GIW 2002
Registration

Advanced Program
The Garden Hall entrance
December 16, 2002 : 13:00 – 17:20
December 17, 2002 : 09:00 – 18:30
December 18, 2002 : 09:00 – 16:45

Monday, December 16, 2002

The Garden Hall

Opening Address
14:00 - 14:10 Richard H. Lathrop (UC Irvine)

Paper Session 1

Data Mining from Genomes
Chair: Limsoon Wong (LIT)

14:10 - 14:35 A String Pattern Regression Algorithm and Its Application to Pattern
Discovery in Long Intron, Hideo Bannai1, Shunsuke Inenaga2, Ayumi
Shinohara2,3, Masayuki Takeda2,3, Satoru Miyano1 (1U. Tokyo, 2Kyushu U.,3JST)
14:35 - 15:00 A Novel Bioinformatic Strategy for Unveiling Hidden Genome Signatures ofEukaryotes: Self-Organizing Map of Oligonucleotide Frequency, Takashi
Abe1,2,3, Shigehiko Kanaya3,4,5, Makoto Kinouchi3,5,6, Yuta Ichiba1,3, Tokio
Kozuki2,3, Toshimichi Ikemura1,3 (1NIG, 2Xanagen, 3ACT-JST, 4NAIST,
5
CREST JST, 6Yamagata U.)
15:00 - 15:25 Detection of Periodicity in Eukaryotic Genomes on the Basis of PowerSpectrum Analysis, Atsushi Fukushima1, Toshimichi Ikemura2, Taku
Oshima1, Hirotada Mori1, Shigehiko Kanaya1 (1NAIST, 2SOKEN)
15:25 - 15:50 Analysis of Common k-mers for Whole Genome Sequences Using
SSB-Tree, Jeong-Hyeon Choi, Hwan-Gue Cho (Pusan Nat’l U.)
BreakPaper Session 2

15:50-16:05

Functional Genomics
Chair: Takatoshi Kawai (Eizai Co., Ltd.)

16:05 - 16:30 Large Scale Statistical Prediction of Protein-Protein Interaction byPotentially Interacting Domain (PID) Pair, Wan Kyu Kim (Object Interaction
Tech. Inc.), Jong Park (Cambridge U.), Jung Keun Suh (LG Life Sci., Ltd.)
16:30 - 16:55 A Comparative Study on Feature Selection and Classification Methods
Using Gene Expression Profiles and Proteomic Patterns, Huiqing Liu ,Jinyan Li, Limsoon Wong (LIT)
16:55 - 17:20 Extraction of Organism Groups from Phylogenetic Profiles Using
Independent Component Analysis, Yoshihiro Yamanishi, Masumi Itoh,
Minoru Kanehisa (Kyoto U.)

Tuesday, December 17, 2002
Paper Session 3

The Garden Hall

Evolution
Chair: Sang Yup Lee (KAIST)

09:00 - 09:25 Origin of Most Primitive mRNAs and Genetic Codes via Interactions
between Primitive tRNA Ribozymes, Koji Ohnishi, Shouken Hokari, Hiroshi
Shutou, Madoka Ohshima, Naotaka Furuichi, Masaki Goda (Niigata U.)
09:25 - 09:50 Very Fast Algorithms for Evaluating the Stability of ML and Bayesian
Phylogenetic Trees from Sequence Data, Peter J. Waddell (U. SouthCarolina), Hirohisa Kishino (U. Tokyo), Rissa Ota (Massey U.)
09:50 - 10:15 An Algorithmic Analysis of the Role of Unequal Crossover in Alpha Satellite
DNA Evolution, Can Alkan, Jeffrey A. Bailey, Evan E. Eichler, S. Cenk
Sahinalp, Eray Tuzun (Case West. Reserve U.)
10:15 - 10:40 Genomic Sorting with Length-Weighted Reversals, Ron Y. Pinter (IsraelInst. Tech.), Steven Skiena (State U. NY)
Break

10:40 - 10:55

Chair: Tetsuo Nishikawa (Hitachi, Ltd.)
10:55 - 11:55 Comparative Genomics for Understanding Ourselves
Yoshiyuki Sakaki (RIKEN)

Keynote Address

Lunch Break

11:55 -13:25

Chair: Kiyoshi Asai (CBRC)
13:25 - 14:25 Inferring Gene Transcription Networks: The Davidson Model
Sorin Istrail (Celera Genomics)

Keynote Address

Paper Session 4

Algorithms
Chair: Tatsuya Akutsu (Kyoto U.)

14:35 - 15:00 Marginalized Kernels for RNA Sequence Data Analysis, Taishin Kin, Koji
Tsuda, Kiyoshi Asai (CBRC)
15:00 - 15:25 Aligning Multiple Protein Sequences by Parallel Hybrid Genetic Algorithm,
Hung Dinh Nguyen1, Ikuo Yoshihara1, Kunihito Yamamori1, Moritoshi
Yasunaga2 (1Miyazaki U., 2U. Tsukuba)
15:25 - 15:50 Inference of Euler Angles for Single Particle Analysis by Using Genetic
Algorithms, Shusuke Saeki1, Kiyoshi Asai2, Katsutoshi Takahashi2, Yutaka
Ueno2, Katsunori Isono3, Hitoshi Iba1 (1U. Tokyo, 2CBRC, 3INTEC W&G
Informatics Corp.)
Break

15:50 -JSBi Annual Meeting
16:00 - 16:30

General MeetingPoster and Software Demonstrations Session 1
16:30 - 18:30

Social Events
18:30 - 21:00(JSBi Session, The Garden Hall Foyer)Award Ceremony & Banquet(The Garden Room)Wednesday, December 18, 2002
Paper Session 5

The Garden Hall

Structural Biology
Chair: Alfonso Valencia (CNB-CSIC)

09:00 - 09:25 Point Matching Under Non-Uniform Distortions and Protein Side Chain
Packing Based on an Efficient Maximum Clique Algorithm, Dukka Bahadur
K. C.1, Tatsuya Akutsu1, Etsuji Tomita2, Tomokazu Seki2, Asao Fujiyama3(1Kyoto U., 2U. Electro-Comm, 3NII)
09:25 - 09:50 The Role of DNA Deformation Energy at Individual Base Steps for theIdentification of DNA-Protein Binding Sites, Nicholas R. Steffen, Scott D.
Murphy, Richard H. Lathrop, Michael L. Opel, Lorenzo Tolleri, G. WesleyHatfield (UC Irvine)
09:50 - 10:15 Folding Pattern Recognition in Proteins Using Spectral Analysis Methods,
Carlos A. Del Carpio Muňoz, Julio Cesar Carbajal L. (Toyohashi U. Tech.)
Poster and Software Demonstrations Session 2
10:15 - 12:15(JSBi Session, The Garden Hall Foyer)
Lunch BreakPaper Session 6

12:15 -14:00
Sequence Analysis
Chair: Makiko Suwa (CBRC)

14:00 - 14:25 Comparative Analysis of the Genomes of Cyanobacteria and Plants, Naoki
Sato (Saitama U.)
14:25 - 14:50 A Novel Index which Precisely Derives Protein Coding Regions fromCross-Species Genome Alignments, Hideki Noguchi1, Tetsushi Yada1,Yoshiyuki Sakaki1,2 (1RIKEN, 2U. Tokyo)
14:50 - 15:15 Using Feature Generation and Feature Selection for Accurate Prediction ofTranslation Initiation Sites, Fanfan Zeng1, Roland H.C. Yap1, Limsoon
Wong2 (1Nat’l U. Singapore, 2LIT)
BreakPaper Session 7

15:15 -15:30Systems Biology / Ontology
Chair: Takako Takai (U. Tokyo)

15:30 - 15:55 Automatic Ontology Construction from the Literature, Christian Blaschke,
Alfonso Valencia (CNB/CSIC)
15:55 - 16:20 In Silico Metabolic Pathway Analysis and Design: Succinic Acid Production
by Metabolically Engineered Escherichia coli as an Example, Sang Yup
Lee, Soon Ho Hong, Soo Yun Moon (KAIST)
16:20 - 16:45 Physical Modeling of the Cellular Arrangement in C. elegans Early Embryo:
Effect of Rounding and Stiffening of the Cells, Atsushi Kajita1,2, Masayuki
Yamamura2, Yuji Kohara1 (1NIG, 2Tokyo Inst. Tech.)
Closing

16:45 -16:55