| From 8:30 at Yebis Garden Hall on December 12, 13. (Registration Desk is open from through the workshop.) |
| Opening Address | |
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| 9:20 - 9:30 | Satoru Miyano (University of Tokyo) |
| Session A | Chair: Satoru Kuhara (Kyushu University) |
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| 9:30 - 9:50 | A New Method for Database Searching and Clustering Antje Krause, Martin Vingron |
| 9:50 - 10:10 | Clustering Molecular Sequences with Their Components Sivasundaram Suharnan, Takeshi Itou, Hideo Matsuda, Hirotada Mori |
| Coffee Break | 10:10 - 10:40 |
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| Session B | Chair: Masaru Tomita (Keio University) |
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| 10:40 - 10:55 | GENOME: A Networked Database Environment for Human Genome Data Andreas M. Kogelnik, Shamkant B. Navathe, Douglas C. Wallace |
| 10:55 - 11:10 | A Novel Approach Towards a Comprehensive Consensus Representation of the Expressed Human Genome Winston Hide, John Burke, Alan Christoffels, Robert Miller |
| Session C | (Invited Talk) Chair: Kiyoshi Asai (ETL) |
|---|---|
| 11:10 - 12:10 | Simple Maximum Likelihood Methods for the Optical Mapping Problem Michael S. Waterman (Univeristy of Southern California) |
| Lunch Break | 12:10 - 13:40 |
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| Session D | Chair: Hiroshi Imai (University of Tokyo) |
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| 13:40 - 14:00 | E-CELL: Software Environment for Whole Cell Simulation Masaru Tomita, Kenta Hashimoto, Kouichi Takahashi, Tom Shimizu, Yuri Matsuzaki, Fumihiko Miyoshi, Kanako Saito, Sakura Tanida, Katsuyuki Yugi, J. Craig Venter, Clyde A. Hutchison |
| 14:00 - 14:20 | DNAinsight: An Image Processing System for 2-D Gel Electrophoresis of Genomic DNA Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe |
| 14:20 - 14:40 | Rhythms Emerge in a Collection of `Blind' Chemicals by the Use of `Genetic Switches' Hiroshi Inayoshi, Hitoshi Iba |
| Coffee Break | 14:40 - 15:10 |
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| Session E | Chair: Hideo Matsuda (Osaka University) |
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| 15:10 - 15:30 | Breakpoint Phylogenies Mathieu Blanchette, Guillaume Bourque, David Sankoff |
| 15:30 - 15:50 | Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models Jeffrey M. Koshi, David P. Mindell, Richard A. Goldstein |
| Session F | (Invited Talk) Chair: Hirotada Mori (AIST-Nara) |
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| 15:50 - 16:50 | The First Laws of Genomics Piotr P. Slonimski |
| Posters and Software Demonstrations |
16:50 - 19:00 |
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| Banquet | ||
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| 19:00 - 21:00 | Foyer, Garden Hall |
| Session G | Chair: Toshihisa Takagi (University of Tokyo) |
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| 9:00 - 9:20 | Automatic Gene Recognition without Using Training Data Kiyoshi Asai, Yutaka Ueno, Katunobu Itou, Tetsushi Yada |
| 9:20 - 9:40 | A Multi-Agent System for Exon Prediction in Human Sequences Laurence Vignal, Frederique Lisacek |
| 9:40 - 10:00 | Prediction of Mitochondrial Targeting Signals Using Hidden Markov Model Yukiko Fujiwara, Minoru Asogawa, Kenta Nakai |
| Coffee Break | 10:00 - 10:30 |
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| Session H | Chair: Kenta Nakai (Osaka University) |
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| 10:30 - 10:45 | Fast Discerning Repeats in DNA Sequences with a Compression Algorithm Eric Rivals, Max Dauchet, Jean-Paul Delahaye, Olivier Delgrange |
| 10:45 - 11:00 | Reading Evolutionary History of Aminoacyl-tRNA Synthetases from Genome Sequences Kiyotaka Shiba, Hiromi Motegi, Tetsuo Noda |
| Session I | (Invited Talk) Chair: Masami Hagiya (University of Tokyo) |
|---|---|
| 11:00 - 12:00 | Title to be announced Jerome Chailloux (GENSET) |
| Lunch Break | 12:00 - 13:30 |
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| Session J | (Invited Talk) Chair: Naotake Ogasawara (AIST-Nara) |
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| 13:30 - 14:30 | The Map of the Cell is in the Chromosome Antoine Danchin (Insitut Pasteur) |
| Coffee Break | 14:30 - 15:45 |
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| Session K | Chair: Tatsuya Akutsu (University of Tokyo) |
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| 14:45 - 15:05 | Sequence Data Analysis for Long Disordered Regions Prediction in the Calcineurin Family Pedro Romero, Zoran Obradovic, A. Keith Dunker |
| 15:05 - 15:20 | Prediction of Hydrophobic Cores of Proteins Using Wavelet Analysis Hideki Hirakawa, Satoru Kuhara |
| 15:20 - 15:35 | Applying an Association Rule Discovery Algorithm to Multipoint Linkage Analysis Nobutaka Mitsuhashi, Haretsugu Hishigaki, Toshihisa Takagi |
| Coffee Break | 15:35 - 15:50 |
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| Session L | Chair: Shinsei Minoshima (Keio University) |
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| 15:50 - 16:05 | Virgil: A Databank of Links between GDB and GenBank Frederic Achard, Emmanuel Barillot |
| 16:05 - 16:20 | GeneMark-RC, a Recursive Procedure for Gene Identification in the Genomic Sequence Data with Self-Consistency Evaluation; Its Application to the Analysis of Several Prokaryotic Genomes Makoto Hirosawa, Katumi Isono |
| Video Break | 16:20 - 16:30 |
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| Session M | Chair: Ayumi Shinohara (Kyushu University) |
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| 16:20 - 16:40 | Sequencing by Hybridization with Positive Faults Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak, Wojciech T. Markiewicz, Jan Weglarz |
| 16:40 - 17:00 | Greedy Algorithms for Finding a Small Set of Primers Satisfying Cover Length Resolution Conditions in PCR Experiments Koichiro Doi, Hiroshi Imai |
| Video Break | 17:00 - 17:10 |
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| Session N | Chair: Qian Ping Gu (University of Aizu) |
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| 17:10 - 17:25 | DP Algorithms for RNA Secondary Structure Prediction with Pseudoknots Tatsuya Akutsu |
| 17:25 - 17:40 | NP-Hardness Results for Protein Side-Chain Packing Tatsuya Akutsu |
| Closing Remarks | ||
|---|---|---|
| 17:40 - 17:50 | Toshihisa Takagi (University of Tokyo) |