GIW 2006
The Seventeenth International Conference on Genome Informatics
Pacifico Yokohama, Japan
December 18–20, 2006
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)
Japanese Society for Bioinformatics (JSBi)
Steering Committee
Minoru Kanehisa (Kyoto University)
Toshihisa Takagi (University of Tokyo)
Satoru Miyano (University of Tokyo)
Program Committee Co-Chair
Yasubumi Sakakibara (Keio University)
Temple F. Smith (Boston University)

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GIW 2006
The Seventeenth International Conference on Genome Informatics
Pacifico Yokohama, Japan
December 18–20, 2006
Registration
Registration should be done at: http://giw.ims.u-tokyo.ac.jp/giw2006/registration.html until December 3, 2006. Registration fee includes a copy of Genome Informatics Vol. 17, No. 2 andcoffee breaks. We offer registration fee discount for JSBi and ISCB members.

Standard
Registration

Student
Registration

until Dec. 3, 2006 after Dec. 3, 2006
Standard
JPY17,000.JPY22,000.ISCB Member
JPY16,000.JPY21,000.JSBi Member
JPY8,000.JPY13,000.JSBi & ISCB Member
JPY7,000.JPY12,000.Standard
JPY12,000.JPY17,000.ISCB Member
JPY11,000.JPY16,000.JSBi Member
JPY5,000.JPY10,000.JSBi & ISCB Member
JPY4,000.JPY9,000.(Banquet on December 19 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: giw2006@ims.u-tokyo.ac.jp
URL: http://giw.ims.u-tokyo.ac.jp/giw2006/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

2Conference Center
2F
Registration Desk
Entrance
3F

3GIW 2006 Advanced Program
Registration
December 18, 2006: 08:30 - 17:30
December 19, 2006: 08:30 - 18:00
December 20, 2006: 08:30 - 15:30

Monday, December 18, 2006
Opening Address
09:00 - 09:10

Yasubumi Sakakibara(Keio U.) and Temple F. Smith(Boston U.)

Paper Session 1
09:10 - 09:35

Chair: Byoung-Tak Zhang (Seoul National U.)
Hybrid Gibbs-Sampling Algorithm for Challenging Motif Discovery: GibbsDST, Kazuhito Shida

09:35 - 10:00

Computational Annotation of Transcription Factor Binding Sites in D.
Melanogaster Developmental Genes, Vipin Narang, Wing-Kin Sung,
Ankush Mittal
A Gram Distribution Kernel Applied to Glycan Classification and Motif
Extraction, Tetsuji Kuboyama, Kouichi Hirata, Kiyoko F. Aoki-Kinoshita,
Hisashi Kashima, Hiroshi Yasuda

10:00 - 10:25

10:25: - 11:00
Keynote Address
11:00 - 12:00

12:00 - 13:30

Break
Chair: Yasubumi Sakakibara (Keio U.)
RNAs Everywhere: Genome-Wide Annotation of Structured RNAs, Ivo L
Hofacker (University of Vienna)
Lunch

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

Chair: Masanori Arita (U.Tokyo)
Discovering Signal Transduction Networks Using Signaling DomainDomain Interactions, Thanh Phuong Nguyen, Tu Bao Ho

14:55 - 15:20

Finding Conserved and Non-Conserved Reactions Using a Metabolic Pathway Alignment Algorithm, José C. Clemente, Kenji Satou, Gabriel Valiente

15:20 - 15:45

A Function-Centric Approach to the Biological Interpretation of Microarray
Time-Series, Pablo Minguez, Fátima Al-Shahrour, Joaquı́n Dopazo

15:45: - 16:15

Break

Paper Session 3
16:15 - 16:40

Chair: Katsuhisa Horimoto (CBRC)RaPiDS: An Algorithm for Rapid Expression Profile Database Search, PaulB. Horton, Larisa Kiseleva, Wataru Fujibuchi

16:40 - 17:05

Development of an Approach for Ab Initio Estimation of CompoundInduced Liver Injury Based on Global Gene Transcriptional Profiles,
Xudong Dai, Yudong D. He, Hongyue Dai, Pek Y. Lum, Christopher J.
Roberts, Jeffrey F. Waring, Roger G. Ulrich

17:05 - 17:30

The Distribution and Deposition Algorithm for Multiple Oligo Nucleotide
Arrays, Kang Ning, Hon Wai Leong

17:30 - 17:55

Detection and Restoration of Hybridization Problems in Affymetrix
GeneChip Data by Parametric Scanning, Tomokazu Konishi
4Tuesday, December 19, 2006
Paper Session 4
09:00 - 09:25

Chair: Kenji Satou (JAIST)
Gene Ontology Annotation by Density and Gravitation Models, Wen-Juan
Hou, Kevin Hsin-Yih Lin, Hsin-Hsi Chen

09:25 - 09:50

Text Mining and Protein Annotations: the Construction and Use of Protein
Description Sentences, Martin Krallinger, Rainer Malik, Alfonso Valencia

09:50 - 10:15

Assessing Clustering Results with Reference Taxonomies, Gabriel Valiente

10:15 - 10:45

Break

Paper Session 5
10:45 - 11:10
11:10 - 11:35

11:35 - 12:00

12:00 - 13:30

Chair: Tetsuo Shibuya (U.Tokyo)
Pairwise Alignment with Rearrangements, Le Sy Vinh, Andrés Varón,
Ward C. Wheeler
Techniques for Multi-Genome Synteny Analysis to Overcome Assembly
Limitations, Arjun Bhutkar, Susan Russo, Temple F. Smith, William M.
GelbartA Markov Chain Model for Haplotype Assembly from SNP Fragments,
Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen
Lunch

Keynote Address
13:30 - 14:30

Chair: Temple F. Smith (Boston U.)
The New Phase of Transcriptome Analysis, Yoshihide Hayashizaki(RIKEN,GSC)

Paper Session 6
14:30 - 14:55

Chair: Hiroyuki Toh (Kyushu U.)
MetaClustering: Discovery of The Different Sample Clusterings in Gene
Expression Data, David Venet, Hugues Bersini, Hitoshi Iba

14:55 - 15:20

Biomarkers for Epithelial Ovarian Cancers, Pritha Mahata

15:20 - 15:45

PepSOM: An Algorithm for Peptide Identification by Tandem Mass Spectrometry Based on SOM, Kang Ning, Hoong Kee Ng, Hon Wai Leong

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 “Pacific” at Inter Continental The Grand Yokohama

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Wednesday, December 20, 2006
Paper Session 7
09:00 - 09:25

Chair: Gabriel Valiente (Tech.U.Catalonia)
DAPID: A 3D-Domain Annotated Protein-Protein Interaction Database,Yung-Chiang Chen, Heng-Chu Chen, Jinn-Moon Yang

09:25 - 09:50

A Method to Detect Important Residues Using Protein Binding Site Comparison, Keunwan Park, Dongsup Kim

09:50 - 10:15

Modeling and Estimation of Dynamic EGFR Pathway by Data Assimilation Approach Using Time Series Proteomic Data, Shinya Tasaki, Masao
Nagasaki, Masaaki Oyama, Hiroko Hata, Kazuko Ueno, Ryo Yoshida, Tomoyuki Higuchi, Sumio Sugano, Satoru Miyano

10:15 - 10:40

A Large-Scale Computational Approach to Drug Repositioning, Yvonne Y.
Li, Jianghong An, Steven J.M. Jones

Posters and Software Demonstrations Session 3
10:40 - 12:00( Even and Odd Number )12:00 - 13:30

Lunch

Keynote Address
13:30 - 14:30

Chair: Hiroshi Mamitsuka (Kyoto U.)
Increasing Confidence of Protein-Protein Interactomes, Limsoon Wong
(National University of Singapore)

Paper Session 8
14:30 - 14:55

Chair: Tatsuya Akutsu(Kyoto U.)
A Generalized Threading Model Using Integer Programming that Allows
for Secondary Structure Element Deletion, Kyle Ellrott, Jun-tao Guo, Victor Olman, Ying Xu

14:55 - 15:20

Protein Topology Classification Using Two-Stage Support Vector Machines, Jayavardhana Gubbi, Alistair Shilton, Michael Parker, Marimuthu
Palaniswami
Robotic Path Planning and Protein Complex Modeling Considering Low
Frequency Intra-Molecular Loop and Domain Motions, Carlos A. Del Carpio, Pei Qiang, Eiichiro Ichiishi, Hideyuki Tsuboi, Michihisa Koyama, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba, Momoji Kubo, Akira
Miyamoto

15:20 - 15:45

Closing and Award Ceremony
15:45 - 16:00

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Commercial Exhibitions
C1:
C2:
C3:
C4:
C5:
C6:
C7:
C8:
C9:

Ryoka Systems Inc.
NABE International Corporation
Mathematical Systems, Inc.
Pathway Solutions Inc.
SGI Japan, Ltd.
Active Motif, Inc.
SCRUM Inc.
HITACHI, LTD
BIOBASE GmbH

Software Demonstrations
S01 Mass Spectral Database for Metabolome Analysis, Hisayuki Horai, Kazuhiro Suwa,
Masanori Arita, Yoshito Nihei, Takaaki Nishioka
S02 CADLIVE: Integration for Large-Scale Network Data, Yuki Shimokawa, Kazuhiro Maeda, Kentaro Inoue, Hiroyuki Kurata
S03 RIKEN Natural Products Depository (RIKEN NPDepo), Hideaki Konno, Takeshi Tomiki,Tomio Saito, Masashi Ueki, Takeo Asaoka, Ryuichiro Suzuki, Masakazu Uramoto,
Hideaki Kakeya, Hiroyuki Osada
S04 PreSPI: Prediction System for Protein Interaction, Woo-Hyuk Jang, Choon-Oh Lee, DongSoo Han
S05 Construction of Candida Albicans Protein Network from Yeast Protein Interactions in System Biology, Chung-Yen Lin,Chieh-Hwa Lin,Chi-Shiang Cho,Fan-Kai Lin,Shu-Hwa Chen,Chao A. Hsiung
S06 ExPlain: Causal Analysis of Gene Expression Data from Promoter Models to Signaling Pathways, Alexander Kel, Holger Karas, Nico Voss, Tagir Waleev, Edgar Wingender
S07 Cell Illustrator3.0: A Platform for Biopathway Modeling and Simulation , Masao Nagasaki,
Atsushi Doi, Ayumu Saito, Emi Ikeda, Kazuko Ueno, Euna Jeong, ChristopherJ. Savoie,
Satoru Miyano
S08 Ajax for Networks and Ontologies, Kinya Okada, Takahisa Furukawa, Kiyoshi Asai

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Posters
P001 Serial Regulation on Cell Cycle System in S.cerevisiae, Sachiyo Aburatani, Katsuhisa Horimoto
P002 Efficient Inferring Method for Extracting Reliable Interactions from Time Series of Gene Expression Profile, Masahiko Nakatsui, Takanori Ueda, Maki Yukihiro, Isao Ono, Masahiro Okamoto
P003 Emerging Needs for Restructuring Biomedical Knowledge and Education System, Tsuguchika Kaminuma, Masumi Yukawa, Yoshitomo Tanaka, Takako Takai-Igarashi, Yoshihiro Takemoto, Hiroshi Tanaka
P004 Relation between Cell Division and Gene Expression by Using Single Cell Tracking System,
Kazumi Hakamada, Satoshi Fujita, Jun Miyake
P005 Identification of Apoptosis-Induced Gene Networks from Time Course Expression Profiles with
Replicated Measurements, Osamu Hirose, Ryo Yoshida, Seiya Imoto, Satoru Miyano
P006 p53 Pathways to Simulate the p53 Transcriptional Activity, Atsushi Doi, Masao Nagasaki,
Kazuko Ueno, Hiroshi Matsuno, Satoru Miyano
P007 An S-System Application for Mammalian Circadian Clock System, Daisuke Tominaga, Katsuhisa Horimoto
P008 Noise-Induced Robust Synchronization in a Multicellular System, Ruiqi Wang, Luonan Chen,
Kazuyuki Aihara
P009 Mathematical Modeling of G1/S Phase in the Cell Cycle with Involving the p53/Mdm2 Network,
Kazunari Iwamoto, Yoshihiko Tashima, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto
P010 Sensitivity Analysis for the E.coli Nitrogen Assimilation System, Koichi Masaki, Hiroyuki Kurata
P011 Analysis for the Conflict between G2/M Phase Arrest in the Cell Cycle and Apoptosis Induction, Yoshihiko Tashima, Yu Kisaka, Hiroyuki Hamada, Taizo Hanai, Yukihiro Eguchi,
Masahiro Okamoto
P012 Spatio-Temporal Dynamics of Molecules on the Cell Surface Studied by Particle Simulation,
Ryuzo Azuma, Hiroshi Kobayashi, Tomoyuki Yamamoto, Akihiko Konagaya
P013 Consistency of the Transition Theory in Computer Simulation of a Genetic Toggle Switch,
Tomohiro Ushikubo, Masaki Sasai
P014 Regulation of Metabolic Networks By Small Molecule Metabolites, Alex Gutteridge, Minoru Kanehisa, Susumu Goto
P015 The Finitely Numerable Effect in the Coupled Molecular Motor Model, Kazunari Mouri, Tetsuya Shimokawa
P016 A Steady-State Approximation-Based Solver for Stiff Biochemical Models, Emi Shiraishi, Hiroyuki Kurata
P017 Genomic Data Assimilation for a Hybrid Functional Petri Net Model of Circadian Rhythmwith Time Course Gene Expression Data, Masao Nagasaki, Rui Yamaguchi, Ryo Yoshida,
Seiya Imoto, Atsushi Doi, Yoshinori Tamada, Hiroshi Matsuno, Satoru Miyano, Tomoyuki Higuchi
P018 Cell Fate Simulation of ASE Cell in Caenorhabditis elegans Using Hybrid Functional Petri Net
with Extension, Ayumu Saito, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano
P019 A Cluster Identification Method without Using a Threshold of Correlation Coefficient in Hierarchical Cluster Analysis, Yuki Miyata, Yoichi Yamada, Ken-ichiro Muramoto
P020 Cluster Analysis of Transcription Factor Binding Sites in the Promoter Regions of Cardiac Genesin Failing Hearts , Masaharu Nakayama, Hiroko Tada, Yasuhide Asaumi, Hiroaki Shimokawa
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P021 Module Discovery in Gene Expression Data Using Closed Itemset Mining Algorithm, Yoshifumi Okada, Wataru Fujibuchi, Paul Horton
P022 A Gene Clustering Method Using Gene Expression Data and Gene Networks, Motoki Shiga,
Ichigaku Takigawa, Hiroshi Mamitsuka
P023 Applying Gaussian Distribution-Dependent Criteria to Decision Trees for High-Dimensional
Microarray Data, Raymond Wan, Ichigaku Takigawa, Hiroshi Mamitsuka
P024 Computational Analysis of Global Expression Profiles in Mouse Natural Antisense Transcripts,
Yuki Okada, Koji Numata, Rintaro Saito, Hidenori Kiyosawa, Akio Kanai, Masaru Tomita
P025 Quantitative Control of Early Transcription by ERK and Akt Signal Transduction,
Takashi Nakakuki, Kaori Ide, Takeshi Nagashima, Kaoru Takahashi, Noriko Yumoto,
Mariko Hatakeyama
P026 Prediction of Ligand- and ErbB Receptor-Specific Transcription Factors from Time-Course Gene
Expression Data of Cancer Cells, Takeshi Nagashima, Jun Horiuchi, Kenji Nakano, Kaori Ide,
Kaoru Takahashi, Mariko Hatakeyama
P027 Modeling of Extracellular Matrix Degradation Processes in Cancer Metastasis Using Covariance
Structure Analysis, Akiko Hatano, Kaoru Mogushi, Hiroshi Tanaka
P028 Gene Expression Profiling of Hepatocellular Carcinoma Using Independent Component Analysis,
Satoshi Nagaie, Kaoru Mogushi, Hiroshi Tanaka
P029 ROKU: An Improved Method for the Detection of Tissue-Specific Expression Patterns,
Koji Kadota, Jiazhen Ye, Yuji Nakai, Tohru Terada, Kentaro Shimizu
P030 Identification of Tissue Specific Transcription Factors Using Microarray Gene Expression Data,
Larisa Kiseleva, Ekaterina Shelest, Edgar Wingender, Paul Horton
P031 Profiling Prostate Cancer Signatures by Statistical Analysis of mRNA Isoform Expression,
T.Murlidharan Nair, Hai-Ri Li, Xiang-Dong Fu
P032 A Comparative Study of Exploratory Analysis versus Statistical Analysis for Oligo-DNA Microarrays, Kenichiro Kanda, Kaoru Azumi, Nori Satoh, Sorin V. Sabau
P033 Genome-Wide Detection of Human Copy Number Variations Using High-Density DNA
Oligonucleotide Arrays, Daisuke Komura, Shumpei Ishikawa, Fan Shen, Kunihiro Nishimura,
Sigeo Ihara, Hiroshi Nakamura, Keith W. Jones, Jing Huang, Hiroyuki Aburatani
P034 Experimental Design for Time-Series Microarray Analysis, Ryosuke Ito, Hiroki Takahashi,
Taku Oshima, Naotake Ogasawara, Md. Altaf-Ul-Amin, Ken Kurokawa, Shigehiko Kanaya
P035 New Gene Filtering Method Using S2N’ Based on the Concept of PART Filtering Method,
Hiro Takahashi, Hiroyuki Honda
P036 Gene Alignment for Cell Division Cycle Microarray Experiments without Sinusoidal Fittings,
Y-h. Taguchi
P037 Power Spectra of Bird-Influenza A Virus (BIV) ssRNA Base Sequences : Possibility of Cooperative Genes or Interferences, Eisei Takushi, Hiroyuki Sakamoto, Mitsuhiro Seino
P038 Gene Finding for Microbial Metagenomics, Jungho Park, Hideki Noguchi, Toshihisa Takagi
P039 Conservation of Regulation Systems in Firmicutes, Nicolas Sierro, Kenta Nakai
P040 Comprehensive Detection of Terminal Oligo-Pyrimidine (TOP)Genes in the Human Genome,
Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Sumio Sugano, Kenta Nakai
P041 Autoimmune Diseases and Evolutionary Trace of the T-Cell Epitopes, Wataru Honda,
Shuichi Kawashima, Minoru Kanehisa
9P042 Analysis of Tissue Specific Expression Patterns of Isozymes, Masataka Takarabe, Akira Tsuchida,
Masashi Fujita, Shujiro Okuda, Akiyasu C. Yoshizawa, Takuji Yamada, Masumi Itoh,
Susumu Goto, Minoru Kanehisa
P043 A Web Application for Identification of Glycosaminoglycan (GAG) Binding Motifs in
Plasmodium Falciparum, Nelson Hayes, Johan Normark, Daniel Nilsson, Craig Wheelock,Mats Wahlgren, Susumu Goto
P044 Analysis of the Sub-Telomeric Region of the Malaria Parasite P. Falciparum Using aCGH Data,
Diego Diez, Ulf Ribacke, Craig Wheelock, Mats Wahlgren, Susumu Goto
P045 Proteins with Charge Periodicity of 28 Residues in Amino Acid Sequences from Total Genomes,
Runcong Ke, Shigeki Mitaku
P046 Characteristic Distribution of GC Contents for Proteins with Charge Periodicity of 28 Residues,
Ryusuke Sawada, Runcong Ke, Noriyuki Sakiyama, Shigeki Mitaku
P047 Analysis and Estimation for the Substituted Sequences of DNA Sequences for Saccharomyces
Cerevisiae with a Kind of Marcov Model, Mitsuhiro Seino, Hiroyuki Sakamoto
P048 Stochastic Local Genome Alignment and Comprehensive Search for Conserved Gene Clusters,
Tsuyoshi Hachiya, Yasubumi Sakakibara
P049 Computational Analysis of Human mRNAs Regulated by GRSF-1, a Positive Regulatorof Influenza Virus, Hikaru Taniguchi, Kosuke Fujishima, Yuka Watanabe, Yuko Osada,
Masaru Tomita, Rintaro Saito, Akio Kanai
P050 Significant Deviation in the Configuration of Tandem Repeats in Prokaryotic Genomes, Shintaro Hirayama, Satoshi Mizuta
P051 RNA Base Pairing Probability Alignment by Genetic Algorithm, Akito Taneda
P052 Detailed Analysis of Reentrant Loops and Neighboring Sites in Alpha-Helical Transmembrane
Proteins, Kinya Matsushiro, Wataru Nakahata, Satoshi Mizuta
P053 Distribution of Relative Mutation Frequency, Hyunchul Kim, Masaru Tomita
P054 MotifCombinator: A Web Tool to Search for Combinations of Cis-Regulatory Motifs,
Mamoru Kato, Tatsuhiko Tsunoda
P055 Frame-Cluster Mapping: Genomewide Analysis for Detection of Localized Signal Regions,
Kou Amano, Hidemitsu Nakamura, Hisataka Numa, Yosiaki Nagamura, Hiroaki Ichikawa,
Kaoru Fukami-Kobayashi
P056 Analysis of Aspergillus oryzae tRNA Genes Using Multivariate Analysis, Jun-Ichi Sagara
P057 Analysis of Amino Acid Sequence by Self Organization Maps, Takeshi Takahashi, Hiroshi Dozono
P058 Prediction of Transcription Factor Binding Sites in Saccharomyces cerevisiae, Takuya Ueno,
Hidetoshi Kono, Sarai Akinori
P059 Structural Breakpoint Prediction and its Application Based on Dimers in Amino Acid Sequence,
Yoshihide Makino, Nobuya Itoh
P060 Ab-initio Identification of Promoter Elements in Antimicrobial Peptide-Coding Genes, Manisha Brahmachary, Christian Schönbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, S.P.T Krishnan, Chin-Yo Lin, David A Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B Bajic
P061 Structural Analysis on Functional Epitope, Jian Huang, Minoru Kanehisa
P062 A GP Based Algorithm for HP-Model Problem, Takahiro Yabuki, Hitoshi Iba
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P063 Combining Molecular Dynamics Simulation with a Graph Theoretical Approach to
Study Protein Complex Flexibility, AbdulRajjak Shaikh, Mohamed Ismael, Pei Qiang,
Hideyuki Tsuboi,Michihisa Koyama, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba,Momoji Kubo, Eiichiro Ichiishi, Carlos A. Del Carpio, Akira Miyamoto
P064 Inferring Domain Combination Pattern and Its Biological Meaning via Association Rules, Sukhoon Jung, Dong-soo Han, Sung-doke Lee
P065 A Novel Method to Determine the Assembling Space between Two Protein Subunits,
Miki Maeda, Hiroya Nobori
P066 Biomolecular Computations toward Enzyme-Catalyzed Transformations of Non-Natural Organic Compounds: Ab initio Fragment Molecular Orbital Calculations, Takahisa Tanaka,
Takatomo Kimura, Yoichiro Yagi, Yoshinobu Naoshima
P067 Can Brownian Dynamics be a Useful Tool for Structure-Based Drug Design?, Akifumi Oda,
Hisao Matsuzaki, Noriyuki Yamaotsu, Shuichi Hirono
P068 A Benchmark Study of the “Soft Docking” Module of MIAX,Using a Set of Unbound Proteins , Pei Qiang, Mohamed Ismael, Abdul Rajjak Shaikh, Hideyuki Tsuboi, Michihisa Koyama,
Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba, Momoji Kubo, Eiichiro Ichiishi, Carlos A. Del Carpio, Akira Miyamoto
P069 Supervised Consensus Scoring Methods for Structure-Based Drug Design, Reiji Teramoto, Hiroaki Fukunishi
P070 Scoring Analysis of DNA Binding Sites of DNA Binding Proteins, Reika Okihara, Yukako Sakatsuji, Ayumi Suzuki, Ichiro Yamato, Satoru Miyazaki
P071 Classification of Protein-DNA Complexes Based on Structural Descriptiors, Ponraj Prabakaran,
Shandar Ahmad, M.Michael Gromiha, Maria G. Singarayan, Akinori Sarai
P072 Comparative Analysis of Amino Acid Residues and Structures between RNase HII and Argonaute Proteins from Pyrococcus furiosus, Sayaka Kitamura, Kosuke Fujishima, Asako Sato,
Arun Krishnan, Masaru Tomita, Akio Kanai
P073 Murlet: A Practical Multiple Alignment Tool for Structural RNA Sequences, Hisanori Kiryu,
Yasuo Tabei, Taishin Kin, Kiyoshi Asai
P074 fRNAdb: A Platform for Mining/Annotating Functional RNA Candidates from Non-Coding
RNA Sequences, Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Takashi Komori, Kiyoshi Asai
P075 RNAmine: Frequent Stem Pattern Miner from RNAs, Michiaki Hamada, Koji Tsuda,
Taku Kudo, Taishin Kin, Kiyoshi Asai
P076 An Evolving Zipper Automaton for RNA Secondary Structure Prediction: Improvement by
Sequence Homology Inclusion, Carlos A. Del Carpio M., Mohamed Ismael, Eiichiro Ichiishi,
Hideyuki Tsuboi, Michihisa Koyama, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba,
Momoji Kubo, Akira Miyamoto
P077 Comprehensive Analysis of miRNA Effect to the Transcripts, Keishin Nishida, Riu Yamashita,
Kengo Kinoshita, Kenta Nakai
P078 Multiple Alignment of RNAs by Maximizing the Sum of the Matching Probability of Stem
Fragments, Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
P079 Phylogenetic Analysis of Essential Genes by Using ORI-GENE, Hirotoshi Kawano,
Hideaki Mizuno, Akinori Sarai
P080 Evidence for Introns-Latehama, Naoya Kenmochi

from Intron Phase Distribution, Hung Dinh Nguyen, Maki Yoshi-

P081 Algebraic Evolution of the Genetic Code, Takashi Kawamura
11

P082 Distance Structure of Homologous Gene Cluster in Cyanobacteria, Naobumi Sasaki, Naoki SatoP083 Tracing Back Xenobiotic Responsive and NR Mediated Pathways/Networks, Yoshitomo Tanaka,
Masumi Yukawa, Hiroshi Tanaka, Tsuguchika Kaminuma
P084 Analyses of the Nutrient Dependency of Parasites to Hosts Using KEGG Database, Ai Muto,
Masahiro Hattori, Wataru Honda, Minoru Kanehisa
P085 Identification of Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood andProtein Architecture, Kenji K. Kojima, Minoru Kanehisa
P086 Comprehensive Analysis of Domain Architectures of Transmembrane Proteins,uichi Yoshida, Yoshihiro Yamazaki, Takuhiro Nishio, Sunao Kaneko, Toshio Shimizu

Syu-

P087 Gene Expression Profile Analysis for Circadian Promoter Activities of Cyanobacterial Bioluminescent Reporter Strains Using Non-Metric Multidimensional Scaling, Tokitaka Oyama, Hiroshi Ito, Takao Kondo, Y-h. Taguchi
P088 Comparative Sequence Analysis between Human and Mouse: Promoter Conservation and Protein Conservation, Hirokazu Chiba, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
P089 Whole-Genome Functional Linkage Network Construction in the Domain Level by Probabilistic
Model, Yong Wang, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen
P090 Systematic Analysis of Functional SNP with Type 2 Diabetes Mellitus (T2DM) in the Korean
Population, Hyo-Jeong Ban, Keun-Joon Park, Ji-Hong Kim, Hyun-Woo Han
P091 Analysis of Disease-Associated Mutations and SNP in Relationship with Protein Structure,
Taku Ashikari, Hidetoshi Kono, Akinori Sarai
P092 Adaptive Threshold for Detecting Significant Fold Changes in Microarray Data, Hidenori Inaoka, Yutaka Fukuoka
P093 Precise Correlation between MLV Integration Sites and Transcription Start Sites in the Human
Genome, Yoshiaki Tanaka, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
P094 Hierarchical Bayes Approach to Array CGH Data Normalization, Shigeyuki Oba, Shin Ishii
P095 Development of a Platform for Functional Genomics under the Generation Challenge Programme(GCP), Masaru Takeya, Kohji Suzuki, Koji Doi, Shoshi Kikuchi, Richard Bruskiewich
P096 Annotating Genes with Labelled and Unlabelled Data, Xing-Ming Zhao, Luonan Chen,
Kazuyuki Aihara
P097 Developing SVM Classifier for GPI-(Like)-Anchored Proteins Prediction, Wei Cao, Shugo Nakamura, Kentaro Shimizu
P098 Enrichment of Protein Utilization in Protein-Protein Interaction Prediction by Adjusting e-valueof InterProScan and Using Gene Ontology, Woo-Hyuk Jang, Hee-Young Hur, Dong-Soo Han
P099 An Approach to Identify Unknown Gene Function through Higher Order Correlations for Gene
Clusters, Akira Funae, Daisuke Komura, Hiroshi Nakamura, Sigeo Ihara
P100 Proposal of Graphic Assessment Method of Attribute Significance for Comprehensive Combination Analysis , Masahiro Nakatochi, Hiroyuki Honda
P101 Predicting Types of Protein-Protein Interactions Using Various Multiple-Instance Learning Algorithms, Hiroshi Yamakawa, Koji Maruhashi, Yoshio Nakao
P102 Relationship between Data Size and Accuracy of Prediction of Protein-Protein Interactions
by Co-Evolutionary Information, Tetsuya Sato, Yoshihiro Yamanishi, Hisako Ichihara, Keiichi Kuma, Minoru Kanehisa, Hiroyuki Toh
P103 Prediction Accuracy Evaluation of Domain and Domain Combination Based Prediction Methods
for Protein-Protein Interaction, Dong-Soo Han, Woo-Hyuk Jang
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P104 Protein Feature Prediction Using Chi-Square in PPI Networks, YongHo Lee, JaeHun Choi,
JongMin Park, SunLee Bang, SooJun Park
P105 Predicting Ligand Binding Sites of Uncharacterized Protein, Mizuki Morita, Shugo Nakamura,
Kentaro Shimizu
P106 Explore MicroRNA Precursors through a High-Throughput Computational Prediction, YuChing Chang, Shih-Je Lan, Yu-Yu Lin, Cheng-Tao Wu
P107 Comparison of the Prediction Abilities of FBA, MOMA and ROOM for a pykF Mutant of E.
coli, Quanyu Zhao, Hiroyuki Kurata
P108 DNA Repair Recognition via Support Vector Machines, J.B. Brown, Tatsuya Akutsu
P109 Discrimination of β-Barrel Membrane Proteins Using Machine Learning Techniques,
M.Michael Gromiha, Makiko Suwa
P110 Prediction of Protein-Protein Interaction Sites with Two-Stage Support Vector Machine,
Masanori Kakuta, Kentaro Shimizu
P111 Prediction of Mucin-Type O-Glycosylation by Layered Neural Networks and Support Vector Machines, Ikue Nouno, Hirotaka Sakamoto, Takeshi Iritani, Kazutoshi Sakakibara, Ikuko Nishikawa,
Masahiro Ito
P112 Computational Prediction of Drosophila MicroRNA Targets and Analysis of their Negative Feedback Control, Yuka Watanabe, Nozomu Yachie, Masaru Tomita, Akio Kanai
P113 Detection of Transcription Units Based on Integration of Non-Targeted Analyses, Hirokazu Kobayashi, Yoshiaki Kiura, Kazuo Kobayashi, Md. Altaf-Ul-Amin, Naotake Ogasawara,
Shigehiko Kanaya, Ken Kurokawa
P114 Prediction of Glycosphingolipid Chemical Structure from MALDI-TOF MS Data, Yuki Matsumuro, Saki Itonori, Mutsumi Sugita, Masahiro Ito
P115 An Expectation-Maximization Algorithm for Reconstructing Heterogeneous Gene-Content Evolution, Wataru Iwasaki, Toshihisa Takagi
P116 From Function Prediction to Pathway Prediction: A New Pipeline Based on KAAS and GENIES,
Yuki Moriya, Yoshihiro Yamanishi, Masumi Itoh, Shinobu Okamoto, Minoru Kanehisa
P117 Proposal of PART (Projective Adaptive Resonance Theory) for Analysis of Gene Expression
Data with Small Samples, Takashi Kawamura, Hiro Takahashi, Hiroyuki Honda
P118 Prediction of Glycan Structures from Gene Expression Data Based on Improved Scoring Scheme,
Akitsugu Suga, Yoshihiro Yamanishi, Kosuke Hashimoto, Minoru Kanehisa
P119 Integrative Estimation of Gene Regulatory Network by Means of AdaBoost, Shinya Nabatame,
Hitoshi Iba
P120 Analysis and Discrimination of Ligand Binding Membrane Proteins Using a Simple Statistical
Approach, M.Xavier Suresh, M.Michael Gromiha, Makiko Suwa
P121 Prediction of Protein Subcellular Localization Using an Artificial Neural Network, Anton Kratz,
Rintaro Saito, Arun Krishnan, Masaru Tomita
P122 A Statistical Framework for Genome Wide Discovery of Biomarker Splice Variations with
GeneChip Human Exon 1.0 ST Arrays, Ryo Yoshida, Kazuyuki Numata, Seiya Imoto,
Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano
P123 A Calibration Technique for Single-Dimensional Distribution of Local GC Content, Tomoyuki Fujimoto, Tadao Sugiura, Takeshi Nagaya, Tetsuo Sato, Kotaro Minato
P124 Nonmetric Distances for Barcode of Life, Hisamitsu Akiba, Y-h. Taguchi
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P125 modEst: A GMOD-Based Framework for Integrating Partial Polyploid Transcripts into CloselyRelated Genomes, Aaron Chuah, Richard Bartfai, Laszlo Orban, Alan Christoffels
P126 In Silico Functional Profiling of Small Molecules for Assessing their Physiological Effects, Tomohiro Sato, Yo Matsuo, Shigeyuki Yokoyama
P127 Probabilistic Ranking for Analyzing Transcriptional Response Variations of Metabolic Gene
Paths, Ichigaku Takigawa, Hiroshi Mamitsuka
P128 Interpreting Patterns of Gene Expression with spherical Self-Organizing Maps (sSOM): Application to Search for Cell Surface Markers , Tuoya, Yuh Sugii, Tadahiro Nagaoka, Takayuki Fukuda,
Hiroko Tada, Hidenori Yamada, Yasaburo Matsuura, Heizo Tokutaka, Masaharu Seno
P129 Gene Subset Selection for Kernel-Based Classifiers, Satoshi Niijima, Satoru Kuhara
P130 Improvement of a Gene Network Discovery Method via Frequent Subtree Mining, Alexandre Termier, Yoshinori Tamada, Kazuyuki Numata, Seiya Imoto, Takashi Washio, Tomoyuki Higuchi
P131 A Graph Mining Approach to Gene Network Motif Extraction, Kazuyuki Numata, Alexandre Termier, Ryo Yoshida, Seiya Imoto, Yoshinori Tamada, Tomoyuki Higuchi, Satoru Miyano
P132 Considering False Negatives in Mixture Oncogenetic Trees Model for Chromosomal Alteration
Data, Kosei Yamoto, Shigeyuki Oba, Shin Ishii
P133 A Novel Clustering Method for Analysis of Biological Networks Using Maximal Components ofGraphs, Morihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi
P134 Extending Multivariate Bernoulli and Multinomial Models for Clustering MEDLINE Records,
Shanfeng Zhu, Ichigaku Takigawa, Shuqin Zhang, Hiroshi Mamitsuka
P135 A Recommendation System of PubMed Articles Based on Content-Based Filtering,Takashi Yoneya, Hiroshi Mamitsuka
P136 Automated Genome Annotation and Analysis of Eukaryotes, Igor Grigoriev, Andrea Aerts,
Alan Kuo, Robert Otillar, Asaf Salamov, Astrid Terry,Kemin Zhou, Kelly Felkins, Jinal Jhavery,
Wayne Huang, Lukasz Szajkowski, Gregory Werner
P137 A Resolution of the Problem of Multiple Inheritance in Gene Ontology, Takako Takai-Igarashi,
Hiroshi Tanaka
P138 A Gene Annotation Tool Based on Sequence Similarity and Biomedical Text, Daisuke Yamaguchi, Asako Koike, Yasunori Yamamoto, Toshihisa Takagi
P139 Classification of Figures in Biomedical Literature toward a Figure Finding System, Natsu Ishii,
Asako Koike, Yasunori Yamamoto, Toshihisa Takagi
P140 A Biomedical Text Mining System from PubMed Abstracts and Patents, Jaesoo Lim,
Hyunchul Jang, Joon-Ho Lim, Soo-Jun ParkP141 Ontology-Based Representation for Cell Systems Markup Language, Euna Jeong, Masao Nagasaki, Ayumu Saito, Satoru Miyano
P142 A New Grid Layout Algorithm with Swap Operation that Extends the Search Space while
Keeping the Time Complexity, Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato,
Satoru Miyano
P143 A Visualization Method for Detecting Pathway Alteration among Subtypes of Lung Carcinoma,
Makoto Kano, Shumpei Ishikawa, Michitaka Hirose, Hiroyuki Aburatani
P144 eXpanda: An Integrated Platform for Network Analysis and Visualization, Yoshiteru Negishi,
Hiroyuki Nakamura, Nozomu Yachie, Rintaro Saito, Masaru Tomita
P145 Pathway Mapping Web-Service Based on KEGG and SVG , Nobuaki Kono, Kazuharu Arakawa,
Masaru Tomita
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P146 Visualization of Metabolic Networks as Networks of Atoms by Pajek: An Application of Connectivity Matrix Method, Jun Ohta
P147 A Hub-Seeded Multilevel Algorithm for Fast Layout of Protein-Protein Interaction Networks,
SunLee Bang, JaeHun Choi, JongMin Park, SooJun ParkP148 Analyzing and Visualizing Complex Metabolite Profiles with MathDAMP, Richard Baran,
Hayataro Kochi, Natsumi Saito, Makoto Suematsu, Tomoyoshi Soga, Takaaki Nishioka, Martin Robert, Masaru Tomita
P149 Correlation Analysis of Sequence and Activity Based on Translation Signal Database, TRSIG,
Takahiro Ishimoto, Alex V. Kochetov, Akinori Sarai
P150 New Features of MutationView : A Module to Search for Disease-Causing Genes fromProtein Functional Domain, Masafumi Ohtsubo, Takashi Kawamura, Susumu Mitsuyama,
Nobuyoshi Shimizu, Shinsei Minoshima
P151 Construction of Biomolecular Network in Structurome and Analysis of Cooperativity, Mitsunobu Sekitou, Akinori Sarai
P152 INOH Pathway Data Ontologies, Noriko Sakai, Satoko Yamamoto, Hiromi Nakamura,
Yukiko Nakanishi, Toshihisa Takagi, KenIchiro Fukuda
P153 Application of AI-Based Database Methods in Purification of Traditional Chinese Pharmacy
Recipes, Yini Cui
P154 Restauro-G: A Rapid Genome Re-Annotation System, Satoshi Tamaki, Kazuharu Arakawa,
Nobuaki Kono, Masaru Tomita
P155 A Web-Based Resource for Glycome Informatics, Kiyoko F. Aoki-Kinoshita, Masao Ichikawa,
Shuichi Ikeda, Kouichi Yamada, Takako Yamaguchi
P156 Gclust Server: Phylogenetic Profiling with Pre-Defined Organism Sets, Naoki Sato
P157 TACT: Transcriptome Auto-Annotation Conducting Tool of H-InvDB, Chisato Yamasaki, Hiroaki Kawashima, Fusano Todokoro, Yasuhiro Imamizu, Makoto Ogawa, Motohiko Tanino,
Takeshi Itoh, Takashi Gojobori, Tadashi Imanishi

15

Program Committee
Yasubumi Sakakibara (Keio U., JP, PC Co-Chair)Temple F. Smith (Boston U., USA, PC Co-Chair)
Tatsuya Akutsu (Kyoto U., JP)
Masanori Arita (U.Tokyo, JP)
Phoebe Chen (Deakin U., Australia)
Oliver Ebenhöh (Humboldt U., Ger.)
Darren R. Flower (EJIVR, UK)
Richard Hughey (U.California Santa Cruz, USA)
Katsuhisa Horimoto (CBRC, JP)
Minoru Kanehisa (Kyoto U., JP)
Taishin Kin (CBRC, JP)
Edda Klipp (MOLGEN,MPG, Ger.)
Stefan Kramer (TUM, Ger.)
Sang Yup Lee (KAIST, South Korea)
Hiroshi Mamitsuka (Kyoto U., JP)
Osamu Maruyama (Kyushu U., JP)
Hideo Matsuda (Osaka U., JP)
Yo Matsuo (RIKEN, JP)
Aleksandar Milosavljevic (BCM, USA)
Satoru Miyano (U.Tokyo, JP)
Kenta Nakai (U.Tokyo, JP)
Haruki Nakamura (Osaka U., JP)
See-Kiong Ng (Inst.Infocomm Res., Singapore) William Stafford Noble (U.Washington, USA)
Shuichi Onami (RIKEN, JP)Elena Rivas (Washington U., USA)
Rintaro Saito (Keio U., JP)
Kenji Satou (JAIST, JP)
Tetsuo Shibuya (U.Tokyo, JP)Jörg Stelling (ETH, Switzerland)
Hideaki Sugawara (NIG, JP)
Toshihisa Takagi (U.Tokyo, JP)
Hiroyuki Toh (Kyushu U., 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)
Eric P. Xing (Carnegie Mellon U., USA)
Ying Xu (U.Georgia, USA)
Tetsushi Yada (Kyoto U., JP)
Byoung-Tak Zhang (Seoul National U., Korea)

16