Final Program

May 31 (Mon.)

Distinguished Lecture
17:00 - 18:00
Bioinformatics and Systems Biology: The E.coli Network of Transcriptional Regulation
Julio-Collado Vides (Universidad Nacional Autónoma de México (UNAM))
Lecture Hall, Joint Research Laboratory (#10 of this map), Uji Campus

Reception
18:30 - 20:30
Restaurant, Uji Campus

June 1 (Tue.)

Registration
8:15 -

Opening Remark
8:50 - 9:00
Minoru Kanehisa (Kyoto University)

Introduction to the three Bioinformatics Education Programs
9:00 - 9:30
Minoru Kanehisa (Kyoto University), Reinhart Heinrich (Humboldt University Berlin), Charles DeLisi (Boston University)

Genomes and Sequences, Chair: Ernst Walter Knapp (Free University Berlin)
9:30 - 12:00

Detection of Inter-Spread Repeat Sequence in Genomic DNA Sequence
Hiroo Murakami, Nobuyoshi Sugaya, Makihiko Sato, Akira Imaizumi, Sachiyo Aburatani, Katsuhisa Horimoto (University of Tokyo)

Clustering of Database Sequences for Fast Homology Search Using Upper Bounds on Alignment Score
Masumi Itoh, Tatsuya Akutsu, Minoru Kanehisa (Kyoto University)

Break (30 minutes)

Markedly Reduced Evolutionary Rates of Transcription Factors and Cytoplasmic Ribosomal RNAs and Proteins in Higher Vertebrates and Their Evolutionary Implications
Daisuke Hoshiyama, Kei-ichi Kuma, Takashi Miyata (Kyoto University)

Causes for the Large Genome Size in a Cyanobacterium Anabaena sp. PCC7120
Nobuyoshi Sugaya, Makihiko Sato, Hiroo Murakami, Akira Imaizumi, Sachiyo Aburatani, Katsuhisa Horimoto (University of Tokyo)

Lunch Break
12:00 - 13:30

Metabolic Pathways, Chair: Zhiping Weng (Boston University)
13:30 - 15:00

Extraction of Phylogenetic Network Modules from Prokaryote Metabolic Pathways
Takuji Yamada, Susumu Goto, Minoru Kanehisa (Kyoto University)

Inferring Dynamic Properties of Biochemical Reaction Networks from Structural Knowledge
Edda Klipp (Berlin Center for Genome Based Bioinformatics (BCB) / Max Planck Institute for Molecular Genetics), Wolfram Liebermeister (Free University Berlin), Christoph Wierling (Max Planck Institute for Molecular Genetics)

Structural Analysis of Expanding Metabolic Networks
Oliver Ebenhöh, Thomas Handorf, Reinhart Heinrich (Humboldt Unversity Berlin)

Break
15:00 - 15:30

Short Paper Talks, Chair: Zhiping Weng (Boston University)
15:30 - 16:30

S17: Study on the Clustering Coefficients in Metabolic Network Using a Hierarchical Framework
Jose C. Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu (Kyoto University)

S27: Stochastic Modelling of Influenza Virus Fusion
Susanne Schreiber (Humboldt University Berlin), Kai Ludwig (Free University Berlin), Herman-Georg Holzhütter, Andreas Herrmann (Humboldt University Berlin)

S30: Bifurcation Analysis of Regulatory Modules in Cell Biology
Maciej Swat (Humboldt University Berlin), Alexander Kel (BIOBASE), Wojciech Swat (Washington University), Hanspeter Herzel (Humboldt University Berlin)

Poster Viewing
16:30 - 18:00
List of Poster Titles

June 2 (Wed.)

Proteins, Ligands and Glycans, Chair: Andreas Hermann (Humboldt University Berlin)
8:30 - 12:00

Optimizing Protein Representations with Information Theory
Julian Mintseris, Zhiping Weng (Boston University)

A Neural Network Method for Identification of RNA-Interacting Residues in Protein
Euna Jeong, I-Fang Chung, Satoru Miyano (University of Tokyo)

ELISA: A Unified Multidimensional View of the Protein Domain Universe
Boris E. Shakhnovich, John Max Harvey, Charles DeLisi (Boston University)

Break (30 minutes)

Cytosolic Processing of Proteasomal Cleavage Products Can Enhance the Presentation Efficiency of MHC-1 Epitopes
Sascha Bulik, Björn Peters, Christian Ebeling, Hergo Holzhütter (Humboldt University Berlin)

Peptide Binding at Class I Major Histocompatibility Complex Scored with Linear Functions and Support Vector Machines
Henning Riedesel, Björn Kolbeck, Oliver Schmetzer, Ernst-Walter Knapp (Free University Berlin)

Extraction of Species-specific Glycan Substructures
Yoshiyuki Hizukuri, Yoshihiro Yamanishi, Kousuke Hashimoto, Minoru Kanehisa (Kyoto University)

Lunch Break
12:00 - 13:30

Proteins, Cells and Interactions, Chair: Temple F. Smith (Boston University)
13:30 - 16:30

Collective Phenomena in Intracellular Processes
Erwin Frey (Free University Berlin), Andrea Parmeggiani (CNRS/ Université Montpellier), Thomas Franosch (Free University Berlin)

A Model of the Mammalian Circadian Oscillator Including the REV-ERB α Module
Sabine Becker-Weimann, Jana Wolf, Achim Kramer, Hanspeter Herzel (Humboldt University Berlin)

Break (30 minutes)

A Versatile Petri Net Based Architecture for Modeling and Simulation of Complex Biological Processes
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano (University of Tokyo)

A Simple Method for Inferring Strengths of Protein-protein Interactions
Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu (Kyoto University)

Constructing Networks with Correlation Maximization Methods
Joseph C. Mellor, Jie Wu, Charles DeLisi (Boston University)

Poster Viewing
16:30 - 18:00
List of Poster Titles

Banquet
19:00 - 21:00
in Sanjo, the city center of Kyoto

June 3 (Thr.)

Signal Transduction and Gene Regulatory Networks, Chair: Susumu Goto (Kyoto University)
8:30 - 11:30

Interrelations between Dynamical Properties and Structural Characteristics of Signal Transduction Networks
Bernd Binder, Reinhart Heinrich (Humboldt University Berlin)

Model Reduction and Analysis of Robustness for the Wnt/β-catenin Signal Transduction Pathway
Roland Krüger, Reinhart Heinrich (Humboldt University Berlin)

Break (30 minutes)

Comparisons of Predicted Genetic Modules: Identification of Co-expressed Genes through Module Gene Flow
Boris E Shakhnovich, Timothy Reddy, Kevin Galinsky, Joseph Mellor, Charles DeLisi (Boston University)

Prediction of Cis-Regulatory Elements of Coregulated Genes
Szymon M. Kielbasa, Nils Blüthgen, Christine Sers, Reinhold Schäfer, Hanspeter Herzel (Humboldt University Berlin)

Gene Expression Module Discovery Using Gibbs Sampling
Chang-Jiun Wu, Yutao Fu (Boston University), T.M. Murali (Virginia Polytechnic Institute and State University), Simon Kasif (Boston University)

Closing Remark
11:30 - 11:40
Minoru Kanehisa (Kyoto University)

Excursion
Afternoon