GIW 2000 Accepted Posters

Identifying Intrinsic Disorder by Sequence Homology	 
     --- Sachiko Takayama, Thomas Marshal, Christopher Oldfield, Andrew Campen, A. Keith Dunker, Celeste J. Brown

AngioDB: Angiogenesis Database
     --- Tae-Kwon Sohn, Eun-Joung Moon, Seok-Ki Lee, Hwan-Gue Cho, Kyu-Won Kim

Novel Method for Primer/Probe Design and Sequence Analysis
     --- Ken-ichi Kurata, Hiroshi Nakamura

A Procedure for Estimating Cluster Boundaries in Gene Expression Profile Data
     --- Katsuhisa Horimoto, Hiroyuki Toh 

Inference of Genetic Networks from Expression Profile by Graphical Gaussian Modeling
     --- Hiroyuki Toh, Katsuhisa Horimoto

Visualization of Genetic Networks: Edge Crossing Minimization of a Graph Drawing with Vertex Pairs
     --- Atsuko Yamaguchi, Hiroyuki Toh

Association of Putative Restriction Modification Genes with Large Genome Polymorphisms Suggested from Comparison of \textit{Pyrococcus} \textit{horikoshii} and \textit{Pyrococcus} \textit{abyssi} Genome Sequences
     --- Akito Chinen, Ikuo Uchiyama, Ichizo Kobayashi

Recent Developments of ProTherm: Thermodynamic Database for Proteins and Mutants
     --- M. Michael Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira, P. Prabakaran, S. Selvaraj, Akinori Sarai

A Comprehensive Comparison between Locations of Orthologs in Circular Microbial Genomes
     --- Hiroaki Saitoh, Kentaro Mori, Satoshi Fukuchi, Katsuhisa Horimoto 

Mining Association Rules Related to Protein-Protein Interactions
     --- Takuya Oyama, Kagehiko Kitano, Kenji Satou, Takashi Ito

Polarity Difference Score: A New Measure for Recognition and Classification of Transmembrane Protein Structures
     --- Makiko Suwa, Henrik T. Yudate, Yasuhiko Masuho, Shigeki Mitaku

\textit{In} \textit{Silico} Differential Display
     --- Hiroo Murakami, Takashi Suzuki, Seon-Yong Jeong, Hideji Hashida, Jun Goto, Ichiro Kanazawa

Multiple Sequence Alignment by Genetic Algorithm
     --- Kenichi Hanada, Tsutomu Yokoyama, Toshio Shimizu

Analysis of the Distributions of 5' Splice Site-Like Sequences in mRNA Precursors by a Position-Tree Method 
     --- Sumie Kitamura-Abe, Nobuyuki Takahashi, Mineichi Kudo, Masaru Shimbo, Akihiro Tsutsumi

An \textit{E.~coli} Pseudo-tRNA Gene Cluster Homologous to the tRNA-Gene Cluster in the \textit{Bacillus} \textit{subtilis} \textit{trrnD} Operon 
     --- Koji Ohnishi, Touru Suzuki, Hiroshi Shutou

A Method for Sequence Analysis Using Multivariate Analysis
     --- Jun-Ichi Sagara, Kentaro Shimizu

Automatic Collection of Functional Sequence Based on Annotations in the GenBank Entry
     --- Yoshifumi Okada, Tomomasa Nagashima

ALL/AML Cancer Classification by Gene Expression Data Using SVM and CSVM Approach
     --- Xuegong Zhang, Haixin Ke

Estimating the Number of Mouse Genes and the Duplicated Regions within the Mouse Genome
     --- Yasuhiko Wada, Tadashi Imanishi, Takashi Gojobori

A Transmembrane Topology Prediction Method Based on Integration Mechanism
     --- Hanako Ito, Demelo Madrazo Lao, Toshio Shimizu

Evaluation of Transmembrane Topology Prediction Methods by Using an Experimentally Characterized Topology Dataset 
     --- Masami Ikeda, Masafumi Arai, Toshio Shimizu

A Novel Method for Identification of Genes Contributing to the Pathological Classification Using cDNA Microarray
     --- Koji Kadota, Yasushi Okazaki, Shugo Nakamura, Hiroshi Shimada, Kentaro Shimizu, Yoshihide Hayashizaki

Computational Analysis of the Strand Bias of the Chi Sequences and Other Oligonucleotides in Bacterial Genomes
     --- Kazuharu Arakawa, Reina Uno, Yoichi Nakayama, Masaru Tomita 

Analysis of \textit{cis}-Acting Elements in Large-Scale Rice Genome Sequence
     --- Atsuko Idonuma, Katsumi Sakata, Takuji Sasaki, Wakako Watanabe, Ikuo Horiuchi, Yuji Shimizu 

Detection of tRNA Based on the Cloverleaf Secondary Structure
     --- Makoto Kinouchi, Shigehiko Kanaya, Toshimichi Ikemura, Yoshihiro Kudo

Super-Motifs of Leucine-Rich Repeats (LRRs) Proteins
     ---  Norio Matsushima, Masakatsu Kamiya, Norio Suzuki, Takanori Tanaka

Computer Simulation of Glycolysis in Pancreatic $\beta$-Cells Using the \textsc{E-Cell} System
     --- Yasuhiro Naito, Hiromu Nakajima, Masaru Tomita

Statistical Analysis of Genomic Information: Long-Range Correlation in DNA Sequences
     --- Atsushi Fukushima, Makoto Kinouchi, Shigehiko Kanaya, Yoshihiro Kudo, Toshimichi Ikemura

Development of DDBJ-XML and Its Application to a Database of cDNA 
     --- Satoru Miyazaki, Hideaki Sugawara

A Dynamic Reconstruction Model for Embryo Development of \textit{C.~elegans}
     --- Tsuguchika Kaminuma, Masumi Yukawa, Makiko Okada, Naomi Komiyama, Noriko Kabuyama, Katsuhiko Taki

Pharmacoinformatics Infrastructure for Genome Based Personalized Medicine
     --- Kotoko Nakata, Tatsuya Nakano, Takako Takai-Igarashi, Tsuguchika Kaminuma

Quantitative Modeling of Gene Regulatory Network: Identifying the Network by Means of Genetic Algorithms
     --- Shin Ando, Hitoshi Iba

Comparison of Geometries and Properties of Protein Molecular Surface for Structure-Based Function Prediction
     --- Kengo Kinoshita, Jun'ichi Furui, Haruki Nakamura

A Sequential-Linking Method for Analysis of Within-Host Viral Evolution
     --- Fengrong Ren, Soichi Ogishima, Hiroshi Tanaka

Correlation between Sequence Conservation of 5' UTR and Codon Usage Bias
     ---  Hiroaki Sakai, Yusuke Ohkuma, Chiaki Imamura, Akira Shinagawa, Masayoshi Itoh, Kazuhiro Shibata, Piero Carninci, Hideaki Konno, Jun Kawai, Yoshifumi Fukunishi, Yoshihide Hayashizaki, Masaru Tomita

Comparison of Affected-Sib-Pair Statistics for Multi-Locus Genetic Disease Models in Multi-Marker Analysis
     --- Osamu Ogasawara, Toshihisa Takagi

A Transcription Regulatory Region Analysis System 
     --- Katsuhiko Murakami, Yohinori Ohta, Koji Tanikawa, Hiroki Nakae, Shigeo Ihara, Toshihisa Takagi

ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions
     --- P. Prabakaran, Jianghong An, M. Michael Gromiha, S. Selvaraj, Hatsuho Uedaira, Hidetoshi Kono, Akinori Sarai

AIGNET: Improvement of a System and Application to the Experimentally Observed Expression Data
     --- Yuji Arikawa, Shoji Watanabe, Yukihiro Eguchi, Yukihiro Maki, Daisuke Tominaga, Masahiro Okamoto

Large-Scale Sequence Analyses in the \textit{Arabidopsis} \textit{thaliana} Genome Sequencing Project: Status 2000
     --- Yasukazu Nakamura, Satoshi Tabata

Design of an Apoptosis-Inducing Short Peptide Using the System for Macromolecular Interaction Assessment MIAX
     --- Taiki Kojima, Atsushi Yoshimori, Akemi Hayakawa, Seiichi Tanuma, Carlos A. Del~Carpio

A Method of Protein Molecular Surface Comparison Based on Geometric Hashing
     --- Keiichirou Matsuura, Norimasa Shoji, Takenao Okawa, Haruki Nakamura

A QSAR Study for Modeling MHC Class-I Binding Oligo-Peptides
     --- Simonetta Fickel, Carlos A. Del~Carpio

MIAX: A System for Assessment of Macromolecular Interaction. 4) Interaction Site Inference by Molecular Hydrophobic and Electrostatic Analysis
     --- Atsushi Yoshimori, Carlos A. Del~Carpio

Selection of Candidate Genes for Polygenic Diseases by Utilizing Protein-Protein Interaction Networks
     --- Tetsuro Toyoda, Yuki Takigawa

Quantitative Modeling of Mitochondrial Energy Metabolism Using \textsc{E-Cell} Simulation Environment
     ---  Katsuyuki Yugi, Masaru Tomita

Gene Discovery of G-Protein Coupled Receptors from Human Genome
     --- Makiko Suwa, Toshiyuki Sato, Ikuo Okouchi, Masamitsu Mikoshiba, Yutaka Akiyama, Kiyoshi Asai, Shinichi Matsumoto, Shuichi Tsutsumi, Hiroyuki Aburatani

Novel Index of Polar Amino Acids Characterizing End Region of Transmembrane Helices
     --- Toshiyuki Hayashibe, Takatsugu Hirokawa, Shigeki Mitaku

Computational Design of Proteinous Drug Employing Hidden Markov Model
     --- Taizo Hanai, Hideki Noguchi, Yukari Matsubara, Kazuya Takeda, Hiroyuki Honda, Vladimir Brusic, Takeshi Kobayashi

An Application of a Pathway Alignment Method to the Analysis of Amino Acid Biosynthesis
     --- Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto

Quantitative Estimation of Cross-Hybridization in DNA Microarrays Based on a Linear Model
     --- Mitsuteru Nakao, Yoshinori K. Okuji, Minoru Kanehisa

Representing Functional Annotations of Mouse cDNA Sequences in XML
     --- Takeya Kasukawa, Hidemasa Bono, Hideo Matsuda, Yasushi Okazaki, Shotaro Koutsuki, Yoshihide Hayashizaki

Practical Organization and Functional Annotation of RIKEN cDNA Microarray
     --- Hidemasa Bono, Takeya Kasukawa, Rika Miki, Koji Kadota, Yasushi Okazaki, Yoshihide Hayashizaki

Development of Data Evaluation Supporting System for Large-Scale Experimental Results
     --- Mikio Yoshida, Hiroshi Fukagawa, Yukari Shibagaki, Hideaki Shimano, Takeshi Mizuno

Emergent of Networks Based on Relationship among Elements
     --- Yasuhiro Suzuki, Qingwei Zhang, Hiroshi Tanaka 

Data Submission System for Cyanobacterial DNA Chip Consortium
     --- Ikuo Uchiyama, Tomoki Miwa, Hiroyo Nishide, Iwane Suzuki, Tatsuo Omata, Masahiko Ikeuchi, Norio Murata, Minoru Kanehisa

A Security System for Human Genome Information Encoded by Chemicals, Not by Electronic Codes
     --- Yumi Kawazoe, Toshikazu Shiba, Masahito Yamamoto, Azuma Ohuchi 

Assessment of Redundancy and Full-Length Rate of Full-Length Enriched cDNA Libraries
     --- Hideaki Konno, Yoshifumi Fukunishi, Piero Carninci, Yoshihide Hayashizaki

Development of a Bioinformatic System for Determination of the 3D Structure of RNA from Secondary Structure Constrains
     --- Yoshimitsu Shigenobu, Carlos A. Del~Carpio

Gene Expression Analysis Using Fuzzy ART Model
     --- Shuta Tomida, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi 

Evaluation of Automatic Term Recognition of Nuclear Receptors from MEDLINE
     --- Sophia Ananiadou, Sylvie Albert, Dietrich Schuhmann

A Database System for cDNA Expression Profile Using ESTs of Oligo-Capping Clones and UniGene
     --- Naoyuki Harada, Katsuhiko Murakami, Tetsuo Nishikawa, Tomoyasu Sugiyama, Toshio Ota, Ryotaro Irie, Keiichi Nagai, Takao Isogai

Sequence Analysis of Less Hydrophobic Transmembrane Segments in Polytopic Membrane Proteins
     --- Hiromitsu Araki, Toshihisa Takagi, Kenta Nakai

Target Prediction of Transcription Factors and Its Application to Genome Analysis
     --- Akinori Sarai, Samuel Selvaraj, YiFei Wang, Jianghong An, Ponraj Prabakaran, Hidetoshi Kono

SOSUIsignal: Software System for Prediction of Signal Peptide and Membrane Protein
     --- Masahiro Gomi, Fumitsugu Akazawa, Shigeki Mitaku

Clustering of Full-Length cDNA Clones Based on Both End Sequences 
     --- Naoki Osato, Hideaki Konno, Masayoshi Itoh, Shinji Kondo, Jun Kawai, Kazuhiro Shibata, Akira Shinagawa, Jun Adachi, Shiro Fukuda, Yoshimi Ota, Yoshihide Hayashizaki

The Construction of a Database on the Intracellular Vesicular Transport
     --- Akiyasu C. Yoshizawa, Shuichi Kawashima, Minoru Kanehisa

A Statistical Analysis Method for Gene Expression Based on EM Algorithm
     --- Ryoko Morioka, Taku Oshima, Yuya Kawagoe, Takeshi Ara, Shin Ishii, Hirotada Mori

HOWDY: The Integrated Human Genome Database of ALIS
     --- Katsuji Matsumura, Mika Hirakawa, Kazuo Takehana, Hiroko Yamaguchi, Sanae Sato, Masako Kuroda

Standardized Phylogenetic Tree 
     --- Toshinori Endo, Soichi Ogishima, Hiroshi Tanaka

Identifying Gene Regulatory Network as Differential Equation by Genetic Programming
     --- Erina Sakamoto, Hitoshi Iba

Extracting Negative Correlation Pattern from Gene Expression Microarray Data
     --- Hwanseok Rhee, Cholhee Jung, Kyongoh Yoon, Hyunseok Park

Contig Ordering Based On Physical Subunit Orders of ATP Synthase 
     --- Cholhee Jung, Hwanseok Rhee, Hyunseok Park, Jinyoung Choi

CGAT: Comparative Genome Analysis Tool for Closely Related Microbial Genomes
     --- Ikuo Uchiyama, Toshio Higuchi, Ichizo Kobayashi 

Computer Modeling of Photosynthesis Using the \textsc{E-Cell} System
     --- Emily Wang, Yoichi Nakayama, Masaru Tomita

Searching the Most Conserved Sequence in Bacterial Whole Genomes
     --- Ken Kurokawa, Naohisa Goto, Teruo Yasunaga

Classification of \textit{Hepatocellular} \textit{Carcinoma} by Gene Expression Profiling Analysis
     --- Shuichi Tsutsumi, Yuko Kobune, Yutaka Midorikawa, Hiroyuki Aburatani

RNA Secondary Structure Based Prediction of Simian Immunodeficiency Virus Nucleocapsid Protein NCp8 Recognition Site
     --- Naoko Takada, Yukio Sugiura

CONSERV: A Tool for Finding Exact Matching Conserved Sequences in Biological Sequences
     --- Naohisa Goto, Ken Kurokawa, Teruo Yasunaga

Phylogenetic Analysis of Mammalian P-Glycoprotein Sequences
     --- Maria Rochelle A. Diswe, Pocholo Joseph R. Capule, Karlo Marco C. Cleto, Francisco S. Chung~Jr., Rhea Vallente Samonte

Classification and Analysis of Eukaryotic ABC Transporters in Complete Eukarya Genomes
     --- Yoshinobu Igarashi, Daisuke Kihara, Minoru Kanehisa

Extraction of Correlated Gene Clusters from Multiple Graph Structures: Theory
     --- Akihiro Nakaya, Susumu Goto, Minoru Kanehisa

Prediction of Dumbbell-Type Soluble Proteins and Their Center Helices
     --- Shun-ya Takahashi, Shigeki Mitaku

The Role of Gene Expression Regulation in Yeast Cell Cycle Pathway
     --- Toshiaki Katayama, Minoru Kanehisa

Sequence Analysis of Redundant Usage of DNA Fragments in Complete Genomes
     --- Masumi Itoh, Toshiaki Katayama, Yoshinori K. Okuji, Minoru Kanehisa

Computer Simulation of Enzyme Deficiency in Human Erythrocyte Using the \textsc{E-Cell} System
     --- Yoichi Nakayama, Ayako Kinoshita, Masaru Tomita

Extraction of Correlated Gene Clusters from Multiple Graph Structures: Application
     --- Shuichi Kawashima, Akihiro Nakaya, Yoshinori Okuji, Susumu Goto, Minoru Kanehisa

Specific PCR Primer and Probe Design Based on Spanning Networks
     --- James Stuart Nelson, Hiroaki Kasai

Automatic Construction of Search Condition for Making an Exhaustive List of Similar Papers
     --- Jianghong An, Takao Nakama, Ponraj Prabakaran, Akinori Sarai

Gene Expression Analysis of Orthologs in \textit{Synechocystis} sp. with Operons in \textit{Escherichia} \textit{coli}
     --- Yoshinori K. Okuji, Yukako Hihara, Ayako Kamei, Masahiko Ikeuchi, Iwane Suzuki, Norio Murata, Minoru Kanehisa 

Transcriptome Analysis Based on Isothermal Sequence Amplification
     --- Kiyoshi Yasukawa, Takahiko Ishiguro

\textsc{HypothesisCreator}: A Framework for Knowledge Discovery Application Development
     --- Yoshinori Tamada, Hideo Bannai, Osamu Maruyama, Satoru Miyano

Automatic Spot Measurement for Genetic Spot Array Images
     --- Naoya Ohta, Youhei Hachisu, Tatsuya Akutsu, Asao Fujiyama

A Local Search Algorithm for Local Multiple Alignment: Special Case Analysis and Application to Cancer Classification
     --- Tatsuya Akutsu

Characterization of Subcellular Localization Signals Using \textsc{HypothesisCreator}
     --- Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano

Predicting Protein Binding Site Presence/Absence in SNP-Related Alleles by Accounting Gel Mobility Shift Assay 
     --- Julia Ponomarenko, Tatyana Merkulova, Gennady Vasiliev, Zoya Levashova, Oleg Fokin, Sergey Lavryushev, Mikhail Ponomarenko, Anatoly Frolov, Galina Orlova, Akinori Sarai

DNA Properties Specific for Protein/DNA Free Energy Changes Caused by Single Nucleotide Substitutions
     --- Mikhail Ponomarenko, Julia Ponomarenko, Galina Orlova, Anatoly Frolov, Nikolay Kolchanov, Akinori Sarai

SIGNAL-ONTOLOGY: Ontology for Cell Signaling
     --- Takako Takai-Igarashi, Toshihisa Takagi

A Method for Predicting Transcription Factors Using Local Regions of Biased Amino Acid Composition
     --- Goro Terai, Takeshi Mizuno, Kenta Nakai, Toshihisa Takagi 

Transmembrane Topology Pattern and Detection of Transmembrane Protein Functions
     --- Natalia Poluliakh, Kohei Saito, Toshio Shimizu

A System for Finding Association Rules from Microarray Data and Public Databases
     --- Takahiro Naitou, Kenji Satou, Emiko Furuichi, Satoru Kuhara, Toshihisa Takagi

Toward Automatic Construction of Extensional Ontology from Genome Databases 
     --- Takuya Yagyuu, Kenji Satou

Toward Automatic Recognition of Field Description Syntax and Parser Generation for Genome Databases
     --- Takeo Sakai, Kenji Satou 

Use of a Full Parser for Information Extraction in Molecular Biology Domain
     --- Akane Yakushiji, Yuka Tateisi, Yusuke Miyao, Jun'ichi Tsujii

The GENIA Project: Knowledge Acquisition from Biology Texts
     --- Nigel Collier, Hideki Mima, San Zoo Lee, Tomoko Ohta, Yuka Tateisi, Akane Yakushiji, Jun'ichi Tsujii

Positional Correlation in Base Occurrence in Splicing Patterns
     --- Yumi Kudo, Yumi Tamada, Toshio Shimizu

A Web Based System for Computation and Management of Massive Number of 2-D Gel Electrophoretograms of Genomic DNA
     --- Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe, Akihiko Konagaya

Autonomous Distributed Genome Database and Its Application to Mouse cDNA and Human Genome Sequence Matching
     --- Yoshiyuki Tanaka, Takeshi Nagashima, Akihiko Konagaya

A Cellular Automata System with Reconfigurable Hardware: Towards a Whole Cell Simulation
     --- Kobori Tomoyoshi, Tsutomu Maruyama, Koshiki Yamaguchi, Akihiko Konagaya

DNA Solution of the Shortest Path Problem by Concentration Control
     --- Masahito Yamamoto, Nobuo Matsuura, Toshikazu Shiba, Azuma Ohuchi

Application of Digital Signal Processing in Clinical Database Management
     --- Pawan Kumar Dhar, S. Vikram, U. C. Niranjan

Finding Sparse Gene Networks
     --- Ayumi Shinohara, Keisuke Iida, Masayuki Takeda, Osamu Maruyama, Satoru Miyano, Satoru Kuhara

On-Web Encyclopedia of Genome Profiles (On-Web GP) for Species-Identification for All Organisms
     --- Mohammed Naimuddin, Takehiro Watanabe, Koichi Nishigaki 

Structure-Revealing Representation of Genome: \textit{Oligostickiness} \textit{Map}
     --- Ayumu Saito, Koichi Nishigaki