GIW ’99
The Tenth Anniversary Workshop
on Genome Informatics
Yebisu Garden Hall
Yebisu Garden Place, Tokyo, Japan
December 14–15, 1999
Yebisu Garden Room
The Anniversary Event
December 13, 1999
The Tenth Workshop on Genome Informatics (GIW
’99) is a forum for researchers, practitioners andusers working on various aspects of Genome Informatics. The aim
is to present recent research results (theory/practice), todemonstrate systems, and to explore directions for future
research and new applications related to Genome Science.

Steering Committee
Minoru Kanehisa (Chair, Kyoto University)
Toshihisa Takagi (University of Tokyo)
Satoru Miyano (University of Tokyo)

Sponsored by
Human Genome Center, University of Tokyo
Grant-in-Aid for Scientiﬁc Research on Priority Areas“GENOME SCIENCE” from MESSC of Japan

Secretary and Local Arrangements
giw@ims.u-tokyo.ac.jp
Human Genome Center
Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Tel:+81-3-5449-5615
Fax:+81-3-5449-5442

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Newest Information
http://giw.ims.u-tokyo.ac.jp/giw99

Program Committee
Kiyoshi Asai (ETL, Japan, PC Chair)
Russ B. Altman (Stanford Univ., USA)
Christopher Burge (MIT, USA)
Antoine Danchin (Institut Pasteur, France)
A. Keith Dunker (Washington State Univ., USA)
Susumu Goto (Kyoto University, Japan)
Lawrence Hunter (National Library of Medicine, USA)
Takashi Ito (University of Tokyo, Japan)
Hiroaki Kitano (SONY, Japan)
Teri Klein (UCSF, USA)
Akihiko Konagaya (JAIST, Japan)
Satoru Kuhara (Kyushu University, Japan)
Hideo Matsuda (Osaka University, Japan)
Satoru Miyano (University of Tokyo, Japan)
Shin-ichi Morishita (University of Tokyo, Japan)
Kenta Nakai (University of Tokyo, Japan)
Naotake Ogasawara (AIST-Nara, Japan)
Christos Ouzounis (EMBL-EBI, U.K.)
Kimmen Sjölander (MAG, USA)
Hideaki Sugawara (DDBJ, Japan)
Gary D. Stormo (University of Colorado, USA)
Satoshi Tabata (KDRI, Japan)
Toshihisa Takagi (University of Tokyo, Japan)
Limsoon Wong (NUS, Singapore)2

Registration
Registration should be done at

http://giw.ims.u-tokyo.ac.jp/giw99/
until November 30, 1999.

Until November 30, 1999: (Japan time)
Registration
Free
Banquet on December 14
JPY6,000.(Student) (JPY3,000)
A copy of workshop book
JPY3,000.Reception Party on December 13 Free
After November 30, 1999: (Japan time)
Registration
Free
Banquet on December 14
JPY7,000.(Student) (JPY4,000)
A copy of workshop book
JPY4,000.Reception Party on December 13 Free

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GIW ’99 Advanced Program
Registration
Dec. 13:
Dec. 14:
Dec. 15:

16:30 - 18:30
9:00 - 18:30
9:00 - 18:00

Garden Room
Garden Hall
Garden Hall

December 13, Monday, Garden Room
The Anniversary Event
16:30 - 18:30
17:30 - 18:00
18:00 - 18:30

18:30 - 21:00

Registration at Garden Room
Event Presented by
Japanese Society for Bioinformatics
Event Presented byInternational Society for Computational
Biology
Reception Party and General Meeting

December 14, Tuesday, Garden Hall
Opening Address
9:20 - 9:30
Kiyoshi Asai (ETL)
Session 1
9:30 - 9:50

Chair: A. Keith Dunker(Washington State University)
MIAX: A Novel System for Assessment ofMacromolecular Interaction in Condensed
Phases. 1) Description of the Interaction
Model and Simulation Algorithm, Carlos
A. Del Carpio Munoz, Atsushi Yoshimori(Toyohashi University of Technology)

9:50 - 10:10

A Generic Criterion for Gene Recongnitions in Genomic Sequences, Chungfan
Kim∗ , Akihiko Konagaya∗ , Kiyoshi Asai† ,(∗ Japan Advanced Institute of Science andTechnology, † ETL)

10:10 - 10:30

Protein Threading Based on Multiple Protein Structure Alignment, Tatsuya Akutsu,
Kim Lan Sim (Univ. of Tokyo)

4Session 2
10:30 - 10:50

Chair: Akihiko Konagaya (JAIST)
Predicting Protein Disorder for N-, C-,
and Internal Regions, Xiaohong Li, Pedro Romero, Meeta Rani, A. Keith
Dunker, Zoran Obradovic (Washington
State Univ.)

10:50 - 11:10

Predicting Binding Regions within Disordered Proteins, Ethan Garner, Pedro Romero, A. Keith Dunker, Celeste
Brown, Zoran Obradovic (Washington
State Univ.)

Break11:10 - 11:20

Invited Talk
11:20 - 12:20

Lunch Break

Chair: Kiyoshi Asai (ETL)
Computational Analysis ofHigh-throughput Genomics Data Using
Hidden Markov Models and Support Vector Machines, David Haussler(UC Santa Cruz)
12:20 - 14:00

Session 3
14:00 - 14:20

Chair: Matsuda Hideo (Osaka Univ.)
A Compression Algorithm for DNA Sequences and Its Applications in Genome
Comparison, Xin Chen∗ , Sam Kwong† ,Ming Li‡ (∗ Univ.of Hong Kong, † Peking
Univ. ‡ Univ.of Waterloo)

14:20 - 14:40

An EM-type Algorithm for Ordered
Restriction Map Alignment, Hirotada
Kobayashi, Hiroshi Imai (Univ.of Tokyo)

14:40 - 15:00

A Greedy Algorithm for Minimizing the
Number of Primers in Multiple PCR Experiments, Koichiro Doi, Hiroshi Imai
(Univ.of Tokyo)

15:00 - 15:20

On the Reconstruction of Ancient Doubled
Circular Genomes Using Minimum Reversals, Nadia El-Mabrouk, David Sankoﬀ(Université de Montréal)Message from International Society for
Computational Biology (ISCB)
15:20 - 15:30 A. Keith Dunker (Board of Director, ISCB)

5

One-Minute Talks for Posters & Software Demonstrations
Chair: Shigeki Mitaku(Tokyo Univ. of Agric. and Tech.)
15:30 - 17:00
Posters & Software Demonstrations
17:00 - 18:30
Banquet18:30 - 21:00
Foyer, Garden Hall

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December 15, Wednesday, Garden Hall
Session 4
9:40 - 10:10

Chair: Satoru Kuhara (Kyushu Univ.)
Genome-scale Gene Expression Analysis
and Pathway Reconstruction in KEGG,
Mitsuteru Nakao, Hidemasa Bono, Shuichi
Kawashima, Tomomi Kamiya, Kazushige
Sato, Susumu Goto, Minoru Kanehisa(Kyoto Univ.)

10:00 - 10:20

Toward Routine Automatic Pathway Discovery from On-line Scientiﬁc Text Abstracts,
See-Kiong Ng∗ , Marie Wong†(∗ Kent Ridge Digital Labs, † Natl. Univ.
Singapore)

10:20 - 10:40

Finding Precursor Compounds in Secondary Metabolism,
Masanori Arita∗ , Kiyoshi Asai∗ , Takaaki
Nishioka† (∗ ETL, † Kyoto Univ.)

Coﬀee Break

10:40 - 11:00

Invited Talk
11:00 - 12:00

Lunch Break

Chair: Toshihisa Takagi (Univ. Tokyo)
Human Genome Analysis and Medicine in
the 21st Century,
Yusuke Nakamura(Director, Human Genome Center, Univ.
Tokyo)
12:00 - 13:30

Posters & Software Demonstrations
13:30 - 15:00

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Session 5
15:00 - 15:20

Chair: Susumu Goto (Kyoto Univ.)
Automated Processing of
2-D Gel Electrophoretograms of Genomic
DNA for Hunting Pathogenic DNA Molecular Changes, Katsutoshi Takahashi∗ ,Masayuki Nakazawa† , Yasuo Watanabe‡
Akihiko Konagaya∗(∗ JAIST, † Kanazawa Technical College,‡
Kanazawa Institute of Technology)

15:20 - 15:40

Bio-calculus: Its Concept and MolecularInteraction,
Masao Nagsaki∗‡ , Shuichi Onami‡ , Satoru
Miyano∗‡ , Hiroaki Kitano†‡(∗ Univ. Tokyo, † SONY CSL, ‡ ERATO)

15:40 - 16:00

Towards Automatic Construction of CellLineage of C.elegans from Nomarski DIC
Microscope Images,
Tomohiro Yasuda∗‡ , Hideo Bannai∗‡ ,Shuichi Onami‡ , Satoru Miyano∗‡ , Hiroaki
Kitano†‡(∗ Univ. Tokyo, † SONY CSL, ‡ ERATO)

Coﬀee Break

16:00 - 16:20

8

Session 6
16:20 - 16:40

Chair: Kenta Nakai (Univ. Tokyo)
Tracing Synergetic Behavior of the QTLs
Aﬀecting Oral Glucose Tolerance in the
OLETF Rat, Akihiro Nakaya∗ , Haretugu
Hishigaki† , Shinichi Morishita∗ (∗ Univ.of
Tokyo, † Otsuka GEN Research Institute)

16:40 - 17:00

Integrating Application Programs for
Bioinformatics Using a web Browser, Yutaka Ueno, Kiyoshi Asai, Masanori Arita(ETL)

17:00 - 17:20

Making High-level Queries on Diverse
Genome Data: A Structured Genome
Document Database System Based on
GXML and GQL, Aaron Stokes∗ , Hideo
Matsuda† , Akihiro Hashimoto† (∗ JST,†
Osaka Univ.)

17:20 - 17:40

A System to Find Genetic Networks
using Weighted Network Model, Tomohiro Moriyama∗ , Ayumi Shinohara∗ ,Masayuki Takeda∗ , Osamu Maruyama† ,Takao Goto† , Satoru Miyano† , Satoru
Kuhara‡ (∗ Kyushu Univ., † Univ.of Tokyo,‡
Graduate School of Genetic Resources
Technology, Kyushu Univ.)

Best Paper
Award Ceremony

17:40 - 17:50

Closing
Remarks

17:50 - 18:00
Akihiko Konagaya (JAIST)

9Software Demonstrations
S01:

PAPIA (Parallel Protein Information Analysis)
System and MolTreC Parallel Molecular Dynamics
Simulator Running on a Compact 8-node Linux PC
Cluster, Yutaka Akiyama∗ , Tamotsu Noguchi∗ ,Kentaro Onizuka∗† , Makoto Ando∗‡(∗ RWCP, † Matsushita Research Inst., ‡ NKK Corp.)

S02:

Ortholog Identiﬁers for Integration of Genomic and
Pathway Information in KEGG, Susumu Goto∗ ,Kotaro Shiraishi† , Kayo Okamoto∗ , Hiroko Ishida∗ ,Toshi Nakatani∗ , Tomoko Deno∗ , Minoru Kanehisa∗(∗ Kyoto Univ., † Fujitsu Kyushu System Ltd.)

S03:

A Keyword Recommendation System for GenBank,
Yasuhiko Kitamura, Tetsuro Nanbu, Shoji Tatsumi(Osaka City Univ.)

S04:

GeneAlign: Java Application Software for Multiple
Sequence Alignment Editor, Ken Kurokawa∗ ,Yoshitaka Hasegawa∗ , Kenichi Kawashima† ,Toshiyuki Okumura† , Tatsuya Takagi∗ ,Teruo Yasunaga∗ (∗ Osaka Univ., † Net Navi)

S05:

KMDB: Keio Mutation Database for Human DiseaseGene, Shinsei Minoshima, Susumu Mitsuyama,
Saho Ohno, Takashi Kawamura, Nobuyoshi Shimizu(Keio Univ.)

S06:

NEXTDB: The Expression Pattern Map Database
for C. elegans, Tadasu Shin-i∗ , Yuji Kohara†(∗ CREST, JST, † NIG)

S07:

ViewDesigner: A Tool for Designing Viewscopes in
Discovery System HypothesisCreator,
Yoshinori Tamada∗ , Satoshi Matsumoto∗ ,Osamu Maruyama† , Satoru Miyano†(∗ Tokai Univ., † Univ. Tokyo)

S08:

Protein Dynamics Observations of Lambda Phageby Hybrid Petri Net, Atsuhi Doi∗ , Rainer Drath† ,Masao Nagasaki‡ , Hiroshi Matsuno∗ Satoru Miyano‡(∗ Yamaguchi Univ., † Technical Univ. of Ilmenau,‡
Univ. Tokyo)

S09:

An Intelligent Tool for Selecting Abstracts in
MEDLINE, Miyako Tanaka∗ , Sanae Nakazono† ,Hiroshi Matsuno† , Satoru Miyano‡ (∗ Ube Natl. Coll.
of Tech., † Yamaguchi Univ., ‡ Univ. Tokyo)

10

Posters
P01:

Development of an Eﬃcient Data Processing Method
for cDNA Microarray and Its Application to Tissue
Expression Proﬁling, Koji Kadota∗† , Rika Miki∗‡ ,Yasushi Okazaki∗§ , Kentaro Shimizu† ,Yoshihide Hayashizaki∗ ‡§ (∗ RIKEN, † Univ. Tokyo,‡
Tsukuba Univ., § CREST, JST)

P02:

DDGEL/DDCHIP: Web-Based Systems for Analysisof 2-D Gel Electrophoresis Images and DNA Macro/
Micro Array Images, Kyotetsu Kanaya∗ ,Akira Ohyama∗ , Tatsuya Akutsu† , Asao Fujiyama‡(∗ Mitsui Knowledge Ind. Co., Ltd., † Univ. Tokyo,
‡
NIG)

P03:

Probe Design for DNA Chip,
Ken-ichi Kurata, Akira Suyama (Univ. Tokyo)

P04:

Discrimination of Drug Sensitivity of Cancer Using
cDNA Microarray and Multivariate Statistical
Analysis, Tatsuhiko Tsunoda∗ , Yoshiaki Hojo† ,Chikashi Kihara∗ , Norihiko Shiraishi∗ ,Osamu Kitahara∗ , Kenji Ono∗ , Toshihiro Tanaka∗ ,Toshihisa Takagi∗ , Yusuke Nakamura∗ (∗ Univ. Tokyo,†
Hitachi, Ltd.)

P05:

Construction of an Integrated Environment for
Sequence, Structure, Property and Function
Analysis of Proteins, Jianghong An∗ , Takao Nakama† ,Yasushi Kubota† , Hiroshi Wako‡ , Akinori Sarai∗(∗ RIKEN, † Advanced Tech. Inst. Inc., ‡ Waseda Univ.)

P06:

Recent Improvements in the Automatic System forProtein Tertiary Structure Prediction GAX, Carlos
Adriel Del Carpio Munoz (Toyohashi Univ. of Tech.)

P07:

Development of an Automated Identiﬁcation
Program for Three-Dimensional Protein Motifs,
Hiroaki Kato, Yoshimasa Takahashi, Hidetsugu Abe(Toyohashi Univ. of Tech.)

P08:

Genius: System for Assigning Protein Coding Regions to 3D Structures, Makiko Suwa∗ , Henrik T. Yudate∗ ,Yasuhiko Masuho∗ , Asaf A. Salamov† , Christine A.
Orengo‡ , Mark B. Swindells§ (∗ Helix Research Inst.,†
The Sanger Centre, ‡ Univ. Coll. London, UK,§
Inpharmatica, Ltd.)P09:

A System for Displaying Protein Structure Information Based on Sequence Fragment Similarity,
Shouji Tatsumoto, Kenji Satou (JAIST)

11

P10:

An Automated Structure Prediction System by
Lattice Model for Seven-Helix-Type Membrane
Proteins, Junichi Uechi∗ , Takatsugu Hirokawa† ,Makiko Suwa‡ , Shigeki Mitaku∗(∗ Tokyo Univ. of Agric. & Tech., † Ryoka Systems
Inc., ‡ Helix Research Inst.)

P11:

BESPA: Software Tools for 3D Structure
Reconstruction from Single Particle Images ofProteins, Yutaka Ueno∗ , Katsutoshi Takahashi† ,Kiyoshi Asai∗ , Chikara Sato∗ (∗ ETL, † JAIST)P12:

Chemical Knowledge for Predicting Biosynthetic
Pathways of Secondary Metabolites, Takaaki Nishioka∗ ,Kimito Funatsu† (∗ Kyoto Univ., † Toyohashi Univ. of
Tech.)

P13:

Prediction of Secondary Metabolism Pathways from
Genomic Information and Compounds Data,
Atsushi Ogiwara (Glaxo Wellcome)

P14:

Methods for Predicting Target Sites of Transcription
Factors, Akinori Sarai∗ , Hidetoshi Kono† ,Michael Gromiha∗ , Fabio Pichierri∗ , Kenji Sayano‡ ,Misako Aida§ (∗ RIKEN, † Univ. of Pennsylvania,‡
ETL, § Hiroshima Univ.)

P15:

Evaluation of a Method for Predicting Transcription
Factors, Goro Terai∗ , Takeshi Mizuno∗ ,Toshihisa Takagi† (∗ INTEC Inc., † Univ. Tokyo)

P16:

Prediction of Cooperative Binding Sites forMultiple Transcription Factors, Yifei Wang,
Akinori Sarai (RIKEN)

P17:

AIGNET: A System That Infers Large Scale Genetic
Networks, Yukihiro Maki∗ , Shoji Watanabe∗ ,Yukihiro Eguchi∗ , Daisuke Tominaga† ,Masahiro Okamoto† (∗ Mitsui Knowledge Industry Co.,
Ltd., † Kyushu Inst. of Tech.)

P18:

Coherent Structural Prediction of a Set of
Paralogous Genes on a Eukaryotic Genome,
Osamu Gotoh (Saitama Cancer Center Reasearch Inst.)

P19:

Interaction-based Analysis of Protein Function and
Network, Haretsugu Hishigaki∗ † , Toshihide Ono† ,Akira Tanigami† , Toshihisa Takagi∗ (∗ Univ. Tokyo,†
OTSUKA Pharmaceutical. Co., Ltd.)

P20:

Prediction of MHC Class II-Peptide Interaction
Using Fuzzy Neural Network, Hideki Noguchi,
Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi(Nagoya Univ.)

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P21:

Prediction of Nuclear Localization Signals by HMM,
Keun-Joon Park, Minoru Kanehisa (Kyoto Univ.)

P22:

A Novel System for Assessment of MacromolecularInteraction in Condensed Phases. 2) Interaction Site
Inference by Molecular Shape and Electrostatic
Complementarity, Atsushi Yoshimori, Carlos Adriel
Del Carpio Munoz (Toyohashi Univ. of Tech.)

P23:

Progress of ProTherm: Theromodynamic Databasefor Proteins and Mutants, Michael Gromiha∗ ,Jianghong An∗ , Hidetoshi Kono∗ , Motohisa Oobatake∗† ,Hatsuho Uedaira∗ , P. Prabakaran∗ , Akinori Sarai∗(∗ RIKEN, † Meijo Univ.)

P24:

Detection of Apoptotic Domains against KEGG
Database by the HMM Search,
Masahiro Hattori, Minoru Kanehisa (Kyoto Univ.)

P25:

Maintenance of Transcription Factor DataBase TFDB,
Masako Kaizawa∗ , Satoru Watanabe∗ ,Takahiro Nobukuni∗ , Masami Horikoshi† , Hiroshi Handa‡ ,Yoshiyuki Kuchino∗ , Takao Sekiya∗ , Hiroshi Mizushima∗(∗ NCCRI, † Exploratory Research for Advanced Tech.,‡Tokyo Institute of Tech.)

P26:

A Database System for the Management andKaryotype Analysis of Chromosome Image Data,
Akihiro Kawaguchi, Kenji Satou (JAIST)

P27:

MAGEST: ESTs and Gene Expression Pattern Databasefor Halocynthia roretzi Maternal cDNA,
Shuichi Kawashima∗ , Takeshi Kawashima∗ ,Hiroki Nishida† , Kazuhiro W. Makabe∗ ,Minoru Kanehisa∗ (∗ Kyoto Univ., † Tokyo Inst. of
Tech.)

P28:

INE: The Rice Genome Sequence Database, Yoshiyuki
Mukai∗ , Hideki Nagasaki∗ , Baltazar A. Antonio∗ ,Katsumi Sakata∗ , Yasumichi Sakai† , Takuji Sasaki∗(∗ NIAR/STAFF, † Mitsubishi Space Software Co., Ltd.)

P29:

Receptor Database (RDB) in 1999, Kotoko Nakata,
Takako Takai, Tsuguchika Kaminuma (Natl. Inst. of
Health Sciences)

P30:

Thermodynamic Database for Protein-Nucleic Acid
Interactions, P. Prabakaran∗ , Jianghong An∗ ,Michael Gromiha∗ , S. Selvaraj∗ , Hatsuho Uedaira∗ ,Hidetoshi Kono† , Akinori Sarai∗ (∗ RIKEN, † Univ.
of Pennsylvania)

P31:

SLAD - An Integrated Swine MHC Database: A
Case Study of Data Warehousing in Molecular

13

Immunology, Christian Schönbach, Vladimir Brusic,
Judice L.Y. Koh (Kent Ridge Digital Labs)
P32:

PDB-DO:Database of Disorder, Kim Lan Sim∗ ,Tomoyuki Uchida† , Satoru Miyano∗ (∗ Univ. Tokyo,†
Hiroshima City Univ.)

P33:

An Aberrant Splicing Database for Finding Rules of
Splice-Site Selection, Takashi Yamanaka∗ ,Tetsushi Yada† , Kenta Nakai∗ (∗ Univ. Tokyo, † RIKEN)

P34:

Construction and Application of Mouse Full-length
cDNA Database, Hideaki Konno∗ ,Yoshifumi Fukunishi∗† , Toshinori Endo∗ ,Yoshihide Hayashizaki∗ (∗ RIKEN† CREST, JST)

P35:

Classiﬁcation of MEDLINE Abstracts,
Katsutoshi Ibushi, Nigel Collier, Jun’ichi Tsujii(Univ. Tokyo)

P36:

A Combined Query Expansion Approach for
Information Retrieval, Hisao Imai, Nigel Collier,Jun’ichi Tsujii (Univ. Tokyo)

P37:

A Semantically Annotated Corpus from MEDLINE
Abstracts, Tomoko Ohta, Yuka Tateisi, Nigel Collier,
Chikashi Nobata, Katsutoshi Ibushi,
Jun’ichi Tsujii (Univ. Tokyo)

P38:

Automatic Extraction of Information on
Protein-Protein Interaction from Scientiﬁc Literature,
Toshihide Ono∗ , Haretsugu Hishigaki∗ † , Akira Tanigami∗ ,Toshihisa Takagi† (∗ OTSUKA Pharmaceutical. Co.,
Ltd., † Univ. Tokyo)

P39:

An Ontology for Biological Reaction Events, Yuka
Tateisi, Tomoko Ohta, Takako Takai, Jun’ichi Tsujii(Univ. Tokyo)

P40:

An Object-Protocol Model Multidatabase Query
System for Rice and Maize, Bal A. Antonio∗ ,Zhiwei Fang† , Hector Sanchez† , Mary Polacco† ,Su-Shing Chen† , Katsumi Sakata∗ , Isamu Ohta∗ ,Yoshiyuki Mukai∗ , Ed Coe, Jr.† , Takuji Sasaki∗(∗ NIAR/STAFF † Univ. of Missouri-Columbia)

P41:

A Preliminary Study in Data Management andVisualization of Signal Transduction Pathway
Data – Viewing Interaction Data,
Ken-ichiro Fukuda, Toshihisa Takagi (Univ. Tokyo)

P42:

Toward a Data Mining Service from Large andHeterogeneous Genome Databases in GenomeNet,
Yoshiki Fuseda, Kenji Satou (JAIST)

14

P43:

P44:
P45:

P46:

P47:

P48:

P49:

P50:

P51:

P52:

P53:

P54:

Cross Database Visualization, David P. Hansen∗ ,Thure Etzold∗ , Guenther Kurapkat†(∗ LION Bioscience Ltd., † LION Bioscience AG)
A Full-Text Search System Covering the Whole
GenomeNet, Takao Kataoka, Kenji Satou (JAIST)WEB Based GENOME Analysis Tools in ALIS Project,
Kazuo Takehana∗ , Takehiko Ito† , Tetsushi Yada‡ ,Mika Hirakawa∗ , Hiroko Yamaguchi∗ , Junko Shimada∗ ,Katsuji Matsumura∗ , Masako Kuroda∗(∗ JST, † Mitsubishi Research Inst., ‡ RIKEN)
Global Integration of Gene Databases by Eigen-ID
Method, Tetsuro Toyoda and Akiko Itai
(Inst. of Medicinal Molecular Design)
Gene Classiﬁcation Method Based on Batch-Learning
SOM, Takashi Abe∗ , Shigehiko Kanaya∗§ ,Makoto Kinouchi∗ , Yoshihiro Kudo∗ , Hirotada Mori§ ¶ ,Hideo Matsuda§  , Carlos Del Carpio† ,Toshimichi Ikemura‡ (∗ Yamagata Univ., † Toyohashi
Univ. of Tech., ‡ NIG, § CREST, JST, ¶ Nara Inst. ofSci. & Tech.,  Osaka Univ.)
Synonymous Codon Usage Based on Codon-Anticodon
Interaction Energy and Gene Expression Level,
Mamoru Kato, Akira Suyama (Univ. Tokyo)
Analysis of Molecular Evolution in Mitochondorial
tRNA Gene Sequences, Jun-Ichi Sagara,
Kentaro Shimizu (Univ. Tokyo)
Unit-Based de novo Drug Design Using a Library ofProtein-Ligand Interaction Sites, Kiminobu X. Sato,
Susumu Goto, Minoru Kanehisa (Kyoto Univ.)
Characterization and Classiﬁcation of Splicing
Patterns, Yumi Tamada, Toshio Shimizu(Hirosaki Univ.)
Application to Gene Cluster Analysis of Inductive
Inference of Languages over Patterns with Conceptual Hierarchy, Yukako Tohsato, Hideo Matsuda,
Akihiro Hashimoto (Osaka Univ.)
Distribution of Species Speciﬁc Gene Family in
Microorganisms, Takeshi Ara∗ , Kenji Suzuki† ,Hideo Matuda∗‡ , Hirotada Mori∗ § (∗ CREST, JST,†
Kyoto Univ., ‡ Osaka Univ., § Nara Inst. of Sci. &Tech.)
Diﬀerences of Translation Termination Sites among
the Three Stop Codons, Yosuke Ozawa,
Satoshi Hanaoka, Rintaro Saito, Masaru Tomita(Keio Univ.)

15

P55:

P56:

P57:
P58:

P59:

P60:

P61:

P62:

P63:

P64:

P65:

P66:

Fop Values, Start Codons, SD Sequence
Conservation, and Their Correlation to Gene
Expression Level, Hiroaki Sakai, Chiaki Imamura,
Hiroshi Ohno, Takanori Washio, Masaru Tomita(Keio Univ.)
Computational Analysis of χ Sequences, Reina Uno,
Yoichi Nakayama, Kenji Yotsutani, Takehito Mogami,
Kazuharu Arakawa, Masaru Tomita (Keio Univ.)
Zipf-Scaling Description in the DNA Sequences,
Yasuo Yonezawa, Hiroyuki Motohasi (Ibaraki Univ.)
Toward Full 3D Structural Investigation of Intron
Splicing in Human Cytochrome P450 2D6 pre-mRNA,
Wayne Dawson∗ † , Kenji Yamamoto∗ (∗ Univ. Tokyo,†
Kitasato Univ.)
Systematic Analyses on Mouse Encyclopedia,
Toshinori Endo∗ , Yoshifumi Fukunishi∗† ,Hideaki Konno∗† , Harukazu Suzuki∗ , Yasuhiro Ozawa∗ ,Masayasu Yoshino∗ , Kazuhiro Shibata∗ , Masayoshi
Itoh∗ , Piero Carninci∗ , Yasushi Okazaki∗ , Yoshihide
Hayashizaki∗ (∗ RIKEN, † CREST, JST)
Sequence Analysis for Discrimination of Signal
Peptides and Signal Anchor Sequences, Masahiro Gomi,
Shigeki Mitaku (Tokyo Univ. of Agric. & Tech.)
Pairwise Alignment on the Loop Structured
Computer, Zhongmin Li, Yoshio Yoshioka,
Toshio Shimizu (Hirosaki Univ.)
A High-throughput Gene Discovery System for
Arabidopsis Genome Sequencing Project,
Yasukazu Nakamura, Satoshi Tabata(Kazusa DNA Research Inst.)
Insertion with Long Target Duplication: A Novel
Mechanism for Bacterial Gene Mobility Suggested
from Genome Comparison, Ayaka Nobusato∗ ,Ikuo Uchiyama† , Seishi Ohashi∗ , Ichizo Kobayashi∗(∗ Univ. Tokyo, † Okazaki Natl. Research Inst.)
Evolutionary Emergence of Early-Peptide-Synthesizing
RNA Machines by Means of HierarchicalSociogenesis of tRNA-riboorganisms, Koji Ohnishi,
Shoken Hokari (Niigata Univ.)
Distances between Completely Matched Tuples in
the Modern Gene Sequences, Nobuyuki Uchikoga,
Akira Suyama (Univ. Tokyo)
Synthesis and Analysis of a Biological System,
Hiroyuki Kurata∗ , Kazunari Taira∗ , Hiroaki Kitano†(∗ Univ. Tokyo, † ERATO, JST)

16

P67:

BioDrive: Simulator for Biochemical andGenetic Networks, Koji M. Kyoda∗† ,Michiko Muraki∗‡ , Shugo Hamahashi∗† ,Mineo Morohashi∗ ‡ , Shuichi Onami∗ ,Hiroaki Kitano∗§ (∗ ERATO, JST, † Keio Univ.,‡
Tokyo Med. & Dent. Univ., § Sony CSL)

P68:

Generic Gene Expression System for ModelingComplex Gene Regulation Network Using
E-Cell System, Kenta Hashimoto,
Fumihiko Miyoshi, Sae Seno, Masaru Tomita(Keio Univ.)

P69:

Parameter Estimation Mechanism of E-Cell
Simulation Environment, Yusuke Saito,
Kouichi Takahashi, Tomoharu Iwata,
Tomohiko Aikawa, Masaru Tomita (Keio Univ.)

P70:

Pathological Analyses of Enzyme Deﬁciency in
Human Erythrocyte Using E-Cell System,
Ryo Matsushima, Yoichi Nakayama, Natsumi Noguchi,
Hironori Tanaka, Ayako Kinoshita, Masaru Tomita(Keio Univ.)

P71:

Towards Kinetic Modeling of DNA Replication
Using the E-Cell System, Fumihiko Miyoshi,
Kenta Hashimoto, Yuki Fujita, Reina Matsuo,
Youhei Yamada, Masaru Tomita (Keio Univ.)

P72:

Computer Simulation of Human Erythrocyte Using
the E-Cell System, Yoichi Nakayama,
Ryo Matsushima, Masaru Tomita (Keio Univ.)

P73:

Mathematical Analysis of Metabolic Networks
Using the E-Cell Simulation Environment,
Masayuki Okayama, Motohiro Yoneda, Yusuke Saito,
Kouichi Takahashi, Masaru Tomita (Keio Univ.)

P74:

Kinetic Modelling of Energy Metabolism in
Mitochondria, Katsuyuki Yugi, Yuko Kanai,
Masaru Tomita (Keio Univ.)

17

Commercial Exhibitions
C1: CTC LABORATORY SYSTEMS CORP.
C2: Ryoka Systems Inc.
C3: Mitsubishi Space Software Ltd.
C4: Mitsui Knowledge Industry Co., Ltd.
C5: Nihon SiliconGraphics K.K.
C6: Hitachi, Ltd.
C7: Teijin Systems Technology Ltd.
C8: PE Biosystems Japan Ltd.

Location
The workshop will take place at the Garden Hall which islocated in the Yebisu Garden Place. Please get oﬀ at JR
Ebisu Station or Ebisu Station on the Eidan Subway Hibiya Line. It takes about 5 minutes walk from the east
exit JR EBISU station to Yebisu Garden Place if you use
the “Yebisu Skywalk” covered moving walkway. The address/TEL/FAX of Yebisu Garden Place are as follows:
1-13-2 Mita, Meguro-ku, Tokyo 153-0062, Japan
TEL: +81-3-5424-0111 FAX: +81-3-5424-1444
URL: http://www.sgi.co.jp/YGP/ (Japanese)18

Getting There
Tokyo is the capital city of Japan.There are direct ﬂights
to Narita International Airport from many countries.You
can take trains from the airport.
After arriving in Narita International Airport,take a
train (either JR line or Keisei line) from the airport station:
1. JR line:
Using Express (Narita Express) train,it takes about
1 hour from the airport station to JR Tokyo station.From JR Tokyo station to JR Ebisu station,take
JR Yamanote line to the direction of Shinagawa andShibuya.It takes about 30 minutes.
2. Keisei line:
Using Express (Skyliner) train,it takes about 1 hourfrom the airport station to Keisei Ueno station.It
takes about 5 minutes walk from Keisei Ueno station to JR Ueno station.From JR Ueno station to
JR Ebisu station,take JR Yamanote line to the direction of Tokyo and Shinagawa. It takes about 40
minutes.
Go along the Sky Walk from the east exit of JR Ebisu
station. After 5 minutes walk, you will ﬁnd the entrance
to the Yebisu Garden Place.

Passport and Visa Requirements
All overseas visitors wishing to enter Japan require a valid
Passport. Visa will also be required for participants comingfrom the countries without visa exemption agreements withJapan.
Entry into Japan for 90 days is very easy to obtaina Visa. Participants requiring visas should apply well inadvance to Japanese consular oﬃces or diplomatic missions
in their countries prior to making ﬁnal travel arrangementswith a travel agent.
For more information about visa,please see
http://www.mofa.go.jp/j info/visit/visa/index.html(The Ministry of Foreign aﬀairs,Japan)
If you require a letter advising your registration for the
conference, please E-mail : giw@ims.u-tokyo.ac.jp.

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