Genome Informatics Vol. 15, No. 2 (2004)

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Genome Informatics Vol. 15, No. 2 (2004)

Presented at the 15th International Conference on Genome Informatics
December 13-15, 2004, Pacifico Yokohama, Japan

Published as: T. Akutsu, V. Brusic, S. Miyano, T. Takagi, and M. Kanehisa (eds.)
“Genome Informatics 2004”
Universal Academy Press, Tokyo, 2004

Preface by Kenta Nakai and Richard H. Lathrop

Program Committee

 


 

Full Talk Papers

Architecture of a Grid-Enabled Research Platform with Location-Transparency for Bioinformatics
Yoshiyuki Kido, Susumu Date, Shingo Takeda, Shoji Hatano, Juncai Ma, Shinji Shimojo, Hideo Matsuda
Genome Informatics 15(2): 3-12 (2004)
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Splicing Profile Based Protein Categorization between Human and Mouse Genomes by Use of the DDBJ Web Services
Åke Västermark, Yasumasa Shigemoto, Takashi Abe, Hideaki Sugawara
Genome Informatics 15(2): 13-20 (2004)
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Computational Methods for the Analysis of Differential Conservation in Groups of Similar DNA Sequences
Nikola Stojanovic
Genome Informatics 15(2): 21-30 (2004)
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Comprehensive Identification of “Druggable” Protein Ligand Binding Sites
Jianghong An, Maxim Totrov, Ruben Abagyan
Genome Informatics 15(2): 31-41 (2004)
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General-Purpose Search Techniques for Genomic Text
Abhijit Chattaraj, Hugh E. Williams, Adam Cannane
Genome Informatics 15(2): 42-51 (2004)
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Graphical Approach to Weak Motif Recognition
Xiao Yang, Jagath C. Rajapakse
Genome Informatics 15(2): 52-62 (2004)
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An Extension and Novel Solution to the (l,d)--Motif Challenge Problem
Mark P Styczynski, Kyle L Jensen, Isidore Rigoutsos, Gregory N Stephanopoulos
Genome Informatics 15(2): 63-71 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Domain Discovery Method for Topological Profile Searches in Protein Structures
Juris Viksna, David Gilbert, Gilleain Torrance
Genome Informatics 15(2): 72-81 (2004)
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A Novel Graph-Based Similarity Measure for 2D Chemical Structures
Si Quang Le, Tu Bao Ho, T.T Hang Phan
Genome Informatics 15(2): 82-91 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

IRIS: Intermolecular RNA Interaction Search
Dmitri D. Pervouchine
Genome Informatics 15(2): 92-101 (2004)
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StructMiner: A Tool for Alignment and Detection of Conserved Secondary Structure
Qian Yang, Mathieu Blanchette
Genome Informatics 15(2): 102-111 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

RNA 3D Structure Prediction: (1) Assessing RNA 3D Structure Similarity from 2D Structure Similarity
Jaime E. Barreda DC, Yoshimitsu Shigenobu, Eiichiro Ichiishi, Carlos A. Del Carpio M.
Genome Informatics 15(2): 112-120 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Inference of Gene Regulatory Networks by Means of Dynamic Differential Bayesian Networks and Nonparametric Regression
Naoya Sugimoto, Hitoshi Iba
Genome Informatics 15(2): 121-130 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Recovering Genetic Regulatory Networks from Micro-Array Data and Location Analysis Data
Fan Li, Yiming Yang
Genome Informatics 15(2): 131-140 (2004)
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Increasing Feasibility of Optimal Gene Network Estimation
Annika Hansen, Sascha Ott, Georgy Koentges
Genome Informatics 15(2): 141-150 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Method for Clustering Gene Expression Data Based on Graph Structure
Shigeto Seno, Reiji Teramoto, Yoichi Takenaka, Hideo Matsuda
Genome Informatics 15(2): 151-160 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Statistical and Integrative Approach for Constructing Biological Network Maps
Hiroyuki Kurata, Natsumi Shimizu, Kanako Misumi
Genome Informatics 15(2): 161-170 (2004)
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PreSPI: Design and Implementation of Protein-Protein Interaction Prediction Service System
Dong-Soo Han, Hong-Soog Kim, Woo-Hyuk Jang, Sung-Doke Lee, Jung Keun Suh
Genome Informatics 15(2): 171-180 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Predicting Protein Secondary Structure by a Support Vector Machine Based on a New Coding Scheme
Long-Hui Wang, Juan Liu, Yan-Fu Li, Huai-Bei Zhou
Genome Informatics 15(2): 181-190 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Support Vector Machines with Profile-Based Kernels for Remote Protein Homology Detection
Steven Busuttil, John Abela, Gordon J. Pace
Genome Informatics 15(2): 191-200 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Kernel Mixture Survival Models for Identifying Cancer Subtypes, Predicting Patient's Cancer Types and Survival Probabilities
Tomohiro Ando, Seiya Imoto, Satoru Miyano
Genome Informatics 15(2): 201-210 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Computational Prediction of Operons in Synechococcus sp. WH8102
Xin Chen, Zhengchang Su, Ying Xu, Tao Jiang
Genome Informatics 15(2): 211-222 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Intercellular Communications Induced by Random Fluctuations
Tianshou Zhou, Luonan Chen, Ruiqi Wang, Kazuyuki Aihara
Genome Informatics 15(2): 223-233 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Knowledge Representation Model for Systems-Level Analysis of Signal Transduction Networks
Dong-Yup Lee, Ralf Zimmer, Sang-Yup Lee, Daniel Hanisch, Sunwon Park
Genome Informatics 15(2): 234-243 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Consistent Re-Modeling of Signaling Pathways and Its Implementation in the TRANSPATH Database
Claudia Choi, Torsten Crass, Alexander Kel, Olga Kel-Margoulis, Mathias Krull, Susanne Pistor, Anatolij Potapov, Nico Voss, Edgar Wingender
Genome Informatics 15(2): 244-254 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Ontological Integration of Data Models for Cell Signaling Pathways by Defining a Factor of Causality Called ‘Signal’
Takako Takai-Igarashi, Riichiro Mizoguchi
Genome Informatics 15(2): 255-265 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Using Protein Motif Combinations to Update KEGG Pathway Maps and Orthologue Tables
Frédéric Nikitin, Bastien Rance, Masumi Itoh, Minoru Kanehisa, Frédérique Lisacek
Genome Informatics 15(2): 266-275 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Systematic DNA-Binding Domain Classification of Transcription Factors
Philip Stegmaier, Alexander E. Kel, Edgar Wingender
Genome Informatics 15(2): 276-286 (2004)
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Mining Yeast Transcriptional Regulatory Modules from Factor DNA-Binding Sites and Gene Expression Data
Tho Hoan Pham, Kenji Satou, Tu Bao Ho
Genome Informatics 15(2): 287-295 (2004)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Keynote Address

The Immune Epitope Database and Analysis Resource: From Vision to Blueprint
Alessandro Sette
Genome Informatics 15(2): 299-299 (2004)
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Revealing the Structure and Dynamics of Cis-Regulation Using Heterogeneous, Genome-Wide, Multi-Species Data
Ron Shamir
Genome Informatics 15(2): 300-301 (2004)
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Complex Systems Biology: Exploring Universal Statistical and Dynamical Features in Cellular Processes
Kunihiko Kaneko
Genome Informatics 15(2): 302-303 (2004)
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