- ``E-CELL: Software Environment for Whole Cell Simulation''
Masaru Tomita, Kenta Hashimoto, Kouichi Takahashi, Tom Shimizu,
J. Craig Venter and Clyde A. Hutchison;
Microbial and Comparative Genomics, Volume 3, Number 1, 1998.
- ``A Virtual Cell with 127 Genes''
Masaru Tomita, Kenta Hashimoto, Kouichi Takahashi, Tom Shimizu, Yuri Matsuzaki,
Fumihiko Miyoshi, Kanako Saito, Sakura Tanida, Katsuyuki Yugi, J. Craig
Venter and Clyde A. Hutchison;
Proceedings of the First International Conference on Bioinformatics
of Genome Regulation and Structure, Volume 1, 97, 1998.
- ``Analysis of Completed Genomes Suggests that Hairpin Formation is
not a Universal Mechanism fir Procaryotic Transription Termination''
Takanori Washio and Masaru Tomita;
Proceedings of the First International Conference on Bioinformatics
of Genome Regulation and Structure, Volume 1, 154, 1998.
- ``On Negative Selection Against ATR Triplets Near Start Codons
in Eucaryotic and Procaryotic Genomes''
Rintaro Saito and Masaru Tomita;
Proceedings of the First International Conference on Bioinformatics
of Genome Regulation and Structure, Volume 1, 224, 1998.
- ``Computer Analysis of Free Energy of Base Paring Between
Shine-Dalgarno Sequence and 3'end of 16SrRNA in Various Procaryotes''
Yuko Osada, Rintaro Saito and Masaru Tomita;
Proceedings of the First International Conference on Bioinformatics
of Genome Regulation and Structure, Volume 1, 228, 1998.
- ``Comparative Analysis of Overlapping Genes in the Genomes
of Mycoplasm genitalium and Mycoplasma pneumoniae''
Yoko Fukuda, Takanori Washio and Masaru Tomita;
Microbial and Comparative Genomics, Volume 3, Number 3, C-66, 1998.
- ``On Low Frequency of CpG Dinucleotide in Bacterial Genomes''
Mami Goto, Takanori Washio and Masaru Tomita;
Microbial and Comparative Genomics, Volume 3, Number 3, C-67, 1998.
- ``The Expression Frequency of the Human Immunoglobulin Lambda
Light Chain Genes and the Role of Their Recombination Signal Sequences''
Taku Okada, Masaru Tomita, Kazuhiko Kawasaki, Shinsei Minoshima and
Nobuyoshi Shimizu;
Microbial and Comparative Genomics, Volume 3, Number 3, C-87, 1998.
- ``Computer Analysis of Free Energy of Base Paring Between
Shine-Dalgarno Sequence and 3'end of 16SrRNA''
Yuko Osada, Rintaro Saito, Sadahiro Kumagai and Masaru Tomita;
Microbial and Comparative Genomics, Volume 3, Number 3, C-87, 1998.
- ``Computer Analyses of Translation Initiation Sites in Complete
Genomes of Mycoplasma genitalium''
Rintaro Saito and Masaru Tomita;
Microbial and Comparative Genomics, Volume 3, Number 3, C-93, 1998.
- ``Sequence Patterns Observed in 5' Flanking Regions of Primate Alu
Elements'' Yoshimi Toda, Rintaro Saito and Masaru Tomita;
Microbial and Comparative Genomics, Volume 3, Number 3, C-97, 1998.
- ``On Periodicity of Adenine-adenine Dinucleotides in Procaryote Genomes''
Masahiko Wada, Yukihiro Kawashima and Masaru Tomita;
Microbial and Comparative Genomics, Volume 3, Number 3, C-99, 1998.
- ``Analysis of Completed Genomes Suggests that Hairpin Formation is
not a Universal Mechanism for Procaryotic Transription Termination''
Takanori Washio and Masaru Tomita;
Microbial and Comparative Genomics, Volume 3, Number 3, C-101, 1998.
- ``E-CELL Project Overview: Towards Integrative Simulation
of Cellular Processes'' Masaru Tomita; 2nd Annual Conference on
Computational Genomics, 1998.
- "Comprehensive Sequence Ana;yses of 5' Flanking Regions of
Primate Alu Elements" Yoshimi Toda, Rintaro Saito and Masaru
Tomita; Genome Informatics 1998, 41-48, Universal Academy Press
Inc., Tokyo (ISBN 4-946443-51-5).
- ``E-CELL Project Overview: Towards Integrative Simulation of
Cellular Processes'' Masaru Tomita, Kenta Hashimoto, Kouichi
Takahashi, Yuri Matsuzaki, Ryo Matsushima, Kanako Saito, Katsuyuki
Yugi, Fumihiko Miyoshi, Hisako Nakano, Sakura Tanida and Thomas
S. Shimizu; Genome Informatics 1998, 242-243, Universal Academy
Press Inc., Tokyo (ISBN 4-946443-51-5).
- ``Modelling of Transcription and DNA Replication Using the E-CELL
Simulation System" Kenta Hashimoto, Fumihiko Miyoshi, Thomas
S. Shimizu, Takeshi Satoyoshi and Masaru Tomita; Genome Informatics
1998, 244-245, Universal Academy Press Inc., Tokyo (ISBN
4-946443-51-5).
- "Modeling of Signal Transduction for Bacterial Chemotaxis Using
the E-CELL Simulation System" Yuri Matsuzaki, Kanako Saito, Thomas
S. Shimizu and Masaru Tomita; Genome Informatics 1998, 246-247,
Universal Academy Press Inc., Tokyo (ISBN 4-946443-51-5).
- "Modeling of Human Red Blood Cell Using the E-CELL Simulation
System" Ryo Matsushima, Akiko Kawase, Naoko Watanabe, Hisako Nakano,
Kanako Saito and Masaru Tomita; Genome Informatics 1998,
248-249, Universal Academy Press Inc., Tokyo (ISBN 4-946443-51-5).
- "Modeling Theory and Software Architecture of the E-CELL
Simulation System" Kouichi Takahashi, Thomas S. Shimizu, Katsuyuki
Yugi and Masaru Tomita; Genome Informatics 1998, 250-251,
Universal Academy Press Inc., Tokyo (ISBN 4-946443-51-5).
- "Multivariate Time Series Analysis of Metabolic Network Using the
E-CELL Simulation System" Yusuke Saito, Kouichi Takahashi and Masaru
Tomita; Genome Informatics 1998, 252-253, Universal Academy
Press Inc., Tokyo (ISBN 4-946443-51-5).
- "Evoluation of Overlapping Genes: Comparative Genomics of
Mycoplasma genitalium and Mycoplasma pneumoniae" Yoko
Fukuda, Takanori Washio and Masaru Tomita; Genome Informatics
1998, 254-255, Universal Academy Press Inc., Tokyo (ISBN
4-946443-51-5).
- "On Periodicity of Adenine-Adenine Dinucleotides in Bacterial
Genomes" Masahiko Wada, Yukihiro Kawashima and Masaru Tomita;
Genome Informatics 1998, 256-257, Universal Academy Press Inc.,
Tokyo (ISBN 4-946443-51-5).
- "Computer Analysis of Base Pairing Free-Energy between
Shine-Dalgarno Sequence and 16S rRNA in Various Procaryotes" Yuko
Osada, Rintaro Saito and Masaru Tomita; Genome Informatics
1998, 258-259, Universal Academy Press Inc., Tokyo (ISBN
4-946443-51-5).
- "On Low Frequency of CpG Dinucleotides in Bacterial Genomes" Mami
Goto, Takanori Washio and Masaru Tomita; Genome Informatics
1998, 260-261, Universal Academy Press Inc., Tokyo (ISBN 4-946443-51-5).
- "Analysis of Translation Initiation Sites in the Complete Genome
of Mycoplasma genitalium Suggests That This Bacterium Uses
Alternative Signal for Translation Initiation" Rintaro Saito and
Masaru Tomita; Genome Informatics 1998, 262-263, Universal Academy
Press Inc., Tokyo (ISBN 4-946443-51-5).
- "Expression Frequency of the Human Immunoglobulin Lambda Light
Chain Genes and the Roles of Their Recombination Signal and Spacer
Sequences" Taku Okada, Masaru Tomita, Kazuhiko Kawasaki, Shinsei
Minoshima and Nobuyoshi Shimizu; Genome Informatics 1998,
264-265, Universal Academy Press Inc., Tokyo (ISBN 4-946443-51-5).
- "原核生物における転写終結部位のコンピュータ解析" 鷲尾尊規、冨田勝;
第21回日本分子生物学会年会, 1998
- "Mycoplasma genitaliumと Mycoplasma pneumoniaeの比較におけるオー
バーラッピング・ジーンの解析" 福田陽子、鷲尾尊規、冨田勝; 第21回日本分
子生物学会年会, 1998
- "Shine-Dalgarno配列と16SrRNA 3'末端の相補鎖の自由エネルギー解析"
長田木綿子、斎藤輪太郎、冨田勝; 第21回日本分子生物学会年会, 1998
- "バクテリアゲノムにおけるCpGジヌクレオチドの頻度低下に関する考察"
後藤マミ、鷲尾尊規、冨田勝; 第21回日本分子生物学会年会, 1998
- "霊長類ALU配列5’外側の近傍領域における共通な塩基パターン"
戸田好美、斎藤輪太郎、冨田勝; 第21回日本分子生物学会年会, 1998
- "バクテリアゲノムにおけるAAジヌクレオチドの周期性について"
和田理彦、川島行弘、冨田勝; 第21回日本分子生物学会年会, 1998
- "ヒトのイムノグロブリンλ軽鎖遺伝子の発現頻度およびりコンビネーショ
ン・シグナル・シーケンスの役割についてのデータベース解析"
岡田拓、冨田勝、川崎和彦、簑島伸生、清水信義; 第21回日本
分子生物学会年会, 1998
- "E-CELLプロジェクトの概要:細胞内全代謝の包括的シミュレーションに
向けて" 冨田勝、橋本健太、高橋恒一、松崎由理、松嶋亮、齋藤佳奈子、柚木
克之、三由文彦、中野寿子、谷田さくら、清水友益; 第21回日本分子生物学会
年会, 1998
- "E-CELLモデリング手法とシステム構築" 高橋恒一、柚木克之、清水友益、
冨田勝; 第21回日本分子生物学会年会, 1998
- "E-CELLシステムを用いた転写、翻訳、複製のモデリング" 橋本健太、三
由文彦、清水友益、里吉健、冨田勝; 第21回日本分子生物学会年会, 1998
- "E-CELLシステムを用いた原核細胞化走性シグナル伝達経路のモデリング
" 松崎由理、齋藤佳奈子、清水友益、谷田さくら、冨田勝; 第21回日本分子生
物学会年会, 1998
- "E-CELLシステムを用いたヒト赤血球のモデリング" 松嶋亮、川瀬晶子、
渡邊奈生子、中野寿子、齋藤佳奈子、冨田勝; 第21回日本分子生物学会年会,
1998
- 「JAVAによるアニメーション入門」
冨田勝、北川宏和; bit, Volume 30, Number 8, 8-14 (1998)
- 「バーチャル細胞の開発:E-CELLプロジェクト」
冨田勝; Human Science, Vol.9, No.6, 27-29 (1998)
- 「E-CELLプロジェクト」
冨田勝; Clinical Neuroscience, Vol.16, No.11, 1296-1299 (1998)
- 「生命情報科学のための遺伝子情報処理実習」
冨田勝;「生物の科学 遺伝」別冊10号(1998)
- 「細胞まるごとシミュレーション」
冨田勝; 三田評論 No.1001 (1998)