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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