Samuel K. Kwofie; Aleksandar Radovanovic; Ulf Schaefer; Sebastian Schmeier; Ekow Oppon; Alan Christoffels; Vladimir B. Bajic (2010)
 DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Research; doi: 10.1093/nar/gkq849.
  7. 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.
  8. 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.
  9. 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
  10. 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.
  11. 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.
  12. V Bajic, S Tan, A Christoffels, C Schombach, L Lipovich, L Yang, O Hofmann, A Kruger, W Hide and C Kai (2006). Mice and Man: Their promoter properties. PLOS Genetics. 2(4) e54. 18 citations
  13. A Christoffels, Sydney Brenner and Byrappa Venkatesh (2006). Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish lineage. Comparative Biochemistry and Physiology Part D. 13-19. 5 citations
  14. The FANTOM Consortium, P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels et al. (2005). The Transcriptional Landscape of the Mammalian Genome. Science 309:1559-1563. 425 citations
  15. L Yang J Chia, R Bartfai, A Christoffels, G.H Yue, K Ding, M.Y Ho, J. Hill, E Stupka and L Orban (2004). Analysis of the adult gonad transcriptomes in zebrafish by combining experimental and computational tools. Comparative and Functional Genomics 5: 403-418. 5 citations
  16. Y.H Loh, A. Christoffels, S Brenner, W Hunziker and B Venkatesh (2004). Extensive expansion of the claudin gene family in the teleost fish, Fugu reveals. Genome Research 14(7): 1248-57. 28 citations
  17. A Christoffels, J Chia, E Koh, S Aparicio, S Brenner and B Venkatesh (2004). Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Molecular Biology Evolution. 21(6): 1146-1151. 144 citations
  18. J Kelso, J Visagie, G Theiler, A Christoffels, S Bardien, D Smedley, D Otgaar, G Greyling, C. V Jongeneel, M I. McCarthy, T Hide, W Hide (2003). EVOC: A Controlled Vocabulary for Unifying Gene Expression Data. Genome Research 13:1222-1230. 65 citations
  19. E Koh, K Lam, A Christoffels, M Erdman, S Brenner and B Venkatesh (2003). Hox gene clusters in the Indonesian coelacanth Latimeria menadoensis. Proceedings of the National Academy of Science. 100: 1084-1088. 28 citations
  20. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, H IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D and Brenner S. (2002). The sequence, assembly and analysis of the compact vertebrate genome of Fugu rubripes. Science 297 1301-1310, USA. 660 citations
  21. J E. Carpenter, A Christoffels, Y Weinbach, W A. Hide (2002). Assessment of the Parallelisation approach of d2-cluster for High-Performance Sequence Clustering. Journal of Computational Chemistry. UK 23(7): 755-757. 9 citations
  22. A Christoffels, A van Gelder, G Greyling, R Miller, T Hide and W Hide (2001). STACKdb: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Research 29(1): 234-238. 64 citations
  23. R. T. Miller, A. G. Christoffels, C. Gopalakrishnan, J. A. Burke, A. A. Ptitsyn, T. R. Broveak and W. A. Hide (1999). A comprehensive approach to clustering of expressed human gene structure: The Sequence Tag Alignment and Consensus Knowledgebase. Genome Research 9(11): 1143-1155.
  24. Christoffels A, Miller R, Hide W (1999). STACK_PACK and STACK (Sequence Tag Alignment and Consensus Knowledgebase): A novel, comprehensive, hierachical EST clustering and consensus generation and analysis system providing unique insight into the human genome. Am J Hum Genet.  65(4): 477 Suppl. S.
  25. Daiger S, Rossiter B, Greenberg J, Christoffels A, Hide W (1999). Data services and computational tools for identification of genes and mutations causing retinal degeneration. Am J Hum Genet. 61(4): 2396 Suppl. S.
  26. Daiger S.P., Rossiter B.F., Greenberg J., Christoffels A., Hide W (1998). Data services and software for identifying genes and mutations causing retinal degeneration. Investigative Ophthalmology & Visual Science 39: S295.

Book Chapters

  1. Christoffels, A (2007). Dealing with duplicated genomes in teleosts. In: Acquaculture Genome technologies. 511-524. Editor:  Zhanjiang Liu. Blackwell Publishers, UK. ISBN 9780813802039.
  2. Christoffels, A (2005). Using UniGene, STACK and TIGER indices. In: Online Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley and Sons Ltd., UK.
  3. Christoffels, A (2005). Molecular phylogenetic analysis: Understanding genome evolution. In: information processing and living systems. 644-651. Editors: Bajic and Tan. Imperial College Press London. ISBN 1860945635.

Conference Proceedings

  1. Bartfai R., Wang X, Sreenivasan R, Cai M, Srinivasan H, Hossain MS, Komen J, Christoffels A and Orban L. (2007) Cyprinid gonad differentiation: A comparative genomics study. Aquaculture.  272: S244-S245. Elsevier Science, Netherlands. ISSN 0044-8486.
  2. A Christoffels, R Bartfai, H Srinivasan, H Komen and L Orban (2006). Comparative genomics in cyprinids: Common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatic 7 Suppl 5:S2. 2 citations
  3. Sin lam Tan, Vidhu Choudhary, Alan Christoffels, Byrappa Venkatesh and Vladimir Bajic.  (2005) Comparison of core promoters in Fugu rubripes and human. Proceedings of the 3rd Asia-pacific bioinformatics conference. pp379. YiPing Chen and Limsoon Wong Eds. Imperial College Press.
  4. Fernandez P, Moolman-Smook H, Brink P, Christoffels A, Hide W, Corfield V (2001). Mapping a cardiac conduction disorder (PFHBII) complicated by DCM to a novel disease-causing locus on chromosome 1q32.1-q41. (Report on the sixth international workshop on human chromosome 1 mapping 2000. Cytogenet Cell Genet  92: (1-2):45  (DOI: 10.1159/000056867)
  5. Hide W., Burke, J., Christoffels, A., Miller, R (1997). A novel approach towards a comprehensive consensus representation of the expressed human genome. Genome Informatics pp187-196. Satoru Miyano and Toshihisa Takagi Eds. Universal Academy Press Inc. Tokyo, Japan. ISSN 0919-9454.

Databases and Software

Switch to our mobile site