Program ver.1108

13 + 14 + 15 + HOME

--------------------- Monday, December 13, 2004 ---------------------

Opening Address
09:00 - 09:10 Tatsuya Akutsu and Vladimir Brusic
Paper Session 1 --- Chair: Limsoon Wong
09:10 - 09:35 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
09:35 - 10:00 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
10:00 - 10:25 Computational Methods for the Analysis of Differential Conservation in Groups of Similar DNA Sequences
Nikola Stojanovic
10:25 - 10:50 Comprehensive Identification of gDruggableh Protein Ligand Binding Sites
Jianghong An, Maxim Totrov, Ruben Abagyan
10:50 - 11:10 Break
Keynote Address --- Chair: Vladimir Brusic
11:10 - 12:10 The Immune Epitope Database and Analysis Resource: From Vision to Blueprint
Alessandro Sette
12:10 - 13:30 Lunch
13:30 - 14:30 Posters and Software Demonstrations Session 1
Paper Session 2 --- Chair: Yixue Li
14:30 - 14:55 General-purpose Search Techniques for Genomic Text
Abhijit Chattaraj, Hugh E. Williams, Adam Cannane
14:55 - 15:20 Graphical Approach to Weak Motif Recognition
Xiao Yang, Jagath C. Rajapakse
15:20 - 15:45 An Extension and Novel Solution to the ( l,d ) -Motif Challenge Problem
Mark P Styczynski, Kyle L Jensen, Isidore Rigoutsos, Gregory N Stephanopoulos
15:45 - 16:10 Domain Discovery Method for Topological Profile Searches in Protein Structures
Juris Viksna, David Gilbert, Gilleain Torrance
16:10 - 16:30 Break
Paper Session 3 --- Chair: Christian Schönbach
16:30 - 16:55 A Novel Graph-Based Similarity Measure for 2D Chemical Structures
Si Quang Le, Tu Bao Ho, T.T Hang Phan
16:55 - 17:20 IRIS: Intermolecular RNA Interaction Search
Dmitri D. Pervouchine
17:20 - 17:45 StructMiner: A Tool for Alignment and Detection of Conserved Secondary Structure
Qian Yang, Mathieu Blanchette
17:45 - 18:10 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.

--------------------- Tuesday, December 14, 2004 ---------------------

Paper Session 4 --- Chair: Tetsuo Shibuya
09:00 - 09:25 Inference of Gene Regulatory Networks by Means of Dynamic Differential
Bayesian Networks and Nonparametric Regression

Naoya Sugimoto, Hitoshi Iba
09:25 - 09:50 Recovering Genetic Regulatory Networks from Micro-Array Data and Location Analysis Data
Fan Li, Yiming Yang
09:50 - 10:15 Increasing Feasibility of Optimal Gene Network Estimation
Annika Hansen, Sascha Ott, Georgy Koentges
10:15 - 10:35 Break
Paper Session 5 --- Chair: Sang Yup Lee
10:35 - 11:00 A Method for Clustering Gene Expression Data Based on Graph Structure
Shigeto Seno, Reiji Teramoto, Yoichi Takenaka, Hideo Matsuda
11:00 - 11:25 Statistical and Integrative Approach for Constructing Biological Network Maps
Hiroyuki Kurata, Natsumi Shimizu, Kanako Misumi
11:25 - 11:50 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
11:50 - 13:30 Lunch
Keynote Address --- Chair: Satoru Miyano
13:30 - 14:30 Revealing the Structure and Dynamics of Cis-Regulation Using Heterogeneous, Genome-Wide, Multi-Species Data
Ron Shamir
Paper Session 6 --- Hiroshi Mamitsuka
14:30 - 14:55 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
14:55 - 15:20 Support Vector Machines with Profile-Based Kernels for Remote Protein
Homology Detection

Steven Busuttil, John Abela, Gordon J. Pace
15:20 - 15:45 Kernel Mixture Survival Models for Identifying Cancer Subtypes, Predicting Patient's Cancer Types and Survival Probabilities
Tomohiro Ando, Seiya Imoto, Satoru Miyano
16:00 - 16:30 JSBi Annual Meeting
16:30 - 18:00 Posters and Software Demonstrations Session 2
18:30 - 21:00 Banquet

--------------------- Wednesday, December 15, 2004 ---------------------

Paper Session 7 --- Kenji Satou
09:00 - 09:25 Computational Prediction of Operons in Synechococcus sp. WH8102
Xin Chen, Zhengchang Su, Ying Xu, Tao Jiang
09:25 - 09:50 Intercellular Communications Induced by Random Fluctuations
Tianshou Zhou, Luonan Chen, Ruiqi Wang, Kazuyuki Aihara
09:50 - 10:15 Knowledge Representation Model for Systems-Level Analysis of Signal Transduction Networks
Dong-Yup Lee, Ralf Zimmer, Sang-Yup Lee, Daniel Hanisch, Sunwon Park
10:15 - 10:40 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
10:40 - 11:05 Ontological Integration of Data Models for Cell Signaling Pathways by Defining a Factor of Causality Called 'Signal'
Takako Takai-Igarashi, Riichiro Mizoguchi
11:05 - 12:15 Posters and Software Demonstrations Session 3
12:15 - 13:30 Lunch
Keynote Address --- Chair: Tatsuya Akutsu
13:30 - 14:30 Complex Systems Biology: Exploring Universal Statistical and Dynamical Features in Cellular Processes
Kunihiko Kaneko
14:30 - 14:50 Break
Paper Session 8 --- Chair: Kenta Nakai
14:50 - 15:15 Using Protein Motif Combinations to Update KEGG Pathway Maps and Orthologue Tables
Frédéric Nikitin, Bastien Rance, Masumi Itoh, Minoru Kanehisa,
Frédérique Lisacek
15:15 - 15:40 Systematic DNA-Binding Domain Classification of Transcription Factors
Philip Stegmaier, Alexander E. Kel, Edgar Wingender
15:40 - 16:05 Mining Yeast Transcriptional Regulatory Modules from Factor DNA-Binding Sites and Gene Expression Data
Tho Hoan Pham, Kenji Satou, Tu Bao Ho
Closing and Award Ceremony
16:05 - 16:20 @


E-mail: giw2004@ims.u-tokyo.ac.jp