Genome Informatics

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Volume 14

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Predict Functionally Important Residues Responsible for Estrogen Receptor Subtype Divergence

Feng Wang, Hirohisa Kishino, Yasuhiko Wada

2003Volume 14 Pages 514-515
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.514

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Protein Classification via Kernel Matrix Completion

Taishin Kin, Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai

2003Volume 14 Pages 516-517
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.516

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On Improving Protein Functional Identification in Pattern Recognition Based on Continuous Density HMM

Dooil Kim, Dae-Sil Lee

2003Volume 14 Pages 518-519
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.518

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Protein Family Classification Using Second-Order Recurrent Neural Networks

Jinmiao Chen, Narendra S. Chaudhari

2003Volume 14 Pages 520-521
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.520

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Profile-Profile Comparison Based on Hidden Markov Model Profiles

Makihiko Sato, Nobuyoshi Sugaya, Hiroo Murakami, Sachiyo Aburatani, Ka ...

2003Volume 14 Pages 522-523
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.522

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Genome Scale Classification of Extended Proteins by a Predictor SOSUIdumbbell

Nobuyuki Uchikoga, Ke Rungcong, Fumitsugu Akazawa, Masashi Sonoyama, S ...

2003Volume 14 Pages 524-525
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.524

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A New Method for Characterizing Functionally-Unknown Proteins Using Specific Amino Acid Frequency and Periodicity at the Proteome Level

Kosuke Fujishima, Jun Imoto, Akio Kanai, Masaru Tomita

2003Volume 14 Pages 526-527
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.526

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Classification of Protein Sequences into Paralog and Ortholog Clusters Using Sequence Similarity Profiles of KEGG/SSDB

Yohsuke Minowa, Toshiaki Katayama, Akihiro Nakaya, Susumu Goto, Minoru ...

2003Volume 14 Pages 528-530
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.528

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Detection of Remote Homologue Using Predicted Structural Information

Daisuke Ishibe, Katsunori Uehara, Takeshi Kawabata, Nobuhiro Go

2003Volume 14 Pages 531-532
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.531

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RiceBLAST: A Comprehensive Homology Search for Rice Specific Sequences

Yoshiaki Nagamura, Baltazar A. Antonio, Hisataka Numa, Ikuo Horiuchi, ...

2003Volume 14 Pages 533-534
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.533

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Scalable BLAST Service in OBIGrid Environment

Fumikazu Konishi, Yukimasa Shiroto, Ryo Umetsu, Akihiko Konagaya

2003Volume 14 Pages 535-536
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.535

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Protein-Ligand Interactions: ProLINT Database and QSAR Analysis

Shandar Ahmad, Kouji Kitajima, Samuel Selvaraj, Hideo Kubodera, Shinji ...

2003Volume 14 Pages 537-538
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.537

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In Silico Prediction of Peroxisomal Proteins in Mouse

Igor V. Kurochkin, Christian Schönbach, Akihiko Konagaya

2003Volume 14 Pages 539-540
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.539

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A Proteomic Approach to Engineer Improved Cell Growth and Increased Production of Serine-Rich Proteins in Escherichia coli

Mee-Jung Han, Jong-Shin Yoo, Sang Yup Lee

2003Volume 14 Pages 541-542
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.541

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Genome-Wide Functional Classification/Identification of Prokaryotic Transmembrane Proteins Based on Transmembrane Topology Similarity

Masafumi Arai, Kosuke Okumura, Masanobu Satake, Toshio Shimizu

2003Volume 14 Pages 543-544
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.543

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Transmembrane Protein Evolution by Internal Gene Duplication

Hironori Mitsuke, Keisuke Noto, Masafumi Arai, Toshio Shimizu

2003Volume 14 Pages 545-546
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.545

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Comprehensive Functional Identification of Transmembrane Proteins Using the BTP Method

Yasuhito Inoue, Toshio Shimizu

2003Volume 14 Pages 547-548
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.547

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Inner Residues in the Transmembrane Helix Bundle are More Conservative

Sukenobu Konishi, Takuhiro Nishio, Toshio Shimizu

2003Volume 14 Pages 549-550
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.549

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The Clusters of Transmembrane Protein Genes in Prokaryotic Genomes

Ichitaro Oya, Satoshi Mizuta, Toshio Shimizu

2003Volume 14 Pages 551-552
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.551

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A Consensus Transmembrane Topology Prediction Method of High-Reliability

Jun-Xiong Xia, Toshio Shimizu

2003Volume 14 Pages 553-554
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.553

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Bioinformatics Studies on Transmembrane Strand Proteins

M. Michael Gromiha, Shandar Ahmad, Makiko Suwa

2003Volume 14 Pages 555-556
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.555

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On the Accuracy of Transmembrane Segment Prediction of Helical Integral Membrane Proteins

Shin Tanimoto, Gautam Basu, Takeshi Kawabata, Nobuhiro Go

2003Volume 14 Pages 557-558
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.557

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PLOC: Prediction of Subcellular Location of Proteins

Keun-Joon Park, Minoru Kanehisa, Yutaka Akiyama

2003Volume 14 Pages 559-560
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.559

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Gene-Distribution Patterns on Cyanobacterial Genomes

Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Satoh, Sachiyo Aburatani, K ...

2003Volume 14 Pages 561-562
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.561

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Omic Space and Totalomics

Tetsuro Toyoda, Akiyoshi Wada

2003Volume 14 Pages 563-564
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.563

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Correlated Mutation Analysis of C2H2 Zinc Finger Domains

Takafumi Nagano, Makiko Suwa, Kiyoshi Asai

2003Volume 14 Pages 565-566
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.565

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Analysis of Horizontal Gene Transfer and Clustering of Microbial ORFs by Use of a GRID Environment

Hideaki Sugawara, Yoji Nakamura, Kazuho Ikeo, Satoru Miyazaki, Takashi ...

2003Volume 14 Pages 567-568
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.567

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Real-Time Mapping System of cDNAs and Genomes Using Grid Computing

Yusuke Saito, Manabu Gomi, Hideo Matsuda, Naohisa Goto, Ken Kurokawa, ...

2003Volume 14 Pages 569-570
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.569

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Space-Gene: Microbial Gene Prediction System Based on Linux Clustering

Jong-won Chang, Chungoo Park, Dong Soo Jung, Mi Hwa Kim, Jae Woo Kim, ...

2003Volume 14 Pages 571-572
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.571

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Pedigree Analysis Programme GTree 1.2 and Its Application

Daisuke Ogino, Shiro Mori, Masato Nose, Hideki Sawada

2003Volume 14 Pages 573-574
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.573

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Self-Organizing Clustering: A Novel Non-Hierarchical Method for Clustering Large Amount of DNA Sequences

Kou Amano, Hidemitsu Nakamura, Hiroaki Ichikawa

2003Volume 14 Pages 575-576
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.575

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PFcDNA: Prediction of a Full Length Gene from Partial Sequence

Soo Young Cho, Myungguen Chung, Seung-baek Han, Hyun Kim, Young Seek L ...

2003Volume 14 Pages 577-578
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.577

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Statistical Significance of Tree Similarity Scores

Kiyoko F. Aoki, Atsuko Yamaguchi, Yasushi Okuno, Tatsuya Akutsu, Nobuh ...

2003Volume 14 Pages 579-580
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.579

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Systematic Analyses of P-Loop Containing Nucleotide Triphosphate Hydrolase Superfamily Based on Sequence, Structure and Function

Yoichi Kawamura, Kiyoshi Asai, Shin Ishii, Nozomi Nagano

2003Volume 14 Pages 581-582
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.581

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TTOP: A System for Phylogenetic Tree Editing and Evolutionary Annotation of Genes

Srinesh Kundu, Masato Hagiwara, Kanako O. Koyanagi, Tadashi Imanishi, ...

2003Volume 14 Pages 583-584
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.583

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Gclust: Genome-Wide Clustering of Protein Sequences for Identification of Photosynthesis-Related Genes Resulting from Massive Horizontal Gene Transfer

Naoki Sato

2003Volume 14 Pages 585-586
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.585

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Comparative Genomics between Drosophila and Human

Masuko Katoh, Masaru Katoh

2003Volume 14 Pages 587-588
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.587

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Novel Types of Two-Domain Multi-Copper Oxidases: Possible Missing Links in the Evolution

Kensuke Nakamura, Takeshi Kawabata, Kei Yura, Nobuhiro Go

2003Volume 14 Pages 589-590
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.589

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SNPAnalyzer: Web-Based Workbench for the SNPs Analysis

Jihho Yoo, Bonghee Seo, Yangseok Kim

2003Volume 14 Pages 591-592
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.591

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Artificial Neural Network Model for Prediction of Childhood Allergic Asthma Using Single Nucleotide Polymorphism Data

Yasuyuki Tomita, Shuta Tomida, Yoichi Suzuki, Taro Shirakawa, Takeshi ...

2003Volume 14 Pages 593-594
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.593

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NAMIHEI: A Novel Algorithm for Genomic Polymorphism Detection from DNA Sequence

Go Maeno, Tomohiro Isobe, Yuko Tokoro, Yuki Ejiri, Nobutaka Mitsuhashi ...

2003Volume 14 Pages 595-596
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.595

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Drug Screening of GPCR Using Active Learning

Yukiko Fujiwara, Yoshiko Yamashita, Tsutomu Osoda, Minoru Asogawa, Shu ...

2003Volume 14 Pages 597-598
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.597

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An Integrated Database of Interaction between Human Proteins and Commonly Used Drugs

Masashi Nemoto, Kenji Araki, Ken Horiuchi, Motoi Tobita, Tetsuo Nishik ...

2003Volume 14 Pages 599-600
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.599

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Common Features in Substrates of Multidrug Resistance Transporters

Yoshinobu Igarashi, Yasushi Okuno, Masahiro Hattori, Susumu Goto, Mino ...

2003Volume 14 Pages 601-602
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.601

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Computational Models of Calcium Signaling in the Pancreas-Temporal and Spatial Regulations

Kojiro Yano, Ole H. Petersen, Alexei V. Tepikin

2003Volume 14 Pages 603-604
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.603

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Model Analysis of Helper T Cell Differentiation

Satoshi Yamada, Akihiko Yoshimura

2003Volume 14 Pages 605-606
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.605

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Kinetics Behavior of G1-to-S Cell Cycle Phase Transition Model

Yoshihiko Tashima, Taizo Hanai, Hiroyuki Hamada, Masahiro Okamoto

2003Volume 14 Pages 607-608
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.607

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CADLIVE-Based Analysis for the Budding Yeast Cell Cycle

Natsumi Shimizu, Shunsuke Yamamichi, Hiroyuki Kurata

2003Volume 14 Pages 609-610
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.609

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Deterministic and Stochastic Models Analyze the Robustness of Circadian Rhythms

Yoshiyuki Sumida, Fumitaka Ohnishi, Hiroyuki Kurata

2003Volume 14 Pages 611-612
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.611

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Integration of Postgenomic Data for GMA to Simulate a Metabolic Circuit

Takayuki Tanaka, Hiroyuki Kurata

2003Volume 14 Pages 613-614
Published: 2003
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.14.613

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