Byrappa VENKATESH

Comparative and Medical Genomics

Profile

Byrappa VENKATESH
Lab Location: #5-04   Email: mcbbv@imcb.a-star.edu.sg   Tel: 65869571

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, an adjunct Professor of the Department of Paediatrics, National University of Singapore and a Joint Scientist at KK Women’s and Children’s Hospital. In recognition of his achievements, 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' project, an international project which aims to catalogue genomes of 10,000 vertebrates.

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.

 

Research

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.

Medical Genomics
We apply our high-throughput next-generation sequencing and bioinformatics capabilities for identifying variants associated with genetic diseases. The main collaborators of our Medical Genomics projects are scientists from the Institute of Medical Biology (IMB) and the Translational Laboratory in Genetic Medicine (TLGM), and clinicians from the KK Women’s and Children’s Hospital and the National University Hospital. A major ongoing project is aimed at identifying variants associated with rare genetic diseases, whose precise diagnosis is often a challenge to clinicians due to the diagnosis odyssey of patients with uncommon symptoms. By sequencing whole-exomes of patients, their unaffected parents and other family members, we have been able to identify causative variants for 150 rare and undiagnosed genetic diseases. Besides helping clinicians in the precise diagnosis of the disease and deciding appropriate therapeutic measures, these findings have improved our understanding of the functions of many human genes. The objective of another ongoing project is to identify germline and somatic mutations associated with neuroblastoma, which is the most common extracranial solid tumour in children. This project is based on sequencing and analysis of a large number of FFPE tumour and normal tissue samples collected by clinicians at the KK Women’s and Children’s Hospital over several years.

Besides sequencing and annotation of whole genomes and transcriptomes, our research interests include the 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 phenotypic diversity of vertebrates.

 

Staff

Department: Byrappa VENKATESH

Name: Ravi VYDIANATHAN

Designation: Research Fellow

Email: raviv@imcb.a-star.edu.sg


Name: Boon Hui TAY

Designation: Laboratory Manager

Email: mcblab46@imcb.a-star.edu.sg


Name: Sumanty TOHARI

Designation: Laboratory Biologist A

Email: toharis@imcb.a-star.edu.sg


Publications

Publications (since 2002)

Lopes-Marques, M., Kabeya, N., Qian, Y., Ruivo, R., Santos, M., Venkatesh, B., Tocher, D., Castro, F. and Monroig, O.
Retention of fatty acyl desaturase 1 (fads1) in Elopomorpha and Cyclostomata provides novel insights into the evolution of long-chain polyunsaturated fatty acid biosynthesis in vertebrates.

BMC Evol. Biol. (2018) 18:157.

Hettiaracchchi, D., Bonnard, C., Jayawardana, S. M. A., Ng, A.Y.J, Tohari, S., Venkatesh, B., Reversade, B., Singaraja, R.and Dissanayake, V. H. W.
Cenani-Lenz syndactyly syndrome - a case report of a family with isolated syndactyly.
BMC Medical Genetics (2018) 19:125.

Hughes, L.C.*, Ortí, G.*, Huang, Y., Sun, Y., Baldwin, C.C., Thompson, A.W.,  Arcila, D., Betancur-R, R., Li, C., Becker, L., Bellora, N., Zhao, X., Li, X., Wang, M., Fang, C., Xie, B, Zhou, Z., Huang, H., Chen, S., Venkatesh, B*. and Shi, Q*.
Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data.
Proc. Natl. Acad. Sci. USA. (2018) 115:6249-6254.

Bonnard, C., Shboul, M., Tonekaboni, S.H., Ng, A.Y.J., Tohari, S., Ghosh, K., Lai, A., Lim, J.Y., Tan, E.C., Devisme, L., Stichelbout, M., Alkindi, A., Banu, N., Yüksel, Z., Ghoumid, J., Elkhartoufi, N., Boutaud, L., Micalizzi, A., Brett, M.S., Venkatesh, B., Valente, E.M., Attié-Bitach, T., Reversade, B. and Kariminejad, A.
Novel mutations in the ciliopathy-associated gene CPLANE1 (C5orf42) cause OFD syndrome type VI rather than Joubert syndrome.
Eur J Med Genet. (2018) 61: 585-595.

Holland, S.J., Berghuis, L., King, J., Iyer, L.M., Sikora, K., Fifield, H., Peter, S., Quinlan, E., Sugahara, F., Shingate, P., Trancoso, I., Iwanami, N., Temereva, E., Strohmeier, C., Kuratani, S., Venkatesh, B., Evanno, G., Aravind, L., Schorpp, M., Larijani, M. and Boehm, T.

Expansions, diversification and inter-individual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys.

Proc. Natl. Acad. Sci. USA. (2018) 115: E3211-E3220.
 

Ravi, V. and Venkatesh, B. 
The divergent genomes of teleosts. 
Annu. Rev. Anim. Biosci. (2018) 6:47-68.

Jung, H., Baek, M., DElia, K.P., Boisvert, C., Tay, B., Currie, P., Venkatesh, B., Stuart M. Brown, S.M., Heguy, A., Schoppik, D. and Dasen, J.S. 
The ancient origins of neural substrates for land walking. 
Cell (2018) 172: 667-682.

Kojo, S., Tanaka, H., Endo, T., Muroi, S., Liu, Y., Seo, W., Tenno, M., Kakugawa, K., Naoe, Y., Nair, K., Moro, K., Katsuragi, Y., Kanai, A., Inaba, T., Egawa, T., Venkatesh, B., Minoda, A., Kominami, R. and Taniuchi, I. 
Priming of lineage-specifying genes by Bcl11b is required for lineage choice in post-selection thymocytes. 
Nat. Commun. (2017) 8:702.

Zakon, H., Li, W., Pillai, N.E., Shingate, P., Tohari, S., Ren, J. and Venkatesh, B. 
Voltage-gated sodium channel gene repertoire of lampreys: gene duplications, tissue-specific expression, and discovery of a long-lost gene. 
Proc. R. Soc. B (2017) 284: 20170824.

Windpassinger, C., et al.
CDK10 mutations in humans and mice cause severe growth retardation, spine malformations and developmental delays.
Am. J. Hum. Genet. (2017) 101: 391-403.

Zhang, H., Ravi, V., Tay, B., Tohari, S., Pillai, N.E., Prasad, A., Lin, Q., Brenner, S. and Venkatesh, B.
Lampreys, the jawless vertebrates, contain only two ParaHox gene clusters.
Proc. Natl. Acad. Sci. USA. (2017) 114: 9146-9151.

Lin, Q., Qiu, Y., Gu, R., Xu, M., Li, J., Bian, C., Zhang, H., Qin, G., Zhang, Y., Luo, W., Chen, J., You, X., Fan, M., Sun, M., Xu, P., Venkatesh, B., Xu, J., Fu, H. and Shi, Q. 
Draft genome of the lined seahorse, Hippocampus erectus
Gigascience (2017) 6: 1-6.

Xue, S., Maluenda, J., Marguet, F., Shboul, M., Quevarec, L., Bonnard, C., Ng, A.Y.J., Tohari, S., Tan, T., Kong, M.K., Monaghan, K.G., Cho, M.T., Siskind, C.E., Sampson, J.B., Rocha, C.T., Alkazaleh, F., Gonzales, M., Rigonnot, L., Whalen, S., Gut, M., Gut, I., Bucourt, M., Venkatesh, B., Laquerrière, A., Reversade, B. and Melki, J. 
Loss-of-function mutations in LGI4, encoding a secreted ligand involved in Schwann cell myelination, are responsible for arthrogryposis multiplex congenital. ?
Am. J. Hum. Genet. (2017) 100: 659-665.

Xu, X., Tay, Y., Sim, B., Yoon, S., Huang, Y., Ooi, J., Utami, K.H., Ziaei, A., Ng, B., Radulescu, C., Low, D., Ng, A.Y.J., Loh, M., Venkatesh, B., Ginhoux, F., Augustine, G.J. and Pouladi, M.A. 
Reversal of phenotypic abnormalities by CRISPR/Cas9-mediated gene correction in Huntington disease patient-derived induced pluripotent stem cells. 
Stem Cell Reports (2017) 8: 619-633.

Fonseca, E., Ruivo, R., Lopes-Marques, M., Zhang, H., Santos, M.M., Venkatesh, B. and Castro, L.F. 
LXRa and LXRb nuclear receptors evolved in the common ancestor of gnathostomes. 
Genome Biol Evol. (2017) 9: 222-230.

Li, J., Bian, C., Hu, Y, Mu, X., Shen, X., Ravi, V., Kuznetsova, I.S., , Sun, Y., You, X., Qiu, Y., Zhang, X., Yu, H., Huang, Y., Xu, P., Gu, R., Xu, J., Orbán, L., Venkatesh, B. and Shi, Q.
A chromosome-level genome assembly of the Asian arowana, Scleropages formosus
Sci. Data (2016) 3:160105.

Lin, Q., Fan, S., Zhang, Y., Xu, M., Zhang, H., Yang, Y., Lee, A.P., Woltering, J.M., Ravi, V., Gunter, H.M., Luo, W., Gao, Z., Lim, Z.W., Qin, G., Schneider, R.F., Wang, X., Xiong, P., Li, G., Wang, K., Min, J., Zhang, C., Qiu, Y., Bai, J., He,W., Bian, C., Zhang, X., Shan, D., Qu, H., Sun, Y., Gao, Q., Huang, L., Shi, Q., Meyer, A. and Venkatesh, B.
The seahorse genome and the evolution of its specialized morphology.
Nature (2016) 540: 395-399.

Pan, H., Yu, H., Ravi, V., Li, C., Lee, A.P., Lian, M.M., Tay, B-H., Brenner, S., Wang, J., Yang, H., Zhang, G. and Venkatesh, B.
The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate.
GigaScience (2016) 5:36.

Tostivint, H., Dettaï, A., Quan, F.B., Ravi, V., Tay, B-H., Rodicio, M., Mazan, S., Venkatesh, B. and Kenigfest, N.B.
Identification of three somatostatin genes in lampreys.
Gen. Comp. Endocrinol. (2016) 237: 89-97.

Sun, Y., Huang, Y., Li, X., Baldwin, C.C. Zhou, Z., Yan, Z., Crandall, K.A., Zhang, Y., Zhao, X., Wang, M., Fang, A., Zhang, X., Huang, H., Lopez, J.V., Kilfoyle, K., Zhang, Y., Ortí, G*., Venkatesh, B.* and Shi, Q*.
Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies.
GigaScience (2016) 5:18.

Bian, C., et al.
The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts.
Sci. Rep. (2016) 6: 24501.

Oud MM, Bonnard C, Mans DA, Altunoglu U, Tohari S, Ng AY, Eskin A, Lee H, Rupar CA, de Wagenaar NP, Wu KM, Lahiry P, Pazour GJ, Nelson SF, Hegele RA, Roepman R, Kayserili H, Venkatesh B, Siu VM, Reversade B and Arts HH.
A novel ICK mutation causes ciliary disruption and lethal endocrine-cerebro-osteodysplasia syndrome.
Cilia (2016) 5:8.

Jamuar SS, Kuan JL, Brett M, Tiang Z, Tan WL, Lim JY, Liew WK, Javed A, Liew WK, Law HY, Tan ES, Lai A, Ng I, Teo YY, Venkatesh B, Reversade B, Tan EC and Foo R.
Incidentalome from genomic sequencing: A barrier to personalized medicine?
EBioMedicine (2016) 5: 211-216.

Braasch, I. et al.
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
Nature Genet. (2016) 48:427-437.

Coffill, C.R., Lee, A.P., Siau, J.W., Chee, S.M., Joseph, T.L., Tan, Y.S., Madhumalar, A., Tay, B., Brenner, S., Verma, C.S., Ghadessy, F.J., Venkatesh, B. and Lane, D.P.
The p53-Mdm2 interaction and the E3 ligase activity of Mdm2/Mdm4 are conserved from lamprey to human.
Genes Dev. (2016) 30: 281-292.

Monroig, O., Lopez-Marques, M., Navarro, J.C., Hontoria, F., Ruivo, R., Santos, M.M., Venkatesh, B., Tocher, D.R. and Castro, L.F.
Evolutionary functional elaboration of the Elovl2/5 gene family in chordates. 
Sci. Rep. (2016) 6: 20510.

Tafakhori, A., Ng, A., Tohari, S., Venkatesh, B., Lee, H., Eskin, A., Nelson, S.F., Bonnard, C., Reversade, B., and Kariminejad, A.
Mutation in TWINKLE in a Large Iranian family with progressive external ophthalmoplegia, myopathy, dysphagia and dysphonia, and behavior change. 
Arch. Iran. Med. (2016) 19: 87-91.

Ravi, V., Yu, W., Pillai, N.E., Lian, M.M., Tay, B., Tohari, S., Brenner, S. and Venkatesh, B.
Cyclostomes lack clustered protocadherins.
Mol. Biol. Evol. (2015) 33: 311-315.

Campanini, E.B., Vandewege, M.W., Pillai, N.E., Tay, B.H., Jones, J.C., Venkatesh, B. and Hoffmann, F.G.
Early evolution of vertebrate Mybs: an integrative perspective combining synteny, phylogenetic, and gene expression analyses.
Genome Biol Evol. (2015) 7: 3009-3012.

Opazo, J.C., Lee, A.P., Hoffmann, F.G., Toloza-Villalobos, J. Burmester, T. Venkatesh, B. and Storz, J.F.
Ancient duplications and expression divergence in the globin gene superfamily of vertebrates: Insights from the elephant shark genome and transcriptome.
Mol. Biol. Evol. (2015) 32: 1684-1694.

Genome 10K Community of Scientists. 
The Genome 10K Project: A way forward. 
Annu. Rev. Anim. Biosci. (2015) 3: 57-111.

Venkatesh, B. and Ohta, Y.
The shark-family (cartilaginous fish) immunogenome.
In: Immunobiology of the shark. Smith, S.L., Sim, R.M. and Flajnik, M.F. (eds.) CRC Press, 326p, 2014.

You, X. et al.
Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes.
Nat. Commun. (2014) 5:5594.

Nah, G.S., Tay, B., Brenner, S., Osato, M. and Venkatesh, B. 
Characterization of the Runx gene family in a jawless vertebrate, the Japanese lamprey (Lethenteron japonicum). 
PLoS ONE (2014) 9 (11):e113445.

Brawand, D., et al.
The genomic substrate for adaptive radiation in African cichlid fish.
Nature (2014) 513: 375-381.

Guerette, P.A., Hoon, S., Ding, D., Amini, S., Masic, A., Ravi, V., Venkatesh, B., Weaver, J.C. and Miserez, A.
Nano-confined
β-sheets mechanically reinforce the supra-biomolecular network of robust squid sucker ring teeth.
ACS NANO (2014) 8: 7170-7179.

Venkatesh, B., Lee, A.P., Ravi, V., Maurya, A.K., Korzh, V., Lim, Z.W., Ingham, P.W., Boehm, T., Brenner, S. and Warren, W.C.
On the origin of SCPP genes.
Evol. Dev. (2014) 16: 125-126.

Jung, H., Mazzoni, E.O., Soshnikova, N., Venkatesh, B., Duboule, D. and Dasen, J.S.
Evolving Hox activity profiles govern diversity in locomotor systems.
Dev Cell (2014) 29: 171-187.

Nah, G.S., Lim, Z.W., Tay, B., Osato, M. and Venkatesh, B.
Runx family genes in a cartilaginous fish, the elephant shark (Callorhinchus milii).
PLoS ONE (2014) 9 (4):e93816. 

Bhatia, S., Monahan, J., Ravi, V., Gautier, P., Murdoch, E., Brenner, S., van Heyningen, V., Venkatesh, B. and Kleinjan, D.A.
A survey of ancient conserved non-coding elements in the PAX6 locus reveals a landscape of interdigitated cis-regulatory archipelagos.
Dev. Biol. (2014) 387: 214-228.

Venkatesh,B., Lee,A.P., Ravi,V., Maurya, A.K., Lian, M.M., Swann, J.B., Ohta,Y., Flajnik, M.F., Sutoh,Y., Kasahara, M., Hoon, S., Gangu,V., Roy, S.W., Irimia, M., Korzh, V., Kondrychyn, I., Lim, Z.W., Tay, B.-H., Tohari, S., Kong, K.W., Ho, S., Lorente-Galdos, B., Quilez, J., Marques-Bonet, T., Raney, B.J., Ingham, P.W., Tay, A., Hillier, L.W., Minx, P., Boehm, T., Wilson, R.K., Brenner, S. and Warren, W.C.
Elephant shark genome provides unique insights into gnathostome evolution.
Nature (2014) 505, 174-179.

Castro, L.F., Gonçalves, O., Mazan, S., Tay, B-H., Venkatesh, B. and Wilson, J.M. 
Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history. 
Proc. R. Soc. B (2014) 281: 20132669.

Mehta, T.K., Ravi, V., Yamasaki, S., Lee, A.P., Lian, M.M., Tay, B., Tohari, S., Yanai, S., Tay, A., Brenner, S. and Venkatesh, B. 
Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum).
Proc. Natl. Acad. Sci. USA. (2013) 110: 16044-16049.

D'Souza, D.G., Rana, K., Milley, K.M., MacLean, H.E., Zajac, J.D., Bell, J., Brenner, S., Venkatesh, B., Richardson, S.J. and Danks, J.A.
Expression of Wnt signaling skeletal development genes in the cartilaginous fish, elephant shark (Callorhinchus milii).
Gen. Comp. Endocrinol. (2013)193:1-9.

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

Yang, W., Thein, S., Guo, X., Xu, F., Venkatesh, B., Sugii, S., Radda, G.K. and Han, W.
Seipin differentially regulates lipogenesis and adipogenesis through a conserved core sequence and an evolutionarily acquired C-terminus. 
Biochem. J. (2013) 452: 37-44.

Lee, A.P. and Venkatesh, B. 
Ultraconserved Elements (UCEs) in the Human Genome. 
Encyclopedia of Life Sciences (eLS). John Wiley & Sons, Ltd: Chichester. (2013) DOI: 10.1002/9780470015902.a0020842.pub2.

Ravi, V. and Venkatesh, B. 
Fugu: A Compact Model Vertebrate Genome. 
Encyclopedia of Life Sciences (eLS). John Wiley & Sons, Ltd: Chichester. (2013). DOI: 10.1002/9780470015902.a0006147.pub3.

Ravi, V., Bhatia, S., Gautier, P., Loosli, F., Tay, B-H., Tay, A., Murdoch, E., Coutinho, P., van Heyningen, V., Brenner, S., *Venkatesh, B. and *Kleinjan, D.A. 
Sequencing of Pax6 loci from the elephant shark reveals a family of Pax6 genes in vertebrate genomes, forged by ancient duplications and divergences. 
PLoS Genetics (2013) 9 (1): e1003177.

Venkatesh, B., Ravi, V., Lee, A.P., Warren, W.C. and Brenner, S.
Basal vertebrates clarify the evolutionary history of ciliopathy-associated genes Tmem138 and Tmem216.
Mol. Biol. Evol. (2013) 30: 62-65.

Davies, W.L., Tay, B-H., Zheng, L. Danks, J.A., Brenner, S., Foster, R.G., Collin, S.P., Hankins, M.W., *Venkatesh, B. *Hunt, D.M.
Evolution and functional characterisation of melanopsins in a deep-sea chimaera (elephant shark, Callorhinchus milii).
PLoS ONE (2012) 7: e51276. 

Tan, Y.Y., Kodzius, R., Tay, B-H., Tay, A., Brenner, S. and Venkatesh, B.
Sequencing and analysis of full-length cDNAs,
5’-ESTs and 3’-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).
PLoS ONE (2012) 7 (10):e47174.

Chauhan, S., Zheng, X., Tan, Y.Y., Tay, B., Lim, S., *Venkatesh, B. and *Kaldis, P.
Evolution of the Cdk-activator Speedy/RINGO in vertebrates.
Cell. Mol. Life Sci. (2012). 69: 3835-3850.

Yamaguchi, Y., Kaiya, H., Konno, N., Iwata, E., Miyazato, M., Uchiyama, M., Bell, J.D., Toop, T., Donald, J.A., Brenner, S., Venkatesh, B. and Hyodo, S.
The fifth neurohypophysial hormone receptor is structurally related to the V2-type receptor but functionally similar to V1-type receptors.
Gen. Comp. Endocrinol. (2012) 178:519-528.

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.
A Trans-species missense SNP in Amhr2 is associated with sex determination in the tiger pufferfish, Takifugu rubripes (fugu).
PLoS Genetics (2012) 8 (7): e1002798.

Wong, P.B.Y., Wiley, E.O., Johnson, W.E., Ryder, O.A., OBrien, S.J., Haussler, D., Koepfli, K., Houck, M.L., Perelman, P., Mastromonaco, G., Bentley, A.C., Venkatesh, B., Zhang, Y., and Murphy, R.W.
Tissue sampling and standards toward initiatives in vertebrate genomics.
GigaScience (2012). 1: 8.

Bernardi G, Wiley E.O., Mansour, H., Miller, M.R., Orti, G., Haussler, D., OBrien, S.J., Ryder, O.A. and Venkatesh, B.
The fishes of Genome 10K. 
Marine Genomics (2012). 7: 3-6.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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. 

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. 

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

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).

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

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.

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.

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.

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.

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.

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.

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. 
Ancient noncoding elements conserved in the human genome. 
Science (2006) 314, 1892.

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

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.

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

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. 

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. 

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.

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

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.

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. 

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

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. 

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.

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. 

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. 

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

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

Koh, E.G.L., Lam, K., Christoffels, A., Erdmann, M.V., Brenner, S. and Venkatesh, B.
Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis. 
Proc. Natl. Acad. Sci. USA (2003) 100, 1084-1088.

Aparicio, S., ...(37 authors)..., Venkatesh, B.,Rokhsar, D. and Brenner, S. 
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
Science (2002) 297, 1301-1310.

 

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