GIW 2005
The Sixteenth International Conference on Genome Informatics
Pacifico Yokohama, Japan
December 19–21, 2005
Scope
GIW is the longest running international bioinformatics conference, which provides unique opportunities that bridge theory and experiments, academia and industry, and East and West. Its scopeincludes all work that is ultimately devoted to the computational understanding of biological systems
on a molecular basis.
Sponsored and Organized by
Bioinformatics Center (Kyoto University)
Human Genome Center (University of Tokyo)
Systems Genomics Towards System-Level Understanding of Life (MEXT of Japan)
Japanese Society for Bioinformatics (JSBi)
Steering Committee
Minoru Kanehisa (Kyoto University)
Toshihisa Takagi (University of Tokyo)
Satoru Miyano (University of Tokyo)

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GIW 2005
The Sixteenth International Conference on Genome Informatics
Pacifico Yokohama, Japan
December 19–21, 2005
Registration
Registration should be done at: http://giw.ims.u-tokyo.ac.jp/giw2005/registration.html until December 4, 2005. Registration fee includes a copy of Genome Informatics Vol. 16, No. 2 andcoffee breaks. We offer registration fee discount for JSBi and ISCB members.
until Dec. 4, 2005 after Dec. 4, 2005
Standard
JPY15,000.JPY20,000.Standard
ISCB Member
JPY14,000.JPY19,000.Registration JSBi Member
JPY8,000.JPY13,000.JSBi & ISCB Member
JPY7,000.JPY12,000.Standard
JPY10,000.JPY15,000.Student
ISCB Member
JPY9,000.JPY14,000.Registration JSBi Member
JPY5,000.JPY10,000.JSBi & ISCB Member
JPY4,000.JPY9,000.(Banquet on December 20 evening : JPY6,000.-)
Secretary and Local Arrangements
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
E-mail: giw@ims.u-tokyo.ac.jp
URL: http://giw.ims.u-tokyo.ac.jp/giw2005/index.html
Location
The conference will take place at PACIFICO YOKOHAMA. Please get off at Minato Mirai Stationon the Minato Mirai Line (connecting from the Tokyu Toyoko Line). It takes about 3 minutes’ walkfrom the Minato Mirai Station to Pacifico Yokohama.
Address: 1-1-1, Minato Miarai, Nishi-ku, Yokohama 220-0012, Japan
Tel: +81-45-221-2155
URL: http://www.pacifico.co.jp/index_e.html

Conference Center
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Posters

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GIW 2005
Registration
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GIW 2005 Advanced Program
Registration
December 19, 2005: 08:30 - 18:00
December 20, 2005: 08:00 - 18:00
December 21, 2005: 08:00 - 16:00

Monday, December 19, 2005
Opening Address
09:00 - 09:10

Reinhart Heinrich (Humboldt U.) and Hiroshi Mamitsuka(Kyoto U.)

Paper Session 1
09:10 - 09:35

Chair: Tetsuo Shibuya (U.Tokyo)
Qualitatively Predicting Acetylation and Methylation Areas in DNA Sequences, Tho Hoan Pham1 , Dang Hung Tran2 , Tu Bao Ho2,3 , Kenji
Satou2,3 , Gabriel Valiente4 (1 Hanoi U. Pedagogy, 2 JAIST, 3 JST, 4 Technical
U. Catalonia)

09:35 - 10:00

Knowledge-Based Prediction of DNA Atomic Structure from Nucleic Sequence,Marcos J. Araúzo-Bravo, Akinori Sarai (U. Vermont)

10:00 - 10:25

Prediction of Functional Modules Based on Gene Distributions in Microbial Genomes, Hongwei Wu1,2 , Fenglou Mao1 , Zhengchang Su1,2 , Victor
Olman1 , Ying Xu1,2 (1 U. Georgia, 2 Oak Ridge National Lab.)

10:25: - 11:00

Break

Keynote Address
11:00 - 12:00
12:00 - 13:30

Chair: Hiroshi Mamitsuka (Kyoto U.)
Chemoinformatics, Drug Design, and Systems Biology, Pierre Baldi (UCIrvine)Lunch

Posters and Software Demonstrations Session 1
13:30 - 14:30( Odd Number )Paper Session 2
14:30 - 14:55

Chair: Oliver Ebenhöh (Humboldt U.)
Supporting the Curation of Biological Databases with Reusable Text Mining, Olivo Miotto1 , Tin Wee Tan1 , Vladimir Brusic2,3 (1 National U. Singapore, 2 U. Queensland, 3 Inst. for Infocomm Res.)

14:55 - 15:20

Reconstruction of Phylogenetic Relationships from Metabolic Pathways
Based on the Enzyme Hierarchy and the Gene Ontology, José C. Clemente1 ,Kenji Satou1 , Gabriel Valiente2 (1 JAIST, 2 Technical U. Catalonia)

15:20 - 15:45

Mass Identification of Chloroplast Proteins of Endosymbiont Origin by
Phylogenetic Profiling Based on Organism-Optimized Homologous Protein Groups, Naoki Sato, Masayuki Ishikawa, Makoto Fujiwara, Kintake
Sonoike (U. Tokyo)

15:45: - 16:15

Break

Paper Session 3
16:15 - 16:40

Chair: Limsoon Wong (Inst.Infocomm Res.)
Strategies for Genome Reduction in Microbial Genomes, Kishore R.
Sakharkar, Vincent T.K. Chow (National U. Singapore)

16:40 - 17:05

Reassembly and Interfacing Neural Models Registered on BiologicalModel Databases, Mihoko Otake1,2 , Toshihisa Takagi1 (1 U. Tokyo,
2 PRESTO,JST)3

17:05 - 17:30

Objective Measurement of Spindle Orientation in Early Caenorhabditis elegans Embryo, Shugo Hamahashi1,2 , Shuichi Onami1,2 (1 Keio U., 2 JST)

17:30 - 17:55

Evolution from Possible Primitive tRNA-Viroids to Early Poly-tRNADerived mRNAs: A New Approach from the Poly-tRNA Theory, Koji
Ohnishi, Madoka Ohshima, Naotaka Furuichi (Niigata U.)

Tuesday, December 20, 2005
Paper Session 4
09:00 - 09:25

Chair: Ying Xu (U. Georgia)
A Study of Fragment-Based Protein Structure Prediction: Biased Fragment Replacement for Searching Low-Energy Conformation, Sung-Joon
Park (Kobe U.)

09:25 - 09:50

Comparison of Protein Structures by Multi-Objective Optimization, Luonan Chen1 Ling-Yun Wu2 , Ruiqi Wang1 , Yong Wang1 Shihua Zhang2 ,Xiang-Sun Zhang2 (1 Osaka Sangyo U., 2 Chinese Acad. of Sci.)

09:50 - 10:15

Statistical Evaluation of a Bottom-Up Clustering for Single Particle Molecular Images, Yutaka Ueno1 , Katsunori Isono1,2 , Katsutoshi Takahashi1 ,Yukio Shimonohara1,3 , Kiyoshi Asai1 (1 CBRC, 2 INTEC Web and Genome
Informatics Corp., 3 Information and Mathematical Science LaboratoryInc.)

10:15 - 10:45

Break

Paper Session 5
10:45 - 11:10

Chair: Koji Tsuda (CBRC)
Inter-Species Validation for Domain Combination Based Protein-Protein
Interaction Prediction Method, Woo-Hyuk Jang 1 , Dong-Soo Han 1,3 ,Hong-Soog Kim 2 , Sung-Doke Lee 1 (1 Information & Communications U.,
2 Electronics & Telecommunications Res. Inst., 3 Correspondence author)

11:10 - 11:35

A Graph Theoretical Approach for Analysis of Protein Flexibility Change
at Protein Complex Formation, Carlos A. Del Carpio M.1 , Abdul Rajjak
Shaikh1 , Eichiro Ichiishi1 , Michihisa Koyama1 , Momoji Kubo1,2 , Kazumi
Nishijima1,3 , Akira Miyamoto1 (1 Tohoku University, 2 PRESTO, JST,3 Mochida Pharmaceutical Co. Ltd.)

11:35 - 12:00

A Fast Protein-Protein Docking Algorithm Using Series Expansion inTerms of Spherical Basis Functions, Kazuya Sumikoshi, Tohru Terada,
Shugo Nakamura, Kentaro Shimizu (U. Tokyo)

12:00 - 13:30

Lunch

Keynote Address
13:30 - 14:30

Chair: Kenta Nakai (U. Tokyo)
Membrane Proteins in Vivo and in Silico: Getting the Best of Two Worlds,
Gunnar von Heijne (Stockholm U.)

Paper Session 6
14:30 - 14:55

Chair: Gabriel Valiente (Tech. U. Catalonia)
Viewing the Proteome from Oligopeptides and Prediction of Protein Function, Hisayuki Horai1,2 , Kouichi Doi1 , Hirofumi Doi1,2 (1 NAIST, 2 Celestar
Lexico-Sciences, Inc.)

14:55 - 15:20

Mass Distributed Clustering: A New Algorithm for Repeated Measurements in Gene Expression Data, Shinya Matsumoto1 , Ken-ichi Aisaki2 ,Jun Kanno2 (1 NCR Japan, Ltd., 2 NIHS)

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15:20 - 15:45

Diagnosis of Early Relapse in Ovarian Cancer Using Serum Proteomic Profiling, Jung Hun Oh1 , Jean Gao1 , Animesh Nandi2 , Prem Gurnani2 , Lynne
Knowles3 , John Schorge3 , Kevin P. Rosenblatt2 (1 U.Texas, 2 UT Southwestern Med. Center, Dallas)

15:45: - 16:00

Break

JSBi Annual Meeting
16:00 - 16:30
Posters and Software Demonstrations Session 2
16:30 - 18:00( Even Number )Banquet18:30 - 20:30

Ballroom “Monaco” at Inter Continental The Grand Yokohama

Wednesday, December 21, 2005
Paper Session 7
09:00 - 09:25

Chair: Tatsuya Akutsu (Kyoto U.)
Reverse Engineering Genetic Networks Using Evolutionary Computation,
Nasimul Noman, Hitoshi Iba (U. Tokyo)

09:25 - 09:50

Toward Integration of Systems Biology Formalism: The Gene Regulatory
Networks Case, Raffaella Gentilini (U. Udine)

09:50 - 10:15

Reconstruction of Gene Regulatory Networks under the Finite State Linear
Model, Dace Ruklisa1 , Alvis Brazma2 , Juris Viksna1 (1 U. Latvia, 2 EBI)

10:15 - 10:40

A Space-Efficient Algorithm for the Constrained Pairwise Sequence Alignment Problem, Dan He, Abdullah N. Arslan (U. Vermont)

Posters and Software Demonstrations Session 3
10:40 - 12:00
12:00 - 13:30

Lunch

Keynote Address
13:30 - 14:30

Chair: Reinhart Heinrich (Humboldt U.)
Cell-Cell Interaction Network That Generates the Skin Pattern of Animal,
Shigeru Kondo (Nagoya U.)

Paper Session 8
14:30 - 14:55

Chair:
Automatic Drawing of Biological Networks Using Cross Cost and Subcomponent Data, Mitsuru Kato, Masao Nagasaki, Atsushi Doi, Satoru Miyano(U. Tokyo)

14:55 - 15:20

Interaction Graph Mining for Protein Complexes Using Local Clique Merging, Xiao-Li Li1 , Soon-Heng Tan1,2 , Chuan-Sheng Foo1,3 , See-Kiong Ng1(1 Inst. for Infocomm Res., 2 National U. Singapore, 3 Stanford U.)

15:20 - 15:45

Topology of Mammalian Transcription Networks, Anatolij P. Potapov1 ,Nico Voss2 , Nicole Sasse1 , Edgar Wingender1,2 (1 U. Göttingen, 2 BIOBASE
GmbH)

Closing and Award Ceremony
15:45 - 16:00

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Commercial Exhibitions
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Ryoka Systems Inc.
CTC Laboratory Systems Corporation
NABE International Corporation
SGI Japan, Ltd.
Mathematical Systems, Inc.
Pathway Solutions Inc.
HITACHI, LTD.
INFOCOM CORPORATIONHIT corporation Ltd.

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Software Demonstrations
S01 Using the Approach of Comparative Proteomics and Systems Biology to Decipher the Human
Protein Network, Chung-Yen Lin, Fan-Kai Lin, Chi-Shyang Cho, Chieh-Hwa Lin, Li-Wei Lai,
Chao A. HsiungS02 b-Src: A Source-Code Search Engine for Bioinformatics Open-Source Packages, Mitsuteru Nakao, Paul Horton
S03 INOH: Pathways and Ontologies, Noriko Sakai, Tatsuya Kushida, Satoko Yamamoto, Emi Hattori, Hiromi Nakamura, Yuki Yamagata, Yukiko Nakanishi, Toshihisa Takagi, Ken Ichiro Fukuda
S04 Fast Retrieval of Useful Information from Literature Database, Hiroko Matsui, Shigeki Tanishima, Norihiro Akasaka, Takafumi Hayashi, Keiko Oketa, Keizoh Uehara
S05 VECT: The Visual Extraction and Conversion Tool, Hui-Hsien Chou
S06 Toxicogenomics: Novel Computational Strategies for Prediction of Long Term Carcinogenicity,
Jochen Koenig, Claire Pallez, Hans Gmuender, Reinhard Doelz, Deepak Thakkar, Frank Staubli
S07 AlignScope : A System for Visualization and Analysis of Whole Genome Alignments, HeeJeong Jin, Hye-Jung Kim, Hwan-Gue Cho
S08 KeyMolnet: An Integrated Platform for Analysis of Molecular Networks, Atsushi Nogi, Hiromi Sato, Miki Fukuda, Makoto Shigetaka, Yohei Ozeki, Misa Ogura, Kyoko Nakanishi,
Rie Taniguchi, Hisako Kuriki, Nakako Iwasaki, Yoko Inoue, Yoko Wakamatsu, Shizuka Homma,
Mikiko Izumi, Yoshinobu Mizoguchi, Yuichi Kikushima, Takeshi Namba, Keiichi Ayabe,Nobuo Tomioka, Akiko Itai
S09 BioRuby+ChemRuby:
An Exploratory Software Project, Toshiaki Katayama, Mitsuteru C. Nakao, Naohisa Goto, Nobuya Tanaka
S10 Cell Illustrator 2.0: A Platform for Biopathway Modeling and Simulation, Masao Nagasaki,
Atsushi Doi, Satoru Miyano
S11 Tools for Supporting Computational Experiments on Genomic Object Net, Toshinori Tanaka,
Katsuyuki Harada, Hironori Kitakaze, Junkichi Yamanaka, Hiroshi Matsuno, Satoru Miyano

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Posters
P001 Systematic Analysis of Structure-Stability Relationship for Proteins and Mutants, Noboru Furukawa, Yuko Takeno, Goran Neshich, Akinori Sarai
P002 Hierarchy of Metabolic Compounds Based on Their Synthesizing Capacity, Thomas Handorf,
Oliver Ebenhöh, Daniel Kahn, Reinhart Heinrich
P003 IBTS: An Extensible System for Integration of Bioinformatics Tools Allowing Cluster Computing, Youngmahn Hahn, Yongseong Cho, Sang Joo Lee
P004 Virtual Drug Screening of Endothelin Receptor Ligands Using Active Learning, Yukiko Fujiwara,
Yoshiko Yamashita, Minoru Asogawa, Chiaki Fukushima, Masaaki Asao, Hideshi Shimadzu,
Kazuya Nakao, Ryo Shimizu
P005 KAAS: KEGG Automatic Annotation Server, Yuki Moriya, Masumi Itoh, Sujiro Okuda, Minoru Kanehisa
P006 Mining Implicit Biological Realted Entities from Literature Using a Probabilistic Model, Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
P007 Constraints Based Dynamic Protein Interaction Network, Dong-Soo Han, Suk-Hoon Jung, WooHyuk Jang, Choon-Ho Lee
P008 New Features of MutationView : Implementation of Various Protein-Oriented Tools to Find out
the Relation between Protein Function and Diseases, Masafumi Ohtsubo, Takashi Kawamura,
Susumu Mitsuyama, Nobuyoshi Shimizu, Shinsei Minoshima
P009 KEGG-Based Pathway Visualization Tool for Complex Omics Data, Nobuaki Kono,
Kazuharu Arakawa, Yohei Yamada, Hirotada Mori, Masaru Tomita
P010 Visualization of Gene Database on WEB Using Self Organizing Maps, Yasuhiko Miyazaki, Hiroshi Dozono, Hisao Tokushima, Yoshio Noguchi
P011 Evolutionary Identifications of Functional Modules in Yeast Protein Interaction Network,
Soichi Ogishima, Yasuhiro Suzuki, Takashi Hase, So Nakagawa, Hiroshi Tanaka
P012 An Integrated Database and Knowledge-Base of Interaction between Human Proteins and Commonly Used Drugs, Hiroyasu Shimada, Masashi Nemoto, Ken Horiuchi, Atsuko Yamaguchi,
Motoi Tobita, Kenji Araki, Tetsuo Nishikawa
P013 Structural Annotation Viewer and Database for Splice-Variant Human cDNA Sequences, Tetsuo Nishikawa, Kouichi Kimura, Jun-ichi Yamamoto, Ai Wakamatsu, Hiroshi Makita, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
P014 PRIME: Platform for RIKEN Metabolomics, Atsushi Fukushima, Miyako Kusano,
Kenji Akiyama, Takeshi Obayashi, Takayuki Tohge, Masami Yokota Hirai, Shigehiko Kanaya,
Masanori Arita, Yoko Shinbo, Kazuo Shinozaki, Tetsuya Sakurai, Kazuki Saito
P015 Construction of Reference Cis-Regulatory Module Database as a Tool for the Pattern Analysis of Cis-Regulatory Regions on Human Genome Sequence, Eri Kibukawa, Yoshiaki Tanaka,
Satoru Miyazaki
P016 BioTextLinker: Dynamic Informative Link Annotation for Biological Text over Heterogeneous
Databases, Hodong Lee, Jong C. Park
P017 MiDB: Mitochondrial Proteomics Database in Human Heart, Hyun Joo, Taeho Kim,
Jae Boum Youm, Nari Kim, Jin Han
P018 FAMSBASE of Human, Rat and Mouse Genomes with Model Quality Estimation, Mitsuo Iwadate, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Hideaki Umeyama
P019 Framework Approach for a Search Platform on Biological Data, Seok Jong Yu, Dan Bi Kim,
Inae Hur, Sang Joo Lee
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P020 PSE: A Tool for Browsing a Large Amount of PubMed Abstracts with Gene Names and Common
Words as the Keywords, Takashi Yoneya
P021 RPAIR: A Database of Chemical Transformation Patterns in Enzymatic Reactions, Takuji Yamada, Masahiro Hattori, Min A. Oh, Susumu Goto, Minoru Kanehisa
P022 A Resource Discovery Service for Bioinformatics Applications in a Grid-Based Environment,
Xiujun Gong, Jitender Jit Singh Cheema, Kensuke Nakamura, Kei Yura, Nobuhiro Go
P023 Gene Annotation Using Proteomic Data, Yoko Ishino, Hisaaki Taniguchi
P024 A Database for Comparative Analysis of Tunicate Promoter Sequences, Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
P025 An Existence of Cooperative (Clustered) Genes in Coliphageφk, Eisei Takushi, Miyako Kawachi
P026 Evaluation Measures of ‘Marker Selection’ and ‘Genotype Membership’ in Large-Scale SNP
Genotyping , Eli Kaminuma, Hiroshi Masuya, Hiromi Motegi, K. Ryo Takahasi, Miki Nakazawa,
Minami Matsui, Yoichi Gondo, Tetsuo Noda, Toshihiko Shiroishi, Shigeharu Wakana, Tetsuro Toyoda
P027 Finding Small and Resistance-Predictable Feature Sets for Bacterium Classification by MultiObjective Optimization, Hiroshi Yamakawa, Yoshio Nakao, Takahisa Suzuki, Yumiko Sanbongi,
Takashi Ida
P028 Sensitizing GO Tools Using Multiple Ratio-Cutoffs for Gene Selection, Kenichi Hirotani,
Yoichi Yamada, Miyuki Onda, Ken-ichiro Muramoto, Kenji Satou, Takashi Ito
P029 Cell-Distance Networks: A Clue for Understanding of Cell Diversity, Larisa Kiseleva, Paul Horton, Wataru Fujibuchi
P030 How Much We Know about Soluble Domains Existing in Loop Regions of Transmembrane
Proteins?, Syuuichi Yoshida, Masafumi Arai, Takuhiro Nishio, Toshio Shimizu
P031 Discovering Novel MicroRNAs from Small RNA Component of the Mouse Embryo Transcriptome, Tatsuya Ando, Sachiko Okamoto, Masahiro Sato, Hiroyuki Izu, Masanori Takayama,
Masanari Kitagawa, Junichi Mineno, Kiyozo Asada, Ikunoshin Kato
P032 Inferring Protein Interaction Network by Boosting Algorithm, Yong Wang, Feng Bao, Jiadong Zhang, Luonan Chen
P033 Construction of Human Gene Catalogue by mRNA Using 1.4 Million of Full-Length cDNAs by Oligo-Capping Method, Ai Wakamatsu, Jun-ichi Yamamoto, Kouichi Kimura,
Keisuke Tsuchiya, Tetsuo Nishikawa, Sumio Sugano, Takao Isogai
P034 Genome Mapping Analysis of Splice Variant One-Pass Sequences of Human Full-Length cDNAs, Kouichi Kimura, Tetsuo Nishikawa, Ai Wakamatsu, Jun’ichi Yamamoto, Keiichi Nagai,
Nobuo Nomura, Sumio Sugano, Takao Isogai
P035 State Space Model with Markov Switching for Estimating Time-Dependent Gene Regulatory Networks from Time Series Microarray Experiments, Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
P036 Knowledge Discovery Using Cross Database Search, Asako Koike, Toshihisa Takagi
P037 Ontology Based Petri Net Modeling of Signaling Networks, Takako Takai-Igarashi
P038 Discovering Reliable Protein Interactions Using Bayesian Networks , Thanh Phuong Nguyen,
Tu Bao Ho, Ngoc Binh Nguyen
P039 Cluster Analysis of Neutrophilic Differentiation by Using Fuzzy K-Means , Akitsugu Suga,
Kazumi Hakamada, Chinatsu Arima, Masahiro Okamoto, Hitoshi Ichikawa, Taizo Hanai
9P040 Validity Index for Fuzzy K-Means Clustering Using the Gap Statistic Method, Chinatsu Arima,
Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai
P041 Validation of Mathematical Model Based Clustering by Using Time-Course Data, Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai
P042 Improvement in the Accuracy of Gene Prediction in Rice cDNA Sequences, Fusano Todokoro,
Takeshi Itoh, Chisato Yamasaki, Hiroaki Kawashima, Tadashi Imanishi, Takashi Gojobori
P043 Co-Expression Analysis Tool for Large Gene Expression Datasets, Hajime Harada, Natalia Polouliakh, Wataru Fujibuchi, Paul Horton
P044 New Reliable Cancer Diagnosis Method Using Boosting and Projective Adaptive Resonance
Theory, Hiro Takahashi, Yasuyuki Murase, Hiroyuki Honda
P045 Classification Method for Prediction of Multifactorial Disease Development by Using Genetic
and Environmental Factors, Yasuyuki Tomita, Mitsuhiro Yokota, Hiroyuki Honda
P046 Ranking Metabolic Paths with Expression Similarities, Ichigaku Takigawa, Hiroshi Mamitsuka
P047 Classifying Microarray Data Using Pairwise Similarity between Gene Profiles, Raymond Wan,Åsa M. Wheelock, Matthew J. Bartosiewicz, Hiroshi Mamitsuka
P048 A Selection Criterion for Robust Classifiers: Cancer Prognosis with Microarray Gene Expression,
Ikumi Suzuki, Shigeyuki Oba, Shin Ishii
P049 Memory-Efficient Clustering Algorithms for Microarray Gene Expression Data, Kazuyuki Numata, Hideo Bannai, Yoshinori Tamada, Michiel de Hoon, Seiya Imoto, Satoru Miyano
P050 Clustering Gene Expression Data with Stepwise Data Envelopment Analysis, Masako Hoshino,
Hiroshige Inazumi
P051 Effective Nearest Neighbor Methods for Multiclass Cancer Classification Using Microarray Data,
Satoshi Niijima, Satoru Kuhara
P052 Algorithm for Predicting Co-Expression Genes by Improvement of Path Consistency Algorithm,
Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto
P053 A New Method for Analyzing Large-Scale Microarray Data Using Biological Knowledge,
Shingo Tsuji, Kouji Nakayama, Masaru Sekijima, Shigeo Ihara, Hiroyuki Aburatani
P054 Non-Negative Matrix Factorization of Lung Adenocarcinoma Expression Profiles, Takeshi Fujiwara, Shumpei Ishikawa, Yujin Hoshida, Kentaro Inamura, Takayuki Isagawa, Miyuki Shimane,
Hiroyuki Aburatani, Yuichi Ishikawa, Hitoshi Nomura
P055 Classification of Cancer Data with Genetic Programming, Topon Kumar Paul, Hitoshi Iba
P056 The Application of Cell Surface Marker DNA Microarray in the Search for Molecular Targets ,Tuoya, Koichi Hirayama, Yuh Sugii, Tadahiro Nagaoka, Takayuki Fukuda, Hiroko Tada, Hidenori Yamada, Yasaburo Matsuura, Heizo Tokutaka, Masaharu Seno
P057 Detection of Cluster Boundary in Microarray Data by Reference to MIPS Functional Catalogue
Database, Yoshifumi Okada, Takehiko Sahara, Satoru Ohgiya, Tomomasa Nagashima
P058 Multiplicative Decomposition of Time- and Dose-Dependent Gene Expression Changes,
Yukitaka Tani, Takeshi Kamimura, Takeshi Nagashima, Kaori Ide, Mariko Hatakeyama,
Hidetoshi Shimodaira
P059 Species-Specific Variation of Alternative Splicing and Transcriptional Initiation in Six Eukaryotes, Hideki Nagasaki, Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, Osamu Gotoh
P060 The Requirements and Problems to Use Draft Sequencing Results in Comparative Genomics ofBacteria, Hidetoshi Yamashita, Yuki Maruyama, Ryuta Komatsu, Toru Suzuki, Seiki Kuramitsu,
Kiyozo Asada, Ikunoshin Kato, Masanari Kitagawa
10P061 Comparative Sequence Analysis of Human and Promoter Regions, Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
P062 Comprehensive Analysis of Triplet Repeats in Vertebrate Genomes, Shigeo Okada, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
P063 A Maximum Likelihood Method for Inference of
Hung Dinh Nguyen, Maki Yoshihama, Naoya Kenmochi

Spliceosomal

IntronEvolution,

P064 Comparative Genomic Analysis of Transcription Regulation Elements in Higher Eukaryotes,
Natalia Polouliakh, Wataru Fujibuchi, Hajime Harada, Tohru Natsume, Paul Horton
P065 Comparative Analysis of Autocorrelations of Electric Charges in Amino Acid Sequences of S.
cerevisiae and E. coli, Runcong Ke, Shigeki Mitaku
P066 Seeking Genomic Duplication in Prokaryotic Genomes by Equivalent Tandem Repeats Distributions, Satoshi Mizuta, Michimasa Koshino, Toshio Shimizu
P067 Statistical Characterization of Transcription Start Sites in Plant Genomes, Shigeo Fujimori,Takanori Washio, Masaru Tomita
P068 A Scale-Free Prior over Graph Structures for Bayesian Inference of Gene Networks,
Takeshi Kamimura, Hidetoshi Shimodaira
P069 Physicochemical and Structural Characterization of Nonapeptides Targeted in Autoimmune
Diseases, Wataru Honda, Shuichi Kawashima, Minoru Kanehisa
P070 Genome-Wide Protein-Protein Interaction Network Prediction for Oryza sativa, Chen-Yu Chen,
Chen-hsiung Chan, Sheng-An Lee, Cheng-Yan Kao
P071 Dependence of the Accuracy of Protein Secondary Structure Prediction on Long-Range Interactions, Daisuke Kihara
P072 Fast Protein-Protein Docking Algorithm Using Pre-Identified Binding Site Patches, Daisuke Kihara, Sael Lee, Karthik Ramani, Srinivasan Turuvekere, Manish Agrawal, Bin Li
P073 Ligand Binding Sites Prediction with the Visibility Criteria, Bin Li, Srinivasan Turuvekere,
Manish Agrawal, Karthik Ramani, Daisuke Kihara
P074 A Weighting Profile Method for Protein-RNA Interaction Prediction,
Satoru Miyano

Euna Jeong,P075 Protein-Protein Docking by the Benzene Clusters Fitting, Grid Scoring and the Pairwise Interaction Potential in CAPRI Rounds 3-5, Genki Terashi, Mayuko Takeda-Shitaka, Daisuke Takaya,
Katsuichiro Komatsu, Hideaki Umeyama
P076 A Software for a New Methodology of Kinetics Analyses of Protein-Ligand Interaction,
Masaki Yamamura, Takuma Shiraki, Takashi S.Kodama, Tatsuo Nakagawa, Natsuhiro Ichinose,
Osamu Gotoh
P077 Identifying Cooperative Transcriptional Regulations Using Protein-Protein Interactions,Nobuyoshi Nagamine, Yuji Kawada, Yasubumi Sakakibara
P078 WoLF PSORT: Protein Localization Prediction Software, Paul Horton, Keun-Joon Park,
Takeshi Obayashi, Kenta Nakai
P079 Online Discrimination of β-Barrel Membrane Proteins from Amino Acid Sequence,
M. Michael Gromiha, Makiko Suwa
P080 Comparison of Prediction Methods for Protein-Protein Interactions Using Co-Evolutionary Information, Tetsuya Sato, Yoshihiro Yamanishi, Hisako Ichihara, Minoru Kanehisa, Hiroyuki Toh
P081 Characterization of Secondary Structure Elements in Riboswitches, Ai Muto, Masahiro Hattori,
Minoru Kanehisa
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P082 Identification of Clinical Data Effect on Aplastic Anemia Treatment Using Multilayer Fuzzy
Neural Network, Hironori Mutoh, Seiji Kojima, Hiroyuki Honda
P083 Reliability Index for 2-class Classification in Diagnosis of Disease: RIbin , Masahiro Nakatochi,
Hiro Takahashi, Hiroyuki Honda
P084 Automatic Assignment of Full EC Numbers Based on Structural Changes of Chemical Compounds, Nobuya Tanaka, Tadashi Kadowaki, Susumu Goto, Minoru Kanehisa
P085 Chemical Genomic Sutdy of Endocrine Disrupting Chemicals in Metabolic Pathways,
Tadashi Kadowaki, Tetsuya Adachi, Shinobu Okamoto, Nobuya Tanaka, Koichiro Tonomura,
Gozoh Tsujimoto, Minoru Kanehisa
P086 Development of a Method for Predicting Biological Functions of Compounds Using Support
Vector Machine, Tomohiro Sato, Yo Matsuo, Shigeyuki Yokoyama
P087 Modeling Tertiary Structure of Complementarity Determining Region of Antibodies,
Toru Hosokawa, Kenta Nakai, Kengo Kinoshita
P088 A New Perspective on an Old Tool: Extending the Coverage of Sequence Similarity-Based
Function Prediction with PFP, Troy Bartholomew Hawkins, Stanislav Luban, Daisuke Kihara
P089 AR(n) Models Applied in Estimation of Genetic Covariance Functions for QTL Mapping,
Yini Cui, Runqing Yang, Shaoqing Huang
P090 Direct Physical Mapping Method Based on Scanning Probe Microscope, Yoshitaka Suetsugu,
Kazumi Tsukamoto, Seigo Kuwazaki, Takeshi Yamauchi, Tomoyuki Yoshino, Motoharu Shichiri,
Hirokazu Takahashi, Junko Narukawa, Shigeru Sugiyama, Kazuei Mita, Toshio Ohtani,
Kimiko Yamamoto
P091 Comprehensive Promoter Analyses Using a Database of Transcription Start Sites, Riu Yamashita, Katsuki Tsuritani, Yutaka Suzuki, Hiroyuki Wakaguri, Sumio Sugano, Kenta Nakai
P092 A Genome-Wide Analysis of p53 Binding Sites Using Tiling Arrays, Shuichi Tsutsumi, Kiyofumi Kaneshiro, Shingo Tsuji, Hiroyuki Aburatani
P093 Discriminative Detection of Transcription Factor Binding Sites from Location Data,
Yuji Kawada, Yasubumi Sakakibara
P094 PPMuSA: PROSITE-Pattern Matcher Using Suffix Array, Aki Hasegawa, Akihiko Konagaya
P095 Sequence-Based Analyses of Biosynthesis Rate Limiting Factors in Wheat Germ Cell-Free
System, Naoya Fujita, Motoaki Seki, Kazuo Shinozaki, Kengo Kinoshita, Tatsuya Sawasaki,
Yaeta Endo, Kenta Nakai
P096 Machine Learning Prediction of Amino Acid Sequence Characterization in Protein NMyristoylation, Ryo Okada, Chigusa Miyakawa, Manabu Sugii, Hiroshi Matsuno, Satoru Miyano
P097 Prediction of Long Disorder Region Using Two-Step SVM, Shuichi Hirose, Kana Shimizu,
Satoru Kanai, Tamotsu Noguchi
P098 Large-Scale Analysis of Expressed Pseudogenes in Higher Eucaryotes, Hayataro Kochi, Rintaro Saito, Masaru Tomita
P099 Development of Translational Signal Database and Analysis of Sequence-Activity Relationship,
Hayato Nishida, Alex. Kochetov, Akinori Sarai
P100 Genome Wide Analysis of the Alternative Splicing Based on Full-Length cDNA Data, Hiroki Sakai, Yutaka Suzuki, Katsuhisa Horimoto, Sumio Sugano, Minoru Kanehisa
P101 An Unsupervised Diplotype Clustering Method to Improve Race-Based Medicine, Junji Tanaka,
Masato Inoue, Naoyuki Kamatani
P102 Toward Full-Automatic Derivation of P450 Gene Database –Performance of Familywise Applied
to Plant Genomes–, Makoto Hirosawa, Daisuke Shibata, Osamu Gotoh
12

P103 Discovery of Protein Coding Genes Through Chromosome-to-Chromosome Sequence Comparison, Osamu Gotoh, Masao Morita, Nobuyuki Ichiyoshi, Tetsushi Yada
P104 Development of a Primer Design Program for Multiplex PCR, Seok Jong Yu, Yong Seong Cho,
Byeong-Jin Jeong, Hyeon S. Son, Sang Joo Lee
P105 Watermark Embedding Techniques for DNA Sequences Using Codon Usage Bias Features,
Toshio Modegi
P106 Genome Analize by Using Spherical SOM, Yasaburo Matsuura, Toshimichi Ikemura,
Takashi Abe, Heizo Tokutaka, Masaaki Ohkita
P107 The Identification of a Cancer Cell Gene by Using SOM, Yasaburo Matsuura, Tuoya, Masaharu Seno, Heizo Tokutaka, Masaaki Ohkita
P108 Bioprocess Optimal
Masahiro Okamoto

Control

Simulator

DesignandDevelopment,

JebrouYoussef,

P109 A System-Biological Approach to Interferon-Based Therapies, Kazunori Miyazaki, Satoshi ItohP110 BAAQ: A Platform for Integrating Bioinformatics Tools and Sharing Knowledge, Jitender Jit Singh Cheema, Xiujun Gong, Kensuke Nakamura, Kei Yura, Nobuhiro Go
P111 Simulation of Light-Induced Phase Response in Mammals with Hybrid Function Petri Net,
Yumi Harada, Natsumi Mito, Yasushi Fujii, Hiroshi Matsuno, Satoru Miyano, Sin-Ichi T. Inouye
P112 Expanding Large Scale Signal Transduction Networks, Kosuke Hashimoto, Bernd Binder, Minoru Kanehisa, Oliver Ebenhoeh, Reinhart Heinrich
P113 Comprehensive Detection of TM Protein Genes which might be Associated with Febrile
Seizure, Yasuhito Inoue, Kazuaki Kanai, Satoshi Mizuta, Motohiro Okada, Sunao Kaneko,
Toshio Shimizu
P114 CADLIVE: Computer-Aided Design of Living Systems, Hiroyuki Kurata, Marie Kajiwara,
Yuki Shimokawa,
P115 Petri Net Based Modeling of Signaling Pathways Including Inhibitory Function, Chen Li, Shunichi Suzuki, Yoko Takeuchi, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano
P116 Interlocked Feedback Is Not the Best Choice for PER Oscillators, Fumitaka Ohnishi, Hiroyuki Kurata
P117 Symbolic-Numeric Estimation of Kinetic Parameters in Biochemical Pathways by Quantifier
Elimination, Shigeo Orii, Hirokazu Anai, Katsuhisa Horimoto
P118 Developing Cardiac Cell Models (Kyoto model) on simBio, Nobuaki Sarai, Satoshi Matsuoka,
Akinori Noma
P119 A Modeling Tool for E-CELL System: Power-Law Model Generator Based on Time-Course
Data, Shigeru Sato, Yasuhiro Naito, Masaru Tomita
P120 Kinetic Modeling of Metabolic Pathways in Acetone-Butanol-Ethanol (ABE) Fermentation Using Novel Simulator, Hideaki Shinto, Yukihiro Tashiro, Mayu Yamashita, Genta Kobayashi,
Tatsuya Sekiguchi, Taizo Hanai, Masahiro Okamoto, Kenji Sonomoto
P121 Theoretical Research on Dynamics of the Genetic Toggle Switch, Tomohiro Ushikubo, Wataru Inoue, Mitsumasa Yoda, Masaki Sasai
P122 Optimization of a Large-Scale Dynamic Model of the Cell Cycle Network Using Multi Objective
GA, Shunsuke Yamamichi, Hiroyuki Kurata
P123 Module Decomposition and Integration Optimizes Gene Regulatory and Metabolic Networks,
Keisuke Yoshida, Hiroyuki Kurata
13

P124 Structure-Based Analysis of Cooperativity in Protain-DNA Recognition, Akinori Sarai,
Satoshi Fujii, Marcos J. Araúzo-Bravo, Hidetoshi Kono
P125 Indirect Readout in Drug-DNA Complexes, Marcos J. Araúzo-Bravo, Akinori Sarai
P126 Prediction of Pseudoknotted RNA Structure by a Structural Alignment Using Genetic Algorithm, Akito Taneda
P127 A New Method of Computing Ligand-Based Pharmacophore Models for Flexible Chemical Compounds, Atsuko Yamaguchi, Hiroyasu Shimada, Ken Horiuchi, Tetsuo Nishikawa
P128 Large Scale Protein Side-Chain Packing Based on Maximum Edge-Weight Clique Finding Algorithms, Dukka Bahadur K. C., J. B. Brown, Etsuji Tomita, Jun’ichi Suzuki, Tatsuya Akutsu
P129 Thermal Adaptations of DNA-Binding Proteins, Masashi Fujita, Minoru Kanehisa
P130 CCG-Based RNA Secondary Structure Prediction, Hee-Jin Lee, Jong C. Park
P131 Comparisons between Dynamic Properties of Homologous Protein Structure in ProMode(Database of Normal Mode Analyses on Proteins), Hiroshi Wako, Motohiro Otsuka,
Yuhki Tomizawa, Masaki Kato, Shigeru Endo
P132 Genome-Wide Protein Structure Characterization of Mycoplasma genitalium, Jun-Wei Hsu,
Chen-hsiung Chan, Cheng-Yan Kao
P133 High Quality Protein Structure Prediction Server, SKE-FAMSD, Kazuhiko Kanou, Mitsuo Iwadate, Genki Terashi, Daisuke Takaya, Mayuko Takeda-Shitaka, Hideaki Umeyama
P134 Computational Analysis of microRNA Recognition Site, Keishin Nishida, Riu Yamashita,
Kengo Kinoshita, Kenta Nakai
P135 RNA Structural Alignment with Conditional Random Fields, Kengo Sato, Yasubumi Sakakibara
P136 Predicting Non-Coding RNAs Based on Free Energy Minimization by Means of Genetic Algorithms, Kouichi Okada, Hitoshi Iba
P137 Sequence and Structural Analysis of Ligand Bindig Sites in Membrane Proteins,
M. Xavier Suresh, M. Michael Gromiha, M. Suwa
P138 Homology Modeling in CASP6 (Critical Assessment of Techniques for Protein Structure Prediction) Using CHIMERA and FAMS, Mayuko Takeda-Shitaka, Genki Terashi, Daisuke Takaya,
Kazuhiko Kanou, Mitsuo Iwadate, Hideaki Umeyama
P139 Pareto-Optimal Motif for Predicting Peptide Binders, Menaka Rajapakse, Bertil Schmidt,
Vladimir Brusic
P140 Fold Recognition and Flexibility of the HIV-1 V3-Loop Crown Structure During the Course of
Adaptation to a Host, Teruaki Watabe, Hirohisa Kishino, Yasuhiro Kitazoe
P141 An Alignment Algorithm by Matching Fixed-Length Stem Fragments for Comparing RNA Sequences, Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai
P142 Non-Arbitrary Judgment for Periodicity of Time-Series Data by an Information Criterion andDiscrete Fourier Transform, Daisuke Tominaga, Paul Horton
P143 Searching for Similar Gene Expression Profiles Across Platforms, Wataru Fujibuchi, Larisa Kiseleva, Paul Horton
P144 Phenotype MicroArray Analysis of Escherichia coli K-12: An in silico Approach, Hiroaki Gobara, Tomoya Baba, Md. Altaf-Ul-Amin, Masanori Arita, Ken Kurokawa, Shigehiko Kanaya,
Hirotada Mori
P145 Inference Engine for Gene Expression by Bayesian Network, Hirofumi Suzaki, Akinori Sarai
14

P146 A Hypothesis of Intrinsic Vital Volatility in Gene Expression, Hiroto Yoshii, Hideki Takayasu
P147 Gene Duplication Models and Reconstruction of Network Evolution, Juris Viksna, David Gilbert,
Dace Ruklisa
P148 Efficient Method for Extracting Common Core Binomial Genetic Interactions, Masahiko Nakatsui, Takanori Ueda, Isao Ono, Masahiro Okamoto
P149 Structural and Functional Analysis of Transiently Expressed Metabolic Networks, Mina Oh,
Wolfram Liebermeister, Minoru Kanehisa, Reinhart Heinrich, Oliver EbenhöhP150 Estimation of Gene Regulatory Network Using Stochastic Differential Equation Model,
Shinya Nabatame, Hitoshi Iba
P151 Comparative Study of State Space Models for Time-Course Gene Expression Data of Yeast,
Rui Yamaguchi, Tomoyuki Higuchi
P152 On Conditions for Morphogenetic Diversity of Multicellular Organisms, Hiroshi Yoshida, Hirokazu Anai, Shigeo Orii, Katsuhisa Horimoto
P153 Orchestration of Gene Systems Inferred from Expression Profiles in Hepatocellular Carcinoma,
Katsuhisa Horimoto, Sachiyo Aburatani, Shigeru Saito, Masao Honda, Shu-ichi Kaneko
P154 Causal Inference of Gene Systems Network in Hepatocellular Carcinoma Progression by Graphical Chain Model, Masao Honda, Shu-ichi Kaneko, Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto
P155 Evaluation of Inference Performance by ASIAN in Transcriptional Regulatory Relationships,
Ritsuko Onuki, Sachiyo Aburatani, Katsuhisa Horimoto, Minoru Kanehisa
P156 Inference of Cell Cycle-Regulatory Systems Network in Saccharomyces cerevisiae, Sachiyo Aburatani, Shigeru Saito, Katsuhisa Horimoto
P157 Inferring Module-Based Gene Networks from Time Course Microarray Data by State Space
Models, Osamu Hirose, Ryo Yoshida, Seiya Imoto, Satoru Miyano
P158 Identification of Drug Active Pathways Based on Gene Networks Estimated by Bayesian
Networks and Gene Expression Data, Yoshinori Tamada, Seiya Imoto, Kousuke Tashiro,
Satoru Kuhara, Satoru Miyano
P159 Scaling-Law and Fluctuation in Gene Expression, Jose C. Nacher, Tomoshiro Ochiai, Tatsuya Akutsu
P160 Stochastic Fluctuation and Relaxation in a Genetic Feedback Loop, Yurie Okabe, Yu Yagi,
Masaki Sasai
P161 Effects of Disease-Associated Mutations and SNP on Protein Structures, Akiyuki Koga,
Hidetoshi Kono, Akinori Sarai
P162 Particle Simulation Approach for Cellular Level Spatio-Temporal Properties, Ryuzo Azuma,
Tetsuji Kitagawa, Hiroshi Kobayashi, Ryo Umetsu, Tomoyuki Yamamoto, Akihiko Konagaya
P163 Theoretical Analysis of Metabolic Networks: Attempt to Express Topological Position of Individual Atoms in a Given Network, Jun Ohta
P164 Objective Distances for Transcriptome Analyses According to the Thermodynamic Model,
Tomokazu Konishi
P165 Elucidation of Xenobiotic Responsive and NR Mediated Pathways/Networks, Tsuguchika Kaminuma, Masumi Yukawa, Naomi Komiyama, Tatsuya Nakano, Kotoko Nakata,
Yoshitomo Tanaka, Hiroshi Tanaka
P166 Improvement of ASIAN Web Site, Kousuke Goto, Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto
P167 Characteristic Chemical Transformation Patterns in Biodegradation Pathways, Mina Oh,
Masahiro Hattori, Susumu Goto, Minoru Kanehisa

15

Program Committee
Reinhart Heinrich (Humboldt U., Ger., PC Co-Chair)
Hiroshi Mamitsuka (Kyoto U., JP, PC Co-Chair)
Tatsuya Akutsu (Kyoto U., JP)
Søeren Brunak (DTU, Den.)
Vladimir Brusic (U.Queensland, Austral.)Oliver Ebenhöh (Humboldt U., Ger.)
Yi-Ping Phoebe Chen (Deakin U., Austral.)Darren R. Flower (EJIVR, UK)
Stefan Hohmann (Goteborg U., Sweden)
Katsuhisa Horimoto (U.Tokyo, JP)
Minoru Kanehisa (Kyoto U., JP)
Edda Klipp (MOLGEN,MPG, Ger.)
Stefan Kramer (TUM, Ger.)
Richard Lathrop (UC Irvine, USA)
Sang Yup Lee (KAIST, South Korea)
Yixue Li (SIBS, China)
Osamu Maruyama (Kyushu U., JP)
Hideo Matsuda (Osaka U., JP)
Aleksandar Milosavljevic (BCM, USA)
Satoru Miyano (U.Tokyo, JP)
Gene W. Myers (UC Berkeley, USA)
Kenta Nakai (U.Tokyo, JP)
Haruki Nakamura (Osaka U., JP)
See-Kiong Ng (Inst.Infocomm Res., Singapore)
William Stafford Noble (U.Washington, USA)
Stephen Oliver (U.Manchester, UK)
Shoba Ranganathan (Macquarie U., Austral.)Kenji Satou (JAIST, JP)
Tobias Scheffer (Humboldt U., Ger.)
Christian Schönbach (RIKEN, JP)
Tetsuo Shibuya (U.Tokyo, JP)Jörg Stelling (ETH, Switzerland)
Hideaki Sugawara (NIG, JP)
Makiko Suwa (CBRC, JP)
Toshihisa Takagi (U.Tokyo, JP)
Hiroyuki Toh (Kyushu U., JP)
Koji Tsuda (CBRC, JP)
Hiroki R. Ueda (RIKEN, JP)
Alfonso Valencia (U. Autonoma, Spain)
Gabriel Valiente (Tech. U. Catalonia, Spain)
Jean-Philippe Vert (Ecole des Mines, France)
Hidemi Watanabe (Hokkaido U., JP)
Limsoon Wong (Inst.Infocomm Res., Singapore) Eric P. Xing (Carnegie Mellon U., USA)
Ying Xu (U.Georgia, USA)
Ueng-Cheng Yang (Nat. Yang-Ming U., Taiwan)

16