Genome Informatics Workshop: Call for Participation

Gotou Susumu goto at kuicr.kyoto-u.ac.jp
Tue Nov 15 14:25:57 EST 1994


                ************ CALL FOR PARTICIPATION ************



                        GENOME INFORMATICS WORKSHOP 1994


                               December 19-20, 1994

                        Pacific Convention Plaza Yokohama

               1-1-1 Minatomirai, Nishi-ku, Yokohama 220, JAPAN


The workshop aims at establishing new research areas bridging biological science 
and computer science, and developing new computational tools for genome research. 
This is the fifth in a  series of workshops organized by the Genome Informatics 
Research Project funded by the Ministry of Education, Science and Culture of Japan.



Tentative_Schedule_____

Monday, December 19
  9 : 30 -   10 : 00  Opening Address

 10 : 00 -   11 : 00  Invited Talk = Tom Marr, Cold Spring Harbor Lab.

 11 : 10 -   12 : 10  Invited Talk = Amos Bairoch, University of Geneva

 12 : 10 -   13 : 10  Lunch

 13 : 10 -   14 : 30  Oral Session 1

 14 : 40 -   15 : 40  Oral Introduction to Poster and Workstation Presentations

 15 : 40 -   17 : 30  Poster and Workstation Sessions

 18 : 00 -   20 : 00  Banquet

Tuesday, December 20
  9 : 00 -   10 : 00  Oral Session 2

 10 : 10 -   10 : 50  Oral Session 3

 11 : 00 -   12 : 00  Invited Talk = Steve Bryant, National Center for Biotechnology 
			Information

 12 : 00 -   13 : 00  Lunch

 13 : 00 -   15 : 00  Poster and Workstation Sessions

 15 : 00 -   16 : 00  Memorial Session for Dr. Seto

 16 : 00 -   17 : 40  Oral Session 4

 17 : 40 -   17 : 50  Closing Remarks


For_registration_contact


Secretariat, Genome Informatics Workshop '94

c/o Human Genome Center, The Institute of Medical Science, The University of Tokyo

4-6-1, Shirokanedai, Minato-ku, Tokyo 108 JAPAN

Facsimile: +81-3-5449-5434, E-mail: workshop at ims.u-tokyo.ac.jp

There is no registration fee.
     ______________________________________________________________________


            Genome Informatics Workshop 1994 December 19-20, 1994


                          Pacific Convention Plaza Yokohama

                    1-1-1 Minatomirai, Nishi-ku, Yokohama 220, Japan
                                     Program


Monday,_December_19


Opening Address    9:30 - 10:00

      Satoru Miyano, Kyushu University


Invited talk   10:00 - 11:00

(Chairperson: Toshihisa Takagi)

Application of the genome topographer system to the study of complex human disease

      Thomas G. Marr, Cold Spring Harbor Laboratory


Invited talk   11:10 - 12:10

(Chairperson: Kenta Nakai)

Protein sequence databases in the context of genome projects

      Amos Bairoch,University of Geneva


Oral Session 1   13:10 - 14:30

(Chairperson: Yukihiro Eguchi)

New Hashing Techniques for Three-Dimensional Protein Structures

      Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa

Prediction of protein structural similarities using a 3D-1D compatibility method

      Yo Matsuo, Ken Nishikawa

Prediction of Beta-Sheet Structures Using Stochastic Tree Grammars

      Hiroshi Mamitsuka, Naoki Abe

Modeling RNA Secondary Structures Using Tree Grammars

      Satoshi Kobayashi, Takashi Yokomori


Oral Introduction to Poster and Workstation Presentations   14:40 - 15:40

(Chairperson: Shigeki Mitaku)


Poster and Workstation Sessions   15:40 - 17:30
     ______________________________________________________________________


Tuesday,_December_20


Oral Session 2   9:00 - 10:00

(Chairperson: Takashi Yokomori)

Protein Motif Discovery from Positive Examples by Minimal Multiple Generalization 
over Regular Patterns

      Hiroki Arimura, Ryoichi Fujino, Takeshi Shinohara, Setsuo Arikawa

Indexing protein sequences with MINOS

      Hugues Ripoche, Engelbert Mephu Nguifo, Jean Sallantin

Comparative Analysis of Amino Acid Sequences based on Rough Sets and Domain 
Knowledge Hierarchy

      Shusaku Tsumoto, Hiroshi Tanaka, Kohei Tsumoto, Izumi Kumagai


Oral Session 3    10:10 - 10:50

(Chairperson: Satoru Kuhara)

Simulative representation of biological knowledge using object-oriented database language

      Makoto Hirosawa, Reiko Tanaka, Hidetoshi Tanaka, Masayuki Akahoshi, Masato Ishikawa

GEISHA SYSTEM:An Environment for Simulating Protein Interaction

      Masanori Arita, Masami Hagiya, Tomoki Shiratori


Invited talk   11:00 - 12:00

(Chairperson: Yutaka Akiyama)

An Integrated Database of Biological Sequences, Scientific Literature, and 3-Dimensional Structure

      Stephen H. Bryant, National Center for Biotechnology Information


Poster and Workstation Sessions   13:00 - 15:00


Memorial Session for Dr. Seto (In Japanese)   15:00 - 16:00

(Chairperson: Minoru Kanehisa)


Oral Session 4   16:00 - 17:40

(Chairperson: Ken Nishikawa)

Fast A* Algorithms for Multiple Sequence Alignment

      Takahiro Ikeda, Hiroshi Imai

Multiple sequence alignment using anchor points through generalized dynamic programming

      Jerome Gracy, Jean Sallantin

Multiple RNA-Sequence Alignment Considering Stem Regions

      Masato Ishikawa, Tomoyuki Toya, Yasushi Totoki, Reiko Tanaka

Molecular Phylogenetic Analysis using both DNA and Amino Acid Sequence Data 
and Its Parallelization

      Hideo Matsuda, Hiroshi Yamashita, Yukio Kaneda

Distribution of Base Composition around the Splice Sites in Different Species

      Masahiko Mizuno, Minoru Kanehisa


Closing Remarks    17:40 - 17:50

Toshihisa Takagi, University of Tokyo
     ______________________________________________________________________

   Poster Session

P1    Construction and analysis of Escherichia coli genome database

          Takeshi Itoh, Minoru Yano, Keiko Takemoto, Yutaka Akiyama,
          Hirotada Mori

P2    YAYOI: Taxonomy Database System over International Computer Networks

          Hajime Kitakami, Yoshio Tateno, Takashi Gojobori

P3    Establishment of Transcription Factor Database and Human Mutation Database

          Hiroshi Mizushima, Kenshi Hayashi

P4    A Signal Transduction Database

          Kenji Suzuki, Susumu Goto, Yutaka Akiyama, Minoru Kanehisa

P5    The Gene Network: Development of a Database System Showing the Relationships
      Among the Genes of All Species

          Nobuyuki Miyajima, Shinobu Nakayama, Mitsuyo Kohara, Satoko Hayashi

P6    Construction of a Membrane Protein Database and an Evaluation of Several 
      Prediction Methods  of Transmembrane Segments

          Toshio Shimizu, Kenta Nakai

P7    The Prediction of Lateral and Rotational Positioning of a-Helices in a Membrane Protein

          Makiko Suwa, Takatsugu Hirokawa, Shigeki Mitaku

P8    Protein Three Dimensional Structure Prediction on Object Oriented Database

          Akira Shimada, Hideki Takehara, Kazunori Toma

P9    Computing Closures of Indirect Similarity Relationships among Structures in Proteins

          Kenji Satou, Emiko Furuichi, Shin'ichi Hashimoto, Yukiko Tsukamoto,
          Satoru Kuhara, Toshihisa Takagi, Kazuo Ushijima

P10   Automatic Labeling of Protein Structures by Hidden Markov Models

          Kiyoshi Asai, Kentaro Onizuka, Masayuki Akahoshi, Hidetoshi Tanaka,
          Katunobu Itou

P11   A New Method for Predicting Long-range Interactions between Amino Acid Residues
      Based-on Homological Correlations

          Hiroshi Mamitsuka

P12   Reverse Evolution of Proteases Studied by a Modified 3D-1D Method

          Haretsugu Hishigaki, Tamio Yasukawa

P13   An Approach to Three-Dimensional Motif Finding in Proteins

          Hiroaki Kato, Yoshimasa Takahashi

P14   Discriminative Analysis of the Conformational Patterns of Protein Amino Acid Residues

          Motokazu Kamimura, Yoshimasa Takahashi

P15   Protein Secondary Structure Analysis Using Neural Network

          Kotoko Nakata

P16   Finding Functional Features of Proteins using Machine Learning Techniques

          Takashi Ishikawa, Shigeki Mitaku, Takao Terano, Takatsugu Hirokawa,
          Makiko Suwa, Seah Boon Chieng

P17   Assignment of Certainty-Factor Parameters with a Given Reasoning Tree for the Prediction
      of Protein Localization Sites

          Kenta Nakai, Ayumi Shinohara, Satoru Miyano

P18   Discrimination of intracellular and extracellular proteins by single residue 
	and residue-pair scores

          Hiroshi Nakashima, Ken Nishikawa

P19   Classification of Possible Proteins from Genome Sequencing

          Yukihiro Eguchi, Yuzo Ueda

P20   Alphabet Indexing by Cluster Analysis:
      A Method for Knowledge Acquisition from Amino Acid Sequences

          Hideaki Nakakuni, Takeo Okazaki, Satoru Miyano

P21   DNA Sequence Analysis using Hidden Markov Model and Genetic Algorithm

          Tetsushi Yada, Masato Ishikawa, Hidetoshi Tanaka, Kiyoshi Asai

P22   Detecting common amino acid sequence patterns with a gap

          Mikita Suyama, Takaaki Nishioka, Jun'ichi Oda

P23   Multiple Sequence Alignment with a Tree-Based Weighting System

          Osamu Gotoh

P24   Integration of Minimum Evolution and Maximum Likelihood Method
      in Constructing Molecular Evolutionary Tree

          Hiroshi Tanaka, Fengrong Ren, Norio Fukuda

P25   Relationship between Gene Function and Codon Usage in Escherichia coli
      on the basis of Principal Component Analysis

          Shigehiko Kanaya, Toshimichi Ikemura, Yoshihiro Kudo

P26   Estimation of protein-production levels for ORFs found by E.coli and yeast genome projects,
      basing on levels of "optimal codon" usage, in connection with feasibility of their protein
      coding ability and with assignment to foreign-type genes.

          Yasukazu Nakamura, Tatsuo Fukagawa, Kimihiko Sugaya,
          Toshimichi Ikemura

P27   A Set of Tools Developed for the Analysis of Open Reading Frames of Yeast (S.cerevisiae)
      Chromosome VI

          Motoe Sasanuma, Zhong-qing Wang, Kazuhiro Shibata,
          Syun-ichi Sasanuma, Masashi Ozawa, Eiko Kohriki,
          Toshihiko Eki, Akinori Sarai, Hideaki Sugawara, Yasufumi Murakami

P28   Evaluation of the Sequence Data Assemble Software "Shotgun"

          Zhong-qing Wang, Yasufumi Murakami, Toshihiko Eki, Akira Oyama,
          Yukihiro Eguchi, Akinori Sarai, Hideaki Sugawara

P29   Rapid identity searching program for DNA sequences and its applications to cDNA grouping

          Tetsuo Nishikawa, Susumu Hiraoka, Naoko Kasahara, Keiichi Nagai

     ______________________________________________________________________

   Workstation Session

W1    Locus-in v.2 and GeneViewPLUS: Computer softwares for entry and analysis of
      the human genome data

          Shinsei Minoshima, Nobuyoshi Shimizu

W2    ContigMaker and SAND: Software Tools for Genome Mapping and Sequencing

          Akira Suyama, Akira Ohyama, Masami Hagiya, Yoshiaki Furuhata,
          Takashi Ito, Asao Fujiyama, Masahira Hattori, Yoshiyuki Sakaki,
          Toshihisa Takagi

W3    Gnome: Recent Developments

          Toshiyuki Niiyama, Atsushi Takeuchi, Kouichi Kotani, Ikuo Uchiyama,
          Atsushi Ogiwara, Kenta Nakai

W4    A server-client version of "Genomatica"
      integrated genome information browser

          Yutaka Akiyama, Takahiro Yakoh, Hirotada Mori, Naotake Ogasawara

W5    Extension of the Integrated Database "HyperGenome" for Genome Maps and Sequence Information

          Susumu Goto, Satoru Kuhara, Toshihisa Takagi, Minoru Kanehisa

W6    Further Improvements on SMART: Sequence Motif Analysis and Retrieval Tool

          Atsushi Ogiwara, Ikuo Uchiyama, Toshihisa Takagi, Minoru Kanehisa

W7    Gidre : Genome Integrated Databases Retrieval Environment

          Kagehiko Kitano, Atsushi Ogiwara, Toshihisa Takagi

W8    GenomeCruiser: A Laboratory Notebook for Human Gene Mapping

          Hiroshi Dohi, Hideaki Sugawara

W9    A DNA Sequencing Project Monitoring and Sequence Data Quality Control System

          Akira Ohyama, Masaki Takazawa, Atsuko Kubota, Nobuyuki Miyajima

W10   Animal Genome Database for Network Users

          Yasuhiko Wada, Kengo Inoue, Hiroshi Yasue

W11   Menu System Based on NCSA Mosaic and Programs Forked from the Menu

          Teruo Yasunaga, Tatsuya Takagi, Takeo Tokimori,
          Kouichi Kotani, Atsushi Takeuchi, Toshiyuki Niiyama

W12   An Attempt to Integrate Various Protein Databases Using an Object-Oriented Database
      Management System

          Hiromi Suzuki, Hiroaki Katoh

W13   A DNA/protein sequence retrieval system: an Xtpanel application

          Akihiro Oda, Jun-ichi Yano, Minoru Kanehisa

W14   Rapid similarity search algorithm of nucleic acid database

          Susumu Hiraoka, Keiichi Nagai

W15   Enhancement of the "PROTEIX" Database System for Three-Dimensional Protein Structures

          Tatsuya Akutsu, Toshio Hyakutake

W16   A computer system for predicting membrane protein structure

          Takatsugu Hirokawa, Seah Boon Chieng, Makiko Suwa, Shigeki Mitaku

W17   BONSAI Garden: Parallel Machine Discovery System for Sequences

          Takayoshi Shoudai, Tomoyuki Uchida, Satoru Miyano, Ayumi Shinohara,
          Shinichi Shimozono, Takeo Okazaki, Takeshi Shinohara,
          Satoru Kuhara, Setsuo Arikawa

W18   SIMFLY: The Simulation of a Fly Embryo

          Masanori Arita, Masami Hagiya, Tomoki Shiratori

W19   A Knowledge Base of Biological Cascades
          Hidetoshi Tanaka, Makoto Hirosawa, Reiko Tanaka, Masayuki Akahoshi,

          Masato Ishikawa

W20   A Knowledge Base for Searching and Browsing Metabolic Pathways

          Susumu Goto, Minoru Kanehisa
                   Genome Informatics Workshop 1994
                       December 19-20, 1994    Yokohama, Japan

     ______________________________________________________________________



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________________________________________________________________________________


  RETURN FORM TO:   Secretariat, Genome Informatics Workshop '94

                    c/o Human Genome Center

                    The Institute of Medical Science

                    The University of Tokyo

                    4-6-1, Shirokanedai, Minato-ku, Tokyo 108, JAPAN

                    Facsimile: +81-3-5449-5434

                    E-mail: workshop at ims.u-tokyo.ac.jp



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