GIW 2001 Advanced Program
December 17, Monday, The Garden HallOpening Address
14:00 - 14:10

Session 1

Limsoon Wong (KRDL)

Gene Expression
Chair: Satoru Kuhara (Kyushu U.)

14:10 - 14:35

Emerging Patterns and Gene Expression Data, Jinyan Li,
Limsoon Wong (Kent Ridge Digital Lab.)

14:35 - 15:00

Selecting Informative Genes with Parallel Genetic Algorithms in Tissue Classification, Juan Liu∗† , Hitoshi Iba† ,Mitsuru Ishizuka† (∗ Wuhan U., † U. Tokyo)

15:00 - 15:25

Minimum Spanning Trees for Gene Expression Data Clustering, Ying Xu, Victor Olman, Dong Xu (Oak Ridge Nat’lLab.)

15:25 - 15:50

Characterizing the Relationship between Protein-Fusion
and Gene Co-Expression, Cary S. Gunther, Terry Gaasterland (Rockefeller U.)

Break

15:50 - 16:05

Session 2

Pathway Analysis
Co-chair: Terry Gaasterland (Rockefeller U.)
Susumu Goto (Kyoto U.)

16:05 - 16:30

Extraction of Correlated Gene Clusters by Multiple Graph
Comparison, Akihiro Nakaya, Susumu Goto, Minoru Kanehisa (Kyoto U.)

16:30 - 16:55

XML Documentation of Biopathways and Their Simulations in Genomic Object Net, Hiroshi Matsuno∗ , Atsushi
Doi∗, Yuichi Hirata† , Satoru Miyano† (∗ Yamaguchi U., † U.
Tokyo)

16:55 - 17:20

Estimation of Bidirectional Metabolic Fluxes from MS andNMR Data Using Positional Representations, Marcos J.
Araúzo-Bravo, Kazuyuki Shimizu (Kyushu Inst. of Tech.)1December 18, Tuesday, The Garden Hall
Session 3

Protein Sequence and Structure
Co-chair: Akihiko Konagaya (JAIST)
Richard Lathrop (UC Irvine)

9:00 - 9:25

A Multi-Queue Branch-and-Bound Algorithm For Anytime
Optimal Search With Biological Applications, Richard H.
Lathrop, Anton Sazhin, Ye Sun, Nick Steﬀen, Sandra S.
Irani (UC Irvine)

9:25 - 9:50

Local Multiple Alignment of Numerical Sequences: Detection of Subtle Motifs from Protein Sequences and Structures, Tatsuya Akutsu (Kyoto U.), Katsuhisa Horimoto(Saga Med. Sch.)A Graph-Based Clustering Method for a Large Set of Sequences Using a Graph Partitioning Algorithm, HideyaKawaji∗† , Yosuke Yamaguchi∗, Hideo Matsuda∗ , Akihiro
Hashimoto∗ (∗ Osaka U., † NTT Software Corp.)

9:50 - 10:15

10:15 - 10:40

Prediction of Subcellular Localizations Using Amino Acid
Composition and Order, Yukiko Fujiwara, Minoru Asogawa(NEC Corp.)

Break

10:40 - 10:55

Invited Talk

Chair: Limsoon Wong (KRDL)

10:55 - 11:55

New Data Driven Research Paradigm for the Post Genome
Era
Charles Lawrence (Wadsworth Center)

Lunch Break

11:55 - 13:30

Invited Talk

Chair: Takashi Ito (Kanazawa U.)

13:30 - 14:30

Protein Interactions
David Eisenberg (UCLA)

Break

14:30 - 14:45
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Session 4

Protein Interaction
Chair: Makiko Suwa (CBRC)

14:45 - 15:10

Automatic Epitope Recognition in Proteins Oriented to theSystem for Macromolecular Interaction Assessment MIAX,Atsushi Yoshimori, Carlos A. Del Carpio (Toyohashi U. ofTech.)

15:10 - 15:35

The Potential Use of SUISEKI as a Protein Interaction Discovery , Christian Blaschke, Alfonso Valencia (CNB/CSIC)

15:35 - 16:00

Conservation of Protein Interaction Network in Evolution,
Jong Park, Dan Bolser (Cambridge U.)

JSBi Annual Meeting
16:00 - 16:30

General Meeting

Poster & Software Demonstrations Session 1
16:30 - 18:30

Social Events
18:30 - 21:00

JSBi Session (The Garden Hall Foyer)
Poster Session: The Garden Hall Foyer
Software Demonstrations: The GardenHall

Award Ceremony and Banquet
The Garden Room3

December 19, Wednesday, The Garden HallSession 5Molecular Phylogeny
Chair: Hideo Matsuda (Osaka U.)

9:00 - 9:25

A Phylogenetic Foundation for Comparative Mammalian
Genomics, Peter J. Waddell∗, Hirohisa Kishino† , Rissa
Ota‡ (∗ U. South Carolina, † U. Tokyo, ‡ Massey U.)

9:25 - 9:50

Bacterial Molecular Phylogeny Using Supertree Approach,Vincent Daubin, Manolo Gouy, Guy Perriére (UCBL)

Break

9:50 - 10:05

Poster & Software Demonstrations Session 2
10:05 - 12:05

JSBi Session (The Garden Hall Foyer)
Poster Session: The Garden Hall Foyer
Software Demonstrations: The Garden Hall

Lunch Break

12:05 - 13:35

Session 6

Genome Analysis
Co-chair: Tatsuya Akutsu (Kyoto U)
Gene Myers (Celera Genomics)

13:35 - 14:00

Optimally Separating Sequences, Gene Myers (Celera Genomics)

14:00 - 14:25

Indexing Huge Genome Sequences for Solving Various
Problems, Kunihiko Sadakane∗ , Tetsuo Shibuya† (∗ TohokuU., † IBM Tokyo Res. Lab.)

14:25 - 14:50

A Mini-Greedy Algorithm for Faster Structural RNA StemLoop Search, Jan Gorodkin∗, Rune B. Lyngsø† , Gary D.
Stormo‡ (∗ U. Aarhus, † UC Santa Cruz, ‡ Washington U.)

Break

14:50 - 15:05415:05 - 15:30

High-Throughput Identification, Database Storage andAnalysis of SNPs in EST Sequences, Francisco José
Useche∗ , Guang Gao∗, Mike Hanafey† , Antoni Rafalski †(∗ U. Delaware, † DuPont Crop Genetics)

15:30 - 15:55

Bioinformatics Issues for Automating the Annotation ofGenomic Sequences, Kim Carter∗ , Akira Oka† , GenTamiya †, Matthew I. Bellgard∗ (∗ Murdoch U., † Tokai U.)

15:55 - 16:20

DNAinsight: A Web Based Image Processing System forLarge Scale RLGS Analysis, Katsutoshi Takahashi∗,
Masayuki Nakazawa† ,Yasuo Watanabe (∗ CBRC,†Kanazawa Tech.
Coll, ‡ Kanazawa Inst.
of Tech.)Closing
16:20 - 16:30

Kenta Nakai (U. Tokyo)

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