GENOME INFORMATICS 2009<br> Genome Informatics Series Vol. 22

GENOME INFORMATICS 2009
Genome Informatics Series Vol. 22
Proceedings of the 9th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2009)

Boston University, Boston, USA, 27 - 29 July 2009

CONTENTS


FRONT MATTER	i
STRUCTURAL FEATURES AND EVOLUTION OF PROTEIN-PROTEIN INTERACTIONS JOACHIM VON EICHBORN, STEFAN GÜNTHER and ROBERT PREISSNER	1
GRAPHICAL ANALYSIS AND EXPERIMENTAL EVALUATION OF SACCHAROMYCES CEREVISIAE P_{TRK_1\|2} AND P_{BMH_1\|2} PROMOTER REGION SUSANNE GERBER, GUIDO HASENBRINK, WOUTER HENDRIKSEN, PAUL VAN HEUSDEN, JOST LUDWIG, EDDA KLIPP and HELLA LICHTENBERG-FRATÉ	11
STRATEGIES OF NON-SEQUENTIAL PROTEIN STRUCTURE ALIGNMENTS AYSAM GUERLER and ERNST-WALTER KNAPP	21
ACTIVE PATHWAY IDENTIFICATION AND CLASSIFICATION WITH PROBABILISTIC ENSEMBLES TIMOTHY HANCOCK and HIROSHI MAMITSUKA	30
THE IMPORTANCE OF COMPARTMENTALIZATION IN METABOLIC FLUX MODELS: YEAST AS AN ECOSYSTEM OF ORGANELLES NIELS KLITGORD and DANIEL SEGRÈ	41
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 and SATORU MIYANO	56
FORMAL REPRESENTATION OF THE HIGH OSMOLARITY GLYCEROL PATHWAY IN YEAST CLEMENS KÜHN, K. V. S. PRASAD, EDDA KLIPP and PETER GENNEMARK	69
PREDICTION OF REGULATORY TRANSCRIPTION FACTORS IN T HELPER CELL DIFFERENTIATION AND MAINTENANCE YUE-HIEN LEE, MANUELA BENARY, RIA BAUMGRASS and HANSPETER HERZEL	84
ANNOTATING GENE FUNCTIONS WITH INTEGRATIVE SPECTRAL CLUSTERING ON MICROARRAY EXPRESSIONS AND SEQUENCES LIMIN LI, MOTOKI SHIGA, WAI-KI CHING and HIROSHI MAMITSUKA	95
A NOVEL META-ANALYSIS APPROACH OF CANCER TRANSCRIPTOMES REVEALS PREVAILING TRANSCRIPTIONAL NETWORKS IN CANCER CELLS ATSUSHI NIIDA, SEIYA IMOTO, MASAO NAGASAKI, RUI YAMAGUCHI and SATORU MIYANO	121
NEW KERNEL METHODS FOR PHENOTYPE PREDICTION FROM GENOTYPE DATA RITSUKO ONUKI, TETSUO SHIBUYA and MINORU KANEHISA	132
EFFICIENT AND DETAILED MODEL OF THE LOCAL Ca²⁺ RELEASE UNIT IN THE VENTRICULAR CARDIAC MYOCYTE THOMAS SCHENDEL and MARTIN FALCKE	142
CO-EVOLUTION OF METABOLISM AND PROTEIN SEQUENCES MORITZ SCHÜTTE, NIELS KLITGORD, DANIEL SEGRÈ and OLIVER EBENHÖH	156
CHARACTERIZATION AND CLASSIFICATION OF ADVERSE DRUG INTERACTIONS MASATAKA TAKARABE, DAICHI SHIGEMIZU, MASAAKI KOTERA, SUSUMU GOTO and MINORU KANEHISA	167
ANALYSIS AND PREDICTION OF NUTRITIONAL REQUIREMENTS USING STRUCTURAL PROPERTIES OF METABOLIC NETWORKS AND SUPPORT VECTOR MACHINES TAKEYUKI TAMURA, NILS CHRISTIAN, KAZUHIRO TAKEMOTO, OLIVER EBENHÖH and TATSUYA AKUTSU	176
ANALYSIS OF A LIPID BIOSYNTHESIS PROTEIN FAMILY AND PHOSPHOLIPID STRUCTURAL VARIATIONS MICHIHIRO TANAKA, YUKI MORIYA, SUSUMU GOTO and MINORU KANEHISA	191
CaMPDB: A RESOURCE FOR CALPAIN AND MODULATORY PROTEOLYSIS DAVID duVERLE, ICHIGAKU TAKIGAWA, YASUKO ONO, HIROYUKI SORIMACHI and HIROSHI MAMITSUKA	202
BACK MATTER	215
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