IBSB2010 - The Tenth Annual International Worksh...

http://sunﬂ￿ower.kuicr.kyoto-u.ac.jp/ibsb2010/IBSB2010
The Tenth Annual International Workshop on
Bioinformatics and Systems Biology

Kyoto, Japan, 26-28 July 2010

IBSB2010 HomeKyoto
Important dates
Programme
Invited speakers
Accepted papers
Paper submission
Poster submission
Poster preparation
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The 10th Annual International Workshop on Bioinformatics and Systems
Biology is part of a collaborative educational program involving several
leading research institutes: Boston University in the United States, Charité Universitätsmedizin Berlin, Humboldt-Universität zu Berlin in Germany,
Kyoto University and the University of Tokyo in Japan. This student-focused
event has been held since 2001 to provide doctoral students and young
researchers with opportunities to present and discuss their research objectives,approaches and results in the emerging field of genomics, systems biology
and bioinformatics.

News
Poster preparation page is open. (16 July 2010)
Programme (tentative) page is open. (25 June 2010)
Poster submission site (requires password) is open. (14 May 2010)
Accepted papers page is open. (13 May 2010)
Confirmed invited speakers page is open. (7 May 2010)
Paper submission site (requires password) is open. (17 Mar. 2010)
Web page is open. (11 Nov. 2009)

Steering committee:
Minoru Kanehisa (Kyoto University)
Edda Klipp (Humboldt-Universität zu Berlin)
Satoru Miyano (University of Tokyo)
Scott Mohr (Boston University)
Thomas Tullius (Boston University)
Iwona Wallach (Charité - Universitätsmedizin Berlin)

Scientific committee:
Boston: Gary Benson, Eric Kolaczyk, Daniel Segrè, Avrum Spira andYu Xia
Berlin: Martin Falcke, Hanspeter Herzel, Hermann-Georg Holzhütter,
Edda Klipp and Ernst-Walter Knapp
Tokyo/Kyoto: Tatsuya Akutsu (Chair), Susumu Goto, Seiya Imoto,1/2

10/07/29 19:58

IBSB2010 - The Tenth Annual International Worksh...

http://sunﬂ￿ower.kuicr.kyoto-u.ac.jp/ibsb2010/

Minoru Kanehisa, Hiroshi Mamitsuka and Satoru Miyano

Organized by
Boston University Graduate Program in Bioinformatics
The International Research Training Group (IRTG) Genomics andSystems Biology of Molecular Networks
International Research and Training Program on Bioinformatics andSystems Biology, Kyoto University Bioinformatics Center
Global COE Program - Center of Education and Research for
Advanced Genome-Based Medicine, University of Tokyo

Local organizing committee:
Tatsuya Akutsu (Chair)
Susumu Goto
Morihiro Hayashida
Motoki Shiga
Takeyuki Tamura

Supported byInstitute for Chemical Research, Kyoto University

Sponsored by

http://sunflower.kuicr.kyoto-u.ac.jp/ibsb2010/2/2

10/07/29 19:58

The Tenth Annual International Workshop on
Bioinformatics and Systems Biology

IBSB 2010
Kyoto, Japan, 26-28 July 2010

Scope
The International Workshop on Bioinformatics and Systems Biology (IBSB) is anannual international forum for doctoral students and young researchers to presentand discuss their research results and approaches in Bioinformatics and SystemsBiology. Since the ﬁrst workshop in Berlin (2001), the workshop has been held inBoston (2002), Berlin (2003), Kyoto (2004), Berlin (2005), Boston (2006), Tokyo(2007), Berlin (2008), and Boston (2009). In 2010, it is held in Kyoto as part of acollaborative educational program involving the leading institutions.
Organized by• Boston - Graduate Program in Bioinformatics, Boston University• Berlin - The International Research Training Group (IRTG) “Genomics andSystems Biology of Molecular Networks”• Kyoto - JSPS International Training Program (ITP) “International Researchand Training Program of Bioinformatics and Systems Biology”• Tokyo - Global COE Program “Center of Education and Research for Advanced Genome-Based Medicine”
Sponsored byJSPS International Training Program (ITP) “International Researchand Training Program of Bioinformatics and Systems Biology”
Supported by
Institute for Chemical Research, Kyoto University
Steering Committee
Minoru Kanehisa Kyoto University
Edda Klipp
Humboldt University Berlin
Satoru Miyano
University of Tokyo
Thomas Tullius
Boston University
Iwona Wallach
Charité - Universitätsmedizin Berlini

Local Organizing Committee
Tatsuya Akutsu (Chair) Kyoto University
Susumu Goto
Kyoto University
Morihiro Hayashida
Kyoto University
Motoki Shiga
Kyoto University
Takeyuki Tamura
Kyoto University
Program Committee
Tatsuya Akutsu
Gary BensonMartin Falcke
Susumu Goto
Hanspeter Herzel
Hermann-Georg HolzhütterSeiya Imoto
Minoru Kanehisa
Edda Klipp
Ernst-Walter Knapp
Eric Kolaczyk
Hiroshi Mamitsuka
Satoru Miyano
Daniel Segrè
Avrum SpiraYu XiaKyoto University, PC Chair
Boston University
Max-Delbrück Center for Molecular Medicine
Kyoto University
Humboldt University Berlin
Charité - Universitätsmedizin Berlin
University of Tokyo
Kyoto University
Humboldt University BerlinFree University Berlin
Boston University
Kyoto University
University of Tokyo
Boston University
Boston University
Boston University

Contact
Laboratory of Biological Information Networks
Bioinformatics Center, Institute for Chemical Research, Kyoto University
Gokasho, Uji, Kyoto 611-0011, Japan
bic2-staﬀ@kuicr.kyoto-u.ac.jp
http://sunﬂower.kuicr.kyoto-u.ac.jp/ibsb2010/
Venue
Obaku Plaza, Uji campus, Kyoto University
Gokasho, Uji, Kyoto 611-0011, Japan
Tel./Fax.: +81-774-38-4394/4395
obaku@uji.kyoto-u.ac.jp
http://www.uji.kyoto-u.ac.jp/campus/facilities.html

ii

IBSB 2010 ProgrammeSunday, 25 July 2010
17:30-19:30

Reception at Hybrid space, Obaku Plaza.

Monday, 26 July 2010 (Kihada Hall, Obaku Plaza)
Invited Talk (Chair: Minoru Kanehisa)
9:00-10:00
Genome Biology and Chromatin Structure,David Landsman (National Institutes of Health, USA)
Invited Talk (Chair: Minoru Kanehisa)
10:00-11:00 Developing Data Mining Methods and Systems for Predictive
Toxicology and Metabolic Prediction,
Stefan Kramer (Technical University of Munich, Germany)
11:00-11:20

BreakOral Talks (Chair: Gary Benson)
11:20-11:40 Phylogenetic Analysis of Lipid Mediator GPCRs,
S. Mizutani, M. Tanaka, C. E. Wheelock, M. Kanehisa and S. Goto
11:40-12:00 Characterizing Common Substructures of Ligands for GPCR Protein
Subfamilies,
B. Erguner, M. Hattori, S. Goto and M. Kanehisa
12:00-14:00

Lunch and Poster Session 1 (Odd Numbers)

Invited Talk (Chair: Susumu Goto)
14:00-15:00 Including Prior Knowledge in Machine Learning for Genomic Data,
Jean-Philippe Vert (Mines ParisTech, France)
Oral Talks (Chair: Susumu Goto)
15:00-15:20 G1 and G2 Arrests in Response to Osmotic Shock Are Robust Properties of the Budding Yeast Cell Cycle,
C. Waltermann, M. Floettmann and E. Klippiii

15:20-15:40

15:40-16:00

Robust Gene Network Analysis Reveals Alteration of the STAT5a
Network as a Hallmark of Prostate Cancer,
A. Reddy, C. C. Huang, H. Liu, C. DeLisi, M. T. Nevalainen, S.
Szalma and G. Bhanot
Integer Programming-based Method for Completing Signaling Pathways and its Application to Analysis of Colorectal Cancer,
T. Tamura, Y. Yamanishi, M. Tanabe, S. Goto, M. Kanehisa, K.
Horimoto and T. Akutsu

16:00-16:20

Break

Oral Talks (Chair: Edda Klipp)
16:20-16:40 Comparison of Gene Expression Proﬁles Produced by Cage, Illumina
Microarray and Real Time RT-PCR,
A. Fujita, M. Nagasaki, S. Imoto, A. Saito, E. Ikeda, T. Shimamura,R. Yamaguchi, Y. Hayashizaki and S. Miyano
16:40-17:00 openSESAME: A New Tool for Discovering Biologically Relevant
Connections in Public Gene Expression Data,*Adam Gower
17:00-17:20 Discovering Causal Signaling Pathways through Gene Expression
Patterns Using SPEED,*Jignesh Parikh
17:20-17:40 Latent Pathway Identiﬁcation Analysis: A Computational Methodfor Predicting Sources of Transcriptional Dysregulation,*Lisa Pham
17:40-18:00 Collocation-based Sparse Estimation For Constructing Dynamic
Gene Networks,
T. Shimamura, S. Imoto, M. Nagasaki, M. Yamauchi, R. Yamaguchi, A. Fujita, Y. Tamada, N. Gotoh and S. Miyano

Tuesday, 27 July 2010 (Kihada Hall, Obaku Plaza)
Invited Talk (Chair: Satoru Miyano)
9:00-10:00
Between Systems and Data-driven Modeling for Computational
Biology: Target Identiﬁcation with Gaussian Processes,
Neil Lawrence (University of Manchester, UK)
Invited Talk (Chair: Satoru Miyano)
10:00-11:00 Using Networks to Elucidate Disease and Drugs,
Roded Sharan (Tel-Aviv University, Israel)iv

11:00-11:20

Break

Oral Talks (Chair: Ernst-Walter Knapp)
11:20-11:40 FluxViz - Cytoscape Plug-In for Visualization of Flux Distributions
in Networks,
M. König and H.-G. Holzhütter
11:40-12:00 A Dynamic Programming Algorithm to Predict Synthesis Processesof Tree-structured Compounds with Graph Grammar,
Y. Zhao, T. Tamura, M. Hayashida and T. Akutsu
12:00-14:00

Lunch and Poster Session 2 (Even Numbers)

Oral Talks (Chair: Tatsuya Akutsu)
14:00-14:20 On the Performance of Methods for Finding a Switching Mechanism
in Gene Expression,
M. Kayano, I. Takigawa, M. Shiga, K. Tsuda and H. Mamitsuka
14:20-14:40 Gene Regulatory Network Clustering for Graph Layout Based on
Microarray Gene Expression Data,K. Kojima, S. Imoto, M. Nagasaki and S. Miyano
14:40-15:00 Analyzing Gene Coexpression Data by an Evolutionary Model,
M. Schütte, M. Mutwil, S. Persson and O. Ebenhöh
15:30-18:30

Excursion to Kiyomizu Temple

18:30-20:30

Banquet at Caﬀe Ristorante OBLIO

Wednesday, 28 July 2010 (Kihada Hall, Obaku Plaza)
Invited Talk (Chair: Hiroshi Mamitsuka)
9:00-10:00
Leveraging Linkage Disequilibrium Structure in Genome-wide
Association Studies,
Eleazar Eskin (University of California, Los Angeles, USA)
Invited Talk (Chair: Hiroshi Mamitsuka)
10:00-11:00 Genome-Phenome Association Analysis of Complex Diseases- a Structured Sparse Regression Approach,Eric P. Xing (Carnegie Mellon University, USA)
11:00-11:20

Breakv

Oral Talks (Chair: Seiya Imoto)
11:20-11:40 A Systems Biology Approach: Modelling of Aquaporin-2 Traﬃcking,
M. Fröhlich, P. M. T. Deen and E. Klipp
11:40-12:00 Induced Pluripotent Stem Cells: Qualitative Modeling of Direct Reprogramming,*Max Flottmann
12:00-14:00

Lunch and Poster Session 3 (All Numbers)

Oral Talks (Chair: Tom Tullius)
14:00-14:20 Predicting Protein Complex Geometries with Linear Scoring Functions,O. Demir-Kavuk, F. Krull, M.-H. Chae and E.-W. Knapp
14:20-14:40 Kinetic Modelling of DNA Replication Initiation in Budding Yeast,
M. Barberis, T. W. Spiesser and E. Klipp
14:40-15:00 Comprehensive Genomic Analysis of Sulfur-relay Pathway Genes,
M. Kotera, T. Kobayashi, M. Hattori, T. Tokimatsu, S. Goto, H.
Mihara and M. Kanehisa
15:00-15:20 Comparison and Modeling of Gene Regulation Using FACS-data,*Manuela Benary
15:20-15:40

BreakOral Talks (Chair: Gyan Bhanot)
15:40-16:00 Next Generation Sequencing of MicroRNA in the Human Airway
Epithelium for Discovery of Novel Biomarkers of Tobacco-smoke Exposure and Lung Cancer,*Joseph Gerrein
16:00-16:20 Genome-wide Analysis of Plant UGT Family Based on Sequence andSubstrate Information,
Y. Nishimura, T. Tokimatsu, M. Kotera, S. Goto and M. Kanehisa
16:20-16:40 Diﬀerent Groups of Metabolic Genes Cluster around Early and Late
Firing Origins of Replication in Budding Yeast,
T. W. Spiesser and E. Klipp
16:40-17:00 The Role of Promoter Methylation in Regulating the Expression ofGenes Associated with COPD Progression,*John Brothers
17:00-17:20 Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate,*Eric Franzosa
17:45-19:45

Closing Dinner at COOP(* means talk without a paper)vi

Conference Venue(Kihada Hall, Obaku Plaza, Uji campus, Kyoto University)

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Uji campus, Kyoto University(Address: Gokasho, Uji, Kyoto 611-0011, Japan, Tel: +81-774-38-3016/3020)

Poster Session (12:00-14:00)
26 July 2010 (Odd Numbers)
27 July 2010 (Even Numbers)
28 July 2010 (All Numbers)
NOTE: Posters should be put by 12:00, 26 July 2010, and must be removed by
17:30, 28 July 2010.

viii