| P 240 [PS file][PDF file] | |
| Title | Annotation of PDB with respect to ``Disordered Regions'' in Proteins |
| Author(s) | Meeta Rani, Pedro Romero, Zoran Obradovic, A. Keith Dunker |
| P 242 [PS file][PDF file] | |
| Title | E-CELL Project Overview: Towards Integrative Simulation of Cellular Processes |
| Author(s) | Masaru Tomita, Kenta Hashimoto, Kouichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Kanako Saito, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Sakura Tanida, Thomas S. Shimizu |
| P 244 [PS file][PDF file] | |
| Title | Modeling of Transcription and DNA Replication Using the E-CELL Simulation System |
| Author(s) | Kenta Hashimoto, Fumihiko Miyoshi, Thomas S. Shimizu, Takeshi Satoyoshi, Masaru Tomita |
| P 246 [PS file][PDF file] | |
| Title | Modeling of Signal Transduction for Bacterial Chemotaxis Using the E-CELL Simulation System |
| Author(s) | Yuri Matsuzaki, Kanako Saito, Tom Shimizu, Masaru Tomita |
| P 248 [PS file][PDF file] | |
| Title | Modeling of Human Red Blood Cell Using the E-CELL Simulation System |
| Author(s) | Riou Matsushima, Akiko Kawase, Naoko Watanabe, Hisako Nakano, Kanako Saito, Masaru Tomita |
| P 250 [PS file][PDF file] | |
| Title | Modeling Theory and Software Architecture of the E-CELL Simulation System |
| Author(s) | Kouichi Takahashi, Tom Shimizu, Katsuyuki Yugi, Masaru Tomita |
| P 252 [PS file][PDF file] | |
| Title | Multivariate Time Series Analysis of Metabolic Network Using the E-CELL Simulation System |
| Author(s) | Yusuke Saito, Kouichi Takahashi, Masaru Tomita |
| P 254 [PS file][PDF file] | |
| Title | Evolution of Overlapping Genes: Comparative Genomics of Mycoplasma genitalium and Mycoplasma pneumoniae |
| Author(s) | Yoko Fukuda, Takanori Washio, Masaru Tomita |
| P 256 [PS file][PDF file] | |
| Title | On Periodicity of Adenine-Adenine Dinucleotides in Bacterial Genomes |
| Author(s) | Masahiko Wada, Yukihiro Kawashima, Masaru Tomita |
| P 258 [PS file][PDF file] | |
| Title | Computer Analysis of Base Pairing Free-Energy between Shine-Dalgarno Sequence and 16S rRNA in Various Procaryotes |
| Author(s) | Yuko Osada, Rintaro Saito, Masaru Tomita |
| P 260 [PS file][PDF file] | |
| Title | On Low Frequency of CpG Dinucleotides in Bacterial Genomes |
| Author(s) | Mami Goto, Takanori Washio, Masaru Tomita |
| P 262 [PS file][PDF file] | |
| Title | Analysis of Translation Initiation Sites in the Complete Genome of Mycoplasma genitalium Suggests That This Bacterium Uses Alternative Signal for Translation Initiation |
| Author(s) | Rintaro Saito, Masaru Tomita |
| P 264 [PS file][PDF file] | |
| Title | Expression Frequency of the Human Immunoglobulin $\lambda$ Light Chain Genes and the Roles of Their Recombination Signal and Spacer Sequences |
| Author(s) | Taku Okada, Masaru Tomita, Kazuhiko Kawasaki, Shinsei Minoshima, Nobuyoshi Shimizu |
| P 266 [PS file][PDF file] | |
| Title | Assessment of Utility of ESTs for Nucleotide Diversity Using Available Assembled Alignments from dbESt, STACK 2.0 and STACK-INDEX |
| Author(s) | Brian Karlak, Winston Hide |
| P 269 [PS file][PDF file] | |
| Title | A Genome-Level Search for Bacterial Genes on Which Positive Selection May Operate: A Means for Identifying Possible Virulence Factors? |
| Author(s) | Junaid Gamieldien, Winston Hide |
| P 271 [PS file][PDF file] | |
| Title | A Statistical Model for Prokaryotic Promoter Prediction |
| Author(s) | Joseph Oppon, Winston Hide |
| P 274 [PS file][PDF file] | |
| Title | Algorithms for Inference of Genetic Networks (AIGNET) |
| Author(s) | Shoji Watanabe, Yukihiro Maki, Yukihiro Eguchi, Daisuke Tominaga, Masahiro Okamoto |
| P 276 [PS file][PDF file] | |
| Title | An Educational Tool for Visualize DNA Structures in vivo |
| Author(s) | Shigehiro Fukase, Masato Wayama |
| P 278 [PS file][PDF file] | |
| Title | Extended Sequence Alignment Method for Protein Secondary Structure Prediction |
| Author(s) | Susumu Hiraoka |
| P 280 [PS file][PDF file] | |
| Title | Detection of Frame-Shift Error in the Yeast Genome Sequences |
| Author(s) | Naoko Kasahara, Naoyuki Harada, Keiichi Nagai |
| P 282 [PS file][PDF file] | |
| Title | Clustering and Detection of 5'Splice Sites of mRNA by $k$ Weight Matrix Model |
| Author(s) | Katsuhiko Murakami, Toshihisa Takagi |
| P 284 [PS file][PDF file] | |
| Title | Automated Metabolic Reconstruction at the Molecular Level |
| Author(s) | Masanori Arita |
| P 286 [PS file][PDF file] | |
| Title | Correlation between Exon and Dispersed Repetitive DNA Distributions on the Human Genome |
| Author(s) | Yoshiaki Hojo, Ikuo Uchiyama, Yataro Daigo, Yusuke Nakamura, Toshihisa Takagi |
| P 288 [PS file][PDF file] | |
| Title | Automatic Construction of Biological Abbreviation Dictionary from Abstracts of Biomedical Papers |
| Author(s) | Mikio Yoshida, Kenichiro Fukuda, Toshihisa Takagi |
| P 290 [PS file][PDF file] | |
| Title | A Workbench for Systematic Construction of Signal Transduction Pathways: Ontologies and Architectures |
| Author(s) | Kenichiro Fukuda, Mikio Yoshida, Toshihisa Takagi |
| P 292 [PS file][PDF file] | |
| Title | Development of Information Extraction Tool: Toward Construction of Protein-Protein Interaction Database |
| Author(s) | Tomoko Okazaki-Ohta, Toshihisa Takagi |
| P 294 [PS file][PDF file] | |
| Title | Palindrome Analysis: Distribution of Complete-Matched Inverted Repeats with a Moderate Length Spacer |
| Author(s) | Masao Fukagawa, Tatsuhiko Tsunoda, Toshihisa Takagi |
| P 296 [PS file][PDF file] | |
| Title | Construction of Ortholog/Paralog Group Table for PTS |
| Author(s) | Takeaki Taniguchi, Minoru Kanehisa |
| P 298 [PS file][PDF file] | |
| Title | A Library of Protein-Ligand Interaction Sites for de novo Ligand Design |
| Author(s) | Kiminobu Sato, Minoru Kanehisa |
| P 300 [PS file][PDF file] | |
| Title | Automatic Detection of Gene Clusters by P-Quasi Complete Linkage Grouping |
| Author(s) | Wataru Fujibuchi, Hiroyuki Ogata, Hideo Matsuda, Minoru Kanehisa |
| P 302 [PS file][PDF file] | |
| Title | The Construction of the Knowledge Base of Immune System |
| Author(s) | Yoshinobu Igarashi, Minoru Kanehisa |
| P 304 [PS file][PDF file] | |
| Title | Detection of Co-regulated Genes by Comparative Analysis of Microbial Genomes |
| Author(s) | Hiroyuki Ogata, Wataru Fujibuchi, Minoru Kanehisa |
| P 306 [PS file][PDF file] | |
| Title | Extracting Regulatory Signals from the Upstream Region of Co-expressed Genes Derived from DNA Microarray Experiments |
| Author(s) | Shuichi Kawashima, Hiroyuki Ogata, Minoru Kanehisa |
| P 308 [PS file][PDF file] | |
| Title | Protein Folding Simulation and Self-Consistent Potential Functions |
| Author(s) | Fumi Takazawa, Masaki Sasaki, Minoru Kanehisa |
| P 310 [PS file][PDF file] | |
| Title | Systematic Classification of B. subtilis Genes and Construction of a Knowledge Base to Represent Functional Information |
| Author(s) | Atsushi Ogiwara |
| P 312 [PS file][PDF file] | |
| Title | Search Pathways for Secondary Metabolites Based on Genome Analysis and Chemical Knowledge on Metabolism |
| Author(s) | Takaaki Nishioka, Kimito Funatsu |
| P 314 [PS file][PDF file] | |
| Title | A Method for Querying Complete Genomes by Viewing Them as Structured Documents |
| Author(s) | Aaron J. Stokes, Hideo Matsuda, Akihiro Hashimoto |
| P 316 [PS file][PDF file] | |
| Title | Maintenance of Transcription Factor DataBase TFDB by TFDB Maintenance System |
| Author(s) | Masako Kaizawa, Satoru Watanabe, Takahiro Nobukuni, Masami Horikoshi, Hiroshi Handa, Yoshiyuki Kuchino, Takao Sekiya, Hiroshi Mizushima |
| P 319 [PS file][PDF file] | |
| Title | ALIS: Data Management Systems for Human Genome Sequencing |
| Author(s) | Mika Hirakawa, Kensaku Imai, Hiroko Yamaguchi, Junko Shimada, Kazuo Takehana, Katsuji Matsumura, Takehiko Itoh, Masako Kuroda |
| P 321 [PS file][PDF file] | |
| Title | Automatic cDNA classification System for Mouse Genome Project |
| Author(s) | Yoshifumi Fukunishi, Hideaki Konno, Yoshihide Hayashizaki |
| P 324 [PS file][PDF file] | |
| Title | Automated cDNA Information System for Large Scale cDNA Project |
| Author(s) | Hideaki Konno, Yuichi Sugahara, Yoshifumi Fukunishi, Kazuhiro Shibata, Yoshihide Hayashizaki |
| P 326 [PS file][PDF file] | |
| Title | Application of the RLGS Image Analysis Tool (RAT) to the Construction of a Genetic Linkage Map of Recombinant Inbred Strain SMXA |
| Author(s) | Yuichi Sugahara, Yoshihide Hayashizaki |
| P 328 [PS file][PDF file] | |
| Title | 3DinSight: An Integrated Database and Search Tool for Structure, Function and Property of Biomolecules |
| Author(s) | Jianghong An, Takao Nakama, Yasushi Kubota, Akinori Sarai |
| P 330 [PS file][PDF file] | |
| Title | ProTherm: Thermodynamic Database for Proteins and Mutants |
| Author(s) | M. Michael Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira, Akinori Sarai |
| P 332 [PS file][PDF file] | |
| Title | Prediction of DNA target Sites by Regulatory Proteins Based on Structure-Derived Potential |
| Author(s) | Hidetoshi Kono, Akinori Sarai |
| P 334 [PS file][PDF file] | |
| Title | Genomic Hypothesis Creator: A Multi-Strategic View Creator for Sequences |
| Author(s) | Osamu Maruyama, Tomoyuki Uchida, Takayoshi Shoudai, Satoru Miyano |
| P 336 [PS file][PDF file] | |
| Title | Development of Web Interface of Image Analysis System DDGEL for 2D Gel Electrophoresis |
| Author(s) | Kyotetsu Kanaya, Akira Ohyama, Tatsuya Akutsu, Asao Fujiyama |
| P 338 [PS file][PDF file] | |
| Title | Subcubic Time Algorithms for RNA Secondary Structure Prediction |
| Author(s) | Tatsuya Akutsu |
| P 340 [PS file][PDF file] | |
| Title | ThreeTree: A New Method to Reconstruct Phylogenetic Trees |
| Author(s) | Satoshi OOta |
| P 342 [PS file][PDF file] | |
| Title | Efficiency of Model-Based Complexity Method for Estimating Unrooted Multifurcate Phylogenetic Tree |
| Author(s) | Fengrong Ren, Hiroshi Tanaka |
| P 344 [PS file][PDF file] | |
| Title | Secondary Structure Prediction Based on Statistical Mechanics |
| Author(s) | Yukio Kobayashi, Nobuhiko Saito |
| P 347 [PS file][PDF file] | |
| Title | Integrating Multiple Evidences by Hidden Markov Models |
| Author(s) | Kiyoshi Asai, Katunobu Itou, Tetsushi Yada |
| P 349 [PS file][PDF file] | |
| Title | Modeling Transcriptional Units of E. coli Genes Using HMM |
| Author(s) | Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Takahiro Ishii, Kenta Nakai |
| P 351 [PS file][PDF file] | |
| Title | A Database of B. subtilis Promoters and Transcription Factors |
| Author(s) | Takahiro Ishii, Kenta Nakai |
| P 353 [PS file][PDF file] | |
| Title | A Study Using Sequence Comparison to Investigate the Molecular Evolution of Mitochondrial tRNA Genes |
| Author(s) | Jun-Ichi Sagara, Shugo Nakamura, Mitsunori Ikeguchi, Kentaro Shimizu |
| P 355 [PS file][PDF file] | |
| Title | Prediction of Initiation Codons in cDNA Fragments Using Statistical Information and Similarity with Protein Sequences |
| Author(s) | Tetsuo Nishikawa, Toshio Ota, Takao Isogai |
| P 357 [PS file][PDF file] | |
| Title | Genome Analysis: Assigning Protein Coding Regions to 3D Structures |
| Author(s) | Asaf A. Salamov, Makiko Suwa, Christine A. Orengo, Mark B. Swindells |
| P 359 [PS file][PDF file] | |
| Title | A Novel Application of GeneMark-RC to the Analysis of Prokaryotic Genomes and Human cDNAs: Sequence Data with Statistical Deviations Are Rich in Important Biological Information |
| Author(s) | Makoto Hirosawa, Osamu Ohara, Katsumi Isono |
| P 361 [PS file][PDF file] | |
| Title | Annotation and Presentation Systems for Arabidopsis Genome Sequencing Project at Kazusa DNA Research Institute |
| Author(s) | Yasukazu Nakamura, Shusei Sato, Satoshi Tabata |
| P 363 [PS file][PDF file] | |
| Title | Charge Distribution of Signal Peptides and Signal Anchor Type II |
| Author(s) | Masahiro Gomi, Takatsugu Hirokawa, Shigeki Mitaku |
| P 365 [PS file][PDF file] | |
| Title | Topology Prediction of Membrane Proteins Based on a Modified ``Positive-Inside'' Rule |
| Author(s) | Koji Kadota, Hiroyuki Sasamoto, Takatsugu Hirokawa, Shigeki Mitaku |
| P 367 [PS file][PDF file] | |
| Title | Classification of Membrane Proteins by Types of Transmembrane Helices Using SOSUI System |
| Author(s) | Shigeki Mitaku, Takatsugu Hirokawa, Mitsuo Ono |
| P 369 [PS file][PDF file] | |
| Title | Gene Classification by Self-Organization Mapping of Codon Usage in Bacteria with Completely Sequenced Genome |
| Author(s) | Shigehiko Kanaya, Yoshihiro Kudo, Takashi Abe, Takanori Okazaki, Carlos Del Carpio, Toshimichi Ikemura |
| P 372 [PS file][PDF file] | |
| Title | GAFLEX: A Hybrid GA Engine for Mapping the Configuration Hyper-Space of Organic Compounds in Solution |
| Author(s) | Carlos A. Del Carpio |
| P 374 [PS file][PDF file] | |
| Title | DYNAX: A New System for Biomolecular Dynamics Simulation in Solution |
| Author(s) | Atsushi Yoshimori, Carlos A. Del Carpio |
| P 376 [PS file][PDF file] | |
| Title | Development of an Antibacterial MAP Homologous to a Loop Region in Human Lactoferrin |
| Author(s) | Masachika Azuma, Taiki Kojima, Masaki Kobayashi, Carlos Adriel Del Carpio |
| P 378 [PS file][PDF file] | |
| Title | MOLDEX:A Computer System for Drug Design. 4)A Combined Electro-Geometric Method for the Identification of Pharmacophoric Structural Patterns in Drugs |
| Author(s) | Hiromi Nakatake, Carlos Adriel Del Carpio |
| P 380 [PS file][PDF file] | |
| Title | A Simulated Annealing Algorithm for Geometrical Assessment of Macromolecular Hydrophobic Interaction |
| Author(s) | Tomoko Hara, Carlos Adriel Del Carpio |
| P 382 [PS file][PDF file] | |
| Title | A Genetic Programming Based System for the Prediction of Secondary and Tertiary Structures of RNA |
| Author(s) | Katsuhisa Yamaguchi, Carlos Adriel Del Carpio |
| P 384 [PS file][PDF file] | |
| Title | Detailed Sequence Analysis of the Distal Down Syndrome Critical Region and the SOD1/AML1 Region on Chromosome 21 |
| Author(s) | Todd Taylor, Masahira Hattori, Kiyoteru Noguchi, Tomomi Shobu, Kazuo Ishii, Atsushi Toyoda, Yoshiyuki Sakaki |
| P 386 [PS file][PDF file] | |
| Title | Genome Wide Survey of the Entire C. elegans alpha-Tubulin Gene Family: cDNA Cloning, Expression, and Structure-Function Analysis |
| Author(s) | Camelia B. Gogonea, M. Y. Ali, Tetsunari Fukushige, M. Afaq Shakir, Takashi Matsuo, Shahid S. Siddiqui |
| P 388 [PS file][PDF file] | |
| Title | Gene Has Its Inherent Significantly Repetitive Tuples |
| Author(s) | Nobuyuki Uchikoga, Akira Suyama |
| P 390 [PS file][PDF file] | |
| Title | Nucleotide Sequence of a Gene Encodes Characteristic Features of an Organism as Well as an Amino Acid Sequence |
| Author(s) | Hiroshi Nakashima, Motonori Ota, Ken Nishikawa, Tatsuo Ooi |
| P 391 [PS file][PDF file] | |
| Title | Application Computer Software in Mapping Quantitative Trait Loci |
| Author(s) | Chindo Hicks, Eiji Kobayashi, Masahiro Satoh, Kazuo Ishii, Tsutomu Furukawa |
| P 393 [PS file][PDF file] | |
| Title | Phosphoglycerate-transporter Protein B as a Most Primitive Protein Predicted by the Poly-tRNA Theory |
| Author(s) | Koji Ohnishi |
| P 395 [PS file][PDF file] | |
| Title | Sequence Analysis of the IRES-Loop III Region of Hepatitis C Virus |
| Author(s) | Takayoshi Sasano, Jun-Ichi Sagara, Shugo Nakamura, Mitsunori Ikeguchi, Kentaro Shimizu |
| [PS file][PDF file] | |
| Title | ORF Clustering Analysis of 17 Complete Genomes |
| Author(s) | Kenji Suzuki, Takeshi Ara, Hideo Matsuda, Hirotada Mori [P77 is not included in the book because the final manuscript was not in time for publication but included in CD-ROM.] |