GIW '99 Program
Registration
Dec. 13: 16:30 - 18:30 Garden Room
Dec. 14: 9:00 - 18:30 Garden Hall
Dec. 15: 9:00 - 18:00 Garden Hall
December 13, Monday, Garden Room
The Anniversary Event
16:30 - 18:30 Registration at Garden Room
17:30 - 18:00 Event Presented by Japanese Society for Bioinformatics
18:00 - 18:30 Event Presented by International Society for Computational Biology
18:30 - 21:00 Reception Party and General Meeting
December 14, Tuesday, Garden Hall
Opening Address
9:20 - 9:30 Kiyoshi Asai (ETL)
Session 1 Chair: A. Keith Dunker (Washington State University)
9:30 - 9:50 MIAX: A Novel System for Assessment of Macromolecular Interaction in
Condensed Phases. 1) Description of the Interaction Model and Simulation
Algorithm, Carlos A. Del Carpio Munoz, Atsushi Yoshimori
9:50 - 10:10 A Generic Criterion for Gene Recongnitions in Genomic Sequences,
Chungfan Kim, Akihiko Konagaya, Kiyoshi Asai
10:10 - 10:30 Protein Threading Based on Multiple Protein Structure Alignment,
Tatsuya Akutsu, Kim Lan Sim
Session 2 Chair: Akihiko Konagaya (JAIST)
10:30 - 10:50 Predicting
Protein Disorder for N-, C-, and Internal Regions,
Xiaohong Li, Pedro Romero, Meeta Rani, A. Keith Dunker, Zoran Obradovic
10:50 - 11:10 Predicting Binding Regions within Disordered Proteins,
Ethan Garner, Pedro Romero, A. Keith Dunker, Celeste Brown, Zoran Obradovic
Break 11:10 - 11:20
Invited Talk David Haussler (UC Santa Cruz) Chair: Kiyoshi Asai (ETL)
11:20 - 12:20 Computational Analysis of High-throughput Genomics Data Using
Hidden Markov Models and Support Vector Machines
Lunch Break 12:20 - 14:00
Session 3 Chair: Matsuda Hideo (Osaka Univ.)
14:00 - 14:20 A Compression Algorithm for DNA Sequences and Its Applications
in Genome Comparison,
Xin Chen, Sam Kwong, Ming Li
14:20 - 14:40 An EM-type Algorithm for Ordered Restriction Map Alignment,
Hirotada Kobayashi, Hiroshi Imai
14:40 - 15:00 A Greedy Algorithm for Minimizing the Number of Primers in Multiple
PCR Experiments,
Koichiro Doi, Hiroshi Imai
15:00 - 15:20 On the Reconstruction of Ancient Doubled Circular Genomes Using Minimum Reversals,
Nadia El-Mabrouk, David Sankoff
Message from International Society for Computational Biology (ISCB)
15:20 - 15:30 A. Keith Dunker (Board of Director, ISCB)
One-Minute Talks for Posters & Software Demonstrations
15:30 - 17:00 Chair: Shigeki Mitaku (Tokyo Univ. of Agric. and Tech.)
Posters & Software Demonstrations
17:00 - 18:30
Banquet
18:30 - 21:00 Foyer, Garden Hall
December 15, Wednesday, Garden Hall
Session 4 Chair: Satoru Kuhara (Kyushu Univ.)
9:40 - 10:10 Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG,
Mitsuteru Nakao, Hidemasa Bono, Shuichi Kawashima, Tomomi Kamiya,
Kazushige Sato, Susumu Goto, Minoru Kanehisa
10:00 - 10:20 Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts,
See-Kiong Ng, Marie Wong
10:20 - 10:40 Finding Precursor Compounds in Secondary Metabolism,
Masanori Arita, Kiyoshi Asai, Takaaki Nishioka
Coffee Break 10:40 - 11:00
Invited Talk Yusuke Nakamura (Director, Human Genome Center, Univ. Tokyo) Chair: Toshihisa Takagi (Univ. Tokyo)
11:00 - 12:00 Human Genome Analysis and Medicine in the 21st Century
Lunch Break 12:00 - 13:30
Posters & Software Demonstrations
13:30 - 15:00
Session 5 Chair: Susumu Goto (Kyoto Univ.)
15:00 - 15:20 Automated Processing of 2-D Gel Electrophoretograms of Genomic DNA
for Hunting Pathogenic DNA Molecular Changes,
Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe, Akihiko Konagaya
15:20 - 15:40 Bio-calculus: Its Concept and Molecular Interaction,
Masao Nagsaki, Shuichi Onami, Satoru Miyano, Hiroaki Kitano
15:40 - 16:00 Towards Automatic Construction of Cell-Lineage of C. elegans from
Nomarski DIC Microscope Images,
Tomohiro Yasuda, Hideo Bannai, Shuichi Onami, Satoru Miyano, Hiroaki Kitano
Coffee Break 16:00 - 16:20
Session 6 Chair: Kenta Nakai (Univ. Tokyo)
16:20 - 16:40 Tracing Synergetic Behavior of the QTLs Affecting Oral Glucose Tolerance
in the OLETF Rat,
Akihiro Nakaya, Haretugu Hishigaki, Shinichi Morishita
16:40 - 17:00 Integrating Application Programs for Bioinformatics Using a web Browser,
Yutaka Ueno, Kiyoshi Asai, Masanori Arita
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
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
Best Paper Award Ceremony
17:40 - 17:50
Closing 17:50 - 18:00
Akihiko Konagaya (JAIST)
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
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
S03: A Keyword Recommendation System for GenBank, Yasuhiko Kitamura, Tetsuro Nanbu, Shoji Tatsumi
S04: GeneAlign: Java Application Software for Multiple Sequence Alignment Editor, Ken Kurokawa, Yoshitaka Hasegawa, Kenichi Kawashima, Toshiyuki Okumura, Tatsuya Takagi, Teruo Yasunaga
S05: KMDB: Keio Mutation Database for Human Disease Gene, Shinsei Minoshima, Susumu Mitsuyama, Saho Ohno, Takashi Kawamura, Nobuyoshi Shimizu
S06: NEXTDB: The Expression Pattern Map Database for C. elegans, Tadasu Shin-i, Yuji Kohara
S07: ViewDesigner: A Tool for Designing Viewscopes in Discovery System HypothesisCreator, Yoshinori Tamada, Satoshi Matsumoto, Osamu Maruyama, Satoru Miyano
S08: Protein Dynamics Observations of Lambda Phage by Hybrid Petri Net, Atsuhi Doi, Rainer Drath, Masao Nagasaki, Hiroshi Matsuno Satoru Miyano
S09: An Intelligent Tool for Selecting Abstracts in MEDLINE, Miyako Tanaka, Sanae Nakazono, Hiroshi Matsuno, Satoru Miyanon
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
P02: DDGEL/DDCHIP: Web-Based Systems for Analysis of 2-D Gel Electrophoresis Images and DNA Macro/Micro Array Images, Kyotetsu Kanaya, Akira Ohyama, Tatsuya Akutsu, Asao Fujiyama
P03: Probe Design for DNA Chip, Ken-ichi Kurata, Akira Suyama
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
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
P06: Recent Improvements in the Automatic System for Protein Tertiary Structure Prediction GAX, Carlos Adriel Del Carpio Munoz
P07: Development of an Automated Identification Program for Three-Dimensional Protein Motifs, Hiroaki Kato, Yoshimasa Takahashi, Hidetsugu Abe
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
P09: A System for Displaying Protein Structure Information Based on Sequence Fragment Similarity, Shouji Tatsumoto, Kenji Satou
P10: An Automated Structure Prediction System by Lattice Model for Seven-Helix-Type Membrane Proteins, Junichi Uechi, Takatsugu Hirokawa, Makiko Suwa, Shigeki Mitaku
P11: BESPA: Software Tools for 3D Structure Reconstruction from Single Particle Images of Proteins, Yutaka Ueno, Katsutoshi Takahashi, Kiyoshi Asai, Chikara Sato
P12: Chemical Knowledge for Predicting Biosynthetic Pathways of Secondary Metabolites, Takaaki Nishioka, Kimito Funatsu
P13: Prediction of Secondary Metabolism Pathways from Genomic Information and Compounds Data, Atsushi Ogiwara
P14: Methods for Predicting Target Sites of Transcription Factors, Akinori Sarai, Hidetoshi Kono, Michael Gromiha, Fabio Pichierri, Kenji Sayano, Misako Aida
P15: Evaluation of a Method for Predicting Transcription Factors, Goro Terai, Takeshi Mizuno, Toshihisa Takagi
P16: Prediction of Cooperative Binding Sites for Multiple Transcription Factors, Yifei Wang, Akinori Sarai
P17: AIGNET: A System That Infers Large Scale Genetic Networks, Yukihiro Maki, Shoji Watanabe, Yukihiro Eguchi, Daisuke Tominaga, Masahiro Okamoto
P18: Coherent Structural Prediction of a Set of Paralogous Genes on a Eukaryotic Genome, Osamu Gotoh
P19: Interaction-based Analysis of Protein Function and Network, Haretsugu Hishigaki, Toshihide Ono, Akira Tanigami, Toshihisa Takagi
P20: Prediction of MHC Class II-Peptide Interaction Using Fuzzy Neural Network, Hideki Noguchi, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi
P21: Prediction of Nuclear Localization Signals by HMM, Keun-Joon Park, Minoru Kanehisa
P22: A Novel System for Assessment of Macromolecular Interaction in Condensed Phases. 2) Interaction Site Inference by Molecular Shape and Electrostatic Complementarity, Atsushi Yoshimori, Carlos Adriel Del Carpio Munoz
P23: Progress of ProTherm: Theromodynamic Database for Proteins and Mutants, Michael Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira, P. Prabakaran, Akinori Sarai
P24: Detection of Apoptotic Domains against KEGG Database by the HMM Search, Masahiro Hattori, Minoru Kanehisa
P25: Maintenance of Transcription Factor DataBase TFDB, Masako Kaizawa, Satoru Watanabe, Takahiro Nobukuni, Masami Horikoshi, Hiroshi Handa, Yoshiyuki Kuchino, Takao Sekiya, Hiroshi Mizushima
P26: A Database System for the Management and Karyotype Analysis of Chromosome Image Data, Akihiro Kawaguchi, Kenji Satou
P27: MAGEST: ESTs and Gene Expression Pattern Database for {\it Halocynthia roretzi} Maternal cDNA, Shuichi Kawashima, Takeshi Kawashima, Hiroki Nishida, Kazuhiro W. Makabe, Minoru Kanehisa
P28: INE: The Rice Genome Sequence Database, Yoshiyuki Mukai, Hideki Nagasaki, Baltazar A. Antonio, Katsumi Sakata, Yasumichi Sakai, Takuji Sasaki
P29: Receptor Database (RDB) in 1999, Kotoko Nakata, Takako Takai, Tsuguchika Kaminuma
P30: Thermodynamic Database for Protein-Nucleic Acid Interactions, P. Prabakaran, Jianghong An, Michael Gromiha, S. Selvaraj, Hatsuho Uedaira, Hidetoshi Kono, Akinori Sarai
P31: SLAD - An Integrated Swine MHC Database: A Case Study of Data Warehousing in Molecular Immunology, Christian Schoenbach, Vladimir Brusic, Judice L.Y. Koh
P32: PDB-DO:Database of Disorder, Kim Lan Sim, Tomoyuki Uchida, Satoru Miyano
P33: An Aberrant Splicing Database for Finding Rules of Splice-Site Selection, Takashi Yamanaka, Tetsushi Yada, Kenta Nakai
P34: Construction and Application of Mouse Full-length cDNA Database, Hideaki Konno, Yoshifumi Fukunishi, Toshinori Endo, Yoshihide Hayashizaki
P35: Classification of MEDLINE Abstracts, Katsutoshi Ibushi, Nigel Collier, Jun'ichi Tsujii
P36: A Combined Query Expansion Approach for Information Retrieval, Hisao Imai, Nigel Collier, Jun'ichi Tsujii
P37: A Semantically Annotated Corpus from MEDLINE Abstracts, Tomoko Ohta, Yuka Tateisi, Nigel Collier, Chikashi Nobata, Katsutoshi Ibushi, Jun'ichi Tsujii
P38: Automatic Extraction of Information on Protein-Protein Interaction from Scientific Literature, Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, Toshihisa Takagi
P39: An Ontology for Biological Reaction Events, Yuka Tateisi, Tomoko Ohta, Takako Takai, Jun'ichi Tsujii
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
P41: A Preliminary Study in Data Management and Visualization of Signal Transduction Pathway Data -- Viewing Interaction Data, Ken-ichiro Fukuda, Toshihisa Takagi
P42: Toward a Data Mining Service from Large and Heterogeneous Genome Databases in GenomeNet, Yoshiki Fuseda, Kenji Satou
P43: Cross Database Visualization, David P. Hansen, Thure Etzold, Guenther Kurapkat
P44: A Full-Text Search System Covering the Whole GenomeNet, Takao Kataoka, Kenji Satou
P45: WEB Based GENOME Analysis Tools in ALIS Project, Kazuo Takehana, Takehiko Ito, Tetsushi Yada, Mika Hirakawa, Hiroko Yamaguchi, Junko Shimada, Katsuji Matsumura, Masako Kuroda
P46: Global Integration of Gene Databases by Eigen-ID Method, Tetsuro Toyoda and Akiko Itai
P47: 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
P48: Synonymous Codon Usage Based on Codon-Anticodon Interaction Energy and Gene Expression Level, Mamoru Kato, Akira Suyama
P49: Analysis of Molecular Evolution in Mitochondorial tRNA Gene Sequences, Jun-Ichi Sagara, Kentaro Shimizu
P50: Unit-Based de novo Drug Design Using a Library of Protein-Ligand Interaction Sites, Kiminobu X. Sato, Susumu Goto, Minoru Kanehisa
P51: Characterization and Classification of Splicing Patterns, Yumi Tamada, Toshio Shimizu
P52: Application to Gene Cluster Analysis of Inductive Inference of Languages over Patterns with Conceptual Hierarchy, Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto
P53: Distribution of Species Specific Gene Family in Microorganisms, Takeshi Ara, Kenji Suzuki, Hideo Matuda, Hirotada Mori
P54: Differences of Translation Termination Sites among the Three Stop Codons, Yosuke Ozawa, Satoshi Hanaoka, Rintaro Saito, Masaru Tomita
P55: Fop Values, Start Codons, SD Sequence Conservation, and Their Correlation to Gene Expression Level, Hiroaki Sakai, Chiaki Imamura, Hiroshi Ohno, Takanori Washio, Masaru Tomita
P56: Computational Analysis of chi Sequences, Reina Uno, Yoichi Nakayama, Kenji Yotsutani, Takehito Mogami, Kazuharu Arakawa, Masaru Tomita
P57: Zipf-Scaling Description in the DNA Sequences, Yasuo Yonezawa, Hiroyuki Motohasi
P58: Toward Full 3D Structural Investigation of Intron Splicing in Human Cytochrome P450 2D6 pre-mRNA, Wayne Dawson, Kenji Yamamoto
P59: 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
P60: Sequence Analysis for Discrimination of Signal Peptides and Signal Anchor Sequences, Masahiro Gomi, Shigeki Mitaku
P61: Pairwise Alignment on the Loop Structured Computer, Zhongmin Li, Yoshio Yoshioka, Toshio Shimizu
P62: A High-throughput Gene Discovery System for Arabidopsis Genome Sequencing Project, Yasukazu Nakamura, Satoshi Tabata
P63: Insertion with Long Target Duplication: A Novel Mechanism for Bacterial Gene Mobility Suggested from Genome Comparison, Ayaka Nobusato, Ikuo Uchiyama, Seishi Ohashi, Ichizo Kobayashi
P64: Evolutionary Emergence of Early-Peptide-Synthesizing RNA Machines by Means of Hierarchical Sociogenesis of tRNA-riboorganisms, Koji Ohnishi, Shoken Hokari
P65: Distances between Completely Matched Tuples in the Modern Gene Sequences, Nobuyuki Uchikoga, Akira Suyama
P66: Synthesis and Analysis of a Biological System, Hiroyuki Kurata, Kazunari Taira, Hiroaki Kitano
P67: BioDrive: Simulator for Biochemical and Genetic Networks, Koji M. Kyoda, Michiko Muraki, Shugo Hamahashi, Mineo Morohash, Shuichi Onami, Hiroaki Kitano
P68: Generic Gene Expression System for Modeling Complex Gene Regulation Network Using E-Cell System, Kenta Hashimoto, Fumihiko Miyoshi, Sae Seno, Masaru Tomita
P69: Parameter Estimation Mechanism of E-Cell Simulation Environment, Yusuke Saito, Kouichi Takahashi, Tomoharu Iwata, Tomohiko Aikawa, Masaru Tomita
P69: Parameter Estimation Mechanism of E-Cell Simulation Environment, Yusuke Saito, Kouichi Takahashi, Tomoharu Iwata, Tomohiko Aikawa, Masaru Tomita
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
P71: Towards Kinetic Modeling of DNA Replication Using the E-Cell System, Fumihiko Miyoshi, Kenta Hashimoto, Yuki Fujita, Reina Matsuo, Youhei Yamada, Masaru Tomita
P72: Computer Simulation of Human Erythrocyte Using the E-Cell System, Yoichi Nakayama, Ryo Matsushima, Masaru Tomita
P73: Mathematical Analysis of Metabolic Networks Using the E-Cell Simulation Environment, Masayuki Okayama, Motohiro Yoneda, Yusuke Saito, Kouichi Takahashi, Masaru Tomita
P74: Kinetic Modelling of Energy Metabolism in Mitochondria, Katsuyuki Yugi, Yuko Kanai, Masaru Tomita
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.