Genome Informatics Vol.22 (2009)


Genome Informatics Vol.22 (2009)

Presented at the The Ninth Annual International Workshop on Bioinformatics and Systems Biology
July 27 - 29, 2009, Boston University, U.S.A.

Published as: Charles DeLisi, Minoru Kanehisa, Satoru Miyano, Scott Mohr and Iwona Wallach
"Genome Informatics Vol.22 (2009)"
Imperial College Press, London

Preface by Charles DeLisi, Minoru Kanehisa, Edda Klipp, Satoru Miyano, Scott Mohr and Iwona Wallach

Program Committee




Structural Features and Evolution of Protein-Protein Interactions
Joachim von Eichborn, Stefan Günther , Robert Preissner
Genome Informatics 22: 1-10 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Graphical Analysis and Experimental Evaluation of Saccharomyces Cerevisiae PTRK1|2 and PBMH1|2 Promoter Region
Susanne Gerver, Guide Hasenbrink, Wouter Hendriksen, Paul van Heusden, Jost Ludwig, Edda Klipp , Hella Lichtenberg-Fraté
Genome Informatics 22: 11-20 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Strategies of Non-Sequential Protein Structure Alignments
Aysam Guerler , Ernst-Walter Knapp
Genome Informatics 22: 21-29 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Active Pathway Identification and Classification with Probabilistic Ensembles
Timothy Hancock , Hiroshi Mamitsuka
Genome Informatics 22: 30-40 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

The Importance of Compartmentalization in Metabolic Flux Models: Yeast as an Ecosystem of Organelles
Niels Klitgord , Daniel Segrè
Genome Informatics 22: 41-55 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A State Space Representation of VAR Models with Sparse Learning for Dynamic Gene Networks
Kaname Kojima, Rui Yamaguchi, Seiya Imoto, Mai Yamauchi, Masao Nagasaki, Ryo Yoshida, Teppei Shimamura, Kazuko Ueno, Tomoyuki Higuchi, Noriko Gotoh , Satoru Miyano
Genome Informatics 22: 56-68 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Formal Representation of the High Osmolarity Glycerol Pathway in Yeast
Clemens Kühn, K. V. S. Prasad, Edda Klipp , Peter Gennemark
Genome Informatics 22: 69-83 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF] [Supplementary Data]

Prediction of Regulatory Transcription Factors in T Helper Cell Differentiation and Maintenance
Yue-Hien Lee, Manuela Benary, Ria Baumgrass , Hanspeter Herzel
Genome Informatics 22: 84-94 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Annotating Gene Functions with Integrative Spectral Clustering on Microarray Expressions and Sequences
Limin Li, Motoki Shiga, Wai-Ki Ching , Hiroshi Mamitsuka
Genome Informatics 22: 95-120 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Novel Meta-analysis Approach of Cancer Transcriptomes Reveals Prevailing Transcriptional Networks in Cancer Cells
Atsushi Niida, Seiya Imoto, Masao Nagasaki, Rui Yamaguchi , Satoru Miyano
Genome Informatics 22: 121-131 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

New Kernel Methods for Phenotype Prediction from Genotype Data
Ritsuko Onuki, Tetsuo Shibura , Minoru Kanehisa
Genome Informatics 22: 132-141 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Efficient and Detailed Model of the Local Ca2+ Release Unit in the Ventricular Cardiac Myocyte
Thomas Schendel , Martin Falcke
Genome Informatics 22: 142-155 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Co-Evolution of Metabolism and Protein Sequences
Moritz Schütte, Niels Klitgord, Daniel Segrè , Oliver Ebenhöh
Genome Informatics 22: 156-166 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Characterization and Classification of Adverse Drug Interactions
Masataka Takarabe, Daichi Shigemizu, Masaaki Kotera, Susumu Goto , Minoru Kanehisa
Genome Informatics 22: 167-175 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Analysis and Prediction of Nutritional Requirements Using Structural Properties of Metabolic Networks and Support Vector Machines
Takeyuki Tamura, Nils Christian, Kazuhiro Takemoto, Oliver Ebenhöh , Tatsuya Akutsu
Genome Informatics 22: 176-190 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Analysis of a Lipid Biosynthesis Protein Family and Phospholipid Structural Variations
Michihiro Tanaka, Yuki Moriya, Susumu Goto , Minoru Kanehisa
Genome Informatics 22: 191-201 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]

CaMPDB: a Resource for Calpain and Modulatory Proteolysis
David duVerle, Ichigaku Takigawa, Yasuko Ono, Hiroyuki Sorimachi , Hiroshi Mamitsuka
Genome Informatics 22: 202-214 (2009)
[Abstract]   [Full-text HTML]   [Full-text PDF]