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Kamiya, T., Kai, W., Tasumi, S., Oka, A., Matsunaga, T., Mizuno, N., Fujita, M., Suetake, H., Suzuki, S., Hosoya, S., Tohari, S., Brenner, S., Miyadai, T., Venkatesh, B., Suzuki, Y., Kikuchi, K. (2012) A Trans-Species Missense SNP in Amhr2 Is Associated with Sex Determination in the Tiger Pufferfish, Takifugu rubripes (Fugu). PLoS Genetics. 8(7): e1002798. [PLoS Genetics Access]

Kai, W., Kikuchi, K., Tohari, S., Chew, A.K., Tay, A., Fujiwara, A., Hosoya, S., Suetake, H., Naruse, K., Brenner, S., Suzuki, Y. and Venkatesh B. (2011) 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. 3: 424-442. [PubMed Access] [Full text]

Lee, A.P., Brenner, S. and Venkatesh, B. (2011) Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus. PLoS ONE. 6(5): e20088. [PubMed Access] [Full text]

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

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

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. (2010) Regulation of protocadherin gene expression by multiple neuron-restrictive silencer elements scattered in the gene cluster. Nucleic Acids Res. 38: 4985-4997. [PubMed Access] [Full text]

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

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

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

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

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

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

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

Kathirvel, P., Yu, W., Venkatesh, B., Lim, C., Lai, P. and Yee, W. (2008) Fugu rubripes and human survival motor neuron genes: Structural and functional similarities in comparative genome studies. Gene 424: 108-114. [PubMed Access]

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

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

Sundström, G., Larsson, T.A., Brenner, S., Venkatesh, B. and Larhammar, D. (2008) Evolution of the neuropeptide Y family: New genes by chromosome duplications in early vertebrates and in teleost fishes. Gen Comp Endocrinol 155: 705-716. [PubMed Access]

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

Ng, C.E.L., Osato, M., Tay, B.H., Venkatesh, B. and Ito, Y. (2007) cDNA cloning of the RUNX family genes from the pufferfish (Fugu rubripes). Gene 399: 162-173. [PubMed Access]

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

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. (2006) Ancient noncoding elements conserved in the human genomee. Science. 314, 1892. [PubMed Access]

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

Wong, E., Yu. W.P., Yap. W.H., Venkatesh. B. and Soong, T.W. (2006) Comparative genomics of the human and Fugu voltage-gated calcium channel alpha(1)-subunit gene family reveals greater diversity in fugu. Gene 366: 117-127. [PubMed Access]

Bromee, T., Venkatesh, B., Brenner, S., Postlethwait, J.H., Yan, Y-L., Larhammar, D. (2006) Uneven evolutionary rates of bradykinin B1 and B2 receptors in vertebrate lineages. Gene 373: 100-108. [PubMed Access]

Lee, A. P., Koh, E.G.L., Tay, A., Brenner, S. and Venkatesh, B. (2006) 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. [PubMed Access][Fugu-Human Hox Conserved Non-coding Sequences (CNS)]

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

Christoffels, A., Brenner, S., and Venkatesh, B. (2005) Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish lineage. Comp. Biochem. Physiol. Part D1, 13-19. [ScienceDirect Access]

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

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

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

Yap, W.H., Yeoh, E., Brenner, S. and Venkatesh, B. (2005) Cloning and expression of the reverse transcriptase component of pufferfish (Fugu rubripes) telomerase. Gene 353(2) 207-217. [PubMed Access]

Larsson, T.A., Olsson, F., Sundstrom, G., Brenner, S., Venkatesh, B. And Larhammar, D. (2005) Pufferfish and zebrafish have five histinct NPY receptor subtypes, but have lost appetite receptors Y1 and Y5. Ann N Y Acad Sci. 1040, 375-377. [PubMed Access]

Sundstrom, G., Larsson, T.A., Brenner, S., Venkatesh, B. And Larhammar, D. (2005) Ray-fin fish tetraploidization gave rise to pufferfish duplicates of NPY and PYY, but zebrafish NPY duplicate was lost. Ann N Y Acad Sci. 1040, 476-478. [PubMed Access]

Bates, M.D., Wells, J.M. and Venkatesh, B.(2005) Comparative genomics of the Hlx homeobox gene and protein: conservation of structure and expression from fish to mammals. Gene 352, 45-6. [PubMed Access]

Venkatesh, B. and Yap, W.H.(2005) Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements. BioEssays 27(1), 100-7. [PubMed Access]

Yu, W.P., Tan, J.M.M., Chew, K.C.M., Oh,T., Kolatkar, P., Venkatesh, B., Dawson, T.M. and Lim, K.L. (2005) The 350-fold compacted Fugu parkin gene is structurally and functionally similar to human Parkin. Gene 346, 97-104. [ScienceDirect Access]

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

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

Loh, Y.H., Christoffels, A., Brenner, S., Hunziker, W. and Venkatesh, B. (2004). Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripes. Genome Res. 7, 1248-1257. [PubMed Access]

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

Davies, S.J., Wise, C., Venkatesh, B., Mirza, G., Jefferson, A., Volpi, E.V. and Ragoussis, J. (2004) Mapping of three translocation breakpoints associated with orofacial clefting within 6p24 and identification of new transcripts within the region. Cytogenet. Genome Res. 105, 47-53. [PubMed Access]

Gilligan, P. and Venkatesh, B. (2004) Application of comparative genomics to the analysis of vertebrate regulatory elements. Briefings in Functional Genomics and Proteomics 3, 7-11. [PubMed Access]

Christoffels, A, Koh, EGL, Chia, JM, Brenner, S, Aparicio, S and Venkatesh,B (2004) Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol. Biol. Evol. 6, 1146-51 [ Supplementary material] [Abstract] [Full text]

Koopman, P, Schepers, G, Brenner, S and Venkatesh, B (2004) Origin and diversity of the Sox transcription factor gene family: Genome-wide analysis in Fugu rubripes. Gene 328, 177-186. [PubMed Access]

Stapleton, T, Luchman, A, Johnston, J, Browder, L, Brenner,S, Venkatesh, B and Jirik, FR (2004) Compact intergenic regions of the pufferfish genome facilitate isolation of gene promoters: characterization of Fugu 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (fPapss2) gene promoter function in transgenic Xenopus. FEBS Lett. 556, 59-63. [PubMed Access]

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

Zhang, T, Tan, YH, Fu, J, Lui, D, Ning, Y, Jirik, FR, Brenner, S and Venkatesh, B (2003) The regulation of retina specific expression of rhodopsin gene in vertebrates. Gene 313, 189-200. [PubMed Access]

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

Gilligan, P., Brenner, S. and Venkatesh, B. Neuron-specific expression and regulation of the pufferfish isotocin and vasotocin genes in transgenic mice. J. Neuroendocrinol. (2003) 15, 1027-1036. [Neuroendocrinology Access]

Yu, WP, Brenner, S and Venkatesh, B (2003) Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu. Trends Genet. 19, 180-183. [PubMed Access]

E Koh, K Lam, A Christoffels, M Erdman, S Brenner and B Venkatesh (2003) Hox gene clusters in the Indonesian coelacanth Latimeria menadoensis. Proc. Natl. Acad. Sci. USA. 100:1084-1088 [PubMed Access]

Yap, WH, Tay, A, Brenner, S and Venkatesh, B (2003) Molecular cloning of the pufferfish (Takifugu rubripes) Mx gene and functional characterization of its promoter. Immunogenetics. 54, 705-713. [PubMed Access]

Williams, H, Brenner, S and Venkatesh, B (2002) Characterization of the platelet-derived growth factor receptor alpha and c-kit genes in the pufferfish Fugu rubripes. DNA Seq. (UK). 13, 263-270. [PubMed Access]

Williams, H, Brenner, S and Venkatesh, B (2002) Identification and analysis of additional copies of the platelet derived growth factor receptor and colony stimulating factor1 receptor in the pufferfish, Fugu rubripes. Gene 295, 255-264. [ScienceDirect Access]

Gilligan, P, Brenner, S and Venkatesh, B (2002) Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences. Gene 294, 35-44. [PubMed Access]

Abrahams, BS, Mak,GM, Berry, ML, Palmquist, DL, Saionz, J, Tay, A, Tan, YH, Brenner, S, Simpson, EM and Venkatesh (2002) Novel vertebrate genes and putative regulatory elements identified at kidney disease and NR2E1/fierce loci. Genomics (2002) 80, 45-53. [PubMed Access]

Brenner,S, Venkatesh,B, Yap,WH, Chou,CF, Tay,A, Ponniah,S, Wang,Y and YH Tan. (2002) "Conserved regulation of the lymphocyte-specific expression of lck in the Fugu and mammals" , Proc. Natl. Acad. Sci. USA. 99:2936-2941. [PubMed Access]

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, Ho 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, Brenner S.(2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-1310 [PubMed Access]