io-port.net

io-port 05329166 Yamada, Takuji; Goto, Susumu; Kanehisa, Minoru; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Extraction of phylogenetic network modules from prokayrote metabolic pathways. (English)

Genome Inform. Online 15, No. 1, 249-258 (2004).

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io-port 05329165 Wu, Chang-Jiun; Fu, Yutao; Murali, T.M.; Kasif, Simon; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Gene expression module discovery using Gibbs sampling. (English)

Genome Inform. Online 15, No. 1, 239-248 (2004).

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io-port 05329164 Sugaya, Nobuyoshi; Sato, Makihiko; Murakami, Hiroo; Imaizumi, Akira; Aburatani, Sachiyo; Horimoto, Katsuhisa; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Causes for the large genome size in a cyanobacterium anabaena sp. PCC7120. (English)

Genome Inform. Online 15, No. 1, 229-238 (2004).

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io-port 05329163 Shakhnovich, Boris E.; Reddy, Timothy E.; Galinsky, Kevin; Mellor, Joseph; Delisi, Charles; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Comparisons of predicted genetic modules: Identification of co-expressed genes through module gene flow. (English)

Genome Inform. Online 15, No. 1, 221-228 (2004).

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io-port 05329162 Shakhnovich, Boris E.; Harvey, John Max; Delisi, Charles; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

ELISA: A unified, multidimensional view of the protein domain universe. (English)

Genome Inform. Online 15, No. 1, 213-220 (2004).

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io-port 05329161 Riedesel, Henning; Kolbeck, Bjoern; Schmetzer, Oliver; Knapp, Ernst-Walter; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Peptide binding at class I major histocompatibility complex scored with linear functions and support vector machines. (English)

Genome Inform. Online 15, No. 1, 198-212 (2004).

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io-port 05329160 Nagasaki, Masao; Doi, Atsushi; Matsuno, Hiroshi; Miyano, Satoru; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

A versatile Petri net based architecture for modeling and simulation of complex biological processes. (English)

Genome Inform. Online 15, No. 1, 180-197 (2004).

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io-port 05329159 Murakami, Hiroo; Sugaya, Nobuyoshi; Sato, Makihiko; Imaizumi, Akira; Aburatani, Sachiyo; Horimoto, Katsuhisa; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Detection of inter-spread repeat sequence in genomic DNA sequence. (English)

Genome Inform. Online 15, No. 1, 170-179 (2004).

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io-port 05329158 Mintseris, Julian; Weng, Zhiping; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Optimizing protein representations with information theory. (English)

Genome Inform. Online 15, No. 1, 160-169 (2004).

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io-port 05329157 Mellor, Joseph C.; Wu, Jie; Delisi, Charles; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Constructing networks with correlation maximization methods. (English)

Genome Inform. Online 15, No. 1, 149-159 (2004).

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io-port 05329156 Krueger, Roland; Heinrich, Reinhart; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Model reduction and analysis of robustness for the $W$nt/β-catenin signal transduction pathway. (English)

Genome Inform. Online 15, No. 1, 138-148 (2004).

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io-port 05329155 Klipp, Edda; Liebermeister, Wolfram; Wierling, Christoph; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Inferring dynamic properties of biochemical reaction networks from structural knowledge. (English)

Genome Inform. Online 15, No. 1, 125-137 (2004).

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io-port 05329154 Kielbasa, Szymon M.; Bluethgen, Nils; Sers, Christine; Schaefer, Reinhold; Herzel, Hanspeter; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Prediction of cis-regulatory elements of coregulated genes. (English)

Genome Inform. Online 15, No. 1, 117-124 (2004).

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io-port 05329153 Jeong, Euna; Chung, I-Fang; Miyano, Satoru; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

A neural network method for identification of RNA-interacting residues in protein. (English)

Genome Inform. Online 15, No. 1, 105-116 (2004).

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io-port 05329152 Itoh, Masumi; Akutsu, Tatsuya; Kanehisa, Minoru; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Clustering of database sequences for fast homology search using upper bounds on alignment score. (English)

Genome Inform. Online 15, No. 1, 93-104 (2004).

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io-port 05329151 Hoshiyama, Daisuke; Kuma, Kei-Ichi; Miyata, Takashi; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Markedly reduced evolutionary rates of transcription factors and cytoplasmic ribosomal rnas and proteins in higher vertebrates and their evolutionary implications. (English)

Genome Inform. Online 15, No. 1, 82-92 (2004).

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io-port 05329150 Hizukuri, Yoshiyuki; Yamanishi, Yoshihiro; Hashimoto, Kosuke; Kanehisa, Minoru; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Extraction of species-specific glycan substructures. (English)

Genome Inform. Online 15, No. 1, 69-81 (2004).

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io-port 05329149 Hayashida, Morihiro; Ueda, Nobuhisa; Akutsu, Tatsuya; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

A simple method for inferring strengths of protein-protein interactions. (English)

Genome Inform. Online 15, No. 1, 56-68 (2004).

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io-port 05329148 Frey, Erwin; Parmeggiani, Andrea; Franosch, Thomas; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Collective phenomena in intracellular processes. (English)

Genome Inform. Online 15, No. 1, 46-55 (2004).

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io-port 05329147 Ebenhoeh, Oliver; Handorf, Thomas; Heinrich, Reinhart; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.

Structural analysis of expanding metabolic networks. (English)

Genome Inform. Online 15, No. 1, 35-45 (2004).

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