KUBIC-NII Joint Seminar on Bioinformatics 2013
organized by
Bioinformatics Center, Institute for Chemical Research, Kyoto University and
National Institute of Informatics


Friday, April 19, 2013


Kyoto University, Uji, Kyoto 611-0011, Japan
Bioinformatics Center, Institute for Chemical Research,
3F, Seminar Room CB316.


Participants (alphabetical)

Tatsuya Akutsu Institute for Chemical Research, Kyoto University, Japan
Earl Bellinger Indiana University Bloomington, USA
J.B. Brown Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
Morihiro Hayashida Institute for Chemical Research, Kyoto University, Japan
Katsumi Inoue National Institute of Informatics, Japan
Jesper Jansson The Hakubi Project, Kyoto University, Japan
Hitoshi Koyano Institute for Chemical Research, Kyoto University, Japan
Morgan Magnin Institut de Recherche en Communications et Cybertétique de Nantes (IRCCyN), École Centrale de Nantes, France
Avraham Melkman Ben-Gurion University of the Negev, Israel
Tenda Okimoto Transdisciplinary Research Integration Center, Japan
Tony Ribeiro The Graduate University for Advanced Studies (SOKENDAI), Japan
Alexandre Rocca Grenoble INP Ensimag, France
Adrien Rougny University Paris-Sud, France
Takeyuki Tamura Institute for Chemical Research, Kyoto University, Japan


9:30 - 10:00 Opening
10:00 - 10:20 Tatsuya Akutsu
A Dominating Set Approach to Controllability of Scale-free Networks.
10:20 - 10:50 J.B. Brown
Drug discovery and the need for new post-ligation downstream network analysis algorithms incorporating contextualization.
10:50 - 11:10 Avraham Melkman
Nested canalyzing SAT-formulae and their satisfaction.
11:10 - 11:20 Break
11:20 - 11:40 Katsumi Inoue*, Tony Ribeiro, Chiaki Sakama
Learning from Interpretation Transition and its Applications to Boolean Networks and Cellular Automata.
11:40 - 12:00 Tony Ribeiro*, Katsumi Inoue, Chiaki Sakama
Learning from Interpretation Transition Using an Efficient OBDD-Like Structure.
12:00 - 13:30 Lunch
13:30 - 14:00 Morgan Magnin*, Maxime Folschette, Katsumi Inoue, Loic Pauleve, Olivier Roux, Olivier Roux, Gilles Bernot, Jean-Paul Comet, Adrien Richard
Inference in Biological Regulatory Networks: From Discrete Parameters to Timing Information.
14:00 - 14:20 Jesper Jansson
Computing the Rooted Triplet Distance between Galled Trees by Counting Triangles.
14:20 - 14:40 Hitoshi Koyano
Probability theory on the monoid of strings and its application to molecular ecology.
14:40 - 15:00 Coffe Break
15:00 - 15:20 Morihiro Hayashida
Predicting protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso.
15:20 - 15:40 Adrien Rougny*, Christine Froidevaux, Katsumi Inoue, Yoshitaka Yamamoto
Translating the Systems Biology Graphical Notation to Logic.
15:40 - 16:00 Takeyuki Tamura
On the complexity of the maximum common subgraph problem for partial k-trees of bounded degree.
16:00 - 16:20 Coffe Break
16:20 - 16:40 Alexandre Rocca*, Morgan Magnin, Katsumi Inoue
CTL and ASP for Model-Checking of Biological Boolean Networks.
16:40 - 17:00 Earl Bellinger*, Hei Chan, Katsumi Inoue
Asynchronously Updated Elementary Cellular Automata with Random Perturbations.
17:00 - 17:20 Tenda Okimoto* and Katsumi Inoue
A Study for Multi-Objective Distributed Constraint Optimization.


Tony Ribeiro: tony_ribeiro at nii.ac.jp

Webmaster: Tony Ribeiro (E-mail tony_ribeiro at nii.ac.jp)