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 rubripesScience (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. et al.
An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement.
Genome Res. (2012) 22: 642-655.

Amemiya, C.T., et.al.,
The African coelacanth genome provides insights into tetrapod evolution.
Nature (2013) 496:311-316.

Mehta, T.K., et al.
Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum).
Proc. Natl. Acad. Sci. USA.(2013) 110: 16044-16049.

Venkatesh,B., et al.
Elephant shark genome provides unique insights into gnathostome evolution
Nature (2014) 505, 174-179.

 

 
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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 under the Nobel Laureate Sydney Brenner at the Medical Research Council (MRC), 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 of 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 member of the Human Genome Organization (HUGO) and a Fellow of the National Academy of Agricultural Sciences, India. He is also a chairperson of the 'Genome 10K', an international project which aims to catalogue genomes of 10,000 vertebrate.

     
  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 Lasker Award (1971 & 2000), British Companion of Honour (1987) and the Nobel Prize for Medicine or Physiology in 2002.
     
  Comparative and Medical Genomics
 


We are using a comparative genomics approach to better understand 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). Fugu genome was the first vertebrate genome to be sequenced soon after the completion of the human genome. It 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). Cartilaginous fishes are the oldest living group of jawed vertebrates (gnathostomes) and serve as a critical reference for understanding the evolution of vertebrate genomes. We have also initiated a genome project for a model jawless vertebrate, the Japanese lamprey (Lethenteron japonicum), which has a smaller genome than the sea lamprey. Jawless vertebrates (cyclostomes), comprising lampreys and hagfishes, are the most basally branching lineage of vertebrates and hence an important reference for understanding the origin and evolution of vertebrates. In addition, we are exploring other model vertebrate genomes such as coelacanth, gar and cichlid fishes that can contribute to our understanding of human and other vertebrate genomes. Our group is also participating in “Genome 10K”, an international project which aims to sequence the genomes of 10,000 vertebrates.



Besides sequencing and annotation of whole genomes and transcriptomes, our research interests include evolution of introns, role of gene and genome duplications in the evolution of vertebrate genomes, and evolution of cis-regulatory elements and its contribution to the morphological diversity of vertebrates. Prediction of conserved noncoding elements and their assay in transgenic zebrafish and mouse have proved to be an effective strategy for discovering cis-regulatory elements in the human genome, and for understanding the role of regulatory evolution in the morphological diversity of vertebrates.

Medical Genomics

We are collaborating with clinicians and scientists in other A*STAR Institutes to identify causative variants associated with metabolic diseases and rare genetic diseases using the next-generation sequencing platform. The main goals of this project are to prioritize therapeutic targets for treatment of chronic metabolic diseases and to understand the biology of rare genetic diseases. For identifying rare genetic variants associated with metabolic diseases we are sequencing candidate genes from individuals selected from the extremes of the population distribution of traits. Sequencing whole exomes of patients with rare genetic diseases and their unaffected parents/siblings is aimed at identifying causative mutations that should help in understanding the biology of such diseases.