The Seventh Workshop on Genome Informatics

The Garden Hall, Yebisu Garden Place, Tokyo, Japan.
December 2 (9:30--17:30), 3 (9:30--17:30), 1996

Electronic Version of Genome Informatics Vol. 7 (1996)

General Information

Location and Accommodation


Poster Presentations

Registration Form

General Information

The Garden Hall, Yebisu Garden Place, Tokyo, Japan.

December 2 (9:30--17:30), 3 (9:30--17:30), 1996

Human Genome Center, The University of Tokyo
Priority Area Research Project ``Genome Science'' from MESSC of Japan

Gordon M. Crippen (University of Michigan)
Pavel A. Pevzner (University of Southern California)
Hiroaki Kitano (SONY CSL)
Susumu Tachi (University of Tokyo)

T.Akutsu (Chair, U. Tokyo) K.Asai(ETL) M.Hagiya(U. Tokyo)
S.Kuhara(Kyushu U.) S.Miyano(U.Tokyo) N.Nakai(Osaka U.)

The Garden Room, Yebisu Garden Place
December 2, 1996 18:30--20:30

Free (not including proceedings or banquet)

Tatsuya AKUTSU
Human Genome Center
Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108, Japan
FAX: +81-3-5449-5434

Location and Accommodation

The workshop will take place at the Garden Hall and banquet will take place at the Garden Room. Both places are located in the Yebisu Garden Place. It takes 5 minutes walk from JR EBISU station to Yebisu Garden Place.
The address/TEL/FAX of Yebisu Garden Place are as follows:

1-13-2 Mita, Meguro-ku, Tokyo 153 JAPAN.
TEL: +81-3-5424-0111
FAX: +81-3-5424-1444

Tokyo is the capital city of Japan. There are direct flights to Narita International Airport from many countries. You can take trains from the airport.

After arriving in Narita International Airport, take a train (either JR line or Keisei line) from the airport station:

  1. JR line:
    Using Express (Narita Express) train, it takes about 1 hour (and 2,890 YEN) from the airport station to JR Tokyo station. From JR Tokyo station to JR Ebisu station, take JR Yamanote line to the direction of Shinagawa and Shibuya. It takes about 30 minutes.

  2. Keisei line:
    Using Express (Skyliner) train, it takes about 1 hour (and 1,740 YEN) from the airport station to Keisei Ueno station. It takes about 5 minutes walk from Keisei Ueno station to JR Ueno station. From JR Ueno station to JR Ebisu station, take JR Yamanote line to the direction of Tokyo and Shinagawa. It takes about 40 minutes.

Go along the Sky Walk from the east exit of JR Ebisu station. After 5 minutes walk, you will find the entrance to the Yebisu Garden Place.

JR Yamanote Line:

     /-- Shibuya ---...---  Shinjuku ---...--- Ikebukuro --\  
    /                                                       \
  Ebisu                                                     .
    |                                                       .
  Meguro                                                    .
    |                                                       . 
    |                                                       | 
    \                                                       /
     \--...-- Shinagawa ---...--- Tokyo ---... --- Ueno ---/
                                    |               |
                                    | JR Keiyou     |  Keisei Line
                                    |    Line       |
                                    v               v
                                  Narita          Narita

From Ebisu Station to Yebisu Garden Place:

                -----------------------------------/   Entrance of
                |                      Sky Walk        Garden Place
                |         East Exit ----------------------------
                |                   |
  Shibuya <---- |   Ebisu sta.      | -------------------> Meguro sta.
  Sta.          ---------------------

You can stay at Westin Hotel Tokyo with conference rate (single room: 20,000YEN, twin room: 24,000YEN, not including service charge or tax). Westin Hotel Tokyo is located in the Yebisu Garden Place. Please contact with ``'' for details about Westin Hotel Tokyo.

Although there are a lot of hotels in Tokyo, only a few of them are listed below. If you prefer the hotels below, you should make reservation for yourselves, by phone or by FAX. All of the hotels below stand near JR Yamanote line stations. It takes at most 15 minutes from each station to JR Ebisu station. Note that service charge and tax are not included except the U-Port hotel.

Shinagawa Prince Hotel (near JR Shinagawa Sta.)
     Single room:   9,700 YEN, 10,200 YEN or 12,700 YEN
     Twin room:    13,500 YEN or 16,500 YEN
     TEL: +81-3-3440-1111
     FAX: +81-3-3441-7092

New Otani Inn Tokyo (near JR Osaki Sta.)
     Single room:  13,000 YEN
     Twin room:    30,000 YEN
     TEL: +81-3-3779-9111
     FAX: +81-3-3779-9181

U-Port (near JR Gotanda Sta.)
     Single room:  8,610 YEN
     Twin room:   13,596 YEN
     (Service charge and tax are included)
     TEL: +81-3-3490-5111
     FAX: +81-3-3779-5785

Preliminary Program

Dec. 2, 1996

9:45--9:50 Opening

9:50--10:50 Session 1 (Chair, S. Miyano)

L. Zhang:
On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies

Qian-Ping Gu, S. Peng, H. Sudborough:
Approximation algorithms for genome rearrangements

H. Matsuda, T. Ishihara, A. Hashimoto:
A clustering method for molecular sequences based on pairwise similarity

10:50--11:10 Break

11:10--12:10 Session 2 (Chair, H. Matsuda)

F. Shi, P. Widmayer:
Approximate multiple strings searching by clustering

T. Shibuya, H. Imai:
Parametric alignment of multiple biological sequences

M. Yamaguchi, S. Shimozono, T. Shinohara:
Finding minimal multiple generalization over regular patterns with alphabet indexing

12:10--13:30 Lunch

13:30--14:30 Invited Lecture 1 (Chair, T. Akutsu)

Gordon M. Crippen (Univ. Michigan)
Failures of inverse folding and threading with gapped alignment

14:30--15:30 Invited Lecture 2 (Chair, H. Imai)

Pavel A. Pevzner (Univ. Southern California)
Transforming Men into Mice

15:30--15:45 Break

15:45--16:30 Posters
1 minute presentation for posters

16:30--18:00 Posters

18:30--20:30 Banquet

Dec. 3, 1996
9:30--10:50 Session 3 (Chair, S. Kuhara)

S. Kanaya, Y. Kudo, S. Suzuki, T. Ikemura:
Systematization of species-specific diversity of genes in codon usage: Comparison of the diversity among bacteria and prediction of the protein production levels in cells

K. Nakai:
Refinement of the prediction methods of signal peptides for the genome analyses of Saccharomyces cerevisiae and Bacillus subtilis

M. S. Gelfand, T. V. Astakhova, M. A. Roytberg:
An algorithm for highly specific recognition of protein-coding regions

K. Asai, T. Yada, K. Itou:
Finding genes by hidden Markov models with a protein motif dictionary

10:50--11:10 Break

11:10--12:10 Session 4 (Chair, K. Nakai)

N. Furukawa, S. Matsumoto, A. Shinohara, T. Shoudai, S. Miyano:
HAKKE: a multi-strategy prediction system for sequences

C. A. Del Carpio, V. Gogonea:
Modeling proteins conformation in solution. Part I: a parallel GA engine for protein conformational space mapping

N. N. Alexandrov, V. V. Solovyev:
Effect of secondary structure prediction on protein fold recognition and database search

12:10--14:00 Lunch and Poster Presentation

14:00--15:00 Invited Lecture 3 (Chair, K. Asai)

Hiroaki Kitano (SONY CSL)
Toward Computer-Aided Biology: A Synthetic Approach for Understanding Life

15:00--16:00 Invited Lecture 4 (Chair, T. Takagi)

Susumu Tachi (U. Tokyo)
Virtual Reality and Tele-Existence

16:00--16:10 Break

16:10--17:30 Session 5 (M. Hagiya)

H. Ogata, H. Bono, W. Fujibuchi, S. Goto, M. Kanehisa:
Analysis of binary relations and hierarchies of enzymes in the metabolic pathways

Y. Kitamura, H. Nakanishi, T. Nozaki, T. Miura, T. Ishida:
MetaViewer and MetaCommander: WWW tools for genome informatics

R. Gras, J. Nicolas:
FOREST, a browser for huge DNA sequences

T. Koike, et al.:
Development of new DDBJ DNA sequence database with data annotation

17:30--17:35 Closing

Poster Presentations

A Taxonomy Database System for Managing Multimedia Contents 
    Hajime Kitakami, Yasuma Mori, Masatoshi Arikawa

Automated Identification of Three-Dimensional Motif in Proteins 
    Hiroaki Kato, Yoshimasa Takahashi

Characterization of Enzyme Structure by Informational Complexity 
    Takayuki Kamei, Yasuo Yonezawa

Java Version of Animal Genome Database 
    Y. Wada, H. Yasue

A Symbolic Representation for RNA Secondary Structures; towards the Construction of RNA Secondary Structures Data Base 
    A. Nakaya, A. Yonezawa, K. Yamamoto

Multiple Sequence Alignment Using a Genetic Algorithm 
    Masamichi Isokawa, Masato Wayama, Toshio Shimizu

Discovering Functional Sites of Amino Acid Sequences Using Sorted Variable Generalization 
    Takashi Ishikawa, Shigeki Mitaku, Takao Terano

Improvement of the Transmembrane Helix Prediction System by Three-Stage Model 
    Takatsugu Hirokawa, Seah Boon-Chieng, Shigeki Mitaku

Sequence Analysis of Short Tandem Repeats in the Genomes of H.influenzae and M.genitalium 
    Takanori Washio, Masahiko Wada, Masaru Tomita

On Correlation between G+C Contents and Introns Lengths: Longer Introns Tend to be More A+T Rich 
    Yasuhiro Asakawa, Masaru Tomita

CpG Dinucleotide Distribution and DNA Methylation 
    Tom Shimizu, Kouichi Takahashi, Masaru Tomita

Computer Analyses of Nucleotide Patterns around Start Codons 
    Rintaro Saito, Hidekazu Sasaki, Yuko Osada, Masaru Tomita

Computer Analyses of Overlapping Genes in Mycoplasma Genitalium 
    Yuko Osada, Ryo Matsushima, Masaru Tomita

Computer Analyses of Site-Specific Variabilities in Human Alu Sequences 
    Michiko Muraki, Masaru Tomita

Inferring History of Genomic Duplication Using Subclassified Alu Elements 
    Yoshimi Toda, Masaru Tomita

Motif Extraction: Normalization of Scores 
    Y. Fujiwara, M. Asogawa

Beta-sheet Prediction Using Inter-strand Residue Pairs and Refinement with Hopfield Neural Network 
    Minoru Asogawa

Building A Receptor Database 
    K. Nakata, M. Hayakawa, T. Igarashi, T. Kaminuma

Direct Comparison DNA and Amino Acid Sequences based on a Dynamic Programming Method 
    Naoko Kasahara, Susumu Hiraoka, Keiichi Nagai

SAKURA: A New Data Submission System of DDBJ to Meet Users' Needs in the Age of Mass Production of DNA Sequences 
    Hikaru Yamamoto, Takuro Tamura, Katsumi Isono, Takashi Gojobori, Hideaki Sugawara, Ken Nishikawa, Naruya Saitou, Tadashi Imanishi, Kaoru Fukami-Kobayashi, Kazuho Ikeo, Yoshio Tateno

Emergent Rhythms in an Artificial Chemical World Using `Genetic Switches' 
    Hiroaki Inayoshi, Hitoshi Iba

A New Software For Visualization of Large Proteins 
    Yutaka Ueno, Kiyoshi Asai

Automatic Discovery of Hidden Markov Representations for Functional Sites within DNA Sequences 
    Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai

GeneHacker: Gene--Finding Program for the Prediction of Precise Protein Coding Regions 
    Makoto Hirosawa, Tetsushi Yada

CyanoBase: The Genome Database for Synechocystis sp. strain PCC6803 
    Yasukazu Nakamura, Nobuyuki Miyajima, Makoto Hirosawa, Takakazu Kaneko, Satoshi Tabata

Management System for Sequencing Data of Human Genome --- As a Part of {\em ALIS} --- 
    Mika Hirakawa, Kensaku Imai, Akira Ohyama, Fumihiko Kikuchi

Establishment and Management of Transcription Factor Database TFDB 
    T. Okazaki, M. Kaizawa, H. Mizushima

Very Fast Identification of tRNA in Genomic DNA 
    F. Lisacek, N. El Mabrouk

Predicting and Learning RNA Secondary Structures 
    Aki Hasegawa, Yasuo Uemura, Satoshi Kobayashi, Takashi Yokomori

Modeling Proteins Conformation in Solution. Part II: A Solvent Effect Model Based on the Evaluation of Solvent-Accessible Surface Area and Generalized Born Equation 
    Valentin Gogonea, Camelia Baleanu-Gogonea, Carlos A. Del Carpio

Sense-Antisense Homology Boxes in Proteins: Structural Motifs Enconded in the DNA? 
    Carlos A. Del Carpio, Valentin Gogonea, Katsuhisa Yamaguchi, Makoto Takei, Kouji Nishimura

Construction of the {\it Bacillus subtilis} ORF Database ({\bf BSORF DB}) 
    A. Ogiwara, N. Ogasawara, M. Watanabe, T. Takagi

Clustering and Evolutional Analysis of E. coli Proteins 
    Suharnan Sivasundaram, Jun-ichi Takeda, Takeshi Itoh, Keiko Takemoto, Hidemi Watanabe, Hideo Matsuda, Hirotada Mori

High-Speed Genome Scanning Analysis Based on Automated Detection and Matching Spots in Autoradiogram Images of 2-D Gel Electrophoresis 
    Tomoyasu Takahashi, Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe

The Inference of Model-based Minimum Complexity in Reconstructing Molecular Phylogenetic Tree 
    F. Ren, H. Tanaka, T. Okayama

3DInSight: An Integrated Relational Database and Search Tool for Molecular Structures and Functional Sites 
    J. An, T. Nakama, Y. Kubota, A. Sarai

Poly-tRNA Structure in the Bacilluis Subtilis rrnB Operon is a Relic of an Early Peptide-Synthesizing Ribozyme Co-Ancestral to the E. coli trpE Gene and the Exon 2 of the Chicken Triose-Phosphate Isomerase Gene 
    Koji Ohnishi, Hiroshi Yanagawa

Mutation View : A Network-Transparent Database System for Mutations in the Human Disease Genes 
    S. Minoshima, S. Mitsuyama, N. Shimizu

Vestiges of Primordial Words in Base Sequences of Modern Genomes 
    Nobuyuki Uchikoga, Akira Suyama

A Prediction Method for Transmembrane Segments in Proteins Utilizing Multiple Discrimination Functions 
    Daisuke Kihara, Toshio Shimizu, Minoru Kanehisa

A Statistical Analysis of Gene Arrangement Patterns in Bacterial and Yeast Genomes 
    Kentaro Tomii, Minoru Kanehisa

Standard Gibbs Free Energy Changes of Enzyme Reactions in Metabolic Pathway Computation 
    Susumu Goto, Nobuhiro Fukushima, Minoru Kanehisa

Deductive Calculation Library for KEGG Pathway Simulation 
    Wataru Fujibuchi, Susumu Goto, Minoru Kanehisa

Genome Scale Prediction of Enzyme Genes Utilizing the Knowledge of Metabolic Interactions 
    Hidemasa Bono, Hiroyuki Ogata, Susumu Goto, Minoru Kanehisa

Java Applets for Handling Genome Maps in KEGG 
    Kazushige Sato, Toyoko Katsurada, Tomomi Kamiya, Mayuko Egoshi, Minoru Kanehisa

Finding Coding Region Using Secondary Hexamer Measure and Two-Dimensional Linear Discriminant Analysis 
    Katsuhiko Murakami, Toshihisa Takagi

Information Finding from Biological Papers 
    Yoshihiro Ohta, Yasunori Yamamoto, Ikuo Uchiyama, Toshihisa Takagi

Constructing a Dictionary of Biological Terms for Information Extraction 
    Yasunori Yamamoto, Yoshihiro Ohta, Ikuo Uchiyama, Toshihisa Takagi

A Refinement System for Large Amount of cDNA Data 
    Haretsugu Hishigaki, Kagehiko Kitano, Yusuke Nakamura, Hiroumi Maekawa, Toshihisa Takagi

Automatic Classification of Protein Structures with Deductive Database System 
    Yoshihisa Yamamura, Yukiko Tsukamoto, Kenji Satou, Emiko Furuichi, Toshihisa Takagi, Satoru Kuhara

Application of Data Mining to Genetic Linkage Analysis 
    Nobutaka Mitsuhashi, Haretsugu Hishigaki, Toshihisa Takagi

Mining Binary Diagram Rules 
    Kazuya Inoue, Osamu Maruyama, Takayoshi Shoudai, Satoru Miyano

A PAC-Learning Algorithm for Conformation Rules and its Experiments 
    Osamu Maruyama, Erika Tateishi, Emiko Furuichi, Satoru Kuhara, Satoru Miyano

An Image Analysis System for Two-Dimensional Gel Electrophoresis 
    Akira Ohyama, Kyotetsu Kanaya, Tatsuya Akutsu, Asao Fujiyama

Multiple Alignment of Biological Sequences Containing Tandem Repeat 
    Hidetoshi Kitada, Kazuhiro Tono, Masahito Yamamoto, Tamotsu Mitamura, Azuma Ohuchi, Toshio ohyanagi, Norio Matsushima

Harmonic Analysis of Protein Sequences 
    Meeta Rani, Chanchal K. Mitra

Registration Form

The Seventh Workshop on Genome Informatics (GIW'96)
December 2--3, 1996     Tokyo, Japan

Registration Form

Please complete the followings.
(If your are Japanese, please use both Kanji and English.)




Mailing Address:_________________________________________


                ______________________________  _________

TEL: _______________________   FAX: _______________________ 

E-MAIL: _________________________________________

Return Form to: Secretariat, The Seventh Workshop on Genome Informatics
                c/o Human Genome Center
                The Institute of Medical Science, The University of Tokyo
                4-6-1 Shirokanedai, Minato-ku, Tokyo 108 JAPAN
                FAX: +81-3-5449-5434