List of Accepted Papers
   
Qualitatively Predicting Acetylation and Methylation Areas in DNA Sequences
ThoHoan Pham, DangHung Tran, TuBao Ho, Kenji Satou, Gabriel Valiente
Knowledge-based Prediction of DNA Atomic Structure from Nucleic Sequence
MarcosJ. Arauzo-Bravo, Akinori Sarai
Linear-Space Algorithm for the Constrained Pairwise Sequence Alignment Problem
Dan He

Supporting the Curation of Biological Databases with Reusable Text Mining
Olivo Miotto, TinWee Tan, Vladimir Brusic

Reconstruction of Phylogenetic Relationships from Metabolic Pathways based on the Enzyme Hierarchy and the Gene Ontology
Jose Clemente, Kenji Satou, Gabriel Valiente

Mass identification of Chloroplast Proteins of Endosymbiont Origin by Phylogenetic Profiling Based on Homologous Protein Groups
Naoki Sato, Masayuki Ishikawa, Makoto Fujiwara, Kintake Sonoike

Strategies for Genome Reduction in Microbial Genomes
Kishore Sakharkar, VincentT.K. Chow
Reassembly and Interfacing Neural Models Registered on Biological Model Databases
Mihoko Otake, Toshihisa Takagi
Objective Measurement of Spindle Orientation in Early Caenorhabditis Elegans Embryo
Shugo Hamahashi, Shuichi Onami
Evolution from Possible Primitive tRNA-viroids to Early Poly-tRNA-derived mRNAs : A New Approach from the Poly-tRNA theory
Koji Ohnishi, Madoka Ohshima, Naotaka Furuichi
A Study of Fragment-Based Protein Structure Prediction: Biased Fragment Replacement for Searching Low-energy Conformation
Sung-Joon Park
Comparison of Protein Structures by Multi-Objective Optimization
Luonan Chen, Ling-Yun Wu, Ruiqi Wang, Shihua Zhang, Xiangsun Zhang
Statistical Evaluation of a Bottom-Up Clustering for Single Particle Molecular Images
Yutaka Ueno, Katsunori Isono, Katsutoshi Takahashi, Yukio Shimonohara, Kiyoshi Asai
Inter-Species Validation for Domain Combination Based Protein-Protein Interaction Prediction Method
Woo-Hyuk Jang, Dong-Soo Han, Hong-Soog Kim, Sung-Doke Lee
A Graph Theoretical Approach for Analysis of Protein Flexibility Change at Protein Complex Formation
Carlos A. DelCarpioM, AbdulRajjak Shaikh, Eiichiro Ichiishi, Akira Miyamoto
A Fast Protein-Protein Docking Algorithm Using Series Expansion in Terms of Spherical Basis Functions
Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
Viewing the Proteome from Oligopeptides and Prediction of Protein Function
Hisayuki Horai, Kouichi Doi, Hirofumi Doi
Mass Distiributed Clustering : A New Clustering Algorithm for Repeated Measurements in Gene Expression Data
Shinya Matsumoto, Kenichi Aisaki, Jun Kanno
Diagnosis of Early Relapse in Ovarian Cancer Using Serum Proteomic
JungHun Oh, Jean Gao, Animesh Nandi, Prem Gurnani, Lynne Knowles, John Schorge, Kevin Rosenblatt
Reverse Engineering Genetic Networks using Evolutionary Computation
Nasimul Noman, Hitoshi Iba
Toward Integration of System Biology Formalism: The Gene Regulatory Networks Case
Raffaella Gentilini
Reconstruction of Gene Regulatory Networks under the Finite State Linear Model
Dace Ruklisa, Alvis Brazma, Juris Viksna
Automatic Drawing of Biological Networks Using Cross Cost and Subcomponent Data
Mitsuru Kato, Masao Nagasaki, Atsushi Doi, Satoru Miyano

Prediction of Functional Modules Based on Gene Distributions in Microbial Genomes
Hongwei Wu, Fenglou Mao, Zhengchang Su, Victor Olman, Ying Xu

Interaction Graph Mining for Protein Complexes Using Local Clique Merging
Li Xiao-li, Tan Soon-Heng, Foo Chuan-Sheng, Ng See-Kiong
Topology of Mammalian Transcription Networks
Anatolij Potapov, Nico Voss, Nicole Sasse, Edgar Wingender

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E-mail: giw2005@ims.u-tokyo.ac.jp