| Monday, December 14 |
8:00 - 18:00 |
| Tuesday, December 15 | 8:30 - 18:00 |
| Wednesday, December 16 | 8:30 - 14:30 |
--------------------- Monday, December 14, 2009 ---------------------
| Opening Address | |
| 09:00 - 09:10 | Yasubumi Sakakibara |
| Keynote Address 1 --- Chair: Shinichi Morishita | |
| 09:10 - 10:10 | Sang Yup Lee Systems Biotechnology |
| 10:10 - 10:40 | Break |
| Paper Session 1 --- Chair: Hideo Matsuda | |
| 10:40 - 11:05 | Comparative Analysis of Topological Patterns in Different Mammalian Networks Bjoern Goemann, AnatolijP. Potapov, Michael Ante, Edgar Wingender |
| 11:05 - 11:30 | The Prediction of Local Modular Structures in a Co-expression Network Based on Gene Expression Datasets Yoshiyuki Ogata, Nozomu Sakurai, Hideyuki Suzuki, Koh Aoki, Kazuki Saito, Daisuke Shibata |
| 11:30 - 11:55 |
Quality Control and Reproducibility in DNA Microarray Experiments Andre Fujita, Joao Sato, Fernando daSilva, Maria Galvao, Mari Sogayar, Satoru Miyano |
| 11:55 - 13:00 | Lunch / Poster Viewing |
| Keynote Address 2 --- Chair: Tetsuo Shibuya | |
| 13:00 - 14:00 | Sean R. Eddy A New Generation of Homology Search Tools Based on Probabilistic Inference |
| Paper Session 2 --- Chair: Tetsuo Shibuya--> | |
| 14:00 - 14:25 |
Gradient-based Optimization of Hyperparamers for Base-pairing Profile Local Alignment Kernels Kengo Sato, Yutaka Saito, Yasubumi Sakakibara |
| 14:25 - 14:50 | Cancer Classification Using Single Genes Xiaosheng Wang, Osamu Gotoh |
| 14:50 - 15:20 | Break |
| Paper Session 3 --- Chair: Satoru Miyano | |
| 15:20 - 15:45 | Comprehensive Analysis of Sequence-structure Relationships In the Loop Regions of Proteins Shugo Nakamura, Kentaro Shimizu |
| 15:45 - 16:10 | Development of a New Meta-score for Protein Structure Prediction from Seven All-atom Distance Dependent Potentials Using Support Vector Regression Matsuyuki Shirota, Takashi Ishida, Kengo Kinoshita |
| 16:10 - 16:35 | Refining Markov Clustering for Protein Complex Prediction by Incorporating Core-attachment Structure Sriganesh Srihari, Kang Ning, HonWai Leong |
| 16:35 - 16:50 | Poster Oral 1 Dynamic Programming Algorithms for RNA Structure Prediction with Binding Sites Unynee Poolsap, Yuki Kato, Tatsuya Akutsu |
| Posters and Software Demonstrations Session 1 | |
| 16:50 - 18:30 | Odd Numbered Posters/Demos |
--------------------- Tuesday, December 15, 2009 ---------------------
| Keynote Address 3 --- Chair: Osamu Gotoh | |
| 9:00 - 10:00 | Mark A. Ragan Thinking Laterally about Genomes |
| Paper Session 4 --- Chair: Osamu Gotoh | |
| 10:00 - 10:25 | Comparative Analysis of Aerobic and Anaerobic Prokaryotes to Identify Correlation between Oxygen Requirement and Gene-Gene Functional Association Patterns Yaming Lin, Hongwei Wu |
| 10:25 - 10:55 | Break |
| Paper Session 5 --- Chair: Christian Schoenbach--> | |
| 10:55 - 11:20 | Calculation of Protein-ligand Binding Free Energy Using Smooth Reaction Path Generation (SRPG) Method; A Comparison the Explicit Water Model, GB/SA Model and Docking Score Function Daisuke Mitomo, Yoshifumi Fukunishi, Haruki Nakamura |
| 11:20 - 11:45 | Structural Insights into the Enzyme Mechanism of a New Family of D-2-hydroxyacid Dehydrogenases, a Close Homolog of 2-ketopantoate Reductase Sukanta Mondal, Kenji Mizuguchi |
| 11:45 - 12:00 | Poster Oral 2 Dissecting protein-protein interaction-mediated cross-talk pathways in hepatocellular carcinoma Chia-Hung Liu, Chun-Nan Hsu, Cheng-Yan Kao, Minoru Kanehisa, Susumu Goto, Chi-Ying F. Huang |
| 12:00 - 13:30 | Lunch / Poster Viewing |
| Keynote Address 4 --- Chair: Yasubumi Sakakibara | |
| 13:30 - 14:30 | Hideyuki Okano Strategies toward CNS-Regeneration Using Induced Pluripotent Stem Cells |
| Paper Session 6 --- Chair: Yasubumi Sakakibara | |
| 14:30 - 14:55 | Localized Suffix Array and Its Application to Genome Mapping Problems for Paired-End Short Reads Kouichi Kimura, Asako Koike |
| 14:55 - 15:20 | Recount: Expectation Maximization Based Error Correction Tool for Next Generation Sequencing Data Edward Wijaya, Martin Frith, Yutaka Suzuki, Paul Horton |
| 15:20 - 15:35 | Poster Oral 3 DDBJ Read Archive and DDBJ Read Annotation Pipeline:An archive database and an analytical tool for next-generation sequence data Eli Kaminuma, Yuichi Kodama, Satoshi Saruhashi, Takeshi Konno, Takako Mochizuki, Hidemasa Bono, Hideaki Sugawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura |
| 15:35 - 15:50 | Yixue Li (2010 AASBi President) GIW2010 announcement |
| 15:50 - 16:00 | Break |
| 16:00 - 16:30 | JSBi Annual Meeting |
| Posters and Software Demonstrations Session 2 | |
| 16:30 - 18:00 | Even Numbered Posters/Demos |
| 18:30 - 20:30 | Banquet (at: banquet room "Silk", Inter Continental THE GRAND YOKOHAMA) |
--------------------- Wednesday, December 16, 2009 ---------------------
| JSBi Special Session - Aspects of synthetic, metabolomic, and systems biology- --- Chairs: Masanori Arita, Tsuyoshi Shirai and Hideo Matsuda |
|
| 9:00 - 9:30 | Masami Hagiya Information Technology for Synthetic Biology |
| 9:30 - 10:00 | MassBank : A Mass Spectral Database for Metabolomics Takaaki Nishioka |
| 10:00 - 10:30 | Cell Illustrator Online 4.0: A Platform for Systems Biology Satoru Miyano |
| 10:30 - 11:00 | Break |
| Paper Session 7 --- Chair: Koji Tsuda | |
| 11:00 - 11:25 | Predicting Protein-Protein Relationships from Literature using Latent Topics Tatsuya Aso, Koji Eguchi |
| 11:25 - 11:50 | A Method for Efficient Execution of Bioinformatics Workflows Junya Seo, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda |
| 11:50 - 12:15 | Tools for Investigating Mechanisms of Antigenic Variation: New Extensions to VarDB C.Nelson Hayes, Diego Diez, Nicolas Joannin, Minoru Kanehisa, Mats Wahlgren, CraigE. Wheelock, Susumu Goto |
| 12:15 - 13:30 | Lunch / Poster Viewing |
| Keynote Address 5 --- Chair: Hiroshi Mamitsuka | |
| 13:30 - 14:30 | Minoru Kanehisa Representation and Analysis of Molecular Networks Involving Diseases and Drugs |
| Paper Session 8 --- Chair: Hiroshi Mamitsuka | |
| 14:30 - 14:55 | An Assessment of Prediction Algorithms for Nucleosome Positioning Yoshiaki Tanaka, Kenta Nakai |
| 14:55 - 15:20 | Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast Michael Fernandez, Satoshi Fujii, Hidetoshi Kono, Akinori Sarai |
| 15:20 - 15:35 | Poster Oral 4
A Parallel Algorithm for Estimating Genome-Wide Gene Networks using Nonparametric Bayesian Networks Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Satoru Miyano |
| Closing and Award Ceremony | |
| 15:35 - 16:00 | |
E-mail: giw2009 AT edelweiss.ims.u-tokyo.ac.jp