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FRONT MATTER
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| Part A Full Papers |
PREDICTING PROTEIN-PROTEIN RELATIONSHIPS FROM LITERATURE USING LATENT TOPICS
TATSUYA ASO and KOJI EGUCHI | 3 |
EVALUATION OF DNA INTRAMOLECULAR INTERACTIONS FOR NUCLEOSOME POSITIONING IN YEAST
MICHAEL FERNANDEZ, SATOSHI FUJII, HIDETOSHI KONO and AKINORI SARAI | 13 |
QUALITY CONTROL AND REPRODUCIBILITY IN DNA MICROARRAY EXPERIMENTS
ANDRÉ FUJITA, JOÃO R. SATO, FERNANDO H.L. DA SILVA, MARIA C. GALVÃO, MARI C. SOGAYAR and SATORU MIYANO | 21 |
COMPARATIVE ANALYSIS OF TOPOLOGICAL PATTERNS IN DIFFERENT MAMMALIAN NETWORKS
BJOERN GOEMANN, ANATOLIJ P. POTAPOV, MICHAEL ANTE and EDGAR WINGENDER | 32 |
TOOLS FOR INVESTIGATING MECHANISMS OF ANTIGENIC VARIATION: NEW EXTENSIONS TO VARDB
C. NELSON HAYES, DIEGO DIEZ, NICOLAS JOANNIN, MINORU KANEHISA, MATS WAHLGREN, CRAIG E. WHEELOCK and SUSUMU GOTO | 46 |
LOCALIZED SUFFIX ARRAY AND ITS APPLICATION TO GENOME MAPPING PROBLEMS FOR PAIRED-END SHORT READS
KOUICHI KIMURA and ASAKO KOIKE | 60 |
COMPARATIVE ANALYSIS OF AEROBIC AND ANAEROBIC PROKARYOTES TO IDENTIFY CORRELATION BETWEEN OXYGEN REQUIREMENT AND GENE-GENE FUNCTIONAL ASSOCIATION PATTERNS
YAMING LIN and HONGWEI WU | 72 |
CALCULATION OF PROTEIN–LIGAND BINDING FREE ENERGY USING SMOOTH REACTION PATH GENERATION (SRPG) METHOD: A COMPARISON OF THE EXPLICIT WATER MODEL, GB/SA MODEL AND DOCKING SCORE FUNCTION
DAISUKE MITOMO, YOSHIFUMI FUKUNISHI, JUNICHI HIGO and HARUKI NAKAMURA | 85 |
STRUCTURAL INSIGHTS INTO THE ENZYME MECHANISM OF A NEW FAMILY OF D-2-HYDROXYACID DEHYDROGENASES, A CLOSE HOMOLOG OF 2-KETOPANTOATE REDUCTASE
SUKANTA MONDAL and KENJI MIZUGUCHI | 98 |
COMPREHENSIVE ANALYSIS OF SEQUENCE-STRUCTURE RELATIONSHIPS IN THE LOOP REGIONS OF PROTEINS
SHUGO NAKAMURA and KENTARO SHIMIZU | 106 |
THE PREDICTION OF LOCAL MODULAR STRUCTURES IN A CO-EXPRESSION NETWORK BASED ON GENE EXPRESSION DATASETS
YOSHIYUKI OGATA, NOZOMU SAKURAI, HIDEYUKI SUZUKI, KOH AOKI, KAZUKI SAITO and DAISUKE SHIBATA | 117 |
GRADIENT-BASED OPTIMIZATION OF HYPERPARAMETERS FOR BASE-PAIRING PROFILE LOCAL ALIGNMENT KERNELS
KENGO SATO, YUTAKA SAITO and YASUBUMI SAKAKIBARA | 128 |
A METHOD FOR EFFICIENT EXECUTION OF BIOINFORMATICS WORKFLOWS
JUNYA SEO, YOSHIYUKI KIDO, SHIGETO SENO, YOICHI TAKENAKA and HIDEO MATSUDA | 139 |
DEVELOPMENT OF A NEW META-SCORE FOR PROTEIN STRUCTURE PREDICTION FROM SEVEN ALL-ATOM DISTANCE DEPENDENT POTENTIALS USING SUPPORT VECTOR REGRESSION
MATSUYUKI SHIROTA, TAKASHI ISHIDA and KENGO KINOSHITA | 149 |
REFINING MARKOV CLUSTERING FOR PROTEIN COMPLEX PREDICTION BY INCORPORATING CORE-ATTACHMENT STRUCTURE
SRIGANESH SRIHARI, KANG NING and HON WAI LEONG | 159 |
AN ASSESSMENT OF PREDICTION ALGORITHMS FOR NUCLEOSOME POSITIONING
YOSHIAKI TANAKA and KENTA NAKAI | 169 |
CANCER CLASSIFICATION USING SINGLE GENES
XIAOSHENG WANG and OSAMU GOTOH | 179 |
RECOUNT: EXPECTATION MAXIMIZATION BASED ERROR CORRECTION TOOL FOR NEXT GENERATION SEQUENCING DATA
EDWARD WIJAYA, MARTIN C. FRITH, YUTAKA SUZUKI and PAUL HORTON | 189 |
| Part B Keynote Addresses |
A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE
SEAN R. EDDY | 205 |
REPRESENTATION AND ANALYSIS OF MOLECULAR NETWORKS INVOLVING DISEASES AND DRUGS
MINORU KANEHISA | 212 |
SYSTEMS BIOTECHNOLOGY
SANG YUP LEE | 214 |
STRATEGIES TOWARD CNS-REGENERATION USING INDUCED PLURIPOTENT STEM CELLS
HIDEYUKI OKANO | 217 |
THINKING LATERALLY ABOUT GENOMES
MARK A. RAGAN | 221 |
BACK MATTER
| 223 |
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