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Research
General Information
ZIRC
ZFIN ID: ZDB-PERS-960805-49
Becker, Thomas S.
Email: tom.becker@sydney.edu.au
URL: http://sydney.edu.au/bmri/research/neurobiology-genomics/tsbecker.php
Affiliation: Becker Lab
Address: Developmental Neurobiology and Genomics Brain and Mind Research Institute University of Sydney 100 Mallet Street Camperdown, NSW 2050 Australia
Country: Australia
Phone: +61-2-93510997
Fax: +61-2-93510599
Orcid ID:


BIOGRAPHY AND RESEARCH INTERESTS
Central nervous system development and the vertebrate genome.


PUBLICATIONS
Watchon, M., Yuan, K.C., Mackovski, N., Svahn, A.J., Cole, N.J., Goldsbury, C., Rinkwitz, S., Becker, T.S., Nicholson, G.A., Laird, A.S. (2017) Calpain inhibition is protective in Machado-Joseph disease zebrafish due to induction of autophagy. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37(32):7782-7794
Soulika, M., Kaushik, A., Mathieu, B., Lourenço, R., Komisarczuk, A.Z., Romano, S.A., Jouary, A., Lardennois, A., Tissot, N., Okada, S., Abe, K., Becker, T.S., Kapsimali, M. (2016) Diversity in cell motility reveals the dynamic nature of the formation of zebrafish taste sensory organs. Development (Cambridge, England). 143(11):2012-24
Giacomotto, J., Carroll, A.P., Rinkwitz, S., Mowry, B., Cairns, M.J., Becker, T.S. (2016) Developmental suppression of schizophrenia-associated miR-137 alters sensorimotor function in zebrafish. Translational psychiatry. 6:e818
Svahn, A.J., Giacomotto, J., Graeber, M.B., Rinkwitz, S., Becker, T.S. (2016) miR-124 contributes to the functional maturity of microglia. Developmental Neurobiology. 76(5):507-18
Laird, A.S., Mackovski, N., Rinkwitz, S., Becker, T.S., Giacomotto, J. (2016) Tissue-specific models of spinal muscular atrophy confirm a critical role of SMN in motor neurons from embryonic to adult stages. Human molecular genetics. 25(9):1728-38
Abu-Siniyeh, A., Owen, D.M., Benzing, C., Rinkwitz, S., Becker, T.S., Majumdar, A., Gaus, K. (2016) The aPKC/Par3/Par6 polarity complex and membrane order are functionally inter-dependent in epithelia during vertebrate organogenesis. Traffic (Copenhagen, Denmark). 17(1):66-79
Ishibashi, M., Manning, E., Shoubridge, C., Krecsmarik, M., Hawkins, T.A., Giacomotto, J., Zhao, T., Mueller, T., Bader, P.I., Cheung, S.W., Stankiewicz, P., Bain, N.L., Hackett, A., Reddy, C.C., Mechaly, A.S., Peers, B., Wilson, S.W., Lenhard, B., Bally-Cuif, L., Gecz, J., Becker, T.S., Rinkwitz, S. (2015) Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene. Human genetics. 134(11-12):1163-82
Rinkwitz, S., Geng, F., Manning, E., Suster, M., Kawakami, K., Becker, T.S. (2015) BAC transgenic zebrafish reveal hypothalamic enhancer activity around obesity associated SNP rs9939609 within the human FTO gene. Genesis (New York, N.Y. : 2000). 53(10):640-51
Giacomotto, J., Rinkwitz, S., Becker, T.S. (2015) Effective heritable gene knockdown in zebrafish using synthetic microRNAs. Nature communications. 6:7378
Punnamoottil, B., Rinkwitz, S., Giacomotto, J., Svahn, A.J., Becker, T.S. (2015) Motor neuron-expressed microRNAs 218 and their enhancers are nested within introns of SLIT2/3 genes. Genesis (New York, N.Y. : 2000). 53(5):321-8
Naville, M., Ishibashi, M., Ferg, M., Bengani, H., Rinkwitz, S., Krecsmarik, M., Hawkins, T.A., Wilson, S.W., Manning, E., Chilamakuri, C.S., Wilson, D.I., Louis, A., Lucy Raymond, F., Rastegar, S., Strähle, U., Lenhard, B., Bally-Cuif, L., van Heyningen, V., FitzPatrick, D.R., Becker, T.S., Roest Crollius, H. (2015) Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome. Nature communications. 6:6904
Chang, G.H., Lay, A.J., Ting, K.K., Zhao, Y., Coleman, P.R., Powter, E.E., Formaz-Preston, A., Jolly, C.J., Bower, N.I., Hogan, B.M., Rinkwitz, S., Becker, T.S., Vadas, M.A., Gamble, J.R. (2014) ARHGAP18: an endogenous inhibitor of angiogenesis, limiting tip formation and stabilizing junctions. Small GTPases. 5(3):1-15
Giacomotto, J., Brouilly, N., Walter, L., Mariol, M.C., Berger, J., Ségalat, L., Becker, T.S., Currie, P.D., and Gieseler, K. (2013) Chemical genetics unveils a key role of mitochondrial dynamics, cytochrome c release and IP3R activity in muscular dystrophy. Human molecular genetics. 22(22):4562-78
Maley, D., Laird, A.S., Rinkwitz, S., and Becker, T.S. (2013) A Simple and Efficient Protocol for the Treatment of Zebrafish Colonies Infected with Parasitic Nematodes. Zebrafish. 10(3):447-50
Ishibashi, M., Mechaly, A.S., Becker, T.S., and Rinkwitz, S. (2013) Using zebrafish transgenesis to test human genomic sequences for specific enhancer activity. Methods (San Diego, Calif.). 62(3):216-25
Svahn, A.J., Graeber, M.B., Ellett, F., Lieschke, G.J., Rinkwitz, S., Bennett, M.R., and Becker, T.S. (2013) Development of ramified microglia from early macrophages in the zebrafish optic tectum. Developmental Neurobiology. 73(1):60-71
Folgueira, M., Bayley, P., Navratilova, P., Becker, T.S., Wilson, S.W., and Clarke, J.D. (2012) Morphogenesis underlying the development of the everted teleost telencephalon. Neural Development. 7(1):32
Coolen, M., Thieffry, D., Drivenes, O., Becker, T.S., and Bally-Cuif, L. (2012) miR-9 Controls the Timing of Neurogenesis through the Direct Inhibition of Antagonistic Factors. Developmental Cell. 22(5):1052-1064
Becker, T.S., and Rinkwitz, S. (2012) Zebrafish as a genomics model for human neurological and polygenic disorders. Developmental Neurobiology. 72(3):415-428
Sundström, E., Komisarczuk, A.Z., Jiang, L., Golovko, A., Navratilova, P., Rinkwitz, S., Becker, T.S., and Andersson, L. (2012) Identification of a melanocyte-specific, microphthalmia-associated transcription factor-dependent regulatory element in the intronic duplication causing hair greying and melanoma in horses. Pigment cell & melanoma research. 25(1):28-36
Rinkwitz, S., Mourrain, P., and Becker, T.S. (2011) Zebrafish: an integrative System for Neurogenomics and Neurosciences. Prog. Neurobiol.. 93(2):231-243
Labalette, C., Bouchoucha, Y.X., Wassef, M.A., Gongal, P.A., Le Men, J., Becker, T., Gilardi-Hebenstreit, P., and Charnay, P. (2011) Hindbrain patterning requires fine-tuning of early krox20 transcription by Sprouty 4. Development (Cambridge, England). 138(2):317-326
Punnamoottil, B., Herrmann, C., Pascual Anaya, J., D'Aniello, S., Garcia-Fernàndez, J., Akalin, A., Becker, T.S., and Rinkwitz, S. (2010) Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes. Developmental Biology. 340(2):269-282
Dong, X., Navratilova, P., Fredman, D., Drivenes, Ø., Becker, T.S., and Lenhard, B. (2010) Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic acids research. 38(4):1071-1085
Navratilova, P., Fredman, D., Lenhard, B., and Becker, T.S. (2010) Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Molecular genetics and genomics : MGG. 283(2):171-184
Ragvin, A., Moro, E., Fredman, D., Navratilova, P., Drivenes, O., Engström, P.G., Alonso, M.E., Mustienes, E.D., Skarmeta, J.L., Tavares, M.J., Casares, F., Manzanares, M., van Heyningen, V., Molven, A., Njølstad, P.R., Argenton, F., Lenhard, B., and Becker, T.S. (2010) Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3. Proceedings of the National Academy of Sciences of the United States of America. 107(2):775-780
Komisarczuk, A.Z., Kawakami, K., and Becker, T.S. (2009) Cis-regulation and chromosomal rearrangement of the fgf8 locus after the Teleost/tetrapod split. Developmental Biology. 336(2):301-312
Navratilova, P., and Becker, T.S. (2009) Genomic regulatory blocks in vertebrates and implications in human disease. Briefings in functional genomics & proteomics. 8(4):333-342
Amsterdam, A., Lai, K., Komisarczuk, A.Z., Becker, T.S., Bronson, R.T., Hopkins, N., and Lees, J.A. (2009) Zebrafish Hagoromo Mutants Up-Regulate fgf8 Postembryonically and Develop Neuroblastoma. Molecular cancer research : MCR. 7(6):841-850
Navratilova, P., Fredman, D., Hawkins, T.A., Turner, K., Lenhard, B., and Becker, T.S. (2009) Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Developmental Biology. 327(2):526-540
Topp, S., Stigloher, C., Komisarczuk, A.Z., Adolf, B., Becker, T.S., and Bally-Cuif, L. (2008) Fgf signaling in the zebrafish adult brain: Association of Fgf activity with ventricular zones but not cell proliferation. The Journal of comparative neurology. 510(4):422-439
Komisarczuk, A.Z., Topp, S., Stigloher, C., Kapsimali, M., Bally-Cuif, L., and Becker, T.S. (2008) Enhancer detection and developmental expression of zebrafish sprouty1, a member of the fgf8 synexpression group. Developmental dynamics : an official publication of the American Association of Anatomists. 237(9):2594-2603
Punnamoottil, B., Kikuta, H., Pezeron, G., Erceg, J., Becker, T.S., and Rinkwitz, S. (2008) Enhancer detection in zebrafish permits the identification of neuronal subtypes that express Hox4 paralogs. Developmental dynamics : an official publication of the American Association of Anatomists. 237(8):2195-2208
Bessa, J., Tavares, M.J., Santos, J., Kikuta, H., Laplante, M., Becker, T.S., Gómez-Skarmeta, J.L., and Casares, F. (2008) meis1 regulates cyclin D1 and c-myc expression, and controls the proliferation of the multipotent cells in the early developing zebrafish eye. Development (Cambridge, England). 135(5):799-803
Hoppmann, V., Wu, J.J., Søviknes, A.M., Helvik, J.V., and Becker, T.S. (2008) Expression of the eight AMPA receptor subunit genes in the developing central nervous system and sensory organs of zebrafish. Developmental dynamics : an official publication of the American Association of Anatomists. 237(3):788-799
Pézeron, G., Mourrain, P., Courty, S., Ghislain, J., Becker, T.S., Rosa, F.M., and David, N.B. (2008) Live analysis of endodermal layer formation identifies random walk as a novel gastrulation movement. Current biology : CB. 18(4):276-281
Meijer, A.H., van der Sar, A.M., Cunha, C., Lamers, G.E., Laplante, M.A., Kikuta, H., Bitter, W., Becker, T.S., and Spaink, H.P. (2008) Identification and real-time imaging of a myc-expressing neutrophil population involved in inflammation and mycobacterial granuloma formation in zebrafish. Developmental and comparative immunology. 32(1):36-49
Weiner, A.M., Allende, M.L., Becker, T.S., and Calcaterra, N.B. (2007) CNBP mediates neural crest cell expansion by controlling cell proliferation and cell survival during rostral head development. Journal of cellular biochemistry. 102(6):1553-1570
Becker, T.S., and Lenhard, B. (2007) The random versus fragile breakage models of chromosome evolution: a matter of resolution. Molecular genetics and genomics : MGG. 278(5):487-491
Herpin, A., Lelong, C., Becker, T., Favrel, P., and Cunningham, C. (2007) A tolloid homologue from the Pacific oyster Crassostrea gigas. Gene expression patterns : GEP. 7(6):700-708
Kikuta, H., Laplante, M., Navratilova, P., Komisarczuk, A.Z., Engstrom, P.G., Fredman, D., Akalin, A., Caccamo, M., Sealy, I., Howe, K., Ghislain, J., Pezeron, G., Mourrain, P., Ellingsen, S., Oates, A.C., Thisse, C., Thisse, B., Foucher, I., Adolf, B., Geling, A., Lenhard, B., and Becker, T.S. (2007) Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome research. 17(5):545-555
Shankaran, S.S., Sieger, D., Schroter, C., Czepe, C., Pauly, M.C., Laplante, M.A., Becker, T.S., Oates, A.C., and Gajewski, M. (2007) Completing the set of h/E(spl) cyclic genes in zebrafish: her12 and her15 reveal novel modes of expression and contribute to the segmentation clock. Developmental Biology. 304(2):615-632
Rinkwitz, S., Laplante, M., Kikuta, H., and Becker, T.S. (2007) A large-scale zebrafish enhancer screen. ZFIN Direct Data Submission.
Kikuta, H., Fredman, D., Rinkwitz, S., Lenhard, B., and Becker, T.S. (2007) Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome biology. 8(1):S4
Pezeron, G., Anselme, I., Laplante, M., Ellingsen, S., Becker, T.S., Rosa, F.M., Charnay, P., Schneider-Maunoury, S., Mourrain, P., and Ghislain, J. (2006) Duplicate sfrp1 genes in zebrafish: sfrp1a is dynamically expressed in the developing central nervous system, gut and lateral line. Gene expression patterns : GEP. 6(8):835-842
Hadrys, T., Punnamoottil, B., Pieper, M., Kikuta, H., Pezeron, G., Becker, T.S., Prince, V., Baker, R., and Rinkwitz, S. (2006) Conserved co-regulation and promoter sharing of hoxb3a and hoxb4a in zebrafish. Developmental Biology. 297(1):26-43
Stigloher, C., Ninkovic, J., Laplante, M., Geling, A., Tannhauser, B., Topp, S., Kikuta, H., Becker, T.S., Houart, C., and Bally-Cuif, L. (2006) Segregation of telencephalic and eye-field identities inside the zebrafish forebrain territory is controlled by Rx3. Development (Cambridge, England). 133(15):2925-2935
Laplante, M., Kikuta, H., Konig, M., and Becker, T.S. (2006) Enhancer detection in the zebrafish using pseudotyped murine retroviruses. Methods (San Diego, Calif.). 39(3):189-198
Gomez-Skarmeta, J.L., Lenhard, B., and Becker, T.S. (2006) New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences. Developmental dynamics : an official publication of the American Association of Anatomists. 235(4):870-885
Amsterdam, A., and Becker, T.S. (2005) Transgenes as screening tools to probe and manipulate the zebrafish genome. Developmental dynamics : an official publication of the American Association of Anatomists. 234(2):255-268
Ellingsen, S., Laplante, M.A., Konig, M., Kikuta, H., Furmanek, T., Hoivik, E.A., and Becker, T.S. (2005) Large-scale enhancer detection in the zebrafish genome. Development (Cambridge, England). 132(17):3799-3811
Herpin, A., Lelong, C., Becker, T., Rosa, F., Favrel, P., and Cunningham, C. (2005) Structural and functional evidence for a singular repertoire of BMP receptor signal transducing proteins in the lophotrochozoan Crassostrea gigas suggests a shared ancestral BMP/activin pathway. The FEBS journal. 272(13):3424-3440
Hardison, A.L., Lichten, L., Banerjee-Basu, S., Becker, T.S., and Burgess, S.M. (2005) The zebrafish gene claudinj is essential for normal ear function and important for the formation of the otoliths. Mechanisms of Development. 122(7-8):949-958
Herpin, A., Lelong, C., Becker, T., Rosa, F.M., Favrel, P., and Cunningham, C. (2005) Structural and functional evidences for a type 1 TGF-beta sensu stricto receptor in the lophotrochozoan Crassostrea gigas suggest conserved molecular mechanisms controlling mesodermal patterning across bilateria. Mechanisms of Development. 122(5):695-705
Kawakami, K., Amsterdam, A., Shimoda, N., Becker, T., Mugg, J., Shima, A., and Hopkins, N. (2000) Proviral insertions in the zebrafish hagoromo gene, encoding an F-box/WD40-repeat protein, cause stripe pattern anomalies. Current biology : CB. 10(8):463-466
Becker, T.S., Burgess, S.M., Amsterdam, A.H., Allende, M.L., and Hopkins, N. (1998) not really finished is crucial for development of the zebrafish outer retina and encodes a transcription factor highly homologous to human Nuclear Respiratory Factor-1 and avian Initiation Binding Repressor. Development (Cambridge, England). 125:4369-4378
Amsterdam, A., Yoon, C., Allende, M., Becker, T., Kawakami, K., Burgess, S., Gaiano, N., and Hopkins, N. (1997) Retrovirus-mediated insertional mutagenesis in zebrafish and identification of a molecular marker for embryonic germ cells. Cold Spring Harbor symposia on quantitative biology. 62:437-450
Allende, M.L., Amsterdam, A., Becker, T., Kawakami, K., Gaiano, N., and Hopkins, N. (1996) Insertional mutagenesis in zebrafish identifies two novel genes, pescadillo and dead eye, essential for embryonic development. Genes & Development. 10(24):3141-3155
Gaiano, N., Amsterdam, A., Kawakami, K., Allende, M., Becker, T., and Hopkins, N. (1996) Insertional mutagenesis and rapid cloning of essential genes in zebrafish. Nature. 383(6603):829-832

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