GIW 2003
The Fourteenth International Conference on Genome Informatics
Pacifico Yokohama,Japan
December 14-17, 2003
Registration
Registration should be done at: http://giw.ims.u-tokyo.ac.jp/giw2003/registration.html
until November 30, 2003. Registration fee includes a copy of Genome Informatics Vol.14 and coffee
breaks. We offer registration fee discount for JSBi and ISCB members.

Standard
Registration

Student
Registration

until Nov. 30, 2003

after Nov. 30, 2003

Standard

JPY12,000.-

JPY15,000.-ISCB Member

JPY11,000.-

JPY14,000.-

JSBi Member

JPY8,000.-

JPY11,000.-

JSBi & ISCB Member

JPY7,000.-

JPY10,000.-

Standard

JPY8,000.-

JPY11,000.-ISCB Member

JPY7,000.-

JPY10,000.-

JSBi Member

JPY5,000.-

JPY8,000.-

JSBi & ISCB Member

JPY4,000.-

JPY7,000.-(Banquet on December 16 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/giw2003/index.html
Location
The conference will take place at PACIFICO YOKOHAMA. Please get off at JR Sakuragicho Station or
Sakuragicho Station on the Tokyu Toyoko Line.

It takes about 12 minutes’ walk from the JR

Sakuragicho station to Pacifico Yokohama via Moving Walkway.
Address: 1-1-1, Minato Miarai, Nishi-ku, Yokohama 220-0012, Japan
Tel:+81-45-221-2155
http://www.pacifico.co.jp/index_e.html

2Conference Center
1F

2F

Entrance

Main Hall

GIW・AIC
Registration

GIW2003
12/15〜17

12/14〜17

3F

303

304

AIC 2003

Posters
GIW & AIC

12/14〜17

12/15〜17※12/14 AASBi

301+302
Posters
andSoftwareDemonstration
GIW & AIC

654

12/15〜17
1

321

1〜11
Commercial
Exhibition

7

2

8

10
3

9
11

316
Office

W.C.

3

317
Internet
ServiceGIW 2003 Advanced Program
Registration
December 14, 2003: 10:00 - 17:45
December 15, 2003: 08:30 - 17:30
December 16, 2003: 08:30 - 18:00
December 17, 2003: 08:30 - 16:20

Monday, December 15, 2003
Opening Address
09:00 - 09:10

Minoru Kanehisa (Kyoto U.)

Paper Session 1
09:10 - 09:35

Chair: Eberhard Voit (USC)
Computational Inference of Regulatory Pathways in Microbes: an Application to
Phosphorus Assimilation Pathways in Synechococcus sp. WH8102, Zhengchang Su1 ,Phuongan Dam1 , Xin Chen2 , Victor Olman1 , Tao Jiang2 , Brian Palenik2 , Ying Xu1(1 U. Georgia, 2 U. California)

09:35 - 10:00

A Case Study of Object-Oriented Bio-Chemistry: A Uniﬁed Speciﬁcation of the Coagulation Cascade, Jacqueline Signorini, Patrick Greussay (U. Paris)

10:00 - 10:25

MetaFluxNet, a Program Package for Metabolic Pathway Construction and Analysis,and Its Use in Large-Scale Metabolic Flux Analysis of Escherichia coli, Sang Yup
Lee, Dong-Yup Lee, Soon Ho Hong, Tae Yong Kim, Hongsoek Yun, Young-Gyun Oh,
Sunwon Park (KAIST)ISCB Address
10:25 - 10:40
10:40 - 11:00
Keynote Address
11:00 - 12:00
12:00 - 13:30

Michael Gribskov (UCSD)
BreakChair: Genshiro Kitagawa (ISM)
On the Art of Modeling; Illustrated with the Analysis of the Golf Swing Motion,
Hirotugu Akaike (ISM)
Lunch

Posters and Software Demonstrations Session 1
13:30 - 15:00
Paper Session 2
15:00 - 15:25

Chair: Vladimir Brusic (Inst. Infocomm Res.)
Reducing False Positives in Molecular Pattern Recognition, Xijin Ge, Shuichi Tsutsumi, Hiroyuki Aburatani, Shuichi Iwata (U. Tokyo)

15:25 - 15:50

On Combining Multiple Microarray Studies for Improved Functional Classiﬁcation by
Whole-Dataset Feature Selection, See-Kiong Ng1 , Soon-Heng Tan1 , V.S. Sundararajan1,2 (1 I2R, 2 Nat’l U. Singapore)

15:50 - 16:15

Statistical Inference Methods for Detecting Altered Gene Associations, Sang-Heon
Yoon, Je-Suk Kim, Hae-Hiang Song (Cath. U. Korea)

Paper Session 3
16:15 - 16:40

Chair: Kenta Nakai (U. Tokyo)
Splice Site Detection with a Higher-Order Markov Model Implemented on a Neural
Network, Loi Sy Ho, Jagath C. Rajapakse (Nanyang Tech U)

16:40 - 17:05

On Selecting Features from Splice Junctions: An Analysis Using Information Theoretic and Machine Learning Approaches, Christina L. Zheng, Virginia R. de Sa,
Michael Gribskov, T. Murlidharan Nair (U. California)

17:05 - 17:30

An In-Silico Method for Prediction of Polyadenylation Signals in Human Sequences,
Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong (I2R)

4

Tuesday, December 16, 2003
Paper Session 4
09:00 - 09:25

Chair: Ueng-Cheng Yang (Yang Ming U.)
Construction of Genetic Network Using Evolutionary Algorithm and Combined Fitness Function, Ando Shin, Hitoshi Iba (U. Tokyo)

09:25 - 09:50

Layout Search of a Gene Regulatory Network for 3-D Visualization, Naoki Hosoyama,
Noman Nasimul, Hitoshi Iba (U. Tokyo)

09:50 - 10:15

Neural-Network-Based Parameter Estimation in S-System Models of Biological Networks, Jonas S. Almeida, Eberhard O. Voit (U. South Carolina)

10:15 - 10:40

Finding Optimal Gene Networks Using Biological Constraints, Sascha Ott, Satoru
Miyano (U. Tokyo)

10:40: - 11:00

Break

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

Chair: Michael Gribskov (UCSD)
Predicting Nucleic Acid Hybridization and Melting Proﬁles, Michael Zuker (Rensselaer Polytechnic Inst.)
Lunch

Keynote Address
13:30 - 14:30

Chair: Minoru Kanehisa (Kyoto U.)
Orthologous Sets of Functional Networks: Inference, Mining and Visualization,Charles DeLisi (Boston U.)

Paper Session 5
14:30 - 14:55

Chair: Mark Ragan (U. Queensland)Eﬃcient Tree-Matching Methods for Accurate Carbohydrate Database Queries,
Kiyoko F. Aoki, Atsuko Yamaguchi, Yasushi Okuno, Tatsuya Akutsu, Nobuhisa Ueda,
Minoru Kanehisa, Hiroshi Mamitsuka (Kyoto U)

14:55 - 15:20

Heuristics for Chemical Compound Matching, Masahiro Hattori, Yasushi Okuno,
Susumu Goto, Minoru Kanehisa (Kyoto U)

15:20 - 15:45

Processing Sequence Annotation Data Using the Lua Programming Language, Yutaka
Ueno1 , Masanori Arita1,2 , Toshitaka Kumagai1 , Kiyoshi Asai1,2 (1 AIST, 2 U Tokyo)

JSBi Annual Meeting
16:00 - 16:30
Posters and Software Demonstrations Session 2
16:30 - 18:00
Banquet18:00 - 21:00

Wednesday, December 17, 2003
Paper Session 6
09:00 - 09:25

Chair: Shinichi Morishita (U. Tokyo)
PatternHunter II: Highly Sensitive and Fast Homology Search, Ming Li1 , Bin Ma2 ,Derek Kisman3 , John Tromp4 (1 U Waterloo, 2 U Western Ontario, 3 Bioinformatics
Solutions Inc, 4 CWI)

09:25 - 09:50
09:50 - 10:15

On Half Gapped Seed, Wei Chen, Wing-kin Sung (Nat’l U Singapore)
Clone-Array Pooled Shotgun Mapping and Sequencing: Design and Analysis of Experiments, Miklós Csűrös1 , Bingshan Li2 , Aleksandar Milosavljevic2 (1 U Montréal,2Baylor Col Med)

Posters and Software Demonstrations Session 3
10:15 - 12:00
12:00 - 13:30
Lunch

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Paper Session 7
13:30 - 13:55

Chair: Kiyoshi Asai (U. Tokyo)
Prediction and Analysis of β-Turns in Proteins by Support Vector Machine, Tho Hoan
Pham1 , Kenji Satou1 ,2 , Tu Bao Ho1 (1 JAIST, 2 JST)

13:55 - 14:20

Multi-Class Protein Fold Classiﬁcation Using a New Ensemble Machine Learning
Approach, Aik Choon Tan1 , David Gilbert1 , Yves Deville2 (1 U Glasgow, 2 U cath
Louvain)14:20 - 14:45

Multi-Class Support Vector Machines for Protein Secondary Structure Prediction,
Minh N. Nguyen, Jagath C. Rajapakse (Nanyang Tech U)

14:45 - 15:05

Break

Paper Session 8
15:05 - 15:30

Chair: Satoru Miyano (U. Tokyo)
Development of an ab initfio Protein Structure Prediction System ABLE, Takashi
Ishida, Takeshi Nishimura, Makoto Nozaki, Tsuyoshi Inoue, Tohru Terada, Shugo
Nakamura, Kentaro Shimizu (U Tokyo)

15:30 - 15:55

Docking Unbound Proteins with MIAX: A Novel Algorithm for Protein-Protein SoftDocking, Carlos A. Del Carpio Muñoz1,2 , Tobias Peissker3 , 4 , Atsushi Yoshimori3 ,Eiichiro Ichiishi1 (1 Tohoku U, 2 U Católica St Moria, 3 Toyohashi U Tech, 4 Zwickau
U App Sci)

15:55 - 16:20

A Domain Combination Based Probabilistic Framework for Protein-Protein Interaction Prediction, Dongsoo Han, Hong-Soog Kim, Jungmin Seo, Woohyuk Jang (Infoand Comm U)

Closing and Award Ceremony
16:20 - 16:35

Commercial Exhibitions
C1: Silicon Genetics
C2: NABE International Corp.
C3: Ryoka Systems Inc.
C4: TOMY DIGITAL BIOLOGY Co., Ltd.
C5: Hitachi, Ltd.
C6: INFOCOM Corp.
C7: Mitsui Knowledge Industry Co., Ltd.
C8: Mathematical Systems Inc.
C9: Hitachi High-Technologies Corp.
C10: SGI Japan, Ltd.
C11: Bioinformatics Center, Institute for Chemical Research, Kyoto University

Software Demonstrations
S01 CADLIVE System: Map-Based Dynamic Simulation of Biochemical Networks, Hiroyuki Kurata, Rei
Iwasaki, Kouichi Masaki, Takayuki Tanaka, Kouji Mitsukiyo, Yoshiyuki Sumida (Kyushu Inst. Tech.)r, New Software Based on
S02 Selection of Causal Gene Sets from Gene Expression Proﬁles Using GeneFis
FNN, Hiroyuki Honda, Takeshi Kobayashi (Nagoya U.)
S03 Development of an Integrated System for Genetic Network Analysis and Microarray Data Management,
Ji-Hung Kim, Kyung-Shin Lee, Pan-Gyu Kim, Hwan-Gue Cho (Pusan Nat. U.)
S04 An Open Source Client-Server System for the Analysis of Aﬀymetrix Microarray Data, Lars Martin Jakt,
Mitsuhiro Okada, Shin-Ichi Nishikawa (RIKEN)

S05 ASIAN: A Web Site for Network Inference, Katsuhisa Horimoto1 , Hiroyuki Toh2 , Sachiyo Aburatani1 ,Nobuyoshi Sugaya1 , Hiroo Murakami1 , Makihiko Sato3 , Shigeru Saito3 , Kousuke Goto3 , Masaki Fumoto3(1 U. Tokyo, 2 Kyoto U., 3 Mitsui Sumitomo Insurance Co., Ltd.)S06 Netview: Application Software for Constructing and Visually Exploring Phylogenetic Networks, Kirill
Kryukov, Naruya Saitou (SOKENDAI)

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S07 Integrated System for Inference of Gene Expression Network, Masahiko Nakatsui, Takanori Ueda, Masahiro
Okamoto (Kyusyu U.)
S08 MutationView : An Integrated Knowledge Base for Mutations and Polymorphisms in Human Disease Genes- Automatical Extraction of Disease-Associated Knowledge -, Masafumi Ohtsubo1 , Susumu Mitsuyama1 ,Takashi Kawamura1 , Nobuyoshi Shimizu1 , Shinsei Minoshima2 (1 Keio U., 2 Hamamatsu U.)
S09 BirdsAnts: Bringing Informative Rules from a Database System, Aimed at Novel Targets Search, Motoi
Tobita, Ken Horiuchi, Kenji Araki, Masashi Nemoto, Tetsuo Nishikawa (REPRORI Co., Ltd.)S10 Ecell2d : Distributed E-CELL2, Andrew Stubbings1 ,4 , Naota Ishikawa2 , Takashi Yamazaki1,4 , Ariya Fujita3 , Iriko Kaneko2 , Yoshinari Fukui2 , Toshikazu Ebisuzaki2 (1 Grid Res. Inc., 2 RIKEN, 3 Swimmy Software, Inc, 4 Best Systems Inc.)
S11 Integrated Distributed Computing Environment on the G-Language GAE v.2, Ryo Hattori, Kazuharu
Arakawa, Hayataro Kouchi, Masaru Tomita (Keio U.)
S12 SuperNORM: A Computer Program for the Parametric Normalization of Microarray Data, Tomokazu
Konishi1 , Masanori Yoshida2 , Kenya Shibahara2 (1 Akita Prefectural U., 2 Skylight-Biotech Inc.)
S13 E-CELL System Version 3: A Software Platform for Integrative Computational Biology, Kouichi Takahashi1 , Takeshi Sakurada1 , Kazunari Kaizu1 , Tomoya Kitayama1 , Satya Arjunan1 , Tatsuya Ishida1 , Gabor
Bereczki1 , Daiki Ito1 , Masahiro Sugimoto1,2 , Takashi Komori3 , Ohta Seiji4 , Masaru Tomita1 (1 Keio U.,
2
Mitsubishi Space Software Co., Ltd., 3 W&G, 4 Mitsui Knowledge Industry Co.,Ltd.)S14 BPE: Biopathway Executer for Large-Scale Biopathway Modeling and Simulation, Masao Nagasaki1 , Atsushi Doi2 , Kazuko Ueno1 , Eri Torikai1 , Hiroshi Matsuno2 , Satoru Miyano1 (1 U. Tokyo, 2 YamaguchiU.)
S15 Bioinformatics and Computational Biology with Biopython, Michiel J.L. de Hoon1 , Brad Chapman2 , Iddo
Friedberg3 (1 U. Tokyo, 2 U. Georgia, 3 The Burnham Inst.)
S16 Representing Metabolic Networks by the Substrate-Product Relationships, Masanori Arita1,2,3 (1 U.
Tokyo, 2 CBRC, 3 Keio U.)

PostersP001 Comprehensive Analysis of Delay in Transcriptional Regulation Using Expression Proﬁles, Koji Ota, Takuji
Yamada, Yoshihiro Yamanishi, Susumu Goto, Minoru Kanehisa (Kyoto U)
P002 Prediction of Glycan Structures from Glycosyltransferase Expression Proﬁles, Shin Kawano1 , Yasushi
Okuno1 , Kosuke Hashimoto1 , Harumi Yamamoto2 , Hiromu Takematsu1 , Yasunori Kozutsumi1,2 , Susumu
Goto1 , Minoru Kanehisa1 (1 Kyoto U, 2 RIKEN)
P003 Statistical Analysis of the Relationship between Gene Expression and Location, Sachiyo Aburatani1 ,Nobuyoshi Sugaya1 , Hiroo Murakami1 , Makihiko Sato1 ,2 , Katsuhisa Horimoto1 (1 U Tokyo, 2 Fujitsu)
P004 Detection of Genes with Tissue-Speciﬁc Patterns Using Akaike’s Information Criterion, Koji Kadota, Katsutoshi Takahashi (AIST)
P005 Operon Prediction by DNA Microarray: An Approach with a Bayesian Network Model, Hitoshi Shimizu,
Shigeyuki Oba, Shin Ishii (NAIST)
P006 Automatic Extraction of Expression-Related Features Shared by a Given Group of Genes, Takuya
Oyama1,5 , Mikio Yoshida1,5 , Satoshi Kamegai1,5 , Kagehiko Kitano1,5 , Fumihito Miura2 , Noriko
Kawaguchi3 ,5 , Miyuki Onda3 , Kenji Satou4 ,5 , Takashi Ito2,3,5 (1 INTEC W&G Info Corp, 2 U Tokyo,
3
Kanazawa U, 4 JAIST, 5 JST)
P007 Dynamics of Repressilator: From Noise to Coherent Oscillation, Tomohiro Ushikubo, Wataru Inoue, Masaki
Sasai (Nagoya U,)
P008 Gene Expression Analysis Reﬁning System (GEARS) via Statistical Approach: A Preliminary Report,
Chen-Hsin Chen1 , Henry Horng-Shing Lu2 , Chen-Tuo Liao3 , Chun-houh Chen1 , Ueng-Cheng Yang4 , YunShien Lee5 (1 Acad Sinica, 2 Nat’l Chiao Tung U, 3 Nat’l Taiwan U, 4 Nat’l Yang-Ming U, 5 Chang Gung U)
P009 CAPIES: DNA Microarray-Based Class Prediction System for Computational Diagnostics, Sung Geun
Lee1 , Bonghee Seo1 , Yang Seok Kim1,2 (1 ISTECH Inc, 2 Yonsei U)
P010 Gene Screening Method for Prognostic Prediction Using Projective ART Model, Hiro Takahashi, Takeshi
Kobayashi, Hiroyuki Honda (Nagoya U)
P011 Features of Gene Extraction by Nonlinear Support Vector Machines in Gene Expression Analysis, Daisuke
Komura, Hiroshi Nakamura, Shuichi Tsutsumi, Hiroyuki Aburatani, Sigeo Ihara (U Tokyo)

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P012 Prognosis Prediction by Microarray Gene Expression Using Support Vector Machine, Chihoko Tago, Taizo
Hanai, Masahiro Okamoto (Kyushu U)
P013 Automatically Finding Good Clusters with Seed K-Means, Miyoung Shin, Eun Mi Kang, Seon Hee Park(ETRI)
P014 Analysis of DNA Microarray Data by Using Self-Organizing Maps, Tomoyuki Kato, Kikuo Fujimura, Heizo
Tokutaka, Yasushi Kawata, Masaaki Ohkita (Tottori U)
P015 Clustering Method Based on Onset and Cessation of Gene Expression, Kazumi Hakamada, Taizo Hanai,
Masahiro Okamoto (Kyushu U)
P016 Signiﬁcance Test of Clusters in Gene Expression Proﬁle Data, Natsuko Kawase, Shigeyuki Oba, Shin Ishii(NAIST)
P017 Gene Expression Analysis Using Fuzzy K-Means Clustering, Chinatsu Arima, Taizo Hanai, Masahiro
Okamoto (Kyushu U)
P018 A Method for Normalization of Gene Expression Data, Makoto Kano1 , Hisashi Kashima1 , Tetsuo Shibuya1 ,Kaori Ide2 , Aiko Kashihara2 , Noriko Nakagawa2 ,3 , Mariko Hatakeyama2 , Seiki Kuramitsu2 ,3 , Akihiko
Konagaya2 (1 IBM, 2 Riken, 3 Osaka U)
P019 Normalization of Target Fluorescence Using Reference Fluorescence for cDNA Microarray Method, Yu
Suzuki, Kenji Hatano, Shigehiko Kanaya, Shunsuke Uemura (NAIST)
P020 A System for Visualizing Gene Expressions Using Metabolic Networks, Ryoko Tamaru, Toshiyuki Amagasa,
Shigehiko Kanaya, Shunsuke Uemura (NAIST)
P021 Image Preprocessing for cDNA Microarray Using Deconvolution Method, Hyo Jung Ban1 , Myungguen
Chung1 ,2 , Yong Sung Lee1 , Jin Hyuk Kim1 , Young Seek Lee1 (1 Han-yang U, 2 ETRI)
P022 On Visualization, Screening, and Classiﬁcation of Cell Cycle-Regulated Genes in Yeast, Henry Horng-Shing
Lu1 , Han-Ming Wu2 (1 Nat’l Chiao-Tung U, 2 Acad Sinica)
P023 A PCA Based Method of Gene Expression Visual Analysis, Kunihiro Nishimura, Koji Abe, Shumpei
Ishikawa, Shuichi Tsutsumi, Koichi Hirota, Hiroyuki Aburatani, Michitaka Hirose (U Tokyo)
P024 Bioinformatics for Oncogenomic Target Identiﬁcation, Masaru Katoh (NCC)
P025 Multiscale Bootstrap Analysis of Gene Networks Based on Bayesian Networks and Nonparametric Regression, Takeshi Kamimura1 , Hidetoshi Shimodaira1 , Seiya Imoto2 , SunYong Kim2 , Kousuke Tashiro3 ,Satoru Kuhara3 , Satoru Miyano2 (1 Tokyo Inst Tech, 2 U Tokyo, 3 Kyushu U)
P026 Combining Gene Expression Data with DNA Sequence Information for Estimating Gene Networks Using
Bayesian Network Model, Yoshinori Tamada1 , SunYong Kim2 , Hideo Bannai2 , Seiya Imoto2 , Kousuke
Tashiro3 , Satoru Kuhara3 , Satoru Miyano2 (1 Kyoto U, 2 U Tokyo, 3 Kyushu U)
P027 Enumeration of Likely Gene Networks and Network Motif Extraction for Large Gene Networks, Sascha
Ott, Satoru Miyano (U Tokyo)
P028 Genetic Networks with Stochastic Fluctuations, Luonan Chen1 , Ruiqi Wang1 , Kazuyuki Aihara2 (1 Osaka
Sangyo U, 2 U Tokyo)
P029 Integrative Method for Identifying Combinatorial Regulation of Transcription Factors, Mamoru Kato1 ,2 ,Naoya Hata2 , Nila Banerjee2 , Michael Q. Zhang2 (1 CSHL, 2 RIKEN)
P030 Pathways/Networks to Syndrome X, Tsuguchika Kaminuma1 , Masumi Yukawa2 , Naomi Komiyama2 , Kotoko Nakata3 , Hiroki Momose4 , Yoshitomo Tanaka4 , Hiroshi Tanaka4 (1 Biodynamics Inc., 2 CBI, 3 NIHS,
4Tokyo Med & Dent U)
P031 Identiﬁcation of Regulation Networks of Lipid Metabolism by Nuclear Receptors, Yoshitomo Tanaka1 ,Tsuguchika Kaminuma2 , Hiroki Momose1 , Kotoko Nakata3 , Hiroshi Tanaka1 (1 Tokyo Med&Dent U,
2
Biodynamics Inc., 3 NIHS)
P032 Analysis of Gene Regulation Network by Nuclear Receptor PPAR, Hiroki Momose1 , Tsuguchika
Kaminuma2 , Yoshitomo Tanaka1 , Kotoko Nakata3 , Hiroshi Tanaka1 (1 Tokyo Med&Dent U, 2 Biodynamics
Inc., 3 NIHS)
P033 Analysis of Reactive Modules in the Metabolic Pathways, Masaaki Kotera, Masahiro Hattori, Susumu
Goto, Minoru Kanehisa (Kyoto U)
P034 Metabolic Pathway Reconstruction for Malaria Parasite Plasmodium falciparum, Vachiranee Limviphuvadh1 , Yasushi Okuno1 , Toshiaki Katayama2 , Susumu Goto1 , Akiyasu C. Yoshizawa1 , Minoru Kanehisa1(1 Kyoto U, 2 U Tokyo)
P035 Extraction of a Thermodynamic Property for Biochemical Reactions in the Metabolic Pathway, Michihiro Tanaka1 , Yasushi Okuno2 , Takuji Yamada2 , Susumu Goto2 , Shunsuke Uemura1 , Minoru Kanehisa2(1 NAIST, 2 Kyoto U)
P036 Crosstalk between Metabolic and Regulatory Pathways, Min Kyung Kim1 , Hyun Seok Park1 , Seong Joon
Yoo2 (1 Ewha Womans U, 2 Sejong U)

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P037 An Eﬃcient Pathway Search Using an Indexing Scheme for RDF, Akiyoshi Matono1 , Toshiyuki Amagasa1 ,Masatoshi Yoshikawa2 , Shunsuke Uemura1 (1 NAIST, 2 Nagoya U)
P038 Graph Complexity of Chemical Compounds in Biological Pathways, Atsuko Yamaguchi, Kiyoko F. Aoki,
Hiroshi Mamitsuka (Kyoto U)
P039 M3 : Merging Module Model for a Network with Scale-Free Properties and Modularity, Kazuhiro Takemoto,
Chikoo Oosawa (Kyushu Inst Tech)
P040 Comparative Analysis Workbench for Genetic Networks, Pan-Gyu Kim1 , Kyung-Shin Lee1 , Hwan-Gue
Cho1 , Seon-Hee Park2 , Miyoung Shin2 , Eun-Mi Kang2 (1 Pusan Nat’l U, 2 ETRI)
P041 KAREIDMAP: A System for Predicting and Mining Gene Regulatory Networks, Hironori Mizuguchi1 , Dai
Kusui2 , Taku Oshima2 , Shigehiko Kanaya2 , Hirotada Mori2,3 (1 NEC Corp, 2 NAIST, 3 Keio U)
P042 Development of a New Gene-Network Estimation System, Shigeyuki Mitsui, Hiroya Nobori, Tuyoshi
Takada, Kunihiro Kishida, Yoshiki Miura, Hiroshi Ikawa (Mitsubishi Space Soft Co Ltd)
P043 3-D Visualization Software of a Gene Regulatory Network, Kouichi Okada, Nasimul Noman, Naoki
Hosoyama, Hitoshi Iba (U Tokyo,)P044 CADLIVE Automatic Visualizing System for Large-Scale Biochemical Maps, Weijiang Li, Hiroyuki Kurata(Kyushu Inst Tech)
P045 Transcriptome Proﬁling and Deciphering the Regulatory Role of Global Transcription Factor fadR, Byung
Hun Kim, Si Jae Park, Sang Yup Lee (KAIST)
P046 Conservation of DNA Curvature Signals in Gene Regulatory Regions, Ruy Jauregui1 , Enrique Merino2(1 Kyoto U, 2 Nat’l Aut U Mexico)
P047 Large Scale Analysis of Transcriptional and Translational Control Mechanism in Human Ribosomal Proteins, Kyota Ishii1 , Tamayo Uechi2 , Takanori Washio1 , Maki Yoshihama2 , Naoya Kenmochi2 , Masaru
Tomita1 (1 Keio U, 2 U Miyazaki)
P048 Regulator Identiﬁcation by Expression Proﬁles of Transcriptional Factor Mutants and Promoter Sequencein Bacillus subtilis, Nobuyuki Fujii, Joe Akitomi, Kazuo Kobayashi, Naotake Ogasawara, Shigehiko Kanaya(NAIST)
P049 Developing Genome-Scale Prediction System for Transcription Factors and Their Targets, Akinori Sarai1 ,Shandar Ahmad1 , Michael M. Gromiha2 , M. D. Shaji Kumar1 , Abdulla Bava1 , Hidetoshi Kono3 (1 Kyushu
Inst Tech, 2 AIST, 3 JAERI)
P050 Prediction of Transcription Factor Binding Sites with Suﬃx Arrays, Myung Eun Lim, Jeong Seop Sim,
Myung Geun Chung, Sun Hee Park (ETRI)
P051 Phylogenetic Analysis of Eubacterial Transcriptional Systems Based on the DBTBS Database of B. subtilis
Transcription Factors and Promoters, Yuko Makita1,2 , Naotake Ogasawara3 , Kenta Nakai1 (1 U Tokyo,
2
Nagoya U, 3 NAIST)
P052 Genome Wide Analysis Reveals Strong Correlation between CpG Islands and Tissue-Speciﬁcity, Riu Yamashita, Yutaka Suzuki, Toshihisa Takagi, Sumio Sugano, Kenta Nakai (U Tokyo)
P053 Extraction of Biological Motifs by Gibbs Sampler from the Promoters of Homo Sapiens, Saccharomyces
cerevisiae and Bacillus subtilis, Natalia Poluliakh1,2 , Kenta Nakai1 (1 U Tokyo, 2 Ochanomizu U)
P054 Detection of Tissue Speciﬁc Genes by Putative Regulatory Motifs in Human Promoter Sequences, Katsuhiko Murakami, Toshio Kojima, Yoshiyuki Sakaki (RIKEN)
P055 Statistical Analysis of Symmetric Exon Sets in Eukaryotic Genes, Yiyu Jia, Chee Keong Kwoh, Meena K.
Sakharkar, Pandjassarame Kangueane (Nanyang Tech U)
P056 Human Full-Length Pre-mRNA Sequence Dataset for Computational Gene Prediction and Alternative
Splicing Analysis, Masahiko Mizuno1 , Osamu Gotoh1 ,2 , Makiko Suwa1 (1 AIST, 2 Kyoto U)
P057 Detect of Novel Alternative Form at Development Stages in Brain, SungHun Lee1 , MyungGuen Chung1 ,2 ,SungHee Park1 , SooJun Park1 , SeonHee Park1 (1 ETRI, 2 HanYang U)
P058 Splice Variant Search with Gene Expression Data, Tadashi Kadowaki, Satoshi Shiojima, Gozoh Tsujimoto(Kyoto U)
P059 Mapping Database of cDNA and Genome Designed to Use for Various Applications, Akifumi Yamashita,
Ken Kurokawa, Teruo Yasunaga (Osaka U)
P060 Finding Signiﬁcant Patterns Characterizing Types of Alternative Splicing, Hiroki Sakai, Osamu Maruyama(Kyushu U)
P061 Towards Splicing Pattern Detection Based on cDNA Sequences, Tomohiro Yasuda, Koichi Kimura, Tetsuo
Nishikawa (Hitachi Ltd)
P062 An Algorithm for Classiﬁcation of Alternative Splicing and Transcriptional Initiation and Its Genome-WideApplication, Hideki Nagasaki1 , Makiko Suwa1 , Osamu Gotoh1 ,2 (1 AIST, 2 Kyoto U)

9

P063 Detection of the Splicing Sites with Kernel Method Approaches Dealing with Nucleotide Doublets, Masaki
Yamamura, Osamu Gotoh (Kyoto U)
P064 Identifying Potential Regulatory Sequences of Alternative Splicing, Hitomi Itoh, Takanori Washio, Masaru
Tomita (Keio U)
P065 A cDNA Evaluation System for Highly Eﬃcient Sequencing of Splicing Variant cDNAs, Jun-ichi Yamamoto1 , Naoto Hatano1 , Kenji Araki1 , Hiroshi Makita1 , Kouichi Kimura2 , Ai Wakamatsu1 , Shizuko
Ishii1 , Tetsuo Nishikawa1,2 , Takao Isogai1 (1 REPRORI, 2 Hitachi Ltd)
P066 Self-Nonself Discrimination Based on Incompatibility of Amino Acid Sequences of Human and Viruses,
Wataru Honda, Shuichi Kawashima, Minoru Kanehisa (Kyoto U)
P067 Analysis of Domain Combinations in Eukaryotic Genomes, Masumi Itoh, Akiyasu C. Yoshizawa, Shujiro
Okuda, Susumu Goto, Minoru Kanehisa (Kyoto U)
P068 Comprehensive Survey of Intracellular Transport System-Related Proteins in Complete Genomes andDraft Genomes, Akiyasu C. Yoshizawa, Masumi Itoh, Shujiro Okuda, Vachiranee Limviphuvadh, Tadahiko
Sakiyama, Shuichi Kawashima, Minoru Kanehisa (Kyoto U)
P069 Extraction of Organism Groups from Whole Genome Comparisons, Yoshihiro Yamanishi1 , Akiyasu C.
Yoshizawa1 , Masumi Itoh1 , Toshiaki Katayama2 , Minoru Kanehisa1 (1 Kyoto U, 2 U Tokyo)
P070 Identifying Obscure Periodic Patterns in Genomic DNA Sequence, Hiroo Murakami1 , Natsuhiro Ichinose2 ,Tetsushi Yada2 , Sachiyo Aburatani1 , Nobuyoshi Sugaya1 , Makihiko Sato1 , Katsuhisa Horimoto1 (1 U Tokyo,
2
Kyoto U)
P071 Distribution of Chromophore-Binding GAF Domains in Genome Sequence, Shinobu Okamoto, Masayuki
Ohomori (U Tokyo)
P072 Newly Identiﬁed Motifs within PAS Domains of Filamentous Cyanobacteria, Rei Narikawa, Shinobu
Okamoto, Masahiko Ikeuchi, Masayuki Ohmori (U Tokyo)
P073 Translational Eﬃciency Prediction Using Structural Learning Method, Koya Mori, Rintaro Saito, Shinichi
Kikuchi, Masaru Tomita (Keio U)
P074 Identiﬁcation of Non-Coding RNAs in the Escherichia coli Genome Using Sequence Speciﬁcity Index (SSI),
Nozomu Yachie, Koji Numata, Rintaro Saito, Akio Kanai, Masaru Tomita (Keio U)
P075 Heterogeneity in Synonymous Codon Usage among Genes of Diverse Bacterial Genomes, Haruo Suzuki,
Rintaro Saito, Masaru Tomita (Keio U)
P076 Detection of Processed Pseudogenes Based on cDNA Mapping to the Human Genome, Hiroaki Sakai1 ,Kanako O. Koyanagi2 , Takeshi Itoh1 , Tadashi Imanishi1 , Takashi Gojobori3 (1 AIST, 2 NAIST, 3 NIG)
P077 Improvement in the Accuracy of Gene Prediction in Human cDNA Sequences, Fusano Todokoro1 , Takeshi
Itoh2 , Chisato Yamasaki2 , Hiroaki Kawashima1,3 , Tadashi Imanishi2 , Takashi Gojobori2 ,4 (1 Dynacom Co
Ltd, 2 AIST, 3 JBIC, 4 NIG)
P078 The Translated Region Inspector for cDNA Sequences, Kouichi Kimura1 , Tetsuo Nisikawa2 , Keiichi Nagai1 , Sumio Sugano2 , Nobuo Nomura3 , Takao Isogai4 (1 Hitachi Ltd, 2 U Tokyo, 3 AIST, 4 REPRORI)
P079 Characterization of One-Pass and Full-Length Sequences of Oligo-Capping cDNA Clones by Genome Mapping, Tetsuo Nishikawa1,2 , Kouichi Kimura1 , Tomohiro Yasuda1 , Jun-ichi Yamamoto2 , Ai Wakamatsu2 ,Shizuko Ishii2 , Masashi Nemoto2 , Jun-ichi Uechi1 , Yutaka Suzuki3 , Keiichi Nagai1 , Sumio Sugano3 , Nobuo
Nomura4 , Takao Isogai2 (1 Hitachi Ltd, 2 REPRORI, 3 U Tokyo, 4 AIST)
P080 Mapping the Genome Sequences on Self Organizing Maps, Hiroshi Dozono, Hisao Tokushima, Yoshio
Noguchi (Saga U)
P081 Mapping of Artiﬁcial Nucleosome Positioning Sequences to the Saccharomyces cerevisiae Genome, Vorathaya Tantoolvesm, Yoichi Takenaka, Satoshi Harashima, Hideo Matsuda (Osaka U)
P082 Analysis of Tandem Repeats Detected in Prokaryotic Genomes, Hikaru Munakata1 , Abulimiti Aimaiti1 ,Akito Taneda1 , Kenji Oosawa2 , Toshio Shimizu1 (1 Hirosaki U, 2 Gunma U)
P083 Genome-Scale Detection of Tandemly-Duplicated Gene Structures, Keisuke Onishi1 , Hao Zhang2 , Takuro
Tamura2 , Takashi Gojobori2,3 , Shintaroh Ueda1 (1 U Tokyo, 2 JBIRC, 3 NIG)
P084 Estimation of the Number of Orphan Genes in the Genome Sequences, Satoshi Fukuchi, Ken Nishikawa(NIG)
P085 A Comparative Study on Formal Grammars for Pseudoknots, Yuki Kato, Hiroyuki Seki, Tadao Kasami(NAIST)
P086 Analysis of 3’/5’ Ratio of Actin and Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Yasuo Oshima, Akio Fujimura (Jichi Med Sch)P087 MGAlign, a Reduced Search Space Approach to the Alignment of mRNA Sequences to Genomic Sequences,
Shoba Ranganathan, Bernett T. K. Lee, Tin Wee Tan (Nat’l U Singapore)

10

P088 Development of Eﬃcient Designing Method for Target Speciﬁc Probe Sets, So Young Yoo1,2 , Hyeong Jun
An1 , Doheon Lee1 , Sang Yup Lee1 (1 KAIST, 2 Medigenes Co Ltd)P089 IMPORT - Integrated Massive Probe’s Optimal Recognition Tools, Cheng Tao Wu, Chung Ya Liao, Hung
Ju Su, Shiu Chieh Lan, Yu Yu Lin, Yu Ching Chang (ITRI)
P090 Algorithms for Computing an Optimal Protein Threading with Proﬁles and Distance Restraints, Tatsuya
Akutsu1 , Morihiro Hayashida1 , Etsuji Tomita2 , Jun’ichi Suzuki2 , Katsuhisa Horimoto3 (1 Kyoto U, 2 UElectro Comm, 3 U Tokyo)
P091 Development of Residue Look-Up Tables and Graphical Representation of Solvent Accessibility in Proteins,
Shandar Ahmad1 , Jung-Ying Wang2 , M. Michael Gromiha3 , Hamed Fawareh4 , Akinori Sarai1 (1 Kyushu
Inst Tech, 2 Lunghwa U Sci&Tech, 3 AIST, 4 Zarka Private U)
P092 Reﬁnement of Comparative-Modeling Structures by Multicanonical Molecular Dynamics, Wei Cao, Tohru
Terada, Shugo Nakamura, Kentaro Shimizu (U Tokyo)
P093 Molecular Modeling for Generation of Structural and Molecular Electronic Descriptors for QSAR Using
Quantum Mechanical Semiempirical and ab initio Methods, Mohd. Shahid Khan1,2 , Zahid H. Khan1(Central U)
P094 Maximum Likelihood Superposition of Protein Structures, Tsuyoshi Kato1 , Koji Tsuda1 ,2 , Kentaro
Tomii1 , Kiyoshi Asai1,3 (1 AIST, 2 MPI Biol Cybernetics, 3 U Tokyo)
P095 Prediction from Sequence to Structure at Oligonucleotide Level by MD Simulations, Manish Biyani, Koichi
Nishigaki (Saitama U)
P096 A Protein Structure Retrieval System Using Atom-Atom Bond-Line Histogram, Sung-hee Park, Soo-jun
Park, Sung-hun Lee, Sun-hee Park (ETRI)
P097 A Combined Experimental and Inferring Interactomes, Chung-Yen Lin, Chi-Shiang Cho, Li-Ming Wang,
Chia-Ling Chen, Pao-Yang Chen, Chen-Zen Lo, Chao A. Hsiung (NHRI)
P098 Prediction of Protein-Protein Interactions from Phylogenetic Trees Using Partial Correlation Coeﬃcient,
Tetsuya Sato1 , Yoshihiro Yamanishi1 , Katsuhisa Horimoto2 , Hiroyuki Toh1 , Minoru Kanehisa1 (1 Kyoto
U, 2 U Tokyo)
P099 Prediction of Protein Functions Based on K-Cores of Protein-Protein Interaction Networks and Amino
Acid Sequences, Md. Altaf-Ul-Amin1,2 , Kensaku Nishikata1 , Toshihiro Koma1 , Teppei Miyasato1 , Yoko
Shinbo1 , Md. Arifuzzaman2 , Chieko Wada3 , Maki Maeda3 , Taku Oshima1 , Hirotada Mori1,4 , Shigehiko
Kanaya1 (1 NAIST, 2 NEDO, 3 JST, 4 Keio U)
P100 Prediction of Protein Interaction Sites and Protein-Protein Interaction Pairs Using Support Vector Machines, Asako Koike1,2 , Toshihisa Takagi1 (1 U Tokyo, 2 Hitachi Ltd)P101 Support Vector Machines for Predicting Protein-Protein Interactions, Shinsuke Dohkan1,2 , Asako Koike1,2 ,Toshihisa Takagi1 (1 U Tokyo, 2 Hitachi Ltd)P102 Inferring Strengths of Protein-Protein Interactions Using Linear Programming, Morihiro Hayashida,
Nobuhisa Ueda, Tatsuya Akutsu (Kyoto U)
P103 Prediction of Residues in Protein-RNA Interaction Sites by Neural Networks, Euna Jeong, I-Fang Chung,
Satoru Miyano (U Tokyo)
P104 Positive Charge Cores in DNA-Binding Proteins, Kimiko Horibe1 , Shigeki Mitaku2 (1 Tokyo U Agri&Tech,
2
Nagoya U)
P105 Structure-Thermodynamic Relationship in Protein-DNA Binding: Heat Capacity Changes, Hatsuho
Uedaira1 , Hidetoshi Kono2 , Prabakaran Ponraj3 , Koji Kitajima4 , Akinori Sarai4 (1 AIST, 2 JAERI, 3 NCI,
4
Kyushu Inst Tech)
P106 Prediction of Interfaces for GPCR Oligomer, Wataru Nemoto1 ,2 , Hiroyuki Toh2 (1 NAIST, 2 Kyoto U)
P107 Predict Functionally Important Residues Responsible for Estrogen Receptor Subtype Divergence, Feng
Wang1,2 , Hirohisa Kishino2,3 , Yasuhiko Wada1,2 (1 Saga U, 2 JST, 3 U Tokyo)
P108 Protein Classiﬁcation via Kernel Matrix Completion, Taishin Kin1 , Tsuyoshi Kato1 , Koji Tsuda1 ,2 ,Kiyoshi Asai1,3 (1 AIST, 2 MPI Biol Cybernetics, 3 U Tokyo)
P109 On Improving Protein Functional Identiﬁcation in Pattern Recognition Based on Continuous Density
HMM, Dooil Kim, Dae-Sil Lee (KRIBB)
P110 Protein Family Classiﬁcation Using Second-Order Recurrent Neural Networks, Jinmiao Chen, Narendra
S. Chaudhari (Nanyang Tech U)
P111 Proﬁle-Proﬁle Comparison Based on Hidden Markov Model Proﬁles, Makihiko Sato1 ,2 , Nobuyoshi Sugaya2 ,Hiroo Murakami2 , Sachiyo Aburatani2 , Katsuhisa Horimoto2 (1 Fujitsu Ltd, 2 U Tokyo)
P112 Genome Scale Classiﬁcation of Extended Proteins by a Predictor SOSUIdumbbell, Nobuyuki Uchikoga1 ,Ke Rungcong1 , 2 , Fumitsugu Akazawa1 , Masashi Sonoyama1 , Shigeki Mitaku1,2 (1 Nagoya U, 2 Tokyo U
Agri&Tech)

11

P113 A New Method for Characterizing Functionally-Unknown Proteins Using Speciﬁc Amino Acid Frequency
and Periodicity at the Proteome Level, Kosuke Fujishima, Jun Imoto, Akio Kanai, Masaru Tomita (KeioU)
P114 Classiﬁcation of Protein Sequences into Paralog and Ortholog Clusters Using Sequence Similarity Proﬁles of KEGG/SSDB, Yohsuke Minowa1 , Toshiaki Katayama2 , Akihiro Nakaya2 , Susumu Goto1 , Minoru
Kanehisa1 (1 Kyoto U, 2 U Tokyo)
P115 Detection of Remote Homologue Using Predicted Structural Information, Daisuke Ishibe1 , Katsunori Uehara1 , Takeshi Kawabata1 , Nobuhiro Go1,2 (1 NAIST, 2 JAERI)
P116 RiceBLAST: A Comprehensive Homology Search for Rice Speciﬁc Sequences, Yoshiaki Nagamura1 , Baltazar A. Antonio1 , Hisataka Numa1 , Ikuo Horiuchi2 , Manabu Akimoto2 , Shigehiro Honda2 , Koichi Sugioka2 , Nana Matoba2 , Yuji Shimizu2 , Katsuaki Watanabe2 , Takuji Sasaki1 , Kenichi Higo1 (1 NIAS,
2
Mitsubishi Space Soft Co. Ltd)P117 Scalable BLAST Service in OBIGrid Environment, Fumikazu Konishi1 , Yukimasa Shiroto2 , Ryo Umetsu1 ,Akihiko Konagaya1 (1 RIKEN, 2 NEC Informatec Systems Ltd)P118 Protein-Ligand Interactions: ProLINT Database and QSAR Analysis, Shandar Ahmad1 , Kouji Kitajima1 ,Samuel Selvaraj1 ,2 , Hideo Kubodera3 , Shinji Sunada4 , Jianghong An5 , Akinori Sarai1 (1 Kyushu Inst Tech,
2
Bharathidasan U, 3 ZoeGene Corp, 4 Mitsubishi Pharma Co, 5 Scripps Res Inst)
P119 In Silico Prediction of Peroxisomal Proteins in Mouse, Igor V. Kurochkin, Christian Schönbach, Akihiko
Konagaya (RIKEN)
P120 A Proteomic Approach to Engineer Improved Cell Growth and Increased Production of Serine-Rich Proteins in Escherichia coli, Mee-Jung Han1 , Jong-Shin Yoo2 , Sang Yup Lee1 (1 KAIST, 2 KBSI)P121 Genome-Wide Functional Classiﬁcation/Identiﬁcation of Prokaryotic Transmembrane Proteins Based on
Transmembrane Topology Similarity, Masafumi Arai1,2 , Kosuke Okumura1 , Masanobu Satake2 , Toshio
Shimizu1 (1 Hirosaki U, 2 Tohoku U)
P122 Transmembrane Protein Evolution by Internal Gene Duplication, Hironori Mitsuke1 , Keisuke Noto1 , Masafumi Arai1,2 , Toshio Shimizu1 (1 Hirosaki U, 2 Tohoku U)
P123 Comprehensive Functional Identiﬁcation of Transmembrane Proteins Using the BTP Method, Yasuhito
Inoue, Toshio Shimizu (Hirosaki U)
P124 Inner Residues in the Transmembrane Helix Bundle are More Conservative, Sukenobu Konishi1 , Takuhiro
Nishio2 , Toshio Shimizu1 (1 Hirosaki U, 2 Hamamatsu U Sch Med)
P125 The Clusters of Transmembrane Protein Genes in Prokaryotic Genomes, Ichitaro Oya, Satoshi Mizuta,
Toshio Shimizu (Hirosaki U)
P126 A Consensus Transmembrane Topology Prediction Method of High-Reliability, Jun-Xiong Xia, Toshio
Shimizu (Hirosaki U)
P127 Bioinformatics Studies on Transmembrane Strand Proteins, M. Michael Gromiha1 , Shandar Ahmad2 ,Makiko Suwa1 (1 AIST, 2 Kyushu Inst Tech)
P128 On the Accuracy of Transmembrane Segment Prediction of Helical Integral Membrane Proteins, Shin
Tanimoto1 , Gautam Basu2 , Takeshi Kawabata1 , Nobuhiro Go1,2 (1 NAIST, 2 JAERI)
P129 PLOC: Prediction of Subcellular Location of Proteins, Keun-Joon Park1 , Minoru Kanehisa2 , Yutaka
Akiyama1 (1 AIST, 2 Kyoto U)
P130 Gene-Distribution Patterns on Cyanobacterial Genomes, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko
Satoh, Sachiyo Aburatani, Katsuhisa Horimoto (U Tokyo)
P131 Omic Space and Totalomics, Tetsuro Toyoda, Akiyoshi Wada (RIKEN)
P132 Correlated Mutation Analysis of C2H2 Zinc Finger Domains, Takafumi Nagano1 , Makiko Suwa2 , Kiyoshi
Asai2 (1 Mitsubishi Electric Corp, 2 AIST)P133 Analysis of Horizontal Gene Transfer and Clustering of Microbial ORFs by Use of a GRID Environment,
Hideaki Sugawara1 , Yoji Nakamura1 , Kazuho Ikeo1 , Satoru Miyazaki1 , Takashi Gojobori1 , Kenji Satou2 ,Akihiko Konagaya3 (1 NIG, 2 JAIST, 3 RIKEN)
P134 Real-Time Mapping System of cDNAs and Genomes Using Grid Computing, Yusuke Saito1 , Manabu
Gomi1 , Hideo Matsuda2 , Naohisa Goto2 , Ken Kurokawa2 , Teruo Yasunaga2 (1 Hewlett-Packard Japan
Ltd, 2 Osaka U)
P135 Space-Gene : Microbial Gene Prediction System Based on Linux Clustering, Jong-won Chang1 , Chungoo
Park1 , Dong Soo Jung1 , Mi-hwa Kim2 , Jae-woo Kim2 , Seung-sik Yoo2 , Hong Gil Nam1 (1 POSTECH,
2POSDATA)
P136 Pedigree Analysis Programme GTree 1.2 and Its Application, Daisuke Ogino1 , Shiro Mori1 , Masato Nose2 ,Hideki Sawada3 (1 Tohoku U, 2 Ehime U, 3 Yamagata U)

12

P137 Self-Organizing Clustering: A Novel Non-Hierarchical Method for Clustering Large Amount of DNA Sequences, Kou Amano1,2 , Hidemitsu Nakamura2 , Hiroaki Ichikawa2 (1 U Lib&Info Sci, 2 NIAS)
P138 PFcDNA: Prediction of a Full Length Gene from Partial Sequence, SooYoung Cho1 , Myungguen Chung1 ,3 ,Seung-baek Han2 , Hyun Kim2 , YoungSeek Lee1 (1 Han-yang U, 2 Korea U, 3 ETRI)
P139 Statistical Signiﬁcance of Tree Similarity Scores, Kiyoko F. Aoki, Atsuko Yamaguchi, Yasushi Okuno,
Tatsuya Akutsu, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka (Kyoto U)
P140 Systematic Analyses of P-Loop Containing Nucleotide Triphosphate Hydrolase Superfamily Based on Sequence, Structure and Function, Yoichi Kawamura1 , Kiyoshi Asai1,2,3 , Shin Ishii1 , Nozomi Nagano3 ,4(1 NAIST, 2 U Tokyo, 3 AIST, 4 JST)P141 TTOP : A System for Phylogenetic Tree Editing and Evolutionary Annotation of Genes, Srinesh Kundu1 ,2 ,Masato Hagiwara1,2 , Kanako O. Koyanagi3 , Tadashi Imanishi1 , Takeshi Itoh1 (1 AIST, 2 AxioHelix Co Ltd,
3
NAIST)
P142 Gclust: Genome-Wide Clustering of Protein Sequences for Identiﬁcation of Photosynthesis-Related Genes
Resulting from Massive Horizontal Gene Transfer, Naoki Sato (Saitama U)
P143 Comparative Genomics between Drosophila and Human, Masuko Katoh1 , Masaru Katoh2 (1 M & M Med
BioInfo, 2 NCC)
P144 Novel Types of Two-Domain Multi-Copper Oxidases: Possible Missing Links in the Evolution, Kensuke
Nakamura1 , Takeshi Kawabata1 , Kei Yura2 , Nobuhiro Go1,2 (1 NAIST, 2 JAERI)
P145 SNPAnalyzer: Web-Based Workbench for the SNPs Analysis, Jihho Yoo1 , Bonghee Seo1 , Yangseok Kim1,2(1 ISTECH Inc, 2 Yonsei U)
P146 Artiﬁcial Neural Network Model for Prediction of Childhood Allergic Asthma Using Single Nucleotide Polymorphism Data, Yasuyuki Tomita1 , Shuta Tomida1 , Yoichi Suzuki2 , Taro Shirakawa3 , Takeshi Kobayashi1 ,Hiroyuki Honda1 (1 Nagoya U, 2 Tohoku U, 3 Kyoto U)
P147 NAMIHEI: A Novel Algorithm for Genomic Polymorphism Detection from DNA Sequence, Go Maeno2∗ ,Tomohiro Isobe1 ∗ , Yuko Tokoro1 , Yuki Ejiri1 , Nobutaka Mitsuhashi1 , Tokuki Sakiyama2 , Ken Aoshima1(1 Mitsui Knowledge Industry Co Ltd, 2 NCC)
P148 Drug Screening of GPCR Using Active Learning, Yukiko Fujiwara1 , Yoshiko Yamashita1 , Tsutomu Osoda1 ,Minoru Asogawa1 , Shun Doi1 , Masaaki Asao2 , Emi Kushiyama2 , Kazuya Nakao2 , Masataka Kuroda2 ,Kazuteru Wada2 , Takanori Ogaru2 , Chiaki Fukushima2 , Ryo Shimizu2 (1 NEC Corp, 2 Tanabe Seiyaku Co
LTD)
P149 An Integrated Database of Interaction between Human Proteins and Commonly Used Drugs, Masashi
Nemoto, Kenji Araki, Ken Horiuchi, Motoi Tobita, Tetsuo Nishikawa (REPRORI)
P150 Common Features in Substrates of Multidrug Resistance Transporters, Yoshinobu Igarashi, Yasushi Okuno,
Masahiro Hattori, Susumu Goto, Minoru Kanehisa (Kyoto U)
P151 Computational Models of Calcium Signaling in the Pancreas - Temporal and Spatial Regulations, Kojiro
Yano, Ole H. Petersen, Alexei V. Tepikin (U Liverpool)
P152 Model Analysis of Helper T Cell Diﬀerentiation, Satoshi Yamada1 , Akihiko Yoshimura2 (1 Mitsubishi Electric Corp, 2 Kyushu U)
P153 Kinetics Behavior of G1-to-S Cell Cycle Phase Transition Model, Yoshihiko Tashima, Taizo Hanai, Hiroyuki Hamada, Masahiro Okamoto (Kyushu U)
P154 CADLIVE-Based Analysis for the Budding Yeast Cell Cycle, Natsumi Shimizu, Shunsuke Yamamichi,
Hiroyuki Kurata (Kyushu Inst Tech)
P155 Deterministic and Stochastic Models Analyze the Robustness of Circadian Rhythms, Yoshiyuki Sumida,
Fumitaka Ohnishi, Hiroyuki Kurata (Kyushu Inst Tech)
P156 Integration of Postgenomic Data for GMA to Simulate a Metabolic Circuit, Takayuki Tanaka, Hiroyuki
Kurata (Kyusyu Inst Tech)
P157 Xenopus Cell Cycle Pathway for Simulating Cell Division Processes by Genomic Object Net, Mika Matsui1,2 , Sachie Fujita1 , Shun-ichi Suzuki1 , Hiroshi Matsuno1 , Satoru Miyano3 (1 Yamaguchi U 2 Oshima
Nat’l Col Maritime Tech 3 U Tokyo)
P158 Simulation of Drosophila Boundary Cell Formation in Forced-Expression of Notch∆E , Rie Yamane1 , Junko
Umezaki1 , Hiroshi Matsuno1 , Ryutaro Murakami1 , Naoyuki Yamasaki1 , Satoru Miyano2 (1 Yamaguchi U,
2
U Tokyo)P159 Distributed Client-Server System Architecture for High Performance Simulations on Genomic Object Net,
Tomokazu Kono1 , Ryuhei Noda1 , Hironori Kitakaze1 , Masao Nagasaki3 , Atsushi Doi2 , Hiroshi Matsuno2 ,Satoru Miyano3 (1 Oshima Nat’l Col Maritime Tech, 2 Yamaguchi U, 3 U Tokyo)

13

P160 OBIYagns: A Biochemical Simulator in Grid Environment, Shuhei Kimura1 , Takuji Kawasaki2 , Mariko
Hatakeyama1 , Takashi Naka3 , Fumikazu Konishi1 , Akihiko Konagaya1 (1 RIKEN, 2 Fuji Res Inst Corp,
3
Kyushu Sangyo U)
P161 Computer Simulation System for Modeling of Reaction-Diﬀusion of Biochemical Pathways, Ryuzo Azuma,
Yoshiki Yamaguchi, Tetsuji Kitagawa, Akihiko Konagaya (RIKEN)
P162 Parallelized Simulation of Molecular Dynamics with a Special-Purpose Computer: MDGRAPE-2, Naoki
Takada1 , Noriyuki Futatsugi1 , Atsushi Suenaga1 , Tetsu Narumi1 , Noriaki Okimoto1 , Hidenori Hirano1 ,Atsushi Kawai2 , Kenji Yasuoka3 , Toshikazu Ebisuzaki1 , Makoto Taiji1 , Akihiko Konagaya1 (1 RIKEN,
2
Saitama Inst Tech, 3 Keio U)
P163 Quantifying the Spiral Leaf Trait of Arabidopsis from the 3D Shape Model Towards Computational Phenomics, Eli Kaminuma, Naohiko Heida, Yuko Tsumoto, Minami Matsui, Tetsuro Toyoda, Akihiko Konagaya (RIKEN)
P164 BioRuby: Open-Source Bioinformatics Library, Naohisa Goto1 , Mitsuteru C. Nakao2 , Shiuichi
Kawashima3 , Toshiaki Katayama2 , Minoru Kanehisa3 (1 Osaka U, 2 U Tokyo, 3 Kyoto U)
P165 G-Language Genome Analysis Environment Version 2, Hayataro Kouchi, Kazuharu Arakawa, Ryo Hattori,
Yohei Yamada, Yusuke Kobayashi, Atsuko Kishi, Kosaku Shinoda, Masaru Tomita (Keio U)
P166 Development of Bacteria Analysis System v.2 on the G-Language Genome Analysis Environment, Daisuke
Kyuma, Kazuharu Arakawa, Koya Mori, Masaru Tomita (Keio U)
P167 Microarray Visualization System on the G-Language GAE, Yohei Yamada1 , Kazuharu Arakawa1 , Hirotada
Mori1,2 , Masaru Tomita1 (1 Keio U, 2 NAIST)P168 Prediction of Biochemical Reactions Using Genetic Programming, Masahiro Sugimoto1,2 , Shinichi
Kikuchi1 , Masaru Tomita1 (1 Keio U, 2 Mitsubishi Space Soft Co Ltd)P169 Automatic Generation of Cell-Wide Pathway Model from Complete Genome, Kazuharu Arakawa, Yohei
Yamada, Hiromi Komai, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita (Keio U)
P170 SIMDEB-ECS : E-CELL Static Model Debugger, Naota Ishikawa, Iriko Kaneko, Toshikazu Ebisuzaki(Riken)P171 In Silico Simulation Represents Adenoviral Gene Knockdown of Myocardial Ventricular Cell, Yasuhiro
Naito1 , Motohiro Yoneda1 , Sayaka Ishinabe1 , Shoko Miyamoto1 , Nobuaki Sarai2 , Satoshi Matsuoka2 , Akinori Noma2 , Masaru Tomita1 (1 Keio U 2 Kyoto U)
P172 Model Construction of the Energy Metabolism Pathway in Myocardial Cell, Motohiro Yoneda1 , Shoko
Miyamoto1 , Yasuhiro Naito1 , Sayaka Ishinabe1 , Nobuaki Sarai2 , Satoshi Matsuoka2 , Akinori Noma2 ,Masaru Tomita1 (1 Keio U, 2 Kyoto U)
P173 FAMSBASE: Modeling Database of 161 Genomes, Mitsuo Iwadate, Kazuhiko Kanou, Daisuke Takaya,
Katsuichiro Komatsu, Mayuko Takeda-Shitaka, Hideaki Umeyama (Kitasato U)
P174 GLYCAN: The Database of Carbohydrate Structures, Kosuke Hashimoto1 , Masami Hamajima1 , Susumu
Goto1 , Shigekazu Masumoto2 , Masayuki Kawasima2 , Minoru Kanehisa1 (1 Kyoto U, 2 Fujitsu Kyushu System Eng)P175 HAPPY: Hypothetical and Putative Protein Database System, Takuya Murakami, Masatomo Najima,
Michihiro Ogawa, Ken Kurokawa, Teruo Yasunaga (Osaka U)
P176 The Construction of a Database for Ubiquitin Signaling Cascade, Tadahiko Sakiyama, Shuichi Kawashima,
Akiyasu C. Yoshizawa, Minoru Kanehisa (Kyoto U)
P177 Development of HocDB (Homology-Based Clustering DataBase), a Sequence Classiﬁcation System for
Database Searching, Motokazu Ishikawa1 , Yoshinori Sato1 , Hiroyuki Toh2 (1 Mitsubishi Space Soft Co
Ltd, 2 Kyoto U)
P178 Development of Community Annotation Databases for Linking Genomes to Cellular Functions, Miho Furumichi1 , Yoko Sato2 , Toshiaki Katayama3 , Shuichi Kawashima1 , Minoru Kanehisa1 (1 Kyoto U, 2 Fujitsu
Kyushu System Eng, 3 U Tokyo)
P179 Gene List of Sphingomonas chungbukensis DJ77, Kwon Hae-Ryong, Hyun-Ju Um, Jeong-Su Oh, Wan-Sup
Cho, Young-Chang Kim (Chungbuk Nat’l U)
P180 Current Status of Rice Annotation Database (RAD), Yuichi Ito1 , Isamu Ohta1 , Yoshiyuki Mukai1 , Baltazar A. Antonio1 , Michie Shibata1 , Mayu Yamamoto1 , Yukiyo Ito1 , Katsumi Sakata2 , Nobukazu Namiki1 ,Takashi Matsumoto1 , Takuji Sasaki1 (1 NIAS, 2 Mitsubishi Space Soft Co Ltd)
P181 Improvements in ProMode (a Database of Normal Mode Analyses of Proteins), Hiroshi Wako1 , Masaki
Kato2 , Shigeru Endo3 (1 Waseda U, 2 Yokohama City U, 3 Kitasato U)
P182 Current Status of ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions, M.D. Shaji
Kumar1 , Ponraj Prabakaran2 , M. Michael Gromiha3 , Hatsuho Uedaira1 , Kouji Kitajima1 , Akinori Sarai1(1 Kyushu Inst Tech, 2 NCI, 3 AIST)

14

P183 Latest Developments in ProTherm: Thermodynamic Database for Proteins and Mutants, K. Abdulla
Bava1 , M. Michael Gromiha2 , Hatsuho Uedaira2 , Koji Kitajima1 , Akinori Sarai1 (1 Kyushu Inst Tech,
2
AIST)P184 Enhancement of the SOAP Server in DDBJ Web Services to Process Tsunami of Biological Data, Yasumasa
Shigemoto1 , Masahito Yamaguchi1 , Satoru Miyazaki2 , Hideaki Sugawara2 (1 Fujitsu Ltd, 2 NIG)
P185 A Prototype of PubMed Central Japan, Hideaki Sugawara1 , Takashi Gojobori1 , Takeshi Konno2 , Yasumasa
Shigemoto2 , Masahito Yamaguchi2 (1 NIG, 2 Fujitsu Ltd)P186 KEGG API: A Web Service Using SOAP/WSDL to Access the KEGG System, Shuichi Kawashima1 ,Toshiaki Katayama2 , Yoko Sato3 , Minoru Kanehisa1 (1 Kyoto U, 2 U Tokyo, 3 Fujitsu Kyushu System Eng)P187 GOODIES: GO Based Data Mining Tool for Characteristic Attribute Interpretation on a Group of Biological Entities, Sung Geun Lee1 , Wan Seon Lee1 , Yang Seok Kim1,2 (1 ISTECH Inc, 2 Yonsei U)
P188 Open Ontology Forge: A Tool for Ontology Creation and Text Annotation Applied to the Biomedical
Domain, Ai Kawazoe, Tony Mullen, Koichi Takeuchi, Tuangthong Wattarujeekrit, Nigel Collier (NII)P189 INOH: A Textual Knowledge Based Pathway Database, Satoko Yamamoto1 , Tatsuya Kushida1 , Naotaka
Ono1 , Yuki Yamagata1 , Toshihisa Takagi2 , Ken-ichiro Fukuda3 (1 JST, 2 U Tokyo, 3 AIST)
P190 UniPath: A Knowledge Representation System for Biological Pathways, Min Su Lee, Seung Soo Park,
Hyun Seok Park (Ewha Womans U)
P191 Extraction of Biological Contexts and Ontological DAG Structures from Gene Groups Using GO Term
Distribution, Sung Geun Lee1 , Jae Seong Yang2 , Wan Seon Lee1 , Miyoung Shin3 , Yang Seok Kim1,4(1 ISTECH Inc, 2 POSTECH, 3 ETRI, 4 Yonsei U)
P192 Ontology Using Role Concept Recognized on Biological Relationships and Its Application, Masaru Takeya,
Hisataka Numa, Koji Doi (NIAS)
P193 Prediction of MHC Class I Binding Peptides Using an Ensemble Learning Approach, Nicolas Majeux1 ,Keiko Udaka2 , Hiroshi Mamitsuka1 (1 Kyoto U, 2 Kochi Med Sch)P194 Development of Construction and Management Tools for Biological Named Entity Dictionary, Hyunchul
Jang, Taehyun Kim, Hyunsook Lee, Soojun Park, Seonhee Park (ETRI)
P195 Language Resource and Rule Construction for Biological Named Entity System Using UMLS, Hyun-Sook
Lee, Tae-Hyun Kim, Soo-Jun Park, Seon-Hee Park (ETRI)
P196 BIOSILICO: A Biochemical Database Retrieval System, Jin Sik Kim1 , Ji Hoon Jun2 , Yong Wook Kim2 ,Sujin Chae2 , Mira Roh2 , Yong Ho In2 , Sang Yup Lee1 (1 KAIST, 2 Bioinformatix Inc)
P197 Development of Lossless Compression Techniques for Biology Information and Its Application for Bioinformatics Database Retrieval, Toshio Modegi (Dai Nippon Printing Co Ltd)P198 An Algorithm to Identify Abbreviations from MEDLINE, Hiroko Ao1,2 , Toshihisa Takagi1 (1 U Tokyo,
2
Kanebo, LTD)
P199 Extracting Information on Protein-Protein Interactions from Biological Literature Based on Machine
Learning Approaches, Kazunari Sugiyama1 , Kenji Hatano1 , Masatoshi Yoshikawa2 , Shunsuke Uemura1(1 NAIST, 2 Nagoya U)
P200 Evaluation System for Information Retrieval in Biomedical Field, Yasunori Yamamoto, Toshihisa Takagi(U Tokyo)P201 Disease-Associated Genes Extraction from Literature Database, Takayuki Takahata1 , Yasuhiro Kouchi1 ,Kaoru Asano1 , Toshihisa Takagi2 (1 Sysmex Corp, 2 U Tokyo)

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