Invited Papers

  1. Yoichiro Nakatani, Hiroyuki Takeda, Yuji Kohara, and Shinichi Morishita. Reconstruction of the Vertebrate Ancestral Genome Reveals Dynamic Genome Reorganization in Early Vertebrates. Medaka: A model for organogenetics, human disease, and evolution. Springer pp.307-322 (2011)
  2. 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.   Medaka: A model for organogenetics, human disease, and evolution. Springer pp.39-48 (2011)
  3. Taro L. Saito, Jun Yoshimura, Budrul Ahsan, Atsushi Sasaki, Reginaldo Kurosh, and Shinichi Morishita. UTGB Toolkit for Personalized Genome Browsers.  Tag-based Next Generation Sequencing (Editted by Harbers and Kahl). pp435-448 Wiley (2011)
  4. Yoichiro Nakataniand Shinichi Morishita. Vertebrate genome evolution examined by comparing the human and fish genomes. (Review) Encyclopedia of Life Sciences, John Wiley & Sons (2007)
  5. 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)
  6. Jun Ogasawaraand Shinichi Morishita. Fast and Sensitive Algorithm for Aligning ESTs to Human Genome. Journal of Bioinformatics and Computational Biology, Vol.1, No.2, 363-386, 2003.
  7. Jun Ogasawara and Shinichi Morishita. Practical Software for Aligning ESTs to Human Genome. Proc. of the Thirteenth Annual Symposium on Combinatorial Pattern Matching (CPM2002) Fukuoka, Japan, July 3-5, 2002.
  8. Jie Cheng, Christos Hatzis, Hisashi Hayashi, Mark-A. Krogel, Shinichi Morishita , David Page, and Jun Sese. KDD Cup 2001 Report. ACM SIGKDD Explorations, Volume 3, Issue 2, Janurary 2002, 47-64. pdf ps
  9. Shinichi Morishita. On Classification and Regression. Proc. of First Int'l Conf. on Discovery Science, Lecture Notes in Artificial Intelligence, Springer, Vol. 1532, pages 40-57, December 1998.
  10. Takeshi Fukuda, Yasuhiko Morimoto, Shinichi Morishita, and Takeshi Tokuyama. Mining Optimized Association Rules for Numeric Attributes. Journal of Computer and System Sciences - Special issue on the 15th ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems, Academic Press. 58(1): 1-12, 1999.
  11. Shinichi Morishita. An Extension of Van Gelder's Alternating Fixpoint to Magic Programs. Journal of Computer and System Sciences - Special Issue on the 12th ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems, Academic Press, Volume 52, Number 3, pp. 506-521, June 1996

Invited Talks

  1. Shinichi Morishita. Searching Massive Epigenome Data for Evolutionarily Conserved Sequence Motifs. 1st IEEE International Conference on Computational Advances in Bio and medical Sciences. Orland, Florida, USA. Feb. 3, 2011.
  2. Shinichi Morishita. Genetic Variation Associated with Nucleosome Structure and DNA Methylation. Fish Genome Meeting 2011, Sanger Center, Cambridge, UK, March 11, 2011.
  3. Shinichi Morishita. Genetic Variation Associated with Nucleosome Structure and DNA Methylation. The 3rd Congress of BioSoft (BioSoft-2011), Beijing, China, March 23, 2011.
  4. Shinichi Morishita. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. The 8th International Workshop on Advanced Genomics. Tokyo, June 17, 2009
  5. Shinichi Morishita. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Third International Workshop on Fish Genomes, Sanger Center, Hinxton, UK, March 13, 2009.
  6. Shinichi Morishita. Vertebrate Genome Evolution Examined by Comparing the Human and Fish Genomes. International Symposium Celebrating Dr. David S. Hogness, Recipient of the 23rd International Prize for Biology. Kyoto, Japan, Nov. 21, 2007
  7. Shinichi Morishita. The medaka draft genome: new insights into vertebrate genome evolution . Origin of Vertebrates, Tokyo, Japan, March 28th, 2007
  8. Shinichi Morishita. Second International Workshop on Fish Genomes, Sanger Center, Hinxton, UK, March 19, 2007.
  9. Shinichi Morishita. Development of Whole Genome Shotgun Assembler for Sequencing Medaka Genome. Medaka Genome and Vertebrate Evolution. Tokyo, Japan, March 3-4, 2004. (Joint work with Masahiro Kasahara, Shin Sasaki, Yukinobu Nagayasu, Tadasu Shin-i, and Yuji Kohara)
  10. Jun Ogasawara and Shinichi Morishita. Practical Software for Aligning ESTs to Human Genome. Proc. of the Thirteenth Annual Symposium on Combinatorial Pattern Matching (CPM2002) Fukuoka, Japan, July 3-5, 2002.
  11. Shinichi Morishita. Gene Resource Locator Project. The 4th International Workshop on Advanced Genomics, Kyoto, Japan, Nov. 13-14, 2001. (Joint work with Jun Ogasawara, Toshihiko Honkura, and Tomoyuki Yamada)
  12. Shinichi Morishita. Enumerating Alternative Spliced Transcripts for Understanding Complexity of the Human Genome. Machine Intelligence 18 Workshop, King's Manor, University of York, 19-21 September 2001. (Joint work with Jun Ogasawara, Toshihiko Honkura, and Tomoyuki Yamada)
  13. Shinichi Morishita. Bridging a gap between DNA sequences & expression patterns of genes. International Symposium on Bioinformatics, Pohang University of Science and Technology, Pohang, Korea, Nov. 22-23, 2000. (Joint work with Jun Ogasawara)
  14. Shinichi Morishita. Association Rules, Boosting, and Genome Mining. DIMACS/IBM Workshop on Data Mining in the Internet Age, IBM - Almaden, San Jose, California, May 1 - 2, 2000. (Joint work with Jun Sese)
  15. Shinichi Morishita. On Classification and Regression. Proc. of First Int'l Conf. on Discovery Science, Lecture Notes in Artificial Intelligence, Springer, Vol. 1532, pages 40-57, December 1998.

List of Domestic Journal Papers

  1. Shinichi Morishita, Masayuki Numao, and Yoshio Tozawa. A Scheduling Expert for Steel-Making Process by Cooperative Scheduling. (In Japanese) Journal of Japan Society for Artificial Intelligence, Volume 5, Number 2, pages 184-193, March 1990
  2. Shinichi Morishita. Theory of Lattice-Valued Programs (In Japanese) Computer Software, Japan Society for Software Science and Technology, pages 66-82, October 1989
  3. Shinichi Morishitaand Masayuki Numao. Visual Compuation Model for Prolog (in Japanese) Transactions of IPSJ, Volumn 28, Number 4, pages 359-366, April 1987