GIW 2004
The Fifteenth International Conference on Genome Informatics
Pacifico Yokohama, Japan
December 13–15, 2004
Registration
Registration should be done at: http://giw.ims.u-tokyo.ac.jp/giw2004/registration.html until November 30, 2004. Registration fee includes a copy of Genome Informatics Vol. 15, No. 2 andcoﬀee breaks. We oﬀer registration fee discount for JSBi and ISCB members.
until Nov. 30, 2004 after Nov. 30, 2004
Standard
JPY12,000.JPY15,000.Standard
ISCB Member
JPY11,000.JPY14,000.Registration JSBi Member
JPY8,000.JPY11,000.JSBi & ISCB Member
JPY7,000.JPY10,000.Standard
JPY8,000.JPY11,000.Student
ISCB Member
JPY7,000.JPY10,000.Registration JSBi Member
JPY5,000.JPY8,000.JSBi & ISCB Member
JPY4,000.JPY7,000.(Banquet on December 14 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/giw2004/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

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GIW 2004 Advanced Program
Registration
December 13, 2004: 08:30 - 18:00
December 14, 2004: 08:30 - 18:00
December 15, 2004: 08:30 - 15:00

Monday, December 13, 2004
Opening Address
09:00 - 09:10

Tatsuya Akutsu (Kyoto U.) and Vladimir Brusic (Inst. Infocomm Res.)

Paper Session 1
09:10 - 09:35

Chair: Limsoon Wong (Inst. Infocomm Res.)
Architecture of a Grid-Enabled Research Platform with LocationTransparency for Bioinformatics, Yoshiyuki Kido1 , Susumu Date2 , Shingo
Takeda2 , Shoji Hatano3 , Juncai Ma3 , Shinji Shimojo2 , Hideo Matsuda2(1 Mitsui Knowledge Industry Co., Ltd., 2 Osaka U., 3 IMCAS)

09:35 - 10:00

Splicing Proﬁle Based Protein Categorization between Human and Mouse
Genomes by Use of the DDBJ Web Services, Åke Västermark1,2 , Yasumasa
Shigemoto3 , Takashi Abe1 , Hideaki Sugawara1 (1 NIG, 2 U. Oxford, 3 FujitsuLtd.)

10:00 - 10:25

Computational Methods for the Analysis of Diﬀerential Conservation inGroups of Similar DNA Sequences, Nikola Stojanovic (U. Texas)

10:25 - 10:50

Comprehensive Identiﬁcation of “Druggable” Protein Ligand Binding Sites,
Jianghong An1 , Maxim Totrov2 , Ruben Abagyan1 (1 The Scripps Res. Inst.,
2 Molsoft, LLC)

10:50: - 11:10

Break

Keynote Address
11:10 - 12:10
12:10 - 13:30

Chair: Vladimir Brusic (Inst. Infocomm Res.)The Immune Epitope Database and Analysis Resource: From Vision toBlueprint, Alessandro Sette (La Jolla Institute for Allergy and Immunology)
Lunch

Posters and Software Demonstrations Session 1
13:30 - 14:30
Paper Session 2
14:30 - 14:55

Chair: Yixue Li (Shanghai Inst. Biol. Sci.)
General-Purpose Search Techniques for Genomic Text, Abhijit Chattaraj,
Hugh E. Williams, Adam Cannane (RMIT U.)

14:55 - 15:20

Graphical Approach to Weak Motif Recognition, Xiao Yang, Jagath C.
Rajapakse (Nanyang Tech. U.)

15:20 - 15:45

An Extension and Novel Solution to the (l,d)–Motif Challenge Problem, Mark P Styczynski1 , Kyle L Jensen1 , Isidore Rigoutsos2 , Gregory N
Stephanopoulos1 (1 MIT, 2 IBM, USA),

15:45 - 16:10

Domain Discovery Method for Topological Proﬁle Searches in Protein
Structures, Juris Viksna1,2 , David Gilbert2 , Gilleain Torrance2 (1 U. Latvia,
2 U. Glasgow)

16:10: - 16:30

Break

Paper Session 3
16:30 - 16:55

Chair: Christian Schönbach (RIKEN)
A Novel Graph-Based Similarity Measure for 2D Chemical Structures, Si
Quang Le1 , Tu Bao Ho1 , T.T Hang Phan2 (1 JAIST, 2 Ube Nat. Coll. Tech.)

16:55 - 17:20

IRIS: Intermolecular RNA Interaction Search, Dmitri D. Pervouchine1,2(1 Boston U., 2 Moscow State U.)3

17:20 - 17:45

StructMiner: A Tool for Alignment and Detection of Conserved Secondary
Structure, Qian Yang, Mathieu Blanchette (McGill U.)

17:45 - 18:10

RNA 3D Structure Prediction: (1) Assessing RNA 3D Structure Similarity from 2D Structure Similarity, Jaime E. Barreda DC1 , Yoshimitsu
Shigenobu2 , Eiichiro Ichiishi3 , Carlos A. Del Carpio M.1,3 (1 The Cath. U.
Santa Maria, 2 Toyohashi U. Tech., 3 Tohoku U.)

Tuesday, December 14, 2004
Paper Session 4
09:00 - 09:25

Chair: Tetsuo Shibuya (U. Tokyo)
Inference of Gene Regulatory Networks by Means of Dynamic Diﬀerential Bayesian Networks and Nonparametric Regression, Naoya Sugimoto,
Hitoshi Iba (U. Tokyo)

09:25 - 09:50

Recovering Genetic Regulatory Networks from Micro-Array Data and Location Analysis Data, Fan Li, Yiming Yang (Carnegie Mellon U.)

09:50 - 10:15

Increasing Feasibility of Optimal Gene Network Estimation, Annika
Hansen, Sascha Ott, Georgy Koentges (U. London)

10:15 - 10:35

Break

Paper Session 5
10:35 - 11:00

Chair: Sang Yup Lee (KAIST)A Method for Clustering Gene Expression Data Based on Graph Structure, Shigeto Seno1 , Reiji Teramoto2 , Yoichi Takenaka1 , Hideo Matsuda1(1 Osaka U., 2 Sumitomo Pharmaceuticals Co., Ltd.)

11:00 - 11:25

Statistical and Integrative Approach for Constructing Biological Network
Maps, Hiroyuki Kurata, Natsumi Shimizu, Kanako Misumi (Kyushu Inst.
Tech.)

11:25 - 11:50

PreSPI: Design and Implementation of Protein-Protein Interaction Prediction Service System, Dong-Soo Han1 , Hong-Soog Kim1 , Woo-Hyuk Jang1 ,Sung-Doke Lee1 , Jung Keun Suh2 (1 Info. Comm. U., 2 LG Life Sci. R&D)

11:50 - 13:30

Lunch

Keynote Address
13:30 - 14:30
Paper Session 6
14:30 - 14:55

Chair: Satoru Miyano (U. Tokyo)
Revealing the Structure and Dynamics of Cis-Regulation Using Heterogeneous, Genome-Wide, Multi-Species Data, Ron Shamir (Tel Aviv U.)
Chair: Hiroshi Mamitsuka (Kyoto U.)
Predicting Protein Secondary Structure by a Support Vector Machine
Based on a New Coding Scheme, Long-Hui Wang, Juan Liu, Yan-Fu Li,
Huai-Bei Zhou (Wuhan U.)

14:55 - 15:20

Support Vector Machines with Proﬁle-Based Kernels for Remote Protein
Homology Detection, Steven Busuttil1 , John Abela2 , Gordon J. Pace2 (1 U.
London, 2 U. Malta)

15:20 - 15:45

Kernel Mixture Survival Models for Identifying Cancer Subtypes, Predicting Patient’s Cancer Types and Survival Probabilities, Tomohiro Ando,
Seiya Imoto, Satoru Miyano (U. Tokyo)

JSBi Annual Meeting
16:00 - 16:30
Posters and Software Demonstrations Session 2
16:30 - 18:00
Banquet18:30 - 21:00
4

Wednesday, December 15, 2004
Paper Session 7
09:00 - 09:25

Chair: Kenji Satou (JAIST)
Computational Prediction of Operons in Synechococcus sp. WH8102, Xin
Chen1 , Zhengchang Su2 , Ying Xu2 , Tao Jiang1 (1 UCR, 2 UGA)

09:25 - 09:50

Intercellular Communications Induced by Random Fluctuations, Tianshou
Zhou1 , Luonan Chen2 , Ruiqi Wang2 , Kazuyuki Aihara3 (1 Tsinghua U.,
2 Osaka Sangyo U., 3 U. Tokyo)

09:50 - 10:15

Knowledge Representation Model for Systems-Level Analysis of Signal Transduction Networks, Dong-Yup Lee1 , Ralf Zimmer2 , Sang-Yup
Lee1 , Daniel Hanisch3 , Sunwon Park1 (1 KAIST, 2 Ludwig-MaximiliansUniversität München, 3 SCAI, Germany)

10:15 - 10:40

Consistent Re-Modeling of Signaling Pathways and Its Implementationin the TRANSPATH Database, Claudia Choi1 , Torsten Crass2 , Alexander Kel1 , Olga Kel-Margoulis1 , Mathias Krull1 , Susanne Pistor1 , Anatolij
Potapov1,2 , Nico Voss1 , Edgar Wingender1,2 (1 BIOBASE, 2 U. Göttingen)

10:40 - 11:05

Ontological Integration of Data Models for Cell Signaling Pathways byDeﬁning a Factor of Causality Called ‘Signal’, Takako Takai-Igarashi1 , Riichiro Mizoguchi2 (1 U. Tokyo, 2 Osaka U.)

Posters and Software Demonstrations Session 3
11:05 - 12:15
12:15 - 13:30
Lunch
Keynote Address
13:30 - 14:30
14:30 - 14:50

Chair: Tatsuya Akutsu (Kyoto U.)
Orthologous Sets of Functional Networks: Inference, Mining
and Visualization, Charles DeLisi (Boston U.)
BreakPaper Session 8
14:50 - 15:15

Chair: Kenta Nakai (U. Tokyo)
Using Protein Motif Combinations to Update KEGG Pathway Maps andOrthologue Tables, Frédéric Nikitin1,4 , Bastien Rance2 , Masumi Itoh3 , Minoru Kanehisa3 , Frédérique Lisacek1,4,5 (1 Geneva Bioinfo., 2 U. Paris XI,
3 U. Kyoto, 4 Swiss Inst. Bioinfo., 5 Génome & Informatique)

15:15 - 15:40

Systematic DNA-Binding Domain Classiﬁcation of Transcription Factors,
Philip Stegmaier1 , Alexander E. Kel1 , Edgar Wingender1,2 (1 BIOBASE,
2 U. Göttingen)

15:40 - 16:05

Mining Yeast Transcriptional Regulatory Modules from Factor DNABinding Sites and Gene Expression Data, Tho Hoan Pham1 , Kenji Satou1,2 ,Tu Bao Ho1 (1 JAIST, 2 JST)

Closing and Award Ceremony
16:05 - 16:20

Commercial Exhibitions
C1:
C2:
C3:
C4:
C5:

SILICON GENETICS / Yokokawa Analytical Systems Inc.
Ryoka Systems Inc.
NABE International Corporation
INFOCOM CORPORATIONBIOBASE GmbH
5

C6:
C7:
C8:
C9:
C10:
C11:
C12:
C13:

Cybernet Systems Co., Ltd.
HITACHI, LTD.
Pathway Solutions Inc.
SGI Japan, Ltd.
Hitachi High-Technologies Corporation
Mitsui Knowledge Industry Co., Ltd.
Sun Microsystems K.K.
Mathematical Systems, Inc.

Software Demonstrations
S01 MPSS: an integrated database system for surveying multitudinous proteins, Pei Hao, Weizhong He, Yi-Xue Li
S02 ASIAN on Personal Computer, Shigeru Saito, Kousuke Goto, Sachiyo Aburatani, Katsuhisa Horimoto
S03 Reﬂection of Knowledge Information in ProMode (A Database of Normal Mode Analyses on
Proteins), Hiroshi Wako, Motohiro Otsuka, Yuhki Tomizawa, Masaki Kato, Shigeru Endo
S04 M y GPS client A Genome Browser Integrating Client-side Private Data and Server-side Largescale Public Annotations, Katsura Hirosawa, Atsushi Moroda, Yoshikazu Hasegawa, Naohiko Heida, Yoshiki Mochizuki, Tetsuro Toyoda
S05 CADLIVE: New Modules for Domain Expansions and Topological Analysis, Hiroyuki Kurata,
Yuki Shimokawa, Tomoko Noguchi, Natsumi Shimizu
S06 Visualization and Cluster Analysis using Spherical SOM, Daisuke Nakatsuka, Heizo Tokutaka
S07 MutationView: Addition of an enhanced search system for the clinical description in the OMIM
based on a new algorithm, Masafumi Ohtsubo, Katsue Daicho, Kouichi Kawaguchi, Susumu Mitsuyama, Takashi Kawamura, Tomoyoshi Horisawa, Nobuyoshi Shimizu, Shinsei Minoshima
S08 Studying the molecular evolution of the SARS-coronavirus on the the DiscoveryNet Environment, Pei Hao, Yuan-Yuan Li, Wei-zhong He, Yi-Xue Li, Vasa Curcin, Moustafa Ghanem,
Yike Guo
S09 GEDA-C: Gene Expression Data Analysis - Clustering based-on seed method, Ho-Youl Jung,
Miyoung Shin, Seon-Hee Park
S10 Care-free Metabolic Map Editor - From Pathways to Maps -, Masanori Arita
S11 Bioinformatics Recipes with BioRuby, Mitsuteru Nakao, Naohisa Goto, Toshiaki Katayama
S12 “Piment” and “Macaroni”: Nervous System Protein Database, Takeshi Tomiki, Naruya Saitou
S13 HiGet: High Performance Database Entry Retrieval System, Kazutomo Ushijima, Chiharu Kawagoe, Kenta Nakai, Shuichi Kawashima, Hideo Bannai, Toshiaki Katayama
S14 Genomic Object Net 1.5: A Platform for Biopathway Modeling and Simulation, Masao Nagasaki,
Atsushi Doi, Satoru Miyano

PostersP001 Prediction of Debacle Parts for Robustness in a Cell by using Recurrent Neural Networks,
Hironori Kitakaze, Ryuhei Noda, Hiroshi Matsuno, Nobuhiko Ikeda, Satoru Miyano
P002 Modeling and Simulation of Cyanobacterial Circadian Clock Mechanism by Hybrid Functional
Petri Net, Mao Yamaji, Hideo Iwasaki, Hiroshi Matsuno, Satoru Miyano
P003 A New Regulatory Interactions Suggested by Simulations for Circadian Genetic Control Mechanism in Mammals, Yasushi Fujii, Yasuki Okitsu, Hiroshi Matsuno, Satoru Miyano, ShinIchi T. Inouye
P004 A New Petri Net Modeling Method for Signaling Pathways with a Focus on Enzyme, Chen Li,
Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano
6P005 CellDesigner2.0: A Process Diagram Editor for Gene-regulatory and Biochemical Networks,
Akira Funahashi, Naoki Tanimura, Yukiko Matsuoka, Naritosi Yosinaga, Hiroaki Kitano
P006 Optimization and System Analysis of the Heat Shock Response by CADLIVE, Kouji Mitsukiyo,
Marie Kajiwara, Hiroyuki Kurata
P007 A Large-Scale Dynamic Model of the Yeast Cell Cycle, Shunsuke Yamamichi, Hiroyuki Kurata
P008 Control Aspect of Common Interactions Extracted from Inferred Network Candidates of Gene
Expression, Masahiko Nakatsui, Takanori Ueda, Isao Ono, Masahiro Okamoto
P009 Simulation for detailed mathematical model of G1-to-S cell cycle phase transition, Yoshihiko Tashima, Taizo Hanai, Hiroyuki Hamada, Masahiro Okamoto
P010 BAAQ: A Grid-based Infrastructure for Integrating Bioinformatics Applications, Xiujun Gong,
Kei Yura, Nobuhiro Go
P011 Simulation of Circadian Rhythms Using Grid Computing, Takayuki Tanaka, Hiroyuki Kurata
P012 Development of a computer simulation system for particle-level molecular interactions,Ryuzo Azuma, Yoshiki Yamaguchi, Tetsuji Kitagawa, Tomoyuki Yamamoto, Akihiko Konagaya
P013 The Molecular Dynamics Simulation of Prion Protein, Masakazu Sekijima, Chie Motono, Tamotsu Noguchi, Tamotsu Noguchi, Kiyotoshi Kaneko, Yutaka Akiyama
P014 Symbolic-Numeric Optimization for Biological Kinetics by Quantiﬁer Elimination, Shigeo Orii,
Hirokazu Anai, Katsuhisa Horimoto
P015 Equilibrium Model of DNA Chip Hybridization Error, John A. Rose, Masami Hagiya,
Akira Suyama
P016 An Analysis Tool Library for Biochemical Modeling on E-Cell System Version 3, Kazunari Kaizu,
Fumihiko Miyoshi, Yoichi Nakayama, Masaru Tomita
P017 Development of Integrated Modeling Environment for E-Cell3 System, Gabor Bereczki,
Kouichi Takahashi, Takeshi Sakurada, Ng Yan Hong, Masaru Tomita
P018 Development of E-Cell kinetic model interoperability
Takeshi Sakurada, Tomoya Kitayama, Masaru Tomita

environment,

Tatsuya Ishida,P019 Development of Distributed Cell Simulations Middleware with E-Cell System, Masahiro Sugimoto, Kouichi Takahashi, Daniel, Muhammad Nurazhar Bin Taher, Lu Yaomin,
Novia Siswanto Be, Tracy Wong, Ng Yan Hong, Masaru Tomita
P020 Modeling Gene Networks Utilizing Evolutionary Information Using Bayesian Network Models, Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Toshiaki Katayama, Minoru Kanehisa,
Satoru Miyano
P021 Estimating Regulatory Networks from DNA Microarrays and Protein-Protein Interactions,
Naoki Nariai, Yoshinori Tamada, Seiya Imoto, Satoru Miyano
P022 Estimating Gene Networks from Expression Data and Binding Location Data via Boolean
Network, Osamu Hirose, Naoki Nariai, Yoshinori Tamada, Hideo Bannai, Seiya Imoto,
Satoru Miyano
P023 Multiscale Bootstrap Analysis of Gene Networks Based on Graphical Gaussian Modeling,
Takeshi Kamimura, Hidetoshi ShimodairaP024 Systematic Identiﬁcation of Weak Connections between Clusters in Biological Network, Hiroki Sakai, Katsuhisa Horimoto, Minoru Kanehisa
P025 Genetic Network Reconstruction in Tryptophan Metabolism from Gene Expression Proﬁles,Akira Imaizumi, Hisashi Yasueda, Sachiyo Aburatani, Katsuhisa Horimoto7

P026 Selective Integration of Multiple Genomic Data for Biological Network Inference, Tsuyoshi Kato,
Koji Tsuda, Kiyoshi Asai
P027 Eﬀective Procedures for the Estimation of Large-scale S-system Parameters, Yukihiro Maki,
Takanori Ueda, Masahiro Okamoto
P028 Correlations Between Scale-free Genetic Regulatory Model Networks and Dynamical Properties,
Chikoo Oosawa, Kazuhiro Takemoto, Genki Hanano
P029 Periodic Oscillation in Gene Networks Modelled by Cyclic Feedback Systems, Ruiqi Wang,
Luonan Chen
P030 A Gibbs Sampling Approach to Detection of Tree Motifs, Lidio Marx Carvalho Meireles, Tatsuya Akutsu
P031 QSAR Analysis with Support Vector Machines and Graph Kernels, Pierre Mahé, Nobuhisa Ueda,
Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert
P032 Stable Stochastic Dynamics in Yeast Cell Cycle , Yurie Okabe, Masaki Sasai
P033 Comparative Analysis of Conditional Regulation Across the Yeast Genomes, Koji Ota,
Susumu Goto, Minoru Kanehisa
P034 An application of multiscale bootstrap resampling to hierarchical clustering of microarray data:
How accurate are these clusters?, Ryota Suzuki, Hidetoshi Shimodaira
P035 Mixed Factors Analysis for Identifying Transcriptional Modules and Clusters on Microarray
Experiments, Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto
P036 Incorporating prior knowledge into clustering of gene expression proﬁles, Daisuke Komura, Hiroshi Nakamura, Shuichi Tsutsumi, Hiroyuki Aburatani, Sigeo Ihara
P037 Mathematical Model Based Clustering of Gene Expression, Kazumi Hakamada, Taizo Hanai,
Masahiro Okamoto
P038 Cleaning Microarray Expression Data with Markov Random Fields Based on Proﬁle Similarity,
Raymond Wan, Hiroshi Mamitsuka
P039 A practical system for the detection of chromosomal aberration in tumor cells by array CGH,
Junya Futagawa, Tomohiro Isobe, Atsushi Moroda, Nobutaka Mitsuhashi, Ken Aoshima, Yasuhito Arai, Fumie Hosoda, Misao Ohki, Issei Imoto, Johji Inazawa, Tokuki Sakiyama
P040 Statistical Analysis of Gene Expression in Repair Mechanism under UV Irradiation,
Sachiyo Aburatani, Nobuyoshi Sugaya, Hiroo Murakami, Katsuhisa Horimoto
P041 Integrated Analysis of Gene Expression Proﬁle and Metabolite Quantity Data of Arabidopsis
thaliana Using BL-SOM, Yukiko Nakamura, Ryoko Morioka, Yoko Shinbo, Masami Yokota Hirai, Md. Altaf-Ul-Amin, Ken Kurokawa, Kotaro Minato, Kazuki Saito, Shigehiko Kanaya
P042 Analysis for time-course proﬁles of transcription arrays, Daisuke Tominaga, Paul Horton
P043 A Step Towards Substructure Exploration from Gene Expression Patterns, Masako Hoshino,
Hiroshige Inazumi
P044 Markov Property and Scale-free Organization of Gene Expression, Tomoshiro Ochiai,
Jose C. Nacher, Tatsuya Akutsu
P045 Expression Analysis of Glycosyltransferase Genes in Human, Mouse, and Rat, Takashi Miyama,
Shin Kawano, Minoru Kanehisa
P046 Yeast Gene Classiﬁcation based on Relevant Biological Functions for Gene Expression Data
Analysis, Satoshi Kamegai, Takuya Oyama, Mikio Yoshida, Fumihito Miura, Kenji Satou,
Takashi Ito
8

P047 Rational Design for Molecular Breeding of Industrially Useful Strains Based on Bioinformatic
Data in Saccharomyces cerevisiae, Takashi Hirasawa, Katsunori Yoshikawa, Kengo Ashitani,
Keisuke Nagahisa, Chikara Furusawa, Yoshio Katakura, Hiroshi Shimizu, Suteaki Shioya
P048 On-chip selection of DNA ligands using a method for generating point mutations, Ryoichi Asai,
Shin I. Nishimura, Takuyo Aita, Katsutoshi Takahashi
P049 Automatic generation of KEGG OC (Ortholog Cluster) and its assignment to draft genomes,
Yuki Moriya, Toshiaki Katayama, Akihiro Nakaya, Masumi Itoh, Akiyasu C. Yoshizawa, Shujiro Okuda, Minoru Kanehisa
P050 Functional Categorization of Multiple Genomes using KEGG OC in the Genome Indices,
Shujiro Okuda, Akiyasu C. Yoshizawa, Yuki Moriya, Masumi Itoh, Toshiaki Katayama,
Susumu Goto, Minoru Kanehisa
P051 Gene-Transpositions on Functional Categories in Prokaryotic Genomes, Nobuyoshi Sugaya, Hiroo Murakami, Sachiyo Aburatani, Kunio Shimizu, Katsuhisa Horimoto
P052 Prediction of DNA-binding sites in proteins using evolutionary proﬁles, Shandar Ahmad, Akinori Sarai
P053 Method for ﬁnding p53 binding sites using tiling array, Shingo Tsuji, Kiyofumi Kaneshiro,
Shuichi Tsutsumi, Sigeo Ihara, Hiroyuki Aburatani
P054 Correlation between signal transduction domains and habitats in cyanobacteria, Shinobu Okamoto, Shuichi Kawashima, Rei Narikawa, Minoru Kanehisa
P055 Transmembrane regions prediction for G-protein-coupled receptors by hidden Markov model,
Kayo Narukawa, Tadashi Kadowaki, Gozoh Tsujimoto
P056 GPCR and G-protein Coupling Selectivity Prediction Based on SVM with Physico-Chemical
Parameters, Makiko Suwa, Yukimitsu Yabuki, Takahiko Muramatsu, Takatsugu Hirokawa,
Hidetoshi Mukai
P057 GLIDA : GPCR and Ligand Database, Jiyoon Yang, Yasushi Okuno, Gozoh Tsujimoto
P058 3DMET: A Database of Three-Dimensional Structures of Natural Metabolites, Miki Maeda
P059 Graph Theoretic Analysis of Chemical Compounds in Biological Pathways, Atsuko Yamaguchi,
Yasushi Okuno, Hiroshi Mamitsuka
P060 Prediction of Glycosyltransferases Synthesizing Glycoconjugates Using Variable-length N-gram
Model, Yeon-Dae Kwon, Shougo Shimizu, Hisashi Narimatsu
P061 An algorithm for graph isomorphism and its application to KEGG Compound Search,
Nobuya Tanaka, Susumu Goto, Minoru Kanehisa
P062 RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions,
Masaaki Kotera, Masahiro Hattori, Min-A Oh, Rumiko Yamamoto, Tomoko Komeno,
Junko Yabuzaki, Koichiro Tonomura, Susumu Goto, Minoru Kanehisa
P063 Glycan Linkage Substitution Matrix Rooted on Tree Alignments, Kiyoko F. Aoki, Hiroshi Mamitsuka, Minoru Kanehisa
P064 Classiﬁcation and Motif Extraction of Glycans in Bloods, Yoshiyuki Hizukuri, Yoshihiro Yamanishi, Osamu Nakamura, Fumio Yagi, Susumu Goto, Minoru Kanehisa
P065 Integrated Quantiﬁcation and Multivariate Analysis Workbench System for Phospholipids,
Kaoru Mogushi, Katsutoshi Takahashi
P066 Power-law Correlations of Connectivities in Biomolecular Networks, Kazuhiro Takemoto,
Chikoo Oosawa
P067 A method for estimation of enzyme kinetics in metabolic pathways using GMA, Tomoya Kitayama, Ayako Kinoshita, Yoichi Nakayama, Masaru Tomita
9P068 A method for customized cross-species metabolic pathway comparison, Eric Lo, Takuji Yamada,Michihiro Tanaka, Masahiro Hattori, Susumu Goto, Chuan-Hsiung Chang, Minoru Kanehisa
P069 Decomposition of kinetically feasible metabolic ﬂux distributions onto elementary modes, JeanMarc Schwartz, Minoru Kanehisa
P070 Global Tree of Known Carbohydrate Structures to Analyze Biosynthetic Pathways, Kosuke Hashimoto, Shin Kawano, Yasushi Okuno, Minoru Kanehisa
P071 Comparative analysis of enzymatic reactions reveals phylogenic evolution of metabolic pathways, Michihiro Tanaka, Naoki Nariai, Thomas Handorf, Oliver Ebenhöh, Satoru Miyano, Minoru Kanehisa, Reinhart Heinrich
P072 Functional Enzyme Exploration combining SIMPLEX screening assisted with Fuzzy Neural
Network, Ryuji Kato, Hiroyuki Konishi, Yuichi Koga, Tsuneo Yamane, Takeshi Kobayashi,
Hideo Nakano, Hiroyuki Honda
P073 Fold-Function Relationship of PLP-Dependent Enzymes, Keiko Matsuda, Takaaki Nishioka,
Kengo Kinoshita, Nobuhiro Go
P074 A novel classiﬁcation of enzyme catalytic reactions, Nozomi Nagano
P075 Phylogenetic Comparison of Human and Mouse Promoter Regions and Visualization of a Variety
of Conserved Elements, Hirokazu Chiba, Kenta Nakai
P076 Conservation of Physicochemical Properties during Protein Evolution, Masashi Fujita, Masumi Itoh, Minoru Kanehisa
P077 A method for comparing microarray data of diﬀerent species, Kenji Hagimoto, Jun Miyazaki,
Shigehiko Kanaya, Naotake Ogasawara, Toshiyuki Amagasa, Shunsuke Uemura
P078 Chromosome Proﬁling: A Clue to Trace The Genome Evolution, Ayumu Saito, Koichi Nishigaki
P079 Searching for cis-elements in Mouse-Human Orthologous Promoter Regions, Natalia Polouliakh,
Wataru Fujibuchi, Tohru Natsume, Paul Horton
P080 Tandem Repeats in 44 Prokaryotic Genomes and Genome Evolution, Satoshi Mizuta, Hikaru Munakata, Abulimiti Aimaiti, Kenji Oosawa, Toshio Shimizu
P081 An approximate maximum likelihood method for phylogenetic tree analysis based on hightemperature Markov Chain Monte Carlo, Ryota Suzuki, Tomoya Taniguchi, Hidetoshi Shimodaira
P082 Extension of Prrn: implementation of a doubly nested randomized iterative reﬁnement strategy
under a piecewise linear gap cost, Shinsuke Yamada, Osamu Gotoh, Hayato Yamana
P083 Sequence Alignment Tool of Membrane Protein, Takahiko Muramatsu, Makiko Suwa
P084 A Rapid peptide based Alignment -free method to construct Genome trees Independent of
sequence annotation, Vikash Kumar, Sunil Kumar
P085 Fast Homology Search using Categorisation Proﬁles, Abhijit Chattaraj, Hugh E. Williams,
Adam Cannane
P086 Measuring the Average Accuracy Performance of Homology Search, XiaoLei Chen, Adam Cannane, Hugh E. Williams
P087 Performance Comparison between Proﬁles from Hidden Markov Models and from PseudocountMethod, Makihiko Sato, Katsuhisa Horimoto
P088 Development of Fast Tandem Repeat Analysis and Lossless Compression Method for DNA
Sequence, Toshio Modegi
P089 Inferring breakpoints from large-scale BAC-end sequences and a complete genome sequence,
Katsuhiko Murakami, Yoshiyuki Sakaki
10P090 CATTAGAT - Web Server for Primer Speciﬁcity Scan, Magnús M. Halldórsson,
Haukur Thorgeirsson, Ýmir Vigfússon, Hans Thormar, Jón Jóhannes Jónsson
P091 Development of a Common Protocol for the Prediction of Microbial Genes, Takehide Kosuge, Toshihisa Okido, Masaki Hirahata, Yasumasa Shigemoto, Satoru Miyazaki, Takashi Abe,
Takashi Gojobori, Hideaki Sugawara
P092 Diverse base composition skews in bacterial chromosomes, Chi Chen, Carton W. Chen
P093 Analysis of the bacterial sequences recognized by RNA-binding proteins and compounds,
Ai Muto, Akiyasu C. Yoshizawa, Shujiro Okuda, Masumi Itoh, Masahiro Hattori, Minoru Kanehisa
P094 Relationship between Chromosome Rearrangement and Repeat Sequences in Human Chromosome 7, Hiroo Murakami, Nobuyoshi Sugaya, Sachiyo Aburatani, Katsuhisa Horimoto
P095 Systematic Survey of Sequence Similarity between Sense and Anti-sense Strands in Escherichia
coli Genome, Kazuhiro Nakamura, Makihiko Sato, Katsuhisa Horimoto
P096 Comprehensive promoter analyses using a database of transcription start sites , Riu Yamashita,
Yutaka Suzuki, Katsuki Tsuritani, Sumio Sugano, Kenta Nakai
P097 Variation Analysis of Transcription Start Sites and ORFs in Splicing Variant cDNAs and Integrated Database System of the Results, Tetsuo Nishikawa, Kouichi Kimura, Ai Wakamatsu,
Jun-ichi Uechi, Hiroshi Makita, Jun-ichi Yamamoto, Tomohiro Yasuda, Masashi Nemoto, Keiichi Nagai, Sumio Sugano, Nobuo Nomura, Takao Isogai
P098 Analysis of GC-compositional Strand Bias in the Transcription Start Sites of Plant and Fungal
Genes, Shigeo Fujimori, Takanori Washio, Masaru Tomita
P099 Power Spectrum of DNA Base Sequence in Human Mitochondrial Genome, Eisei Takushi, Yukinobu Chinen
P100 A Possible Existence of Cooperative Gene and Transition in Bacteriophage φX174 Genome,
Eisei Takushi
P101 Quantitative analysis of synonymous codon usage bias, Haruo Suzuki, Rintaro Saito,
Masaru Tomita
P102 The kingdom of Plantae EST Indices: a resource for plant genomics community, Ali MasoudiNejad, Ruy Jauregui, Shuichi Kawashima, Susumu Goto, Minoru Kanehisa, Takashi R. Endo
P103 Exhaustive analysis for screening of susceptible interactions between genetic and environmental factors for multifactorial disease, Yasuyuki Tomita, Mitsuhiro Yokota, Takeshi Kobayashi,
Hiroyuki Honda
P104 Exhaustive combination search method for SNPs combination Related to Helicobacter pylori
infection susceptibility Using Artiﬁcial Neural Network, Hironori Mutoh, Nobuyuki Hamajima,
Takeshi Kobayashi, Hiroyuki Honda
P105 Investigating the Optimal Dataset Size for SNP Hunting, Toshiko Matsumoto, Yasuyuki Nozaki, Ryo Nakashige, Minori Shinya, Yoko Yoshikawa, Shuhei Mano, Tadashi Imanishi, Hidetoshi Inoko, Gen Tamiya, Takashi Gojobori
P106 Logistic Regression Model of Binary Disease Trait for Case-Control Study Considering Interactions between SNPs and Environments, Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano
P107 Prediction of regulatory SNPs inﬂuencing Gene expression on Chromosome 5q31-33, Gil-Mi Ryu,
Jee Yeon Heo, Sangbae Kim, Ka Kyung Kim, Chan Park, Kuchan Kimm, InSong Koh
P108 Clustering and Multiple Alignment for a Large Number of cDNA Sequences Including Splicing
Variants, Tomohiro Yasuda
11

P109 Analysis of splicing variants of human full-length cDNAs, Ai Wakamatsu, Jun-ichi Yamamoto,
Kouichi Kimura, Tetsuo Nishikawa, Yutaka Suzuki, Sumio Sugano, Keiichi Nagai, Nobuo Nomura, Takao Isogai
P110 Development of ASTRA: database of human alternative splicing patterns, Hideki Nagasaki,
Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, Osamu Gotoh
P111 Alternative splicing of transmembrane regions in human gene, Masateru Yamamoto,Chie Motono, Hideki Nagasaki, Makiko Suwa
P112 Non-coding RNA ﬁnding based on probabilistic secondary structure information, Taishin Kin,
Koji Tsuda, Kiyoshi Asai
P113 Detection of tRNA genes from DNA sequences of Eukaryotes, Makoto Kinouchi, Yoshihiro Kudo
P114 Scarna: Stem Candidate Aligner for RNA, Kiyoshi Asai, Taishin Kin
P115 Detection of non-coding RNAs by properties of stems, Hiroki Ueda, Jun-Ichi Sagara, Minoru Nakazawa, Shimmi Hattori
P116 A genetic algorithm approach for ﬁnding the common structure of two homologous RNAs,
Akito Taneda
P117 Hierarchical Alignment of RNA Secondary Structures Including Pseudoknots, Shinnosuke Seki,
Atsushi Kijima, Satoshi Kobayashi, Gen-ichi Sanpei
P118 Integrated Reliability-Assessment for Protein-Protein Interaction Data, Akihito Tokuda,
Asako Koike, Toshihisa Takagi
P119 Conserved Protein-Protein Interactions in Diﬀerent Species, Yoko Shinbo, Toshihiro Koma,
Md. Altaf-Ul-Amin, Ken Kurokawa, Hirotada Mori, Naotake Ogasawara, Yukiko Nakamura,
Shigehiko Kanaya
P120 Validation and prediction of protein-protein interactions by pairwise analysis of functional protein families, Sarah Mohseni-Zadeh, Jacques Camonis, Jérôme Wojcik, Emmanuel Barillot
P121 Using Sequence Homology to Filter High-throughput Protein-protein Interaction Data, Ashwini Patil, Haruki Nakamura
P122 Prediction of Protein-Protein Interactions Based on Real-Valued Phylogenetic Proﬁles Using
Partial Correlation Coeﬃcient, Tetsuya Sato, Yoshihiro Yamanishi, Minoru Kanehisa, Hiroyuki Toh
P123 A Function Prediction of Unknown Proteins in Protein-Protein Interaction Data, JaeYoung Jung, Jae-Hun Choi, Jong-Min Park, Seon-Hee Park
P124 Prediction of uncharacterized protein functions by integrating protein-protein interaction data
and domain information, Kinya Okada, Kiyoshi Asai
P125 Analysis of protein interaction networks in neurodegenerative disorders, Vachiranee Limviphuvadh, Seigo Tanaka, Susumu Goto, Kunihiro Ueda, Minoru Kanehisa
P126 A Fast Method for Inferring Strengths of Protein-Protein Interactions and A Hardness Result,
Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu
P127 Improving Prediction of MHC Class I Binding Peptides with Additional Binding Data, Shanfeng Zhu, Kiyoko F. Aoki, Keiko Udaka, Hiroshi Mamitsuka
P128 GreenPepper: The docking prediction software of protein complex, Toshiharu Kondo, Hirokazu Ishida, Ryo Yamauchi, Eijiro Watanabe, Chizuru Hirose, Mitiko Gō
P129 Computer Modeling of Enzyme Protein-Chiral Ligand Interactions: Enantioselectivity of Lipase
Enzyme, Yoshinobu Naoshima, Yoshihiro Mori, Yoichiro Yagi
12

P130 Selection of Proper Template Complex for Modeling Protein-Protein Complex, Naoshi Fukuhara,
Takeshi Kawabata, Nobuhiro Go
P131 The analysis between functions and densities in yeast intercomplex protein-protein interactions,
So Nakagawa, Soichi Ogishima, Takeshi Hase, Yashuhiro Suzuki, Hiroshi Tanaka
P132 Deciphering the Protein Network of Caenorhabditis elegans in the Approach of Systems Biology, Chung-Yen Lin, Chi-Shiang Cho, Chia-Ming Chang, Chia-Ling Chen, Fan-Kai Lin, PaoYang Chen, Chen-Zen Lo, Chao A. Hsiung
P133 Hierarchical Structure of the Protein-protein Interaction Networks, Ka-Lok Ng, Po-Han Lee,
Chien-Hung Huang
P134 InteractionViewer: A Visualization Tool for Protein-Protein Interaction Networks, Jun-Wei Hsu,
Tao-Wei Huang, Yao-Lin Chang, Cheng-Yen Kao
P135 Design and Implementation of Navigation System for Protein Interaction Networks, JongMin Park, Jae-Hun Choi, Jae-Young Jung, Seon-Hee ParkP136 In Silico Search for Nuclear Receptor Target Genes, Yoshitomo Tanaka, Tsuguchika Kaminuma,
Kotoko Nakata, Hiroshi Tanaka
P137 Universal Proteomics tools for Protein Quantitation and Data Management - Xome & Mass Navigator, Koji Yanagisawa, Yasuto Yokoi, Ken Aoshima, Yuji Miura, Yoshiya Oda, Yasushi Ishihama, Tsuyoshi Tabata, Takatoshi Kawai, Takeshi Nagasu
P138 WoLF PSORT: Protein Localization Prediction Program, Paul Horton, Koon-Jeun Park
P139 Identiﬁcation of novel chloroplast proteins of endosymbiotic origin by phylogenetic proﬁling
using homolog groups, Naoki Sato, Masayuki Ishikawa
P140 Translational Polymorphism as an Important Source of Eukaryotic Proteins Variety, Alex V. Kochetov, Nikolay A. Kolchanov, Akinori Sarai
P141 Extended proteins with negative net charges in total proteomes, Nobuyuki Uchikoga, Runcong Ke, Fumitsugu Akazawa, Masashi Sonoyama, Shigeki Mitaku
P142 Analysis of Amino Acid Conservation in Transmembrane Helices,
Sukenobu Konishi, Takuhiro Nishio, Toshio Shimizu

Satoshi Hamada,P143 A Transmembrane Topology Prediction Procedure for Identifying GPCR Sequences, Yasuhito Inoue, Takao Kimura, Toshio Shimizu
P144 Domain Architecture of Prokaryotic Single-Spanning Transmembrane Proteins, Masafumi Arai,
Takafumi Fukushi, Satoshi Mizuta, Masanobu Satake, Toshio Shimizu
P145 Detection of conformational changes in the membrane proteins by using PDB-REPRDB, Tamotsu Noguchi
P146 Simulation of electric charge distribution of all proteins in Saccharomyces cerevisiae proteome,
Runcong Ke, Shigeki Mitaku
P147 De novo peptide sequencing using ion-peak intensity and amino acid cleavage intensity ratio,
Mitsuhiro Kanazawa, Atsushi Ogiwara, Hisae Anyoji, Umpei Nagashima
P148 Quantitative Proteomics Analysis System i-OPAL, Atsushi Ogiwara, Hsiao-kun Tu, Mitsuhiro Kanazawa, Hisae Anyoji, Takao Kawakami, Toshihide Nishimura
P149 Mutation eﬀect on number distribution of transmembrane helices in total proteome of Drosophilamelanogaster, Ryusuke Sawada, Masashi Sonoyama, Shigeki Mitaku
P150 Predicting the protein disordered region using modiﬁed position speciﬁc scoring matrix,
Kana Shimizu, Shuichi Hirose, Tamotsu Noguchi, Yoichi Muraoka
13

P151 Sequence and Structural Analysis of Outer Membrane Proteins: Applications to Discrimination
and Prediction, M. Michael Gromiha, Shandar Ahmad, Makiko Suwa
P152 Conservation of Domain Geometry in Proteins,
Cyrus Chothia, Sarah TeichmannJung-Hoon Han,

Nicola Kerrison,

P153 A Structural Sequence Representation of Protein: Secondary Structure Element Sequence (SSES), Sung-Hee Park, Chan-Yong Park, Dae-Hee Kim, Seon-Hee Park
P154 Computational Method for Determining Global Protein Topology from Distance Restraints by
Chemical Cross-Linking, Akira R. Kinjo, Ken Nishikawa, Tatsuya Akutsu, Katsuhisa Horimoto
P155 GATS: Grid Aided Target Selection for molecular simulation, Yuichi Hirata, Said Mirza Pahlevi,
Masaaki Kawata, Isao Kojima, Nagashima Unpei, Mitsuo Yokokawa, Satoshi Sekiguchi
P156 A new protein classiﬁcation method using dynamic classiﬁer, Chan-Yong Park, Sung-Hee Park,
Dae-Hee Kim, Seon-Hee Park, Chi-Jung Hwang
P157 Functional Classiﬁcation of Coiled-Coil Proteins in Multiple Genomes, Akiyasu C. Yoshizawa,
Shujiro Okuda, Yuki Moriya, Masumi Itoh, Toshiaki Katayama, Shin Kawano, Shinobu Okamoto, Shuichi Kawashima, Minoru Kanehisa
P158 Structural diversity as a source of quasispeciation in human immunodeﬁciency virus type 1,
Teruaki Watabe, Hirohisa Kishino, Yasuhiro Kitazoe
P159 FAMSBASE: Modeling Database of 277 Genomes, Mitsuo Iwadate, Kazuhiko Kanou,
Genki Terashi, Mayuko Takeda-Shitaka, Eiichiro Suzuki, Hideaki Umeyama
P160 Question Answering System in Biomedical Domain, Kouji Takahashi, Asako Koike, Toshihisa Takagi
P161 New cancer diagnosis method on the basis of fuzzy theory and boosting, Hiro Takahashi, Hiroyuki Honda
P162 Model Analysis of Foam Cell Formation in Atherosclerosis, Satoshi Yamada, Nobuhiro Yamada
P163 Building Patterns for Biomedical Event Extraction, Hong-Woo Chun, Tomoko Ohta, JinDong Kim, Jun’ichi Tsujii
P164 A Generic Pipeline Architecture for Bioinformatics System, Hsiao-Kun Tu, Mitsuhiro Kanazawa,
Hisae Anyoji, Atsushi Ogiwara
P165 A Support System for Creating the Minimum Yeast Genom by Searching Non-Essential Area,
Takahiro Sumiya, Masafumi Nishizawa, Yukinori Kitadai, Tatsuo Tomita, Atsushi Nakamura
P166 Construction of Subcellular Locations prediction tool for Three Kingdoms: Fungi, Animal and
Plant, Keun-Joon Park, Paul Horton
P167 Moleview : A program for molecular visualization, Chan-Yong Park, Sung-Hee Park, DaeHee Kim, Seon-Hee Park, Chi-Jung Hwang
P168 Intris: A Viewer for Splice Variants and their Expression Proﬁles — Summarization into Variant
Types, Kouichi Kimura, Tetsuo Nishikawa, Ai Wakamatsu, Jun-ichi Yamamoto, Ken’ichi Nagai, Nobuo Nomura, Takao Isogai
P169 Three-dimensional visualization of allelic copy number data, Kunihiro
Shumpei Ishikawa, Koichi Hirota, Hiroyuki Aburatani, Michitaka Hirose

Nishimura,P170 Polymorphism Markup Language (PML) for the interoperability of data on SNPs and other sequence variations, Hideaki Sugawara, Hiroshi Mizushima, Tokio Kano, Yasumasa Shigemoto,
Yoichi Hashimoto, Isao Tomabechi, Masayuki Ikawa, Naoki Sakagami, Toshiyuki Katagiri,
Takashige Oroguchi
P171 MFAML: an XML-based standard format for metabolic ﬂux analysis, Hongseok Yun, DongYup Lee, Seunghyun Lee, Joonwoo Jeong, Sang Yup Lee
14

P172 The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate
structures, Norihiro Kikuchi, Akihiko Kameyama, Shuuichi Nakaya, Hiromi Ito, Takashi Sato,
Toshihide Shikanai, Yoriko Takahashi, Hisashi Narimatsu
P173 Improving Parsing Precision of an Existing Parser for Extracting Biological Relation Events,
Hyunchul Jang, Jaesoo Lim, Hyun-Sook Lee, Soo-Jun Park, Seon-Hee Park, Kyu-Chul Lee
P174 Corpus Tagging Tool for Tagging Biological Named Entities and Their Relation Events,
Hyunchul Jang, Hyun-Sook Lee, Jaesoo Lim, Soo-Jun Park, Seon-Hee Park, Kyu-Chul Lee
P175 Extraction of the cooccurrence sentences of gene names and keywords from Pubmed abstracts,
Takashi Yoneya
P176 Evaluation of the Article Collecting System Based on Rough Reading Strategy, Ryo Okada,Manabu Sugii, Miyako Tanaka, Hiroshi Matsuno, Satoru Miyano
P177 Knowledge discovery based on conceptual network, Asako Koike, Toshihisa Takagi
P178 Domain Independent Named Entity Recognition from Biological Literature, Hyun-Sook Lee,
Soo-Jun Park, Hyunchul Jang, Jaesoo Lim, Seon-Hee Park
P179 INOH: A Pathway Database of Biological Events, Takao Asanuma, Tatsuya Kushida, Satoko Yamamoto, Yuki Yamagata, Azumi Sekiguchi, Toshihisa Takagi, Ken Ichiro Fukuda
P180 Ontology of Experiments for Bioinformatics , Larissa N. Soldatova, Ross D. KingP181 KAIKOGAAS: An Automated Annotation System for Silkworm Genome, Michihiko Shimomura,
Yuji Shimizu, Shun-ichi Sasanuma, Baltazar A. Antonio, Yoshiaki Nagamura, Kazuei Mita,
Takuji Sasaki
P182 Construction of H-Invitational Database CIB-DDBJ Flat File Server, Toshihisa Okido, Yasumasa Shigemoto, Masashi Matsuo, Tadashi Koike, Satoshi Fukuchi, Tadashi Imanishi,
Satoru Miyazaki, Yoshio Tateno, Takashi Gojobori
P183 DNA conformational energy from molecular dynamics simulations: Toward the understandingof the indirect readout mechanism in protein-DNA recognition, Marcos J. Araúzo-Bravo, Shandar Ahmad, Satoshi Fujii, Shigeori Takenaka, Hidetoshi Kono, Nobuhiro Go, Akinori Sarai
P184 Algorithms for Direct Clone-mapping Technology using Scanning Near-ﬁeld Optical/Atomic
Force Microscopy, Yoshitaka Suetsugu, Tomoyuki Yoshino, Seigo Kuwazaki, Hirokazu Takahashi, Junko Narukawa, Motoharu Shichiri, Daisuke Fukushi, Kazuei Mita, Shigeru Sugiyama,
Toshio Ohtani, Kimiko Yamamoto
P185 A Novel Method for Screening Arabidopsis Mutants in silico based on Statistical Modeling,
Eli Kaminuma, Naohiko Heida, Takeshi Yoshizumi, Miki Nakazawa, Minami Matsui, Tetsuro Toyoda

15