Venkatesh, B.  
Fugu: The Pufferfish Model Genome.
In: Nature Encyclopedia of the Human Genome. Cooper DN (ed.) Vol 2, pp 535-539. London: Nature Publishing Group, 2003.

Venkatesh, B.
Genome Size.
In: Nature Encyclopedia of the Human Genome. Cooper DN (ed.) Vol 3, pp 33-37. London: Nature Publishing Group, 2003.

Venkatesh, B.. 
Evolution and diversity of fish genomes.
Curr. Opin. Genet. Dev. (2003) 13, 588-592.

Stapleton, T, Luchman, A., Johnston, J., Browder, L., Brenner,S., Venkatesh, B. and Jirik, F.R.
Compact intergenic regions of the pufferfish genome facilitate isolation of gene promoters: characterization of Fugu 3'-phosphoadenosine 5'-phosphosulfate synthase 2 gene promoter function in transgenic Xenopus.
FEBS Lett. (2004) 556, 59-63.

Brinkmann, H., Venkatesh, B.., Brenner, S. and Meyer, A.
Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates.
Proc. Natl. Acad. Sci. USA (2004) 101, 4900-4905.

Gilligan, P. and Venkatesh, B.
Application of comparative genomics to the analysis of vertebrate regulatory elements.
Brief. Funct. Genomic. Proteomic. (2004) 3, 7-11.

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. (2004) 21, 1146-1151.

Loh, Y.H., Christoffels, A., Brenner, S., Hunziker, W. and Venkatesh, B.
Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripes.
Genome Res. (2004). 14, 1248-1257.

Chou, C.F., Tohari, S., Brenner, S. and Venkatesh, B.
Erythropoietin gene from a teleost fish, Fugu rubripes.
Blood (2004) 104:1498-1503.

Yeo, G., Hoon, S., Venkatesh, B. and Burge, C.B.
Variation in sequence and organization of splicing regulatory elements in vertebrate genes.
Proc. Natl. Acad. Sci. USA. (2004) 101, 15700-15705.

Venkatesh, B. and Yap, W.H.
Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements.
BioEssays (2005) 27, 100-107.

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

Kai, W., Kikuchi, K., Fujita, M., Suetake, H., Yoshiura, Y., Ototake, M., Fujiwara, A., Venkatesh, B., Miyaki, K. and Suzuki, Y.
A genetic linkage map for the tiger pufferfish, Takifugu rubripes.
Genetics (2005) 171: 227-238.

Yap, W.H., Yeoh, E., Tay, A., Brenner, S. and Venkatesh, B.
STAT4 is a target of the hematopoietic zinc-finger transcription factor Ikaros in T cells.
FEBS Lett (2005) 579: 4470-4478.

Venkatesh, B.., Lu, S.Q., Dandona, N., See, S.L., Brenner, S. and Soong, T.W.
Genetic basis of tetrodotoxin resistance in pufferfishes.
Curr. Biol. (2005) 15: 2069-2072.

Venkatesh, B., Dandona, N. and Brenner, S.
Fugu genome does not contain mitochondrial pseudogenes.
Genomics (2006) 87, 307-310.

Bliss, J.M., Venkatesh, B. and Colicelli, J.
The RIN family of RAS effectors.
In Methods in Enzymology. Vol 407 Regulators and Effectors of small GTPase: RAS family. Eds. Balch, W.E., Der, C.J. and Hall, A. Academic Press, New York. p 335-344. 2006.

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. (2006) 103, 6994-6999.

Soong, T.W. and Venkatesh, B.
Adaptive evolution of tetrodotoxin resistance in animals.
Trends Genet. (2006) 22, 621-626.

Venkatesh, B., Kirkness, E.F., Loh, Y.H., Halpern, A.L., Lee, A.P., Johnson, J., Dandona, N., Viswanathan, L.D., Tay, A., Venter, J.C., Strausberg, R.L. and Brenner, S.
Ancient noncoding elements conserved in the human genome.
Science (2006) 314, 1892.

Yu, W.P., Yew, K., Rajasegaran, V. and Venkatesh, B.
Sequencing and comparative analysis of fugu protocadherin clusters reveal diversity of protocadherin genes among teleosts.
BMC Evol.Biol. (2007) 7:49.

Venkatesh, B., Kirkness, E.F., Loh, Y.H., Halpern, A.L., Lee, A.P., Johnson, J., Dandona, N., Viswanathan, L.D., Tay, A., Venter, J.C., Strausberg, R.L. and Brenner, S.
Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. 
PLoS Biol. (2007) 5(4): e101.

Lee, A.P., Yang, Y.C., Brenner, S. and Venkatesh, B.
TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements.
BMC Genomics (2007) 8: 441.

Ruhe, J.E., Streit, S. Hart, S., Wong, C., Specht, K., Knyazev, P., Knyazeva, T., Tay, L.S., Loo, H.L., Foo, P., Wong, W., Pok, S., Lim, S.J., Ong, H., Luo, M., Ho, H.K., Peng, K., Lee, T.C., Bezler, M., Mann, C., Gaertner, S., Hoefler, H., Iacobelli, S., Peter, S., Tay, A., Brenner, S., Venkatesh, B. and Ullrich, A.
Genetic alterations in the tyrosine kinase transcriptome of human cancer cell lines.
Cancer Res. (2007) 67: 11368-11376.

Loh, Y.H., Brenner, S. and Venkatesh, B.
Investigation of loss and gain of introns in the compact genomes of pufferfishes (fugu and Tetraodon).
Mol.Biol. Evol. (2008)25: 526-535.

Yu, W.P., Rajasegaran, V., Yew, K., Loh, W.,  Tay, B.H., Amemiya, C.T., Brenner, S. and Venkatesh, B.
Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: a comparative analysis of the protocadherin cluster.
Proc. Natl. Acad. Sci. USA. (2008) 105: 3819-3824.

Gwee, P.C., Amemiya, C.T., Brenner, S. and Venkatesh, B.
Sequence and organization of coelacanth neurohypophysial hormone genes: evolutionary history of the vertebrate neurohypophysial hormone gene locus.
BMC Evol. Biol. (2008) 8:93.

Venkatesh, B.
Fugu: The Pufferfish Model Genome.
In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. (April 2008).

Lee, A.P. and Venkatesh, B.
Ultraconserved DNA Sequence Elements in the Human Genome.
In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. (April 2008).

Larsson, T.A., Olsson, F., Sundstrom, G., Lundin, L., Brenner, S., Venkatesh, B. and Larhammar, D.
Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions.
BMC Evol. Biol. (2008) 8: 184.

Ravi, V. and Venkatesh, B.
Rapidly evolving fish genomes and teleost diversity.
Curr. Opin. Genet. Dev. (2008) 18: 544-550.

Larsson, T.A., Tay, B.H., Sundstrom, G., Fredriksson, R., Brenner, S., Larhammar, D. and Venkatesh, B. Neuropeptide Y-family peptides and receptors in the elephant shark, Callorhinchus milii confirm gene duplications before the gnathostome radiation.
Genomics (2009) 93: 254-260.

Wang, J., Lee, A.P., Kodzius, R., Brenner, S. and Venkatesh, B.
Large number of ultraconserved elements were already present in the jawed vertebrate ancestor.
Mol. Biol. Evol. (2009) 26: 487-490.

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.

Gwee, P.C., Tay, B., Brenner, S. and Venkatesh, B.
Characterization of the neurohypophysial hormone gene loci in elephant shark and the Japanese lamprey: origin of the vertebrate neurohypophysial hormone genes.
BMC Evol. Biol. (2009) 9: 47.

Yeo, G.H., Cheah, F.S.H., Winkler, C., Jabs, E.W., Venkatesh, B. and Chong, S.S.
Phylogenetic and evolutionary relationships and developmental expression patterns of the zebrafish twist gene family. 
Dev. Genes Evol. (2009) 219: 289-300.

Bajoghli, B., Aghaallaei, N., Hess, I., Rode, I., Netuschil, N., Tay, B.H., Venkatesh, B., Yu, K.,  Kaltenbach, S.L., Holland, N.D., Diekhoff, D., Happe, C., Schorpp, M. and Boehm, T.
Evolution of genetic networks underlying the emergence of thymopoiesis in vertebrates.
Cell (2009) 138: 186-197.

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.

Jiang, X., Li, S., Ravi, V., Venkatesh, B. and Yu, W-P.
Identification and comparative analysis of the protocadherin cluster in a reptile, the green anole lizard.
PLoS ONE (2009) 4: e7614.

Genome 10K community of Scientists.
Genome 10K: A proposal to obtain whole-genome sequence for 10,000 vertebrate species.
J. Hered. (2009) 100: 659-674.

MacDonald, R.B., Debiais-Thibaud, M., Martin, K., Poitras, L., Tay, B-H., Venkatesh, B. and Ekker, M.
Functional conservation of a forebrain enhancer from the elephant shark (Callorhinchus milii) in zebrafish and mice.
BMC Evol. Biol. (2010) 10:157.

Tan, Y-P., Li, S., Jiang, X-J., Loh, W., Foo, Y.K., Loh, C-B., Xu, Q., Yuen, W-H., Jones, M., Fu, J., Venkatesh, B. and Yu, W-P.
Regulation of protocadherin gene expression by multiple neuron-restrictive silencer elements scattered in the gene cluster.
Nucleic Acids Res. (2010) 38: 4985-4997.

Kulkarni, R.P., Tohari, S., Ho, A., Brenner, S. and Venkatesh, B.
Characterization of a hypoxia-response element in the Epo locus of the pufferfish, Takifugu rubripes.
Marine Genomics (2010) 3: 63-70.

Inoue, J.G., Miya, M., Lam, K., Tay, B-H., Danks, J.A., Bell, J., Walker, T.I. and Venkatesh, B.
Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): A mitogenome perspective.
Mol. Biol. Evol. (2010) 27: 2576-2586.

Liu, Y., Ibrahim, A.S., Tay, B.-H., Richardson, S.J., Bell, J., Walker, T.I., Brenner, S., Venkatesh, B. and Danks, J.A.
Parathyroid hormone gene family in a cartilaginous fish, the elephant shark (Callorhinchus milii).
J. Bone Miner. Res. (2010) 25: 2337-2347.

Gill, T., Lowe, L., Nguyen, J., Liu, P.P., Venkatesh, B. and Aplan, P.D.
Enforced expression of SV40 large T antigen leads to testicular germ cell tumors in zebrafish.
Zebrafish (2010) 7: 333-341.

Lee, A.P., Kerk, S.Y., Tan, Y.Y., Brenner, S. and Venkatesh, B.
Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes.
Mol. Biol. Evol. (2011) 28: 1205-1215.

Lee, A.P., Brenner, S. and Venkatesh, B.
Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus.
PLoS ONE (2011) 6: e20088.

Kai, W., Kikuchi, K., Tohari, S., Chew AH, Tay, A., Fujiwara, A., Hosoya, S., Suetake, H., Naruse, K., Brenner, S., Suzuki, Y. and Venkatesh, B.
Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals.
Genome Biol. Evol.(2011) 3: 424-442.

Dos Santos, S., Mazan, S., Venkatesh, B., Cohen-Tannoudji, J. and Quérat, B.
Emergence and evolution of the glycoprotein hormone and neurotrophin gene families in vertebrates.
BMC Evol Biol (2011) 11:332.

Lane, D.P., Madhumala, A., Lee, A.P., Tay, B-H., Verma, C., Brenner, S. and Venkatesh, B.
Conservation of all three p53 family members and Mdm2 and Mdm4 in the cartilaginous fish.
Cell Cycle(2011) 10: 4272-4279.