Genome Informatics

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Volume 12

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BIOCAD Project for Constructing a Biological System in Silico

Tadashi Adachi, Nana Matoba, Hiroyuki Kurata

2001Volume 12 Pages 284-285
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.284

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Simulation and System Analysis of Gene Regulatory Networks Using the Two-phase Partition Method

Hiroyuki Kurata, Takahiro Inoue, Yoshiyuki Sumida, Shin Tanaka, Takesh ...

2001Volume 12 Pages 286-287
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.286

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Simulation of the Pattern Formation in Multicellular Organism by Genomic Object Net

Atsushi Doi, Rie Yamane, Naoyuki Yamasaki, Haruka Yoshimori, Ryutaro M ...

2001Volume 12 Pages 288-289
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.288

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Biopathway Model Conversion from E-CELL to Genomic Object Net

Mika Matsui, Atsushi Doi, Hiroshi Matsuno, Yuichi Hirata, Satoru Miyan ...

2001Volume 12 Pages 290-291
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.290

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Genomic Object Net: Petri Net Enhancement for Multi-Cellular Processes

Yuichi Hirata, Hiroshi Matsuno, Makiko Sasaki, Satoru Miyano

2001Volume 12 Pages 292-293
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.292

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Gene Toggle Switches Only with Positive Feedback Loops

Tetsuya Kobayashi, Luonan Chen, Kazuyuki Aihara

2001Volume 12 Pages 294-295
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.294

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Regulation Analysis by Combining the Information Obtained from the mRNA Expression, Protein Expression and Metabolic Fluxes

Chen Yang, Qiang Hua, Kazuyuki Shimizu

2001Volume 12 Pages 296-297
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.296

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In Silico Metabolic Pathway Modeling and Analysis of Mycoplasma pneumoniae

Jin Sik Kim, Sang Yup Lee

2001Volume 12 Pages 298-299
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.298

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Circadian Oscillation and Stochastic Noises

Nobukazu Ohki, Masatoshi Hagiwara

2001Volume 12 Pages 300-301
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.300

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A Study of Spatial Formation of Immune Cells

Shin I. Nishimura

2001Volume 12 Pages 302-303
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.302

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Pathway Finding from Given Time-Courses Using Genetic Algorithm

Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Masaru Tomita

2001Volume 12 Pages 304-305
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.304

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Modeling Photorespiration Pathway through E-CELL

Pawan Dhar, Emily Wang, Yoichi Nakayama, Masaru Tomita

2001Volume 12 Pages 306-307
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.306

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Estimation of Genetic Networks of the Circadian Rhythm in Cyanobacterium Using the E-CELL System

Fumihiko Miyoshi, Yoichi Nakayama, Masaru Tomita

2001Volume 12 Pages 308-309
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.308

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A Simulation Model of Diabetes Using E-Cell System

Yasuhiro Naito, Hiroshi Ohno, Sae Seno, Yuki Oguchi, Atsumi Sano, Hiro ...

2001Volume 12 Pages 310-311
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.310

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Towards Simulation of Whole Metabolic Pathways in Human Erythrocyte

Ayako Kinoshita, Yoichi Nakayama, Masaru Tomita

2001Volume 12 Pages 312-313
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.312

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An Electrophysiological Simulation Model of the Myocardial Cell Using E-CELL System

Motohiro Yoneda, Yasuhiro Naito, Shoko Miyamoto, Sayaka Ishinabe, Shin ...

2001Volume 12 Pages 314-315
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.314

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Design and Development of Software Environment for Whole-Cell Simulation

Yusuke Saito, Kenta Hashimoto, Takeshi Sakurada, Yuki Fujita, Kouichi ...

2001Volume 12 Pages 316-317
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.316

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E-CELL Simulation Environment Version 3: System Architecture of Simulation Engine

Kouichi Takahashi, Takeshi Sakurada, Yohei Yamada, Tomoya Kitayama, Ma ...

2001Volume 12 Pages 318-319
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.318

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Computer Simulation of the Asymmetric Cell Division in Early Development of C. elegans Embryo Using E-CELL System

Azusa Kuroki, Akio Kanai, Masaru Tomita

2001Volume 12 Pages 320-321
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.320

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Modeling Environment for Large-Scale Models Using the E-CELL System

Yoichi Nakayama, Katsuyuki Yugi, Yohei Yamada, Masaru Tomita

2001Volume 12 Pages 322-323
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.322

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Development of the Bacteria Analysis System on G-Language Genome Analysis Environment

Koya Mori, Kazuharu Arakawa, Masaru Tomita

2001Volume 12 Pages 324-325
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.324

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G-Language Genome Analysis Environment

Kazuharu Arakawa, Koya Mori, Masaru Tomita

2001Volume 12 Pages 326-327
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.326

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Prediction System for Dumbbell-Type Proteins: SOSUIdumbbell

Nobuyuki Uchikoga, Shun-ya Takahashi, Ke Runcong, Fumitsugu Akazawa, M ...

2001Volume 12 Pages 328-329
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.328

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Molecular Dynamics Simulation of Protein Translocation across a Membrane

Mitsuharu Okazaki, Tomoki Watanabe, Naohito Urakami, Takashi Yamamoto

2001Volume 12 Pages 330-331
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.330

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Classification and Analysis of Inter-Helical Loop Segments in Membrane Proteins

Takatsugu Hirokawa, Makiko Suwa, Yutaka Akiyama

2001Volume 12 Pages 332-333
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.332

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Comprehensive Functional Identification of Prokaryotic Transmembrane Proteins by Binary Topology Pattern

Yoshiaki Sugiyama, Masafumi Arai, Toshio Shimizu

2001Volume 12 Pages 334-335
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.334

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Classification of Eukaryotic 7-tms Transmembrane Proteins by Binary Topology Pattern

Yasuhito Inoue, Yoshiaki Sugiyama, Masami Ikeda, Toshio Shimizu

2001Volume 12 Pages 336-337
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.336

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Comprehensive Analysis of Transmembrane Protein Sequences in 39 Microbial Genomes

Masafumi Arai, Keisuke Noto, Demelo Madrazo Lao, Masami Ikeda, Toshio ...

2001Volume 12 Pages 338-339
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.338

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Methods for Detecting the Signal Peptide in Transmembrane and Globular Proteins

Demelo Madrazo Lao, Toshio Shimizu

2001Volume 12 Pages 340-342
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.340

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Detection of Hidden Periodicity in Protein Sequences and Its Correlation with Structure and Function of Proteins

Andrew A. Laskin, Eugene V. Korotkov, Nikolai A. Kudryashov

2001Volume 12 Pages 343-344
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.343

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Analysis of Complementarity of Protein-Protein and Protein-DNA Interactions Using the Molecular Surface Database, eF-site

Kengo Kinoshita, Yuko Tsuchiya, Haruki Nakamura

2001Volume 12 Pages 345-347
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.345

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Functional Proteomics in Silico: Putative Protein Interaction Analysis

Chung-Yen Lin, Chen-Zen Lo, Chao A. Hsiung

2001Volume 12 Pages 348-349
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.348

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Protein Classification Comparison Server

Jun-Hyung Park, Sung-Ryong Ryu, Cheolmin Kim, In Song Koh, Jong Park

2001Volume 12 Pages 350-351
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.350

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Discovery and Classification of Peptide Family G-Protein Coupled Receptors in the Human Genome Sequence

Maria E. Levchenko, Toshiaki Katayama, Minoru Kanehisa

2001Volume 12 Pages 352-353
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.352

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A Novel Protein Soft Docking Algorithm Based on Spectral Analysis of Shape Complementarity

Atsushi Yoshimori, Carlos A. Del Carpio M.

2001Volume 12 Pages 354-355
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.354

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Scoring Protein-Substrate Complex Decoys Based on Electrostatic and Hydrophobic Complementarities: Evaluation of Hormone-Receptor Interactions

Yoshihiro Katsuta, Atsushi Yoshimori, Carlos A. Del Carpio M.

2001Volume 12 Pages 356-357
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.356

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Protein Folding Recognition Based on Amino Acid Physicochemical Property Profiles

Daisuke Komatsu, Atsushi Yoshimori, Carlos A. Del Carpio M.

2001Volume 12 Pages 358-359
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.358

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A Bioinformatic Approach for RNA 3D Structure Prediction: Development of a Knowledge-Base for 2D-to-3D Structural Elements Compatibility Analysis

Yoshimitsu Shigenobu, Carlos A. Del Carpio

2001Volume 12 Pages 360-361
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.360

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Conformational Search and Potential Energy Analysis of Protein β-Hairpin Formations by Parallel Exhaustive Tree Search

Makoto Ando, Yutaka Akiyama, Hideo Matsuda

2001Volume 12 Pages 362-363
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.362

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Comparative Analysis of Protein Charge Distribution in Genome Scale

Ke Runcong, Shigeki Mitaku

2001Volume 12 Pages 364-365
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.364

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PepAssem, a Peptide Assembly Algorithm for a Complex Protein Mixture

Sang-Hee Shim, Doo Soo Chung

2001Volume 12 Pages 366-367
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.366

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Multiple Zinc Finger Motifs with Comparison of Plant and Insect

Nobuyuki Kawagashira, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsuba ...

2001Volume 12 Pages 368-369
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.368

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Analysis of Amino Acid Substitution Rate in Proteins between Hyperthermophilic and Mesophilic Organisms Using Complete Genome Data

Tomoya Yamashita, Goki Kashima, Akio Kanai, Asako Sato, Kenji Higashi, ...

2001Volume 12 Pages 370-371
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.370

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Structural Affectivity of Protein Chain Growth by t-RNA System

Yasuo Yonezawa, Sadaharu Ueno

2001Volume 12 Pages 372-373
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.372

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An Approach for Homology Search with Reconfigurable Hardware

Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya

2001Volume 12 Pages 374-375
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.374

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Aligning and Scoring Motifs Based on Secondary Characteristics

Pedro Gonnet, Frédérique Lisacek

2001Volume 12 Pages 376-377
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.376

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Heuristic Probe Mining Based on Multiple Sequence Analysis

Byeong-Chul Kang, Heung-Soo Park, Ho-Young Kang, Hee-Kyung Park, Cheol ...

2001Volume 12 Pages 378-379
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.378

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Amino Acid Substitution Matrices Estimated by Maximum Likelihood

Leonardo De Oliveira Martins, Paolo M. De A. Zanotto

2001Volume 12 Pages 380-381
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.380

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A Web Server for Multiple Sequence Alignment Using Genetic Algorithm

Tsutomu Yokoyama, Takumi Watanabe, Akito Taneda, Toshio Shimizu

2001Volume 12 Pages 382-383
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.382

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Target Prediction of Transcription Factors: Refinement of Structure-Based Method

Akinori Sarai, Samuel Selvaraj, M. Michael Gromiha, Joerg-Gerald Siebe ...

2001Volume 12 Pages 384-385
Published: 2001
Released on J-STAGE: July 11, 2011

DOIhttps://doi.org/10.11234/gi1990.12.384

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