Genome Informatics Vol. 11 (2000)

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Genome Informatics Vol. 11 (2000)

Presented at the Genome Informatics Workshop 2000
December 18-19, 2000, Garden Hall, Yebisu Garden Place, Tokyo, Japan

Published as: A.K. Dunker, A. Konagaya, S. Miyano, and T.Takagi (eds.) "Genome Informatics 2000"
Universal Academy Press, Tokyo, 2000

Preface by A. Keith Dunker and Akihiko Konagaya

Program Committee

 


 

Full Talk Papers

Rice at the Forefront of Plant Genome Informatics
Bal A. Antonio, Katsumi Sakata, Takuji Sasaki
Genome Informatics 11: 3-11 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

An Integrated Analysis and Database System for Full-Length cDNA
Tetsuo Nishikawa, Katsuhiko Murakami, Naoyuki Harada, Toshio Ota, Tomoyasu Sugiyama, Keiichi Nagai, Ryotaro Irie, Hiroshi Matui, Makiko Suwa, Takao Isogai
Genome Informatics 11: 12-23 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

An Infrastructure for Comparative Genomics to Functionally Characterize Genes and Proteins
Clemens Suter-Crazzolara, Gunther Kurapkat
Genome Informatics 11: 24-32 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Intelligent DNA Chips: Logical Operation of Gene Expression Profiles on DNA Computers
Yasubumi Sakakibara, Akira Suyama
Genome Informatics 11: 33-42 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Biological Sequence Compression Algorithms
Toshiko Matsumoto, Kunihiko Sadakane, Hiroshi Imai
Genome Informatics 11: 43-52 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Sequencing by Hybridization in the Presence of Hybridization Errors
Koichiro Doi, Hiroshi Imai
Genome Informatics 11: 53-62 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Visualization and Manipulation of Pedigree Diagrams
Limsoon Wong
Genome Informatics 11: 63-72 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Intelligent System for Topic Survey in MEDLINE by Keyword Recommendation and Learning Text Characteristics
Miyako Tanaka, Sanae Nakazono, Hiroshi Matsuno, Hideki Tsujimoto, Yasuhiko Kitamura, Satoru Miyano
Genome Informatics 11: 73-82 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Correspondence Analysis of Genes and Tissue Types and Finding Genetic Links from Microarray Data
Hirohisa Kishino, Peter J. Waddell
Genome Informatics 11: 83-95 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Environmental Factor Dependent Maximum Likelihood Method for Association Study Targeted to Personalized Medicine
Tatsuhiko Tsunoda, Ryo Yamada, Toshihiro Tanaka, Yozo Ohnishi, Naoyuki Kamatani
Genome Informatics 11: 96-105 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Expression Profiles and Biological Function
Juan Carlos Oliveros, Christian Blaschke, Javier Herrero, Joaquín Dopazo, Alfonso Valencia
Genome Informatics 11: 106-117 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Inferring Genetic Networks from DNA Microarray Data by Multiple Regression Analysis
Mamoru Kato, Tatsuhiko Tsunoda, Toshihisa Takagi
Genome Informatics 11: 118-128 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Cluster Inference Methods and Graphical Models Evaluated on NCI60 Microarray Gene Expression Data
Peter J. Waddell, Hirohisa Kishino
Genome Informatics 11: 129-140 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Protein Sequence-Structure Alignment Based on Site-Alignment Probabilities
Sanzo Miyazawa
Genome Informatics 11: 141-150 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Clustering and Averaging of Images in Single-Particle Analysis
Kiyoshi Asai, Yutaka Ueno, Chikara Sato, Katsutoshi Takahashi
Genome Informatics 11: 151-160 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Intrinsic Protein Disorder in Complete Genomes
A. Keith Dunker, Zoran Obradovic, Pedro Romero, Ethan C. Garner, Celeste J. Brown
Genome Informatics 11: 161-171 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Comparing Predictors of Disordered Protein
Xiaohong Li, Zoran Obradovic, Celeste J. Brown, Ethan C. Garner, A. Keith Dunker
Genome Informatics 11: 172-184 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Gene Network Inference Method from Continuous-Value Gene Expression Data of Wild-Type and Mutants
Koji M. Kyoda, Mineo Morohashi, Shuichi Onami, Hiroaki Kitano
Genome Informatics 11: 196-204 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

MIAX: A System for Assessment of Macromolecular Interaction. 3) A Parallel Hybrid GA for Flexible Protein Docking
Carlos Adriel Del Carpio M., Atsushi Yoshimori
Genome Informatics 11: 205-214 (2000)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Software Demonstration Abstracts

FANTOM+: The Interface for Functional Annotation of Mouse cDNA
Hidemasa Bono, Takeya Kasukawa, Toshihisa Okido, Katsunaga Sakai, Masaaki Furuno, Shotaro Kohtsuki, Kiyoshi Yoshida, Yasushi Okazaki, Yoshihide Hayashizaki
Genome Informatics 11: 219-221 (2000)
[Full-text PDF]

KEGG/EXPRESSION: A Database for Browsing and Analysing Microarray Expression Data
Susumu Goto, Shuichi Kawashima, Yoshinori Okuji, Tomomi Kamiya, Satoshi Miyazaki, Youjiro Numata, Minoru Kanehisa
Genome Informatics 11: 222-223 (2000)
[Full-text PDF]

A New Version of the KMDB/MutationView: A Keio Mutation Database for Human Disease Genes
Shinsei Minoshima, Susumu Mitsuyama, Masafumi Ohtsubo, Takashi Kawamura, Sachiko Ito, Sayumi Shibamoto, Fumiaki Ito, Nobuyoshi Shimizu
Genome Informatics 11: 224-226 (2000)
[Full-text PDF]

A Simulation Tool for Regulatory Network of Gene Expressions in the Patterning of Multicellular Organisms
Shin-Ichi Koga, Hiroshi Matsuno, Ryutaro Murakami
Genome Informatics 11: 227-228 (2000)
[Full-text PDF]

Genomic Object Net: Object Oriented Representation of Biological Systems
Hiroshi Matsuno, Atsushi Doi, Rainer Drath, Satoru Miyano
Genome Informatics 11: 229-230 (2000)
[Full-text PDF]

Poster Abstracts

Quantitative Estimation of Cross-Hybridization in DNA Microarrays Based on a Linear Model
Mitsuteru Nakao, Yoshinori K. Okuji, Minoru Kanehisa
Genome Informatics 11: 231-232 (2000)
[Full-text PDF]

Gene Expression Analysis of Orthologs in Synechocystis sp. with Operons in Escherichia coli
Yoshinori K. Okuji, Yukako Hihara, Ayako Kamei, Masahiko Ikeuchi, Iwane Suzuki, Norio Murata, Minoru Kanehisa
Genome Informatics 11: 233-234 (2000)
[Full-text PDF]

Data Submission System for Cyanobacterial DNA Chip Consortium
Ikuo Uchiyama, Tomoki Miwa, Hiroyo Nishide, Iwane Suzuki, Tatsuo Omata, Masahiko Ikeuchi, Norio Murata, Minoru Kanehisa
Genome Informatics 11: 235-236 (2000)
[Full-text PDF]

ALL/AML Cancer Classification by Gene Expression Data Using SVM and CSVM Approach
Xuegong Zhang, Haixin Ke
Genome Informatics 11: 237-239 (2000)
[Full-text PDF]

Classification of Hepatocellular Carcinoma by Gene Expression Profiling Analysis
Shuichi Tsutsumi, Yuko Kobune, Yutaka Midorikawa, Hiroyuki Aburatani
Genome Informatics 11: 240-241 (2000)
[Full-text PDF]

Inference of Genetic Networks from Expression Profile by Graphical Gaussian Modeling
Hiroyuki Toh, Katsuhisa Horimoto
Genome Informatics 11: 242-244 (2000)
[Full-text PDF]

Visualization of Genetic Networks: Edge Crossing Minimization of a Graph Drawing with Vertex Pairs
Atsuko Yamaguchi, Hiroyuki Toh
Genome Informatics 11: 245-246 (2000)
[Full-text PDF]

A Procedure for Estimating Cluster Boundaries in Gene Expression Profile Data
Katsuhisa Horimoto, Hiroyuki Toh
Genome Informatics 11: 247-248 (2000)
[Full-text PDF]

Finding Sparse Gene Networks
Ayumi Shinohara, Keisuke Iida, Masayuki Takeda, Osamu Maruyama, Satoru Miyano, Satoru Kuhara
Genome Informatics 11: 249-250 (2000)
[Full-text PDF]

Gene Expression Analysis Using Fuzzy ART Model
Shuta Tomida, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi
Genome Informatics 11: 251-252 (2000)
[Full-text PDF]

Extracting Negative Correlation Pattern from Gene Expression Microarray Data
Hwanseok Rhee, Cholhee Jung, Kyongoh Yoon, Hyunseok Park
Genome Informatics 11: 253-254 (2000)
[Full-text PDF]

A Statistical Analysis Method for Gene Expression Based on EM Algorithm
Ryoko Morioka, Taku Oshima, Yuya Kawagoe, Takeshi Ara, Shin Ishii, Hirotada Mori
Genome Informatics 11: 255-256 (2000)
[Full-text PDF]

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
Genome Informatics 11: 257-259 (2000)
[Full-text PDF]

Practical Organization and Functional Annotation of RIKEN cDNA Microarray
Hidemasa Bono, Takeya Kasukawa, Rika Miki, Koji Kadota, Yasushi Okazaki, Yoshihide Hayashizaki
Genome Informatics 11: 260-261 (2000)
[Full-text PDF]

Automatic Spot Measurement for Genetic Spot Array Images
Naoya Ohta, Youhei Hachisu, Tatsuya Akutsu, Asao Fujiyama
Genome Informatics 11: 262-263 (2000)
[Full-text PDF]

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
Genome Informatics 11: 264-265 (2000)
[Full-text PDF]

In Silico Differential Display
Hiroo Murakami, Takashi Suzuki, Seon-Yong Jeong, Hideji Hashida, Jun Goto, Ichiro Kanazawa
Genome Informatics 11: 266-267 (2000)
[Full-text PDF]

The Role of Gene Expression Regulation in Yeast Cell Cycle Pathway
Toshiaki Katayama, Minoru Kanehisa
Genome Informatics 11: 268-269 (2000)
[Full-text PDF]

Extraction of Correlated Gene Clusters from Multiple Graph Structures: Theory
Akihiro Nakaya, Susumu Goto, Minoru Kanehisa
Genome Informatics 11: 270-271 (2000)
[Full-text PDF]

Extraction of Correlated Gene Clusters from Multiple Graph Structures: Application
Shuichi Kawashima, Akihiro Nakaya, Yoshinori Okuji, Susumu Goto, Minoru Kanehisa
Genome Informatics 11: 272-273 (2000)
[Full-text PDF]

Classification and Analysis of Eukaryotic ABC Transporters in Complete Eukarya Genomes
Yoshinobu Igarashi, Daisuke Kihara, Minoru Kanehisa
Genome Informatics 11: 274-275 (2000)
[Full-text PDF]

The Construction of a Database on the Intracellular Vesicular Transport
Akiyasu C. Yoshizawa, Shuichi Kawashima, Minoru Kanehisa
Genome Informatics 11: 276-277 (2000)
[Full-text PDF]

Quantitative Modeling of Gene Regulatory Network: Identifying the Network by Means of Genetic Algorithms
Shin Ando, Hitoshi Iba
Genome Informatics 11: 278-280 (2000)
[Full-text PDF]

Identifying Gene Regulatory Network as Differential Equation by Genetic Programming
Erina Sakamoto, Hitoshi Iba
Genome Informatics 11: 281-283 (2000)
[Full-text PDF]

An Application of a Pathway Alignment Method to the Analysis of Amino Acid Biosynthesis
Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto
Genome Informatics 11: 284-285 (2000)
[Full-text PDF]

Selection of Candidate Genes for Polygenic Diseases by Utilizing Protein-Protein Interaction Networks
Tetsuro Toyoda, Yuki Takigawa
Genome Informatics 11: 286-288 (2000)
[Full-text PDF]

Emergent of Networks Based on Relationship among Elements
Yasuhiro Suzuki, Qingwei Zhang, Hiroshi Tanaka
Genome Informatics 11: 289-290 (2000)
[Full-text PDF]

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
Genome Informatics 11: 291-292 (2000)
[Full-text PDF]

Target Prediction of Transcription Factors and Its Application to Genome Analysis
Akinori Sarai, Samuel Selvaraj, YiFei Wang, Jianghong An, Ponraj Prabakaran, Hidetoshi Kono
Genome Informatics 11: 293-294 (2000)
[Full-text PDF]

A Method for Predicting Transcription Factors Using Local Regions of Biased Amino Acid Composition
Goro Terai, Takeshi Mizuno, Kenta Nakai, Toshihisa Takagi
Genome Informatics 11: 295-296 (2000)
[Full-text PDF]

A Transcription Regulatory Region Analysis System
Katsuhiko Murakami, Yohinori Ohta, Koji Tanikawa, Hiroki Nakae, Shigeo Ihara, Toshihisa Takagi
Genome Informatics 11: 297-298 (2000)
[Full-text PDF]

Transcriptome Analysis Based on Isothermal Sequence Amplification
Kiyoshi Yasukawa, Takahiko Ishiguro
Genome Informatics 11: 299-300 (2000)
[Full-text PDF]

Detection of tRNA Based on the Cloverleaf Secondary Structure
Makoto Kinouchi, Shigehiko Kanaya, Toshimichi Ikemura, Yoshihiro Kudo
Genome Informatics 11: 301-302 (2000)
[Full-text PDF]

RNA Secondary Structure Based Prediction of Simian Immunodeficiency Virus Nucleocapsid NCp8 Protein Recognition Site
Naoko Takada, Yukio Sugiura
Genome Informatics 11: 303-304 (2000)
[Full-text PDF]

Development of a Bioinformatic System for Determination of the 3D Structure of RNA from Secondary Structure Constrains
Yoshimitsu Shigenobu, Carlos A. Del Carpio
Genome Informatics 11: 305-306 (2000)
[Full-text PDF]

CONSERV: A Tool for Finding Exact Matching Conserved Sequences in Biological Sequences
Naohisa Goto, Ken Kurokawa, Teruo Yasunaga
Genome Informatics 11: 307-308 (2000)
[Full-text PDF]

Searching the Most Conserved Sequence in Bacterial Whole Genomes
Ken Kurokawa, Naohisa Goto, Teruo Yasunaga
Genome Informatics 11: 309-310 (2000)
[Full-text PDF]

Computational Analysis of the Strand Bias of the Chi Sequences and Other Oligonucleotides in Bacterial Genomes
Kazuharu Arakawa, Reina Uno, Yoichi Nakayama, Masaru Tomita
Genome Informatics 11: 311-312 (2000)
[Full-text PDF]

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
Genome Informatics 11: 313-314 (2000)
[Full-text PDF]

Statistical Analysis of Genomic Information: Long-Range Correlation in DNA Sequences
Atsushi Fukushima, Makoto Kinouchi, Shigehiko Kanaya, Yoshihiro Kudo, Toshimichi Ikemura
Genome Informatics 11: 315-316 (2000)
[Full-text PDF]

Multiple Sequence Alignment by Genetic Algorithm
Kenichi Hanada, Tsutomu Yokoyama, Toshio Shimizu
Genome Informatics 11: 317-318 (2000)
[Full-text PDF]

Positional Correlation in Base Occurrence in Splicing Patterns
Yumi Kudo, Yumi Tamada, Toshio Shimizu
Genome Informatics 11: 319-320 (2000)
[Full-text PDF]

Sequence Analysis of Redundant Usage of DNA Fragments in Complete Genomes
Masumi Itoh, Toshiaki Katayama, Yoshinori K. Okuji, Minoru Kanehisa
Genome Informatics 11: 321-322 (2000)
[Full-text PDF]

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
Genome Informatics 11: 323-324 (2000)
[Full-text PDF]

An E. coli Pseudo-tRNA Gene Cluster Homologous to the tRNA-Gene Cluster in the Bacillus subtilis trrnD Operon
Koji Ohnishi, Touru Suzuki, Hiroshi Shutou
Genome Informatics 11: 325-326 (2000)
[Full-text PDF]

Estimating the Number of Mouse Genes and the Duplicated Regions within the Mouse Genome
Yasuhiko Wada, Tadashi Imanishi, Takashi Gojobori
Genome Informatics 11: 327-328 (2000)
[Full-text PDF]

Specific PCR Primer and Probe Design Based on Spanning Networks
James Stuart Nelson, Hiroaki Kasai
Genome Informatics 11: 329-330 (2000)
[Full-text PDF]

Novel Method for Primer/Probe Design and Sequence Analysis
Ken-ichi Kurata, Hiroshi Nakamura
Genome Informatics 11: 331-332 (2000)
[Full-text PDF]

A Comprehensive Comparison between Locations of Orthologs in Circular Microbial Genomes
Hiroaki Saitoh, Kentaro Mori, Satoshi Fukuchi, Katsuhisa Horimoto
Genome Informatics 11: 333-334 (2000)
[Full-text PDF]

A Method for Sequence Analysis Using Multivariate Analysis
Jun-Ichi Sagara, Kentaro Shimizu
Genome Informatics 11: 335-336 (2000)
[Full-text PDF]

A Local Search Algorithm for Local Multiple Alignment: Special Case Analysis and Application to Cancer Classification
Tatsuya Akutsu
Genome Informatics 11: 337-338 (2000)
[Full-text PDF]

Association of Putative Restriction Modification Genes with Large Genome Polymorphisms Suggested from Comparison of Pyrococcus horikoshii and Pyrococcus abyssi Genome Sequences
Akito Chinen, Ikuo Uchiyama, Ichizo Kobayashi
Genome Informatics 11: 339-340 (2000)
[Full-text PDF]

CGAT: Comparative Genome Analysis Tool for Closely Related Microbial Genomes
Ikuo Uchiyama, Toshio Higuchi, Ichizo Kobayashi
Genome Informatics 11: 341-342 (2000)
[Full-text PDF]

Super-Motifs of Leucine-Rich Repeats (LRRs) Proteins
Norio Matsushima, Masakatsu Kamiya, Norio Suzuki, Takanori Tanaka
Genome Informatics 11: 343-345 (2000)
[Full-text PDF]

Identifying Intrinsic Disorder by Sequence Homology
Sachiko Takayama, Thomas Marshal, Christopher Oldfield, Andrew Campen, A. Keith Dunker, Celeste J. Brown
Genome Informatics 11: 346-347 (2000)
[Full-text PDF]

Large-Scale Sequence Analyses in the Arabidopsis thaliana Genome Sequencing Project: Status 2000
Yasukazu Nakamura, Satoshi Tabata
Genome Informatics 11: 348-349 (2000)
[Full-text PDF]

Analysis of cis-Acting Elements in Large-Scale Rice Genome Sequence
Atsuko Idonuma, Katsumi Sakata, Takuji Sasaki, Wakako Watanabe, Ikuo Horiuchi, Yuji Shimizu
Genome Informatics 11: 350-351 (2000)
[Full-text PDF]

Contig Ordering Based on Physical Subunit Orders of ATP Synthase
Cholhee Jung, Hwanseok Rhee, Hyunseok Park, Jinyoung Choi
Genome Informatics 11: 352-353 (2000)
[Full-text PDF]

Structure-Revealing Representation of Genome: Oligostickiness Map
Ayumu Saito, Koichi Nishigaki
Genome Informatics 11: 354-355 (2000)
[Full-text PDF]

A System for Finding Association Rules from Microarray Data and Public Databases
Takahiro Naitou, Kenji Satou, Emiko Furuichi, Satoru Kuhara, Toshihisa Takagi
Genome Informatics 11: 356-357 (2000)
[Full-text PDF]

Mining Association Rules Related to Protein-Protein Interactions
Takuya Oyama, Kagehiko Kitano, Kenji Satou, Takashi Ito
Genome Informatics 11: 358-359 (2000)
[Full-text PDF]

HypothesisCreator: A Framework for Knowledge Discovery Application Development
Yoshinori Tamada, Hideo Bannai, Osamu Maruyama, Satoru Miyano
Genome Informatics 11: 360-361 (2000)
[Full-text PDF]

Characterization of Subcellular Localization Signals Using HypothesisCreator
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano
Genome Informatics 11: 362-363 (2000)
[Full-text PDF]

Development of Data Evaluation Supporting System for Large-Scale Experimental Results
Mikio Yoshida, Hiroshi Fukagawa, Yukari Shibagaki, Hideaki Shimano, Takeshi Mizuno
Genome Informatics 11: 364-365 (2000)
[Full-text PDF]

On-Web Encyclopedia of Genome Profiles (On-Web GP) for Species-Identification for All Organisms
Mohammed Naimuddin, Takehiro Watanabe, Koichi Nishigaki
Genome Informatics 11: 366-367 (2000)
[Full-text PDF]

A Dynamic Reconstruction Model for Embryo Development of C. elegans
Tsuguchika Kaminuma, Masumi Yukawa, Makiko Okada, Naomi Komiyama, Noriko Kabuyama, Katsuhiko Taki
Genome Informatics 11: 368-369 (2000)
[Full-text PDF]

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
Genome Informatics 11: 370-371 (2000)
[Full-text PDF]

Assessment of Redundancy and Full-Length Rate of Full-Length Enriched cDNA Libraries
Hideaki Konno, Yoshifumi Fukunishi, Piero Carninci, Yoshihide Hayashizaki
Genome Informatics 11: 372-373 (2000)
[Full-text PDF]

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
Genome Informatics 11: 374-375 (2000)
[Full-text PDF]

Representing Functional Annotations of Mouse cDNA Sequences in XML
Takeya Kasukawa, Hidemasa Bono, Hideo Matsuda, Yasushi Okazaki, Shotaro Kohtsuki, Yoshihide Hayashizaki
Genome Informatics 11: 376-377 (2000)
[Full-text PDF]

Autonomous Distributed Genome Database and Its Application to Mouse cDNA and Human Genome Sequence Matching
Yoshiyuki Tanaka, Takeshi Nagashima, Akihiko Konagaya
Genome Informatics 11: 378-379 (2000)
[Full-text PDF]

Development of DDBJ-XML and Its Application to a Database of cDNA
Satoru Miyazaki, Hideaki Sugawara
Genome Informatics 11: 380-381 (2000)
[Full-text PDF]

HOWDY: The Integrated Human Genome Database of ALIS
Katsuji Matsumura, Mika Hirakawa, Kazuo Takehana, Hiroko Yamaguchi, Sanae Sato, Masako Kuroda
Genome Informatics 11: 382-383 (2000)
[Full-text PDF]

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
Genome Informatics 11: 384-385 (2000)
[Full-text PDF]

ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions
P. Prabakaran, Jianghong An, M. Michael Gromiha, S. Selvaraj, Hatsuho Uedaira, Hidetoshi Kono, Akinori Sarai
Genome Informatics 11: 386-387 (2000)
[Full-text PDF]

AngioDB: Angiogenesis Database
Tae-Kwon Sohn, Eun-Joung Moon, Seok-Ki Lee, Hwan-Gue Cho, Kyu-Won Kim
Genome Informatics 11: 388-389 (2000)
[Full-text PDF]

Application of Digital Signal Processing in Clinical Database Management
Pawan Kumar Dhar, S. Vikram, U.C. Niranjan
Genome Informatics 11: 390-391 (2000)
[Full-text PDF]

Pharmacoinformatics Infrastructure for Genome Based Personalized Medicine
Kotoko Nakata, Tatsuya Nakano, Takako Takai-Igarashi, Tsuguchika Kaminuma
Genome Informatics 11: 392-393 (2000)
[Full-text PDF]

Computational Design of Proteinous Drug Employing Hidden Markov Model
Taizo Hanai, Hideki Noguchi, Yukari Matsubara, Kazuya Takeda, Hiroyuki Honda, Vladimir Brusic, Takeshi Kobayashi
Genome Informatics 11: 394-395 (2000)
[Full-text PDF]

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
Genome Informatics 11: 396-398 (2000)
[Full-text PDF]

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
Genome Informatics 11: 399-401 (2000)
[Full-text PDF]

Comparison of Affected-Sib-Pair Statistics for Multi-Locus Genetic Disease Models in Multi-Marker Analysis
Osamu Ogasawara, Toshihisa Takagi
Genome Informatics 11: 402-403 (2000)
[Full-text PDF]

Standardized Phylogenetic Tree
Toshinori Endo, Soichi Ogishima, Hiroshi Tanaka
Genome Informatics 11: 404-405 (2000)
[Full-text PDF]

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
Genome Informatics 11: 406-407 (2000)
[Full-text PDF]

A Sequential-Linking Method for Analysis of Within-Host Viral Evolution
Fengrong Ren, Soichi Ogishima, Hiroshi Tanaka
Genome Informatics 11: 408-409 (2000)
[Full-text PDF]

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
Genome Informatics 11: 410-411 (2000)
[Full-text PDF]

Polarity Difference Score: A New Measure for Recognition and Classification of Transmembrane Protein Structures
Makiko Suwa, Henrik T. Yudate, Yasuhiko Masuho, Shigeki Mitaku
Genome Informatics 11: 412-413 (2000)
[Full-text PDF]

SOSUIsignal: Software System for Prediction of Signal Peptide and Membrane Protein
Masahiro Gomi, Fumitsugu Akazawa, Shigeki Mitaku
Genome Informatics 11: 414-415 (2000)
[Full-text PDF]

Novel Index of Polar Amino Acids Characterizing End Region of Transmembrane Helices
Toshiyuki Hayashibe, Takatsugu Hirokawa, Shigeki Mitaku
Genome Informatics 11: 416-417 (2000)
[Full-text PDF]

Prediction of Dumbbell-Type Soluble Proteins and Their Center Helices
Shun-ya Takahashi, Shigeki Mitaku
Genome Informatics 11: 418-419 (2000)
[Full-text PDF]

Sequence Analysis of Less Hydrophobic Transmembrane Segments in Polytopic Membrane Proteins
Hiromitsu Araki, Toshihisa Takagi, Kenta Nakai
Genome Informatics 11: 420-421 (2000)
[Full-text PDF]

Transmembrane Topology Pattern and Detection of Transmembrane Protein Functions
Natalia Poluliakh, Kohei Saito, Toshio Shimizu
Genome Informatics 11: 422-423 (2000)
[Full-text PDF]

A Transmembrane Topology Prediction Method Based on Integration Mechanism
Hanako Ito, Demelo Madrazo Lao, Toshio Shimizu
Genome Informatics 11: 424-425 (2000)
[Full-text PDF]

Evaluation of Transmembrane Topology Prediction Methods by Using an Experimentally Characterized Topology Dataset
Masami Ikeda, Masafumi Arai, Toshio Shimizu
Genome Informatics 11: 426-427 (2000)
[Full-text PDF]

Comparison of Geometries and Properties of Protein Molecular Surface for Structure-Based Function Prediction
Kengo Kinoshita, Jun'ichi Furui, Haruki Nakamura
Genome Informatics 11: 428-429 (2000)
[Full-text PDF]

A Method of Protein Molecular Surface Comparison Based on Geometric Hashing
Keiichirou Matsuura, Norimasa Shoji, Takenao Okawa, Haruki Nakamura
Genome Informatics 11: 430-431 (2000)
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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
Genome Informatics 11: 432-433 (2000)
[Full-text PDF]

MIAX: A System for Assessment of Macromolecular Interaction. 4) Interaction Site Inference by Molecular Hydrophobic and Electrostatic Analysis
Atsushi Yoshimori, Carlos A. Del Carpio
Genome Informatics 11: 434-435 (2000)
[Full-text PDF]

A QSAR Study for Modeling MHC Class-I Binding Oligo-Peptides
Simonetta Fickel, Carlos A. Del Carpio
Genome Informatics 11: 436-437 (2000)
[Full-text PDF]

Automatic Collection of Functional Sequence Based on Annotations in the GenBank Entry
Yoshifumi Okada, Tomomasa Nagashima
Genome Informatics 11: 438-439 (2000)
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SIGNAL-ONTOLOGY: Ontology for Cell Signaling
Takako Takai-Igarashi, Toshihisa Takagi
Genome Informatics 11: 440-441 (2000)
[Full-text PDF]

Toward Automatic Construction of Extensional Ontology from Genome Databases
Takuya Yagyuu, Kenji Satou
Genome Informatics 11: 442-443 (2000)
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Toward Automatic Recognition of Field Description Syntax and Parser Generation for Genome Databases
Takeo Sakai, Kenji Satou
Genome Informatics 11: 444-445 (2000)
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Use of a Full Parser for Information Extraction in Molecular Biology Domain
Akane Yakushiji, Yuka Tateisi, Yusuke Miyao, Jun'ichi Tsujii
Genome Informatics 11: 446-447 (2000)
[Full-text PDF]

The GENIA Project: Knowledge Acquisition from Biology Texts
Nigel Collier, Hideki Mima, San Zoo Lee, Tomoko Ohta, Yuka Tateisi, Akane Yakushiji, Jun'ichi Tsujii
Genome Informatics 11: 448-449 (2000)
[Full-text PDF]

Evaluation of Automatic Term Recognition of Nuclear Receptors from MEDLINE
Sophia Ananiadou, Sylvie Albert, Dietrich Schuhmann
Genome Informatics 11: 450-451 (2000)
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Automatic Construction of Search Condition for Making an Exhaustive List of Similar Papers
Jianghong An, Takao Nakama, Ponraj Prabakaran, Akinori Sarai
Genome Informatics 11: 452-453 (2000)
[Full-text PDF]

Computer Simulation of Glycolysis in Pancreatic beta-Cells Using the E-CELL System
Yasuhiro Naito, Hiromu Nakajima, Masaru Tomita
Genome Informatics 11: 454-455 (2000)
[Full-text PDF]

Quantitative Modeling of Mitochondrial Energy Metabolism Using E-Cell Simulation Environment
Katsuyuki Yugi, Masaru Tomita
Genome Informatics 11: 456-457 (2000)
[Full-text PDF]

Computer Modeling of Photosynthesis Using the E-CELL System
Emily Wang, Yoichi Nakayama, Masaru Tomita
Genome Informatics 11: 458-459 (2000)
[Full-text PDF]

Computer Simulation of Enzyme Deficiency in Human Erythrocyte Using the E-Cell System
Yoichi Nakayama, Ayako Kinoshita, Masaru Tomita
Genome Informatics 11: 460-461 (2000)
[Full-text PDF]

A Cellular Automata System with Reconfigurable Hardware: Towards a Whole Cell Simulation
Kobori Tomoyoshi, Tsutomu Maruyama, Koshiki Yamaguchi, Akihiko Konagaya
Genome Informatics 11: 462-463 (2000)
[Full-text PDF]

A Security System for Human Genome Information Encoded by Chemicals, Not by Electronic Codes
Yumi Kawazoe, Toshikazu Shiba, Masahito Yamamoto, Azuma Ohuchi
Genome Informatics 11: 464-465 (2000)
[Full-text PDF]

DNA Solution of the Shortest Path Problem by Concentration Control
Masahito Yamamoto, Nobuo Matsuura, Toshikazu Shiba, Azuma Ohuchi
Genome Informatics 11: 466-467 (2000)
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Invited Talks

Whole Genome Assemblies of the Drosophila and Human Genomes
Gene Myers
Genome Informatics 11: 217-217 (2000)
[Full-text PDF]

RIKEN Structural Genomics Initiative
Shigeyuki Yokoyama
Genome Informatics 11: 218-218 (2000)
[Full-text PDF]