Byrappa VENKATESH / Sydney BRENNER   
                       
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  Byrappa VENKATESH  
  Lab Location: #5-04

email:
mcbbv@imcb.a-star.edu.sg
tel:65869571
  
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  Key Publications  
 

Aparicio, S.et al.
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.  Science (2002) 297, 1301-1310.

Christoffels, A., Koh, E.G.L., Chia, J., Brenner, S., Aparicio, S. and Venkatesh, B.
Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes.
Mol. Biol. Evol. 21, 1146-1151. 2004.

Venkatesh, B., Tay, A., Dandona, N., Patil, J.G. and Brenner, S.
A compact cartilaginous fish model genome.
Curr. Biol. 15, R82-R83, 2005.

Lee, A. P., Koh, E.G.L., Tay, A., Brenner, S. and Venkatesh, B.
Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters.
Proc. Natl. Acad. Sci. USA. 103, 6994-6999, 2006.

Venkatesh, B., et al.,
Ancient noncoding elements conserved in the human genome.
Science 314, 1892. 2006.

Venkatesh, B., et al.
Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome.
PLoS Biol. 5(4): e101, 2007.

Davies, W.L., Carvalho, L.S., Tay, B.H., Brenner, S., Hunt, D.M. and Venkatesh, B.
Into the blue: gene duplication and loss underlie colour vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii.
Genome Res. (2009) 19: 415-426.

Ravi, V., Lam, K., Tay, B-H., Tay, A., Brenner, S. and Venkatesh, B.
Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes. Proc. Natl. Acad. Sci. USA. (2009). 106: 16327-16332.

Maeso, I., Irimia, M., Tena, J.T., González-Pérez, E., Tran, D., Ravi, V., Venkatesh, B., Campuzano, S., Gómez-Skarmeta, J.L. and Garcia-Fernàndez, J.
An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement.
Genome Res. (2012) 22: 642-655.

  
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  Byrappa VENKATESH


Byrappa Venkatesh obtained his BSc and MSc from the University of Agricultural Sciences, Bangalore, India and PhD from the National University of Singapore. He did his postdoctoral studies in Dr Sydney Brenner's lab at the Medical Research Council, Cambridge, UK and returned to Singapore in 1992 to set up this Lab. He is currently a Professor and Research Director in IMCB, and an adjunct Professor with the Department of Paediatrics, National University of Singapore. For his work on the fugu genome, Venkatesh was honored with Singapore's "National Science Award" in 2004. He is a chairperson of the 'Genome 10K' project.

     
  Sydney BRENNER
   

Sydney Brenner received his DPhil from Oxford University in 1954. He was a member of the Scientific Staff of the MRC Laboratory of Molecular Biology in Cambridge, UK from 1957-1993, and served as its Director from 1979-1986. He is the recipient of many awards and honors in recognition of his contributions to molecular biology, including the Nobel Prize for Medicine or Physiology in 2002.
     
  Comparative and Medical Genomics
 


We are using a comparative genomics approach for better understanding the structure, function and evolution of the human genome. Our group is one of the pioneers in the field of comparative genomics. We proposed the compact genome of the fugu (Takifugu rubripes) as a model vertebrate genome in 1993 (Nature 366: 265-268, 1993) and determined its whole genome sequence in 2002 (Science 297: 1301-1310, 2002) (http://www.fugu-sg.org/). Fugu genome is being widely used as a reference genome for comparative analysis of human and other vertebrate genomes. More recently, we identified elephant shark (Callorhinchus milii) as having the smallest genome among cartilaginous fishes and initiated the Elephant Shark Genome Project (PLoS Biol 5(4): e101, 2007) (http://esharkgenome.imcb.a-star.edu.sg/). Cartilaginous fishes are the oldest living group of jawed vertebrates (gnathostomes) and serve as critical reference for understanding the evolution of vertebrate genomes. The elephant shark genome is currently being sequenced with funding from the National Institutes of Health (NIH), USA. In addition, we are exploring other potential model vertebrate genomes that can contribute to our understanding of human and other vertebrate genomes. Our group is also participating in the “Genome 10K” project which aims to sequence the genomes of 10,000 vertebrates.

Besides sequencing and annotation of genomes, our research interests include whole genome comparisons aimed at studying the role of gene and genome duplications in the evolution of vertebrate genomes, genome organization and gene structure (loss and gain of introns), prediction of ancient conserved noncoding elements (CNEs) in the human genome, and evolution of CNEs. Functional assay of CNEs in transgenic zebrafish and mouse has proved to be an effective strategy for discovering a large number of cis-regulatory elements in the human genome. Mutations in some cis-regulatory elements have been associated with genetic diseases and hence a catalogue of functional cis-regulatory elements will be valuable for identifying disease-associated regulatory mutations.

Medical Genomics

We are collaborating with clinicians in identifying rare genetic variants associated with Type 2 diabetes and dyslipidemia. The main goals of this project are to understand the genetic basis of chronic metabolic diseases, and to prioritize therapeutic targets for their treatment. We are targeting candidate genes in individuals selected from extremes of the population distribution of the trait that are likely to be enriched for rare variants with large effects.

     
     
   
         
 
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