Taro L. Saito, DBLP Entry

Refereed Conference/Journal Papers

  • Toshiya Nishimura, Amaury Herpin, Tetsuaki Kimura, Ikuyo Hara, Toshihiro Kawasaki, Shuhei Nakamura, Yasuhiro Yamamoto, Taro L. Saito, Jun Yoshimura, Shinichi Morishita, Tatsuya Tsukahara, Satoru Kobayashi, Kiyoshi Naruse, Shuji Shigenobu, Noriyoshi Sakai, Manfred Schartl, and Minoru Tanaka. Analysis of a novel gene, Sdgc, reveals sex chromosome-dependent differences of medaka germ cells prior to gonad formation. Development 2014 141:3363-3369; July 30, 2014, doi:10.1242/dev.106864.

  • Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Kazuki Ichikawa, Takayoshi Otsuka, Katsumi Ogoshi, Taro L. Saito, Kouji Matsushima, Sumio Sugano, Shinichi Hashimoto, Yutaka Suzuki, Shinichi Morishita, and Hiroyuki Takeda. Large hypomethylated domain serves as strong repressive machinery for key developmental genes in vertebrate. Development 2014, doi:10.1242/dev.108548.

  • Taro L. Saito, Shin-ichi Hashimoto, Sam Guoping Gu, J. Jason Morton, Michael Stadler, Thomas Blumenthal, Andrew Fire(*), and Shinichi Morishita(*). The Transcription Start Site Landscape of C. elegans. Genome Research 2013 Aug;23(8):1348-61. *: joint corresponding authors

  • Ishikawa T, Okada T, Ishikawa-Fujiwara T, Todo T, Kamei Y, Shigenobu S, Tanaka M, Saito TL, Yoshimura J, Morishita S, Toyoda A, Sakaki Y, Taniguchi Y, Takeda S, Mori K. ATF6α/β-mediated adjustment of ER chaperone levels is essential for development of the notochord in medaka fish. Mol Biol Cell. 24(9):1387-1395. (2013)

  • Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul JP Bonnal, Brad Chapman, Peter JA Cock, Tore Eriksson, Paul MK Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R Kinjo, Fumikazu Konishi, Kyung-Hoon Kwon, Alberto Labarga, Anna-Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Pjotr Prins, Taro L Saito, Matthias Samwald, Venkata P Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger A Vos, David Withers, Chisato Yamasaki, Christian M Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. Journal of Biomedical Semantics doi:10.1186/2041-1480-4-6 (2013)

  • Wei Qu, Shin-ichi Hashimoto, Atsuko Shimada, Yoichiro Nakatani, Kazuki Ichikawa, Taro L Saito, Katsumi Ogoshi, Kouji Matsushima, Yutaka Suzuki, Sumio Sugano, Hiroyuki Takeda, Shinichi Morishita. Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns. Genome Research 22:1419-1425 (2012)

  • Higasa K(*), Nikaido M(*), Saito TL(*), Yoshimura J(*), Suzuki Y, Suzuki H, Nishihara H, Aibara M, Ngatunga BP, Kalombo HW, Sugano S, Morishita S(#), Okada N (#). Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths. Gene. 505(2):324-32 (2012) (* first authors, # corresponding authors)

  • Mitsui J, Matsukawa T, Ishiura H, Higasa K, Yoshimura J, Saito TL, Ahsan B, Takahashi Y, Goto J, Iwata A, Niimi Y, Riku Y, Goto Y, Mano K, Yoshida M, Morishita S, Tsuji S. CSF1R mutations identified in three families with autosomal dominantly inherited leukoencephalopathy. Am J Med Genet B Neuropsychiatr Genet. 159B(8):951-7. (2012)

  • Accelerating Path-free XML Queries in RDBMS. Hongyan Wu, Taro L. Saito, Shinichi Morishita. IPSJ Online Transactions. Vol. 3, pp.206-217 (2010)

  • UTGB Toolkit for Personalized Genome Browsers. Taro L. Saito, Jun Yoshimura, Shin Sasaki, Budrul Ahsan, Atsushi Sasaki, Reginaldo Kuroshu and Shinichi Morishita. Bioinformatics (2009) 25 (15): 1856-1861. doi: 10.1093/bioinformatics/btp350

  • Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites. Shin Sasaki, Cecilia C. Mello, Atsuko Shimada, Yoichiro Nakatani, Shin-ichi Hashimoto, Masako Ogawa, Kouji Matsushima, Sam Guoping Gu, Masahiro Kasahara, Budrul Ahsan, Atsushi Sasaki, Taro L. Saito, Yutaka Suzuki, Sumio Sugano, Yuji Kohara, Hiroyuki Takeda, Andrew Fire, Shinichi Morishita. Science 16, January 2009:401-404.

  • MachiBase: A Drosophila Melanogaster 5’-end mRNA Transcription Database. Budrul Ahsan (*), Taro L. Saito (*), Shin-ichi Hashimoto, Keigo Muramatsu, Manabu Tsuda, Atushi Sasaki, Kouji Matsushima, Toshiro Aigaki, Shinichi Morishita. Nucleic Acids Research (Database Issue) 2009. (* joint first authors)

  • Relational-Style XML Query. Taro L. Saito, Shinichi Morishita. SIGMOD 2008, Vancouver, June 2008. (PDF), (Presentation Slides).

  • UTGB/Medaka: Genomic Resource Database for Medaka Biology. Budrul Ahsan, Daisuke Kobayashi, Tomoyuki Yamada, Masahiro Kasahara, Shin Sasaki, Taro L. Saito, Yukinobu Nagayasu, Koichiro Doi, Yoichiro Nakatani, Wei Qu, Tomoko Jindo, Atsuko Shimada, Kiyoshi Naruse, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi Shimizu, Shin-ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-I, Hiroyuki Takeda, Yuji Kohara, and Shinichi Morishita. Nucleic Acids Research, published on October 11, 2007. doi:10.1093/nar/gkm765

  • Efficient Integration of Structure Indexes of XML. Taro L. Saito, Shinichi Morishita. The 12th International Conference on Database Systems for Advanced Applications (DASFAA 2007). (PDF)

  • Amoeba Join: Overcoming Structural Fluctuations of XML Data. Taro L. Saito, Shinichi Morishita. In proc. of the Ninth International Workshop on the Web and Databases (WebDB 2006). (PDF)

  • Evaluation of Image Processing Programs for Accurate Measurement of Budding and Fission Yeast Morphology. Genjiro Suzuki, Hiroshi Sawai, Miwaka Ohtani, Satoru Nogami, Fumi Sano-Kumagai, Ayaka Saka, Masashi Yukawa, Taro L. Saito, Jun Sese, Dai Hirata, Shinichi Morishita and Yoshikazu Ohya. *Current Genetics. 2006 Jan 6

  • High-Dimensional and Large-Scale Phenotyping of Yeast Mutants. Yoshikazu Ohya, Jun Sese(*), Masashi Yukawa(*), Fumi Sano, Yoichiro Nakatani, Taro L. Saito, Ayaka Saka, Tomoyuki Fukuda, Satoru Ishihara, Satomi Oka, Genjiro Suzuki, Machika Watanabe, Aiko Hirata, Miwaka Ohtani, Hiroshi Sawai, Nicolas Fraysse, Jean-Paul Latge, Jean M. Francois, Markus Aebi, Seiji Tanaka, Sachiko Muramatsu, Hiroyuki Araki, Kintake Sonoike, Satoru Nogami, and Shinichi Morishita. PNAS published December 19, 2005, 10.1073/pnas.0509436102 (Genetics) (* equally contributed authors)

  • Data Mining Tools for The Saccharomyces Cerevisiae Morphological Database. Taro L. Saito(*), Jun Sese(*), Yoichiro Nakatani, Fumi Sano, Masashi Yukawa, Yoshikazu Ohya and Shinichi Morishita. Nucleic Acids Research 2005. Vol. 33 (Web Server Issue). (* equally contributed authors)

  • SCMD: Saccharomyces Cerevisiae Morphological Database. Taro L. Saito, Miwaka Ohtani, Hiroshi Sawai, Fumi Sano, Ayaka Saka, Daisuke Watanabe, Masashi Yukawa, Yoshikazu Ohya, and Shinichi Morishita. Nucleic Acids Research Vol. 32: D319-D322 (2004).

    • SCMD http://scmd.gi.k.u-tokyo.ac.jp is an web database server that provides millions of micrographs of yeast mutants. Each micrograph is processed by our image processing software, and various kinds of phenotype data are now available in SCMD. Its database server is implemented by using the technologies of Xerial.
  • Xerial: An Update Tolerant and High Concurrent XML Database. Taro L. Saito, Shinichi Morishita. In Proceedings of Fourth Data Mining Workshop 2004, JSSST. p. 13-20 (PDF)

  • Transaction management for XML (in Japanese). Taro L. Saito, Shinichi Morishita. In Proceedings of Joint Symposium on Parallel Processing (JSPP 2002), May 2002, p. 103-110 (PDF), (Presentation Slides) (in Japanese)

Theses

  • Purifying XML Structures. Taro L. Saito. PhD thesis, Department of Computer Science, Graduate School of Information Science and Technology, the University of Tokyo, December 2006 (PDF) (presentation slides).

  • On Concurrency and Updatability of XML databases. Taro L. Saito. Master thesis, Department of Computer Science, Graduate School of Information Science and Technology, the University of Tokyo, January 2004. (PDF) (Presentation Slides (in Japanese))

  • Transaction Management for XML. Taro L. Saito. Senior thesis submitted to Department of Information Science, Faculty of Science, University of Tokyo, February 2002. (PDF), (MS PowerPoint file).

Invited Talks

Talks

  • Create Your Own Genome Browser with UTGB Toolkit. Taro L. Saito, Shin Sasaki, Budrul Ahsan, Reginaldo Kuroshu and Shinichi Morishita. BMB2008, December 2008.

Posters

  • UTGB Toolkit for Personalized Genome Browsers. Taro L. Saito, Jun Yoshimura, Shin Sasaki, Budrul Ahsan, Atsushi Sasaki, Reginaldo Kuroshu and Shinichi Morishita. The 8th International Workshop on Advanced Genomics, June 16th-18th, 2009.

  • UTGB Shell: An Open-Source Browser Framework for the Integration of Biological Data. Taro L. Saito, Shin Sasaki, Budrul Ahsan and Shinichi Morishita. Cold Spring Harbor Laboratory (CSHL) Conference, THE BIOLOGY OF GENOMES, May 2008 (PPT).

  • SCMD - Saccharomyces Cerevisiae Morphological Database. Taro L. Saito, Miwaka Ohtani, Hiroshi Sawai, Fumi Sano, Ayaka Saka, Daisuke Watanabe, Masashi Yukawa, Yoshikazu Ohya and Shinichi Morishita. Cold Spring Harbor Laboratory (CSHL) Conference, THE BIOLOGY OF GENOMES, May 2004. (PPT)