Alan Christoffels

Name: Alan Christoffels

Role: Associate Professor

Contact Details

Telephone: +27-(0)21-9592969

Facsimile: +27-(0)21-9592512

Mobile:

Email: alan at sanbi ac za

Skype: gillyjake

Research Areas:

Tsetse fly Comparative Genomics

Genome Annotation & Evolution

Web-based Bioinformatics support services

Cyprinid Genomics

Lab Members:

Sarah Wambui

Mushal Allam

Edwin Murungi

Ruben Cloete

Musa Nur Gabere

Mark Wamalwa

Ashley Pretorius

Teaching:

Comparative Genomics

I have relocated to South Africa and currently setting up my laboratory at the South African National Bioinformatics Institute. Over the last 6 years my research has focused on annotating vertebrate genomes and studying evolutionary mechanisms that shape genome structure in fish.

Evolutionary genomics of pathogens
My laboratory at SANBI uses comparative genomics tools and in-house technologies to investigate host-pathogen interactions with a view of developing intervention methods. Currently, projects in the lab are focused on sleeping sickness and malaria in collaboration with Profs Bajic and Hide.

1. Glossina genome evolution

Tsetse flies serve as a vector for African trypanosomes that cause sleeping sickness in humans and livestock. However, these flies are normally refractory to trypanosome infection with half the fly population becoming infected. Research has suggested that tsetse fly immunity factors are key determinants in the success or failure of infection and maturation process of parasites.

The production of genomics resources related to tsetse genome are coordinated by the International Glossina Genome Initiative (IGGI). In lieu of a sequenced tsetse fly genome and a subsequent genome annotation effort, a number of expressed sequence tags (ESTs) have been generated. Currently, our efforts are targeted towards developing a system to manage this data resource and the analysis of immunity related genes in the context of other characterized vector genomes.

2. Regulatory mechanisms of immunity-related genes

Novel mechanisms were recruited for specialization of immunity-related genes in chordates. It is very likely that insects and particularly tsetse flies would have specialized mechanisms to cope with various environmental challenges including infection by trypanosomes. In collaboration with Prof Bajic we are investing the promoter regions of immunity-related genes in the tsetse fly genome with a view of modeling regulatory networks that fine-tune immunological responses.

3. Web-based bioinformatics support for biologists
We aim to meet the routine bioinformatics needs of biologists on campus with the development of tools through collaborative research. Currently, we have development GDD and EMAP.

EST Management and Analysis Protocols (eMAP)

Expressed sequence tags (ESTs) are single-read, error-prone transcripts that are generated on a large-scale. As part of our effort to support database management and analyses of in-house generated ESTs, we are developing a system for (1) relational database storage and (2) configurable analysis pipeline of EST data.

Gene duplication detection (GDD)

Gene and/or genome duplication has been postulated as the driving force for the introduction of novel gene functions. The analysis of the impact of gene expansion on the introduction of novel gene functions is made possible through the availability of sequenced genomes for a range of species. At present, comprehensive identification of gene duplications in an organism requires powerful computational resources and bioinformatics expertise to execute various protocols including phylogenetic software such as PHYLIP and LINTREE on a genome-scale in addition to implementing protocols for system and data management. We have addressed these issues through development of GDD application. Protocols for gene duplication analysis as outlined in Christoffels et al. 2004 are implemented here in GDD. Using the GDD tool, the biologist can submit one or many protein families online.

Selected Publications

2008

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.

2007

Christoffels, A (2007). Dealing with duplicated geomes in teleosts. In: Acquaculture Genome technologies. 511-524. Editor: Zhanjiang Liu. Blackwell Publishers, UK. ISBN 9780813802039.

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.

2006

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 Bioinformatics 7 Suppl 5:S2.

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.

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.

2005

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, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. T. Krishnan, A. Kruger, S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. Lazarevic, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. Ruan, S. L. Salzberg, A. Sandelin, C. Schneider, C. Schönbach, K. Sekiguchi, C. A. M. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, D. Silva, B. Sinclair, S. Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, H. R. Ueda, E. van Nimwegen, R. Verardo, C. L. Wei, K. Yagi, H. Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. Wahlestedt, J. S. Mattick, D. A. Hume, RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group), C. Kai, D. Sasaki, Y. Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki, M. Tagami, K. Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. Kawai, and Y. Hayashizaki. (2005). The Transcriptional Landscape of the Mammalian Genome. Science 309:1559-1563.

Christoffels, A (2005). Using UniGene, STACK and TIGER indices. In: Online Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley and Sons Ltd., UK.

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.

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.

2004

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.

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.

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.

2003

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.

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.

2002

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.

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.

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.