Publications: Barrero, Roberto

2012

Appels, R., Barrero, R. and Bellgard, M. (2012) Advances in biotechnology and linking outputs to variation in complex traits: Plant and Animal Genome meeting January 2012. Functional & Integrative Genomics, 12 (1). pp. 1-9.

Edwards, D., Wilcox, S., Barrero, R.A., Fleury, D., Cavanagh, C.R., Forrest, K.L., Hayden, M.J., Moolhuijzen, P., Keeble-Gagnère, G., Bellgard, M.I., Lorenc, M.T., Shang, C.A., Baumann, U., Taylor, J.M., Morell, M.K., Langridge, P., Appels, R. and Fitzgerald, A. (2012) Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnology Journal, 10 (6). pp. 703-708.

Black, M., Moolhuijzen, P., Chapman, B., Barrero, R., Howieson, J., Hungria, M. and Bellgard, M. (2012) The genetics of symbiotic nitrogen fixation: Comparative genomics of 14 rhizobia strains by resolution of protein clusters. Genes, 3 (1). pp. 138-166.

McCooke, J.K., Appels, R., Barrero, R.A., Ding, A., Ozimek-Kulik, J.E., Bellgard, M.I., Morahan, G. and Phillips, J.K. (2012) A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8. BMC Genomics, 13 (1). p. 393.

Taniya, T., Tanaka, S., Yamaguchi-Kabata, Y., Hanaoka, H., Yamasaki, C., Maekawa, H., Barrero, R.A., Lenhard, B., Datta, M.W., Shimoyama, M., Bumgarner, R., Chakraborty, R., Hopkinson, I., Jia, L., Hide, W., Auffray, C., Minoshima, S., Imanishi, T. and Gojobori, T. (2012) A prioritization analysis of disease association by data-mining of functional annotation of human genes. Genomics, 99 (1). pp. 1-9.

2011

Bellgard, M.I., Moolhuijzen, P.M., Guerrero, F.D., Schibeci, D., Rodriguez-Valle, M., Peterson, D.G., Dowd, S.E., Barrero, R., Hunter, A., Miller, R.J. and Lew-Tabor, A.E. (2011) CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus. International Journal for Parasitology, 42 (2). pp. 161-169.

Murray, D.C., Bunce, M., Cannell, B.L., Oliver, R., Houston, J., White, N.E., Barrero, R.A., Bellgard, M.I. and Haile, J. (2011) DNA-based faecal dietary analysis: A comparison of qPCR and high throughput sequencing approaches. PloS one, 6 (10). e25776.

Barrero, R.A., Chapman, B., Yang, Y., Moolhuijzen, P., Keeble-Gagnère, G., Zhang, N., Tang, Q., Bellgard, M.I. and Qiu, D. (2011) De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes. BMC Genomics, 12 (1). p. 600.

Barrero, R.A., Bellgard, M. and Zhang, X. (2011) Diverse approaches to achieving grain yield in wheat. Functional & Integrative Genomics, 11 (1). pp. 37-48.

Barrero, R.A., Keeble-Gagnère, G., Zhang, B., Moolhuijzen, P., Ikeo, K., Tateno, Y., Gojobori, T., Guerrero, F.D., Lew-Tabor, A. and Bellgard, M. (2011) Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus. BMC Genomics, 12 (1). Article No. 328.

Lew-Tabor, A.E., Kurscheid, S., Barrero, R., Gondro, C., Moolhuijzen, P.M., Rodriguez Valle, M., Morgan, J.A.T., Covacin, C. and Bellgard, M.I. (2011) Gene expression evidence for off-target effects caused by RNA interference-mediated gene silencing of Ubiquitin-63E in the cattle tick Rhipicephalus microplus. International Journal for Parasitology, 41 (9). pp. 1001-1014.

Appels, R., Adelson, D.L., Moolhuijzen, P., Webster, H., Barrero, R. and Bellgard, M. (2011) Genome studies at the PAG 2011 conference. Functional & Integrative Genomics, 11 (1). pp. 1-11.

Lew-Tabor, A., Rodriguez-Valle, M., Kurscheid, S., Barrero, R., Gondro, C., Moolhuijzen, P.M., Morgan, J.A.T., Bruyeres, A.B., Zhang, B. and Bellgard, M.I. (2011) Microarray evidence for off target effects in tick RNA interference experiments, and the lack of strong correlation between DSRNA and antibody phenotypes in tick In vitro treatments for vaccine candidate screening. In: Ticks and Tick-borne Pathogens International Conference (TTP-7) 2011, 28 August - 2 September 2011, Zaragoza, Spain.

Bellgard, M., Moolhuijzen, P., Guerrero, F.D., Appels, R., Schibeci, D., Rodriguez-Valle, M., Barrero, R., Hunter, A. and Lew-Tabor, A. (2011) A new web-based genomics resource for bioinformatics analysis of Rhipicephalus (Boophilus) microplus: CattleTickBase. In: Ticks and Tick-borne Pathogens International Conference (TTP-7) 2011, 28 August - 2 September 2011, Zaragoza, Spain.

2010

Appels, R., Barrero, R., Keeble, G. and Bellgard, M. (2010) Advances in genome studies: the PAG 2010 conference. Functional & Integrative Genomics, 10 (1). pp. 1-9.

Guerrero, F.D., Moolhuijzen, P., Peterson, D.G., Bellgard, M.I., Schibeci, D., Hunter, A., Rodriguez-Valle, M., Barrero, R., Nene, V.M. and Lew-Tabor, A.E. (2010) Cot filtration approach for advancing genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus. In: Entomology 2010: ESA 58th Annual Meeting, 12 - 15 December 2010, San Diego, CA.

Matsumura, H., Yoshida, K., Luo, S., Kimura, E., Fujibe, T., Albertyn, Z., Barrero, R.A., Krüger, D.H., Kahl, G., Schroth, G.P. and Terauchi, R. (2010) High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing. PLoS ONE, 5 (8). e12010.

Bellgard, M., Guerrero, F.D., Moolhuijzen, P., Schibeci, D., Hunter, A., Rodriguez-Valle, M., Barrero, R., Gondro, C. and Lew-Tabor, A.E. (2010) Toward a genome sequence for Rhipicephalus (Boophilus) microplus: Cattle tick base available resources for the research community. In: XIIth International Conference for Parasitology (ICOPA), 15 - 20 August , Melbourne, Australia.

Wanchanthuek, P., Bellgard, M., La, T., Ryan, K., Moolhuijzen, P., Chapman, B., Black, M.L., Schibeci, D., Hunter, A., Barrero, R., Phillips, N.D. and Hampson, D.J. (2010) The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes. PLoS ONE, 5 (7). pp. 1-16.

Moolhuijzen, P., Kulski, J.K., Dunn, D.S., Schibeci, D., Barrero, R., Gojobori, T. and Bellgard, M. (2010) The transcript repeat element: the human Alu sequence as a component of gene networks influencing cancer. Functional & Integrative Genomics, 10 (3). pp. 307-319.

2009

Kurscheid, S., Lew-Tabor, A.E., Rodriguez Valle, M., Bruyeres, A.G., Doogan, V.J, Munderloh, U.G., Guerrero, F.D., Barrero, R.A. and Bellgard, M.I. (2009) Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss-of-function phenotypes in Drosophila. BMC Molecular Biology, 10 (1). p. 26.

Bellgard, M., Wanchanthuek, P., La, T., Ryan, K., Moolhuijzen, P., Albertyn, Z., Shaban, B., Motro, Y., Dunn, D.S., Schibeci, D., Hunter, A., Barrero, R., Phillips, N.D. and Hampson, D.J. (2009) Genome sequence of the pathogenic intestinal spirochete Brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine. PLoS ONE, 4 (3). e4641.

Kawazoe, A., Jin, L., Shigematsu, M., Bekki, D., Barrero, R.A., Taniguchi, K. and Collier, N. (2009) The development of a schema for semantic annotation: Gain brought by a formal ontological method. Applied Ontology, 4 (1). pp. 5-20.

2008

Yamasaki, C., Murakami, K., Fujii, Y., Sato, Y., Harada, E., Takeda, J-I, Taniya, T., Sakate, R., Kikugawa, S., Shimada, M., Tanino, M., Koyanagi, K.O., Barrero, R.A., Gough, C., Chun, H-W, Habara, T., Hanaoka, H., Hayakawa, Y., Hilton, P.B., Kaneko, Y., Kanno, M., Kawahara, Y., Kawamura, T., Matsuya, A., Nagata, N., Nishikata, K., Noda, A.O., Nurimoto, S., Saichi, N., Sakai, H., Sanbonmatsu, R., Shiba, R., Suzuki, M., Takabayashi, K., Takahashi, A., Tamura, T., Tanaka, M., Tanaka, S., Todokoro, F., Yamaguchi, K., Yamamoto, N., Okido, T., Mashima, J., Hashizume, A., Jin, L., Lee, K-B, Lin, Y-C, Nozaki, A., Sakai, K., Tada, M., Miyazaki, S., Makino, T., Ohyanagi, H., Osato, N., Tanaka, N., Suzuki, Y., Ikeo, K., Saitou, N., Sugawara, H., O’Donovan, C., Kulikova, T., Whitfield, E., Halligan, B., Shimoyama, M., Twigger, S., Yura, K., Kimura, K., Yasuda, T., Nishikawa, T., Akiyama, Y., Motono, C., Mukai, Y., Nagasaki, H., Suwa, M., Horton, P., Kikuno, R., Ohara, O., Lancet, D., Eveno, E., Graudens, E., Imbeaud, S., Debily, M., Hayashizaki, Y., Amid, C., Han, M., Osanger, A., Endo, T., Thomas, M.A., Hirakawa, M., Makalowski, W., Nakao, M., Kim, N-S, Yoo, H-S, De Souza, S.J., Bonaldo, M., Niimura, Y., Kuryshev, V., Schupp, I., Wiemann, S., Bellgard, M., Shionyu, M., Jia, L., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Zhang, Q., Go, M., Minoshima, S., Ohtsubo, M., Hanada, K., Tonellato, P., Isogai, T., Zhang, J., Lenhard, B., Kim, S., Chen, Z., Hinz, U., Estreicher, A., Nakai, K., Makalowska, I., Hide, W., Tiffin, N., Wilming, L., Chakraborty, R., Soares, M.B., Chiusano, M.L., Suzuki, Y., Auffray, C., Yamaguchi-Kabata, Y., Itoh, T., Hishiki, T., Fukuchi, S., Nishikawa, K., Sugano, S., Nomura, N., Tateno, Y., Imanishi, T. and Gojobori, T. (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research, 36 (Supp 1). D793-D799.

Kurscheid, S., Rodriguez-Valle, M., Moolhuijzen, P.M., Barrero, R., Guerrero, F.D., Lew-Tabor, A.E. and Bellgard, M.I. (2008) In silico prediction of tick vaccine candidates. In: ASP & ARC/NHMRC Research Network for Parasitology Annual Conference, 6 - 9 July 2008, Glenelg, S.A..

Tanaka, T., Antonio, B.A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J.-i., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y-C, Wei, F-J, Hsing, Y-i, Zhao, Q., Bin, H., Kramer, M.R., McCombie, R.W., Lonsdale, D., O’Donovan, C.C., Whitfield, E.J., Apweiler, R., Koyanagi, K.O., Khurana, J.P., Raghuvanshi, S., Singh, N.K., Tyagi, A.K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R.M., Hoen, D.R., Bureau, T.E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R.A., Sato, Y., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., OOta, S., Fuks, G., Messing, J., Christie, K.R., Lieberherr, D., Kim, H-R, Zuccolo, A., Wing, R.A., Nobuta, K., Green, P.J., Lu, C., Meyers, B.C., Chaparro, C., Piegu, B., Panaud, O. and Echeverria, M. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Research, 36 (Supp 1). D1028-D1033.

2007

Itoh, T., Tanaka, T., Barrero, R.A., Yamasaki, C., Fujii, Y., Hilton, P.B., Antonio, B.A., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., Costa de Oliveira, A., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A.T., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, Y., Kawamura, T., Kawashima, H., Khurana, J.P., Kikuchi, S., Komatsu, S., Koyanagi, K.O., Kubooka, H., Lieberherr, D., Lin, Y-C, Lonsdale, D., Matsumoto, T., Matsuya, A., McCombie, W.R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Nam, J., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., OOta, S., Osato, N., Palmer, L.E., Quetier, F., Raghuvanshi, S., Saichi, N., Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, F., Sato, Y., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N.K., Smith-White, B., Takeda, J.-i., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A.K., Vanavichit, A., Wang, A., Wing, R.A., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Yu, Y., Zhang, H., Zhao, Q., Higo, K., Burr, B., Gojobori, T. and Sasaki, T. (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research, 17 (2). pp. 175-183.

Collier, N., Kawazoe, A., Jin, L., Shigematsu, M., Dien, D., Barrero, R.A., Takeuchi, K. and Kawtrakul, A. (2007) A multilingual ontology for infectious disease surveillance: rationale, design and challenges. Language Resources and Evaluation, 40 (3-4). pp. 405-413.

2006

Takeda, J-I, Suzuki, Y., Nakao, M., Barrero, R.A., Koyanagi, K.O., Jin, L., Motono, C., Hata, H., Isogai, T., Nagai, K., Otsuki, T., Kuryshev, V., Shionyu, M., Yura, K., Go, M., Thierry-Mieg, J., Thierry-Mieg, D., Wiemann, S., Nomura, N., Sugano, S., Gojobori, T. and Imanishi, T. (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Research, 34 (14). pp. 3917-3928.

2005

Yamasaki, C., Koyanagi, K.O., Fujii, Y., Itoh, T., Barrero, R., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., Takeda, J-I, Fukuchi, S., Miyazaki, S., Nomura, N., Sugano, S., Imanishi, T. and Gojobori, T. (2005) Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene, 364 . pp. 99-107.

Nakao, M., Barrero, R.A., Mukai, Y., Motono, C., Suwa, M. and Nakai, K. (2005) Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals. Nucleic Acids Research, 33 (8). pp. 2355-2363.

Sakurai, H., Barrero, R.A. and Gojobori, T. (2005) Prediction of miRNAs and their target genes. In: Nakamura, Y. and Ouchi, M., (eds.) RNA Frontiers of Engineering. CMC Publishing, pp. 113-125.

2004

Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., Yura, K., Miyazaki, S., Ikeo, K., Homma, K., Kasprzyk, A., Nishikawa, T., Hirakawa, M., Thierry-Mieg, J., Thierry-Mieg, D., Ashurst, J., Jia, L., Nakao, M., Thomas, M.A., Mulder, N., Karavidopoulou, Y., Jin, L., Kim, S., Yasuda, T., Lenhard, B., Eveno, E., Suzuki, Y., Yamasaki, C., Takeda, J-I, Gough, C., Hilton, P., Fujii, Y., Sakai, H., Tanaka, S., Amid, Clara, Bellgard, M., Bonaldo, M., Bono, H., Bromberg, S.K., Brookes, A.J., Bruford, E., Carninci, P., Chelala, C., Couillault, C., Souza, S., Debily, M., Devignes, M., Dubchak, I., Endo, T., Estreicher, A., Eyras, E., Fukami-Kobayashi, K., R. Gopinath, G., Graudens, E., Hahn, Y., Han, M., Han, Z-G., Hanada, K., Hanaoka, H., Harada, E., Hashimoto, K., Hinz, U., Hirai, M., Hishiki, T., Hopkinson, I., Imbeaud, S., Inoko, H., Kanapin, A., Kaneko, Y., Kasukawa, T., Kelso, J., Kersey, P., Kikuno, R., Kimura, K., Korn, B., Kuryshev, V., Makalowska, I., Makino, T., Mano, S., Mariage-Samson, R., Mashima, J., Matsuda, H., Mewes, H-W, Minoshima, S., Nagai, K., Nagasaki, H., Nagata, N., Nigam, R., Ogasawara, O., Ohara, O., Ohtsubo, M., Okada, N., Okido, T., Oota, S., Ota, M., Ota, T., Otsuki, T., Piatier-Tonneau, D., Poustka, A., Ren, S-X, Saitou, N., Sakai, K., Sakamoto, S., Sakate, R., Schupp, I., Servant, F., Sherry, S., Shiba, R., Shimizu, N., Shimoyama, M., Simpson, A.J., Soares, B., Steward, C., Suwa, M., Suzuki, M., Takahashi, A., Tamiya, G., Tanaka, H., Taylor, T., Terwilliger, J.D., Unneberg, P., Veeramachaneni, V., Watanabe, S., Wilming, L., Yasuda, N., Yoo, H-S, Stodolsky, M., Makalowski, W., Go, M., Nakai, K., Takagi, T., Kanehisa, M., Sakaki, Y., Quackenbush, J., Okazaki, Y., Hayashizaki, Y., Hide, W., Chakraborty, R., Nishikawa, K., Sugawara, H., Tateno, Y., Chen, Z., Oishi, M., Tonellato, P., Apweiler, R., Okubo, K., Wagner, L., Wiemann, S., Strausberg, R.L., Isogai, T., Auffray, C., Nomura, N., Gojobori, T. and Sugano, S. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology, 2 (6). e162.

2003

Barrero, R.A., Umeda, M., Yamamura, S. and Uchimiya, H. (2003) Over-expression of arabidopsis CAP causes decreased cell expansion leading to organ size reduction in transgenic tobacco plants. Annals of Botany, 91 (5). pp. 599-603.

2002

Barrero, R.A., Umeda, M., Yamamura, S. and Uchimiya, H. (2002) Arabidopsis CAP Regulates the Actin Cytoskeleton Necessary for Plant Cell Elongation and Division. The Plant Cell Online, 14 (1). pp. 149-163.

2000

Matsukura, C., Kawai, M., Toyofuku, K., Barrero, R.A., Uchimiya, H. and Yamaguchi, J. (2000) Transverse vein differentiation associated with gas space formation - Fate of the middle cell layer in leaf sheath development of rice. Annals of Botany, 85 (1). pp. 19-27.

1999

Samarajeewa, P.K., Barrero, R.A., Umeda-Hara, C., Kawai, M. and Uchimiya, H. (1999) Cortical cell death, cell proliferation, macromolecular movements and rTip1 expression pattern in roots of rice ( Oryza sativa L.) under NaCl stress. Planta, 207 (3). pp. 354-361.

1998

Kawai, M., Samarajeewa, P.K., Barrero, R.A., Nishiguchi, M. and Uchimiya, H. (1998) Cellular dissection of the degradation pattern of cortical cell death during aerenchyma formation of rice roots. Planta, 204 (3). pp. 277-287.