People

List of Doctral Theses

• [2011] Reginaldo Kuroshu. Computational approaches for high-throughput sequencing and assembly of clone sequences.
  • Kuroshu RM, Watanabe J, Sugano S, Morishita S, Suzuki Y, Kasahara M. Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly. PLoS One.  7;5(5):e10517 (2010)
• [2011] Hiroshi Hatsuda. Marked Point Process to Analyze Biological Data.
  • Hiroshi Hatsuda, Keigo Muramatsu, Toshiro Aigaki, and Shinichi Morishita. Robust and Accurate Recognition of Veins in Fruit Fly Wings.IEEE 6th International Symposium on Image and Signal Processing and Analysis.pp. 146-151(2009)
• [2011] Hongyan Wu. Accelerating Path-free XML Queries in RDBMS.
  • Hongyan Wu, Taro L Saito, Shinichi Morishita. Accelerating Path-free XML Queries in RDBMS. IPSJ Online Transactions. Vol. 3, pp.206-217 (2010)
• [2009] Masahiro Kasahara. RAMEN: Genome Assembler.
  • Masahiro Kasahara(*), Kiyoshi Naruse(*), Shin Sasaki(*), Yoichiro Nakatani(*), Wei Qu, Budrul Ahsan, Tomoyuki Yamada, Yukinobu Nagayasu, Koichiro Doi, Yasuhiro Kasai, Tomoko Jindo, Daisuke Kobayashi, Atsuko Shimada, 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(#), Shinichi Morishita(#), and Yuji Kohara(#).The medaka draft genome and insights into vertebrate genome evolution. Nature 447, 714-719 (2007)* joint first authors. # joint corresponding authors. doi:10.1038/nature05846
• [2009] Wei Qu. Efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing.
  • Wei Qu, Shin-ichi Hashimoto, Shinichi Morishita. Efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing. Genome Research 19(7): 1309-1315 (2009)
• [2008] Shin Sasaki. Medaka genome sequencing and synchronization between genome evolution and nucleosome structure in medaka genome.
  • 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 Saito, Yutaka Suzuki, Sumio Sugano, Yuji Kohara, Hiroyuki Takeda, Andrew Fire(#), Shinichi Morishita(#) Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites.Science323(5912):401-4 (2009)

• [2008] Tomoyuki Yamada. Research on searching for unique and repetitive regions from large-scale biological sequence information.
  • Tomoyuki Yamada and Shinichi Morishita. Accelerated off-target search algorithm for siRNA. Bioinformatics, 21(8):1316-1324, 2005
  • Tomoyuki Yamada and Shinichi Morishita. Computing Highly Specific and Noise Tolerant Oligomers Efficiently, Journal of Bioinformatics and Computational Biology, Vol. 2, No. 1, pp21-46, 2004.
• [2007] Taro Saito. Purifying XML Structures.
  • Taro L. Saito and Shinichi Morishita. Relational-Style XML Query. Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data (ACM SIGMOD), Vancouver, 303-314 (2008)
• [2007] Yoichiro Nakatani. Whole genome duplication and reconstruction of ancestor genomes.
  • Yoichiro Nakatani, Hiroyuki Takeda, Yuji Kohara, and Shinichi Morishita. Reconstruction of the Vertebrate Ancestral Genome Reveals Dynamic Genome Reorganization in Early Vertebrates. Genome Research 17(9): 1254-1265 (2007)
• [2005] Jun Sese. Classified Clustering for Quantitative Biological Data Analysis.
  • Jun Sese, Yukinori Kurokawa, Morito Monden, Kikuya Kato and Shinichi Morishita.Constrained Clusters of Gene Expression Profiles with Pathological Features, Bioinformatics, 20: 3137 – 3145, 2004.
  • Jun Sese and Shinichi Morishita. Itemset Classified Clustering. Proc. of the 8th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), Lecture Notes in Computer Science, Vol. 3202, 398-409, 2004.
• [2000] Akihiro Nakaya. Parallel data mining for analysis of correlated genetic factors.
  • Akihiro Nakaya, Harutsugu Hishigaki and Shinichi Morishita. Mining the Quantitative Trait Loci Associated with Oral Glucose Tolerance in the Oletf Rat. Proc. of Pacific Symposium on Biocomputing, pages 367-379, January 4-9, 2000.
  • Akihiro Nakaya, Hideharu Furukawa and Shinichi Morishita. Weighted Majority Decision among Several Region Rules for Scientific Discovery. Proc. of Second Int’l Conf. on Discovery Science, Lecture Notes in Artificial Intelligence, Springer, pages 15-29, December 1999.