Genome Informatics 2009

GIW09Poster.gif

Genome Informatics 2009

Presented at the 20th International Conference on Genome Informatics
December 14-16, 2009, Yokohama Pacifico, Japan

Poster and Software Demonstrations

 


 

  • Short Talks Selected from Posters
  •  

  • Software Demonstration Abstracts
  •  

  • Poster Abstracts
    1. Genome Analysis
    2. Sequence Analysis
    3. Phylogenetics
    4. Structural bioinformatics
    5. Gene Expression
    6. Genetic and Population Analysis
    7. Systems Biology
    8. Data and Text Mining
    9. Databases and Ontologies
    10. Chemoinformatics and Chemical Biology
    11. Biomedical Informatics

     


     

    Short Talks Selected from Posters

    Dynamic Programming Algorithms for RNA Structure Prediction with Binding Sites
    Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu
    T001/P036[PDF file]

    Dissecting Protein-Protein Interaction-Mediated Cross-Talk Pathways in Hepatocellular Carcinoma
    Chia-Hung Liu, Chun-Nan Hsu, Cheng-Yan Kao, Minoru Kanehisa, Susumu Goto, Chi-Ying F. Huang
    T002/P081[PDF file]

    DDBJ Read Archive and DDBJ Read Annotation Pipeline:An Archive Database and an Analytical Tool for Next-Generation Sequence Data
    Eli Kaminuma, Yuichi Kodama, Satoshi Saruhashi, Takeshi Konno, Takako Mochizuki, Hidemasa Bono, Hideaki Sugawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
    T003/P120[PDF file]

    A Parallel Algorithm for Estimating Genome-Wide Gene Networks using Nonparametric Bayesian Networks
    Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Satoru Miyano
    T004/P086[PDF file]

    Software Demonstrations

    Microbial Genome Annotation Pipeline (MiGAP) for Diverse Users
    Hideaki Sugawara, Akira Ohyama, Hiroshi Mori, Ken Kurokawa
    S001[PDF file]

    Bridging the Gap between Biologists and Bioinformaticians with Subio Platform
    Akio Tanabe, Fumio Naito, Taro Fukasa, Shiro Terashima
    S002[PDF file]

    cyto-Hubba: a Cytoscape Plug-in for Hub Object Analysis in Network Biology
    Shu-Hwa Chen, Chia-Hao Chin, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin
    S003[PDF file]

    Extended CADLIVE: Multi-User Framework and Data Integrator
    Sayaka Tomeda, Shinpei Tonami, Kentaro Inoue, Kazuhiro Maeda, Hiroyuki Kurata
    S004[PDF file]

    Cell Illustrator Online 4.0: A Platform for Systems Biology
    Masao Nagasaki, Kazuko Ueno, Emi Ikeda, Chen Li, Kaname Kojima, Ayumu Saito, Satoru Miyano
    S005[PDF file]

    New Functions of MassBank: Mass Spectral Database for Metabolome Analysis - Peak Search by Formula, Web API and Database Maintenance -
    Hisayuki Horai, Masanori Arita, Yoshito Nihei, Tasuku Ikeda, Yuya Ojima, Takaaki Nishioka
    S006[PDF file]

    COPICAT: A Software System for Predicting Interactions between Chemical Compounds and Proteins by Using Two-Layer Support Vector Machine
    Masahiro Yokota, Nobuyoshi Nagamine, Yohei Sugawara, Kris Popendorf, Miho Uchida, Tatsuo Kitahashi, Takashi Komori, Yasubumi Sakakibara
    S007[PDF file]

    Pathway Prediction Focusing on Inclusive Relation of Substructures
    Kenichi Tanaka, Kensuke Nakamura, Tamio Saito, Hiroyuki Osada, Hiroki Takahashi, Aki Hirai, Shigehiko Kanaya, Md. Altaf-Ul-Amin
    S008[PDF file]

    Poster Abstracts

    ♦ Genome Analysis

    GC Content Provides New Insights into Exon Recognition
    Eddo Kim, Amir Goren, Maayan Amit, Gil Ast
    P001[PDF file]

    Immigrants to the Nucleus; Analysis of Mitochondrial-like Fragments in Human Genome
    Junko Tsuji, Paul Horton
    P002[PDF file]

    How (not) to align Genomes
    Martin C. Frith, Michiaki Hamada, Paul Horton
    P003[PDF file]

    Expression Profile in Various Stages of Gametogenesis Correlates with the Alu Distribution Pattern in Human Genome
    Hiroki Ashida, Toutai Mituyama, Kiyoshi Asai
    P004[PDF file]

    Properties of the Word Set for Estimating Similarities between Prokaryotic Genomes in Linguistic Approach
    Keishin Hanya, Satoshi Mizuta
    P005[PDF file]

    Comparative Genomic Analysis of Unicellular to Seed Plants by Using Gene Functions of A.thaliana
    Mai Kawazoe, Hiroki Takahashi, Masayoshi Wada, Aki Hirai, Kensuke Nakamura, Md. Altaf-Ul-Amin, Shigehiko Kanaya
    P006[PDF file]

    The Evolution of Metazoan Mitochondrial Genome and Latent Biological Mechanisms
    Haidong Tan, Masaharu Seno
    P007[PDF file]

    Detection of Mosaic Structure of Syntenic Segments in Marine Cyanobacterial Genomes
    Naobumi V. Sasaki, Naoki Sato
    P008[PDF file]

    Contribution of Mobile Genetic Elements on Variation in Gene Content among Bacteria
    Haruo Suzuki, Michael J. Stanhope
    P009[PDF file]

    Comparative Analysis of Information Contents Relevant to Intron Recognition in Many Species
    Hiroaki Iwata, Osamu Gotoh
    P010[PDF file]

    Plant Gene Identification Based on Cross-Species Mapping of Full-Length cDNAs
    Naoki Amano, Tsuyoshi Tanaka, Hisataka Numa, Hiroaki Sakai, Takeshi Itoh
    P011[PDF file]

    Integrated Transcriptional Regulatory Networks Identify Differences in Iron Regulation Across and within Yersinia Species
    Xin-Yi Chua, James Hogan
    P012[PDF file]

    The Functional Diversity of GPCR Genes Observed from Comparative Genome Analysis.
    Makiko Suwa, Yukiteru Ono, Wataru Fujibuchi
    P013[PDF file]

    ♦Sequence Analysis

    A Method for Extracting Optimal Sequence Related to Biological Activity
    Tatsuya Nosho, Ko Kato, Hiroki Takahashi, Md. Altaf-Ul-Amin, Shigehiko Kanaya
    P014[PDF file]

    Evolution of Human Phosphorylation Sites
    Dong Seon Kim, Yoonsoo Hahn
    P015[PDF file]

    Prediction of the O-glycosylation by Support Vector Machine and Independent Component Analysis for Amino Acid Sequence around O-glysocylation
    Yukiko Nakajima, Kazutoshi Sakakibara, Masahiro Ito, Ikuko Nishikawa
    P016[PDF file]

    Detection of Tissue-Specific Genes and Computational Analysis of Testis-Specific Gene Expression Regulatory Regions
    Akifumi Yamashita, Naohisa Goto, Seiji Nishiguchi, Kazunori Shimada, Hiromichi Yamanishi, Teruo Yasunaga
    P017[PDF file]

    Pairwise RNA Pseudoknotted Structure Prediction Based on Stochastic Grammar
    Nobuyoshi Mizoguchi, Yuki Kato, Hiroyuki Seki
    P018[PDF file]

    The Effect Read Length has on the Performance of Adaptive Seeds for Sequence Alignment
    Raymond Wan, Szymon M. Kielbasa, Paul Horton, Martin C. Frith
    P019[PDF file]

    Prediction of Eukaryotic Translation Initiation Sites Using Machine Learning
    Yoko Ishino
    P020[PDF file]

    Selectivity of Cis-Element Data and its Analysis with an Informatics Approach
    Yuya Yamazaki, Tomonori Suzuki, Satoru Miyazaki
    P021[PDF file]

    Comprehensive Analysis of Polyketide Synthase Families
    Yugo Shimizu, Masaaki Kotera, Toshiaki Tokimatsu, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
    P022[PDF file]

    A Multi-Objective Genetic Algorithm for Pairwise RNA Sequence Alignment
    Akito Taneda
    P023[PDF file]

    Molecular Evolutionary Analysis of Primary Immunodeficiency Associated Genes
    Tomotaka Koyama, Katsuhiko Mineta, Toshinori Endo
    P024[PDF file]

    ♦Phylogenetics

    Inference of Geographic Transmission Probability of Influenza Viruses from a Large Phylogenetic Tree
    Fumiaki Yanagihashi, Kimihito Ito, Hiroki Arimura
    P025[PDF file]

    New trend of Biodiversity Informatics Based on Global Biodiversity Information Facility (GBIF) and Barcode of Life (BoL)
    Yasumasa Shigemoto, Yoshikazu Kuwana, Hideaki Sugawara
    P026[PDF file]

    Analysis of Plant UGT Family Sequences and Substrate Specificity
    Yosuke Nishimura, Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto, Minoru Kanehisa
    P027[PDF file]

    Complicated Evolutionary History of Wild and Cultivated Asian Rice Disclosed by Gene Tree Incongruence Analysis
    Ching-chia Yang, Hiroaki Sakai, Takeshi Itoh
    P028[PDF file]

    ♦Structural bioinformatics

    TANGLE: an Integrated Server for Protein Backbone Torsion Angle Prediction
    Jiangning Song, Hao Tan, Khalid Mahmood, Geoffrey Webb, Tatsuya Akutsu, James Whisstock
    P029[PDF file]

    Analysis of Glycan Recognition Sites of Viruses
    Shota Yamada, Sayaka Takase, Kiyoko F. Aoki-Kinoshita
    P030[PDF file]

    Development of a New Glycan Score Matrix
    Yukie Akune, Kiyoko F. Aoki-Kinoshita
    P031[PDF file]

    Identifying Functional Motifs on Protein Surfaces by Structural Alignment with Sequence Information
    Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Takashi Yamamoto, Xiang-Sun Zhang, Luonan Chen
    P032[PDF file]

    Improvement of All-to-All Protein-Protein Interaction Prediction System MEGADOCK
    Masahito Ohue, Yusuke Matsuzaki, Yuri Matsuzaki, Yutaka Akiyama
    P033[PDF file]

    Classification of Protein Fragments with a Graph Spectral Technique
    Jun-ichi Ito, Junichi Higo, Kentaro Tomii
    P034[PDF file]

    Classification and Identification of Indiscernible Metal Binding Sites of Proteins
    Yuki Sakashita, Jun-ichi Ito, Kiyoshi Asai, Kentaro Tomii
    P035[PDF file]

    ♦Gene Expression

    Identification of DNA Methylation Which Leads to Differences of Gene Interaction Network between Cell Types
    Michio Kamiya, Kenji Satou, Yoichi Yamada
    P037[PDF file]

    Gene-Expression-Based Disease Class Classification Using Probit Model
    Hideyuki Takahashi, Toshimasa Yamazaki, Hiroki Sasaki
    P038[PDF file]

    Finding Informative Genes Related to Alzheimer Disease using Supervised Independent Component Analysis
    Faezeh Dorri, Houshang Hassibi, Seyed Hassan Paylakhi, Elahe Elahi
    P039[PDF file]

    Correction and Integration of Normalized Microarray Data
    Takashi Yoneya, Tatsuya Miyazawa
    P040[PDF file]

    Microarray-Based Classification of Seed-Specific Gene Expression for Pigmentation in Colored Rice
    Changkug Kim, Unghan Yoon, Dowon Yun, Gangseob Lee, Yonghwan Kim
    P041[PDF file]

    Annotating Gene Functions by Spectral Clustering for Combining Gene Expressions and Sequences
    Limin Li, Motoki Shiga, Wai-ki Ching, Hiroshi Mamitsuka
    P042[PDF file]

    Molecular Network Analysis Suggests Aberrant CREB-Mediated Gene Regulation in the Alzheimer's Disease Hippocampus
    Jun-ichi Satoh, Shinya Obayashi, Hiroko Tabunoki
    P043[PDF file]

    Analyzing Histone Codes by a Computational Approach
    Yayoi Natsume-Kitatani, Motoki Shiga, Hiroshi Mamitsuka
    P044[PDF file]

    Genome-Wide Three-Way Gene Interactions from Transcript and Genotype Data
    Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka
    P045[PDF file]

    Prevailing Cancer Transcriptional Networks Revealed by Meta-Analysis of Cancer Transcriptomes
    Atsushi Niida, Seiya Imoto, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano
    P046[PDF file]

    Subspace Clustering of Gene Expression Data with Prior Knowledge
    Yoko Omura, Jun Sese
    P047[PDF file]

    Cytokine Productions and Gene Expressions Caused by Mechanical Stretching of Normal Human Pulmonary Artery Endothelial Cells
    Kozue Kobayashi, Masumi Tanaka, Hidenori Inaoka, Satoru Nebuya, Yutaka Fukuoka, Hirosuke Kobayashi, Makoto Noshiro
    P048[PDF file]

    Data Analysisf of Genomic Alteration by Environmental Toxicant
    Yu Ri An, Seung Jun Kim, Hye-Won Park, Jong Pil Youn, Jung Mi Ha, Moon-Ju Oh, Seung Yong Lee, Jung-Hwa Oh, Seok-Joo Yoon, Seung Yong Hwang
    P049[PDF file]

    Co-Expression Analysis in Close Physical Proximity Using Tumor Data
    Hidenori Inaoka, Yutaka Fukuoka, Makoto Noshiro
    P050[PDF file]

    Distinguishing Tumors from Normal by Cell Surface Maker with Spherical SOM
    Yuh Sugii, Ling Chen, Heizo Tokutaka, Masaharu Seno
    P051[PDF file]

    Aspergillus Niger: Mapping Fungal Specific Zinc-Finger Transcription Factors to Gene Co-Expression Networks
    Benjamin M. Nitsche, Vera Meyer, Arthur FJ. Ram
    P052[PDF file]

    Comparison of Transcriptional Regulatory Network Based on Cis-Module Database
    Shizu Akasaka, Tomoko Urushibara, Tomonori Suzuki, Satoru Miyazaki
    P053[PDF file]

    Quality Control and Reproducibility in DNA Microarray Experiments
    André Fujita, João Sato, Fernando H.L da Silva, Maria C. Galvaõ, Mari C. Sogayar, Satoru Miyano
    P054[PDF file]

    A Statistical Method of Analyzing Global Gene Expression Data Obtained from Experiments Using Japanese Herbal Medicine
    Masayuki Shojo, Akira Katoh, Tatsuhiko Ikeda, Yuka Ninomiya, Masatomo Sakurai, Tomoyuki Hayasaki, Toshihiko Hanawa, Hiroki Takahashi, Md. Altaf-Ul-Amin, Kyosuke Nomoto, Shigehiko Kanaya
    P055[PDF file]

    A Web Tool for Expression Pattern-Based Data Retrieval and Relevant Network Discovery from vast Public Microarray Database
    Chunlai Feng, Michihiro Araki, Ryo Kunimoto, Akiko Tamon, Hiroki Makiguchi, Satoshi Niijima, Gozoh Tsujimoto, Yasushi Okuno
    P056[PDF file]

    A Method of Estimation of Crosstalk Genes with Multiple Time-Series Gene Expression Profiles
    Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    P057[PDF file]

    Reinterpretation of the Database Search Result Using Trans-Proteomics Pipeline in Mass Spectrometry-Based Proteomics
    Kyung-Hoon Kwon, Sang Kwang Lee, Kun Cho, Gun Wook Park, Byeong Soo Kang, Young Mok Park
    P058[PDF file]

    Time and Space Efficient Implementation of Robust Biclustering Algorithm (ROBA)
    Muhammad Ibrahim, Nasimul Noman, Hitoshi Iba
    P059[PDF file]

    ♦Genetic and Population Analysis

    A Study of Different Rule Selection Strategies for Rule Based SNP Imputation
    Yue Wang, Guimei Liu, Limsoon Wong
    P060[PDF file]

    Discovering CNVs from Read Depth Analysis of Next Generation Sequencing Data
    Alexej Abyzov, Alexander Eckehart Urban, Michael Snyder, Mark Gerstein
    P061[PDF file]

    Accurate Assignment of Short Pyrosequencing Reads in a 16S rRNA Taxonomy
    José C. Clemente, Jesper Jansson, Gabriel Valiente
    P062[PDF file]

    ♦Systems Biology

    Bayesian Analysis of Perturbed Escherichia coli metabolism
    Seung Min Yoo, Hyun Uk Kim, Tae Yong Kim, Sang Yup Lee
    P063[PDF file]

    Adjustable Diffusion Matrix-Based Spectral Clustering for Protein-Protein Interaction Network
    Kentaro Inoue, Hiroyuki Kurata
    P064[PDF file]

    Novel Robustness Analysis Reveals Remarkable Robustness of Dual Feedback Loops in a Circadian Clock
    Kazuhiro Maeda, Hiroyuki Kurata
    P065[PDF file]

    Module Decomposition and Integration Method Optimizes a Large-Scale Cell Cycle Model
    Daichi Nitta, Hiroyuki Kurata
    P066[PDF file]

    Metabolite Essentiality Analysis Using Genome-Scale Metabolic Networks of Pathogens for the Drug Discovery
    Sang Yup Lee, Hyun Uk Kim, Tae Yong Kim
    P067[PDF file]

    Metabolic Network Reconstruction and Pathway Analysis of Mannheimia Succiniciproducens
    Seung Min Yoo, Tae Yong Kim, Hyung Rok Choi, Sang Yup Lee
    P068[PDF file]

    Proteome Analysis of the Succinic Acid Producer Mannheimia Succiniciproducens and Byproduct Elimination Strategy
    Yu Hyun Lee, Jeong Wook Lee, Meehee Kim, Sang Yup Lee
    P069[PDF file]

    Adaptive Response to Low Level of an Alkylating Agent in Escherichia coli K-12 and ada Mutant Strains by Transcriptome and Proteome Analyses
    Yu Hyun Lee, Mee-Jung Han, Jong Hwan Baek, Sang Yup Lee, Meehee Kim
    P070[PDF file]

    Genome-Wide Mutational and Expression Analyses of Evolved Escherichia Coli Strains Under Ethanol Stress
    Takaaki Horinouchi, Kuniyasu Tamaoka, Chikara Furusawa, Takashi Hirasawa, Naoaki Ono, Shingo Suzuki, Tetsuya Yomo, Hiroshi Shimizu
    P071[PDF file]

    Modeling of Early Sporulation in Bacillus Subtilis with Hybrid Functional Petri Net
    Jin Hwan Do, Masao Nagasaki, Satoru Miyano
    P072[PDF file]

    Model Analysis of Helper T Cell Differentiation with Transcriptional Factor's Interactions in Th0
    Satoshi Yamada, Akihiko Yoshimura
    P073[PDF file]

    Systematic Identification of Differential Expression Networks in Chemosensitive and Chemoresistant Ovarian Cancer
    Shih-Yi Chao, A-Mei Huang
    P074[PDF file]

    Comparing Biological Networks via Graph Compression
    Morihiro Hayashida, Tatsuya Akutsu
    P075[PDF file]

    Prediction of Transcriptional Patterns of Gene Deletion Mutants by Modified Control Effective Flux
    Quanyu Zhao, Hiroyuki Kurata
    P076[PDF file]

    Construction of Transcriptional Regulatory Network during Rice Anther Development
    Luonan Chen, Wenjuan Zhang, Takashi Yamamoto, Shunsuke Okuzumi, Zhiping Liu
    P077[PDF file]

    Elucidation of Metabolic Pathway under the Influence of Gene Regulatory Network
    Yuta Hamano, Kozo Nishida, Takuya Morimoto, Hiroki Takahashi, Md Altaf-Ul-Amin, Shigehiko Kanaya
    P078[PDF file]

    Kinetic Modeling of Central Metabolic Pathway for Phenotype MicroArray Analysis
    Yusaku Mazaki, Hirotada Mori, Masahiro Ito, Yukako Tohsato
    P079[PDF file]

    A Method for the Inference of Gene Regulatory Networks based on Dynamic Bayesian Network with Clustering of Time-Series Subsequences
    Yuya Shuto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    P080[PDF file]

    Estimating Dynamic Gene Networks Under Different Biological Conditions
    Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano
    P082[PDF file]

    Cancer Related Pathways are Enriched Among Common Human Targets in Viruses-Human Interactions
    Dai-Shin Chen, Wen-Chih Cheng, Wan-Jing Lu, Chen-hsiung Chan
    P083[PDF file]

    Effective Multi-Scale Graph Navigation System Powered by Fast and Biologically Meaningful Hierarchical Clustering
    Thanet Praneenararat, Wataru Iwasaki, Toshihisa Takagi
    P084[PDF file]

    Robustness Analysis on Lateral Propagation Mechanism of EGF Signaling by L2induced Gain
    Makoto Ogawa, Takashi Nakakuki
    P085[PDF file]

    Active State Transition Diagram Analysis from Time Course Simulation Data: an HFPNe Approach
    Chen Li, Masao Nagasaki, Ayumu Saito, Satoru Miyano
    P087[PDF file]

    Network Based Analysis of Hepatitis C Virus Infection
    Lokesh Tripathi, Kohji Moriishi, Yoshio Mori, Yoshiharu Matsuura, Yi-an Chen, Kenji Mizuguchi
    P088[PDF file]

    Gene Network Comparison by State Space Models Based on Time Course Microarray Data
    Kaname Kojima, Rui Yamaguchi, Seiya Imoto, Mai Yamauchi, Masao Nagasaki, Ryo Yoshida, Teppei Shimamura, Kazuko Ueno, Tomoyuki Higuchi, Noriko Gotoh, Satoru Miyano
    P089[PDF file]

    Sensitivity Analysis of MAPK-Induced Transcription Control of Fos Protein by using $L_2$-induced Gain
    Hiroki Ishiyama, Takashi Nakakuki
    P090[PDF file]

    PGFeval: Software Tool and Web Server for Evaluation and Visualization of Proteogenomic Features
    Mohamed Helmy, Masaru Tomita, Yasushi Ishihama
    P091[PDF file]

    Pathway Projector: an Interactive Pathway Browser with Zoomable User Interface
    Nobuaki Kono, Kazuharu Arakawa, Ryu Ogawa, Nobuhiro Kido, Kazuki Oshita, Keita Ikegami, Satoshi Tamaki, Masaru Tomita
    P092[PDF file]

    Temporal Gene Expression Patterns Reveal Mass Conservation in TNF-α Signaling
    Kentaro Hayashi, Masaru Tomita, Masa Tsuchiya, Kumar Selvarajoo
    P093[PDF file]

    Reconstruction and Analysis of Integrated Metabolic Reaction Network of Bacillus Subtilis
    Kozo Nishida, Hiroki Takahashi, Kensuke Nakamura, Md Altaf-Ul Amin, Shigehiko Kanaya
    P094[PDF file]

    Quantitative Cell Division Dynamics Information from Early C.elegans Embryos
    Koji Kyoda, Eru Adachi, Junko Kuramochi, Kumiko Shimada, Shuichi Onami
    P095[PDF file]

    Robustness of Attractor in Complex Networks with Scale-Free Topology III
    Shu-ichi Kinoshita, Kazumoto Iguchi, Hiroaki S. Yamada
    P096[PDF file]

    ♦Data and Text Mining

    Gene Function Prediction via Discriminative Graph Embedding
    Canh Hao Nguyen, Hiroshi Mamitsuka
    P097[PDF file]

    Using Local Reaction Structure to Build a Global Metabolic Network Classifier
    Timothy Hancock, Hiroshi Mamitsuka
    P098[PDF file]

    REST/SOAP Web Service API for G-language System
    Kazuharu Arakawa, Nobuhiro Kido, Kazuki Oshita, Masaru Tomita
    P099[PDF file]

    Efficient Computation of Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles
    Yang Cong, Takeyuki Tamura, Tatsuya Akutsu, Wai-Ki Ching
    P100[PDF file]

    Improvements to Profile PSTMM for Glycan Recognition Profile Prediction
    Sakiko Kaiya, Masae Hosoda, Kiyoko F. Aoki-Kinoshita
    P101[PDF file]

    Semantic Classification of Nouns in UMLS Using Google Web 1T 5-gram
    Aika Myosho, Kenji Nakano, Yoichi Yamada, Kenji Satou
    P102[PDF file]

    KBWS: an EMBASSY Package for Effective Utilization of Bioinformatics Web Services
    Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita
    P103[PDF file]

    Classification of Adrenergic Receptors Using the Multi-Dimentional Method
    Yasuhito Inoue, Yuki Kinoshita, Jyunpei Seki, Ryosuke Hanbayashi
    P104[PDF file]

    Classification of Neuroimaging Figures toward Automatic Figure Annotation System
    Natsu Ishii, Asako Koike, Toshihisa Takagi
    P105[PDF file]

    Biomedical Figure Search Using Combination of Bag of Keypoints and Bag of Words
    Asako Koike, Natsu Ishii, Toshihisa Takagi
    P106[PDF file]

    Mining Significant Substructure-Substructure Pairs in Strucural Associations
    Ichigaku Takigawa, Koji Tsuda, Hiroshi Mamitsuka
    P107[PDF file]

    Graph Summarization for Finding Relations of Protein Functions
    Aika Terada, Jun Sese
    P108[PDF file]

    Reliable Augmentation of Protein Interaction Data with Interologs for Protein Function Prediction
    Chern Han Yong, Limsoon Wong
    P109[PDF file]

    A New Approach to Analyzing DNA Microarray Data Using Principal Component Analysis
    Jun-Ichi Sagara, Hideaki Koike, Yasunobu Terabayashi, Motoaki Sano, Noriko Yamane, Noriko Yamane, Mitsuko Dohmoto, Ken Oda, Eiji Ohshima, Kuniharu Tachibana, Yoshimasa Higa, Shinichi Ohashi, Masayuki Machida
    P110[PDF file]

    ♦Databases and Ontologies

    FUJI Database Provides Functional and Structural Annotation of Proteins On Demand
    Keiichi Homma, Hideaki Sugawara
    P111[PDF file]

    MetalMine: a Database of Functional Metal-Binding Sites in Proteins
    Kensuke Nakamura, Aki Hirai, Hiroki Takayashi, Md. Altaf-Ul-Amin, Shigehiko Kanaya
    P112[PDF file]

    On-the-Fly Link Generation for Workflows in Biology
    Yeondae Kwon, Yasumasa Shigemoto, Yoshikazu Kuwana, Hideaki Sugawara
    P113[PDF file]

    CaMPDB: a Resource for Calpain and Modulatory Proteolysis
    David A. du Verle, Ichigaku Takigawa, Yasuko Ono, Hiroyuki Sorimachi, Hiroshi Mamitsuka
    P114[PDF file]

    Incorporation of New Data and Development of User Management and Feedback System in RINGS
    Junichi Araki, Masatoshi Shimahara, Anna Kokubu, Kiyoko F. Aoki-Kinoshita
    P115[PDF file]

    Consecutive Update of the Microbial Genome Re-Annotation Database, GTPS
    Takehide Kosuge, Yasumasa Shigemoto, Yoshikazu Kuwana, Hideaki Sugawara
    P116[PDF file]

    SDOPDB: Comparative Standardized-Protocol Database for Mouse Phenotyping Analyses
    Nobuhiko Tanaka, Kazunori Waki, Hideki Kaneda, Tomohiro Suzuki, Ikuko Yamada, Tamio Furuse, Kimio Kobayashi, Hiromi Motegi, Hideaki Toki, Maki Inoue, Osamu Minowa, Tetsuo Noda, Keizo Takao, Tsuyoshi Miyakawa, Tsuyoshi Koide, Shigeharu Wakana, Hiroshi Masuya
    P117[PDF file]

    FlyGlycoDB: a Database of Glycan-Related Genes and Proteins in Drosophila
    Kiyoshi Tadahisa, Shoko Nishihara, Kiyoko F. Aoki-Kinoshita
    P118[PDF file]

    Omics Data Analysis Using SOP (Search of Omics Pathway) Web Tool
    Seung Yong Lee, Jun-Sub Kim, Seung-Jun Kim, Ji-Hoon Kim, Hye-Won Park, Yu Ri An, Moon-Ju Oh, Seung Yong Hwang
    P119[PDF file]

    CyanoClust: Protein Cluster Database for Comparative genomics of Cyanobacteria and Plastids
    Naoki Sato, Naobumi V. Sasaki
    P121[PDF file]

    Evaluating Protein Sequence Signatures Inferred from Protein-Protein Interaction Data Using Gene Ontology Annotations
    Osamu Maruyama, Hideki Hirakawa, Takao Iwayanagi, Yoshiko Ishida, Shizu Takeda, Jun Otomo, Satoru Kuhara
    P122[PDF file]

    Creation and Management of Information Platform in Targeted Proteins Research Program
    Hisashi Mizutani, Takao Iwayanagi, Keiichi Homma, Yoshie Ohno, Miyuki Konishi, Haruki Nakamura, Junko Sato, Akihito Kaneko, Tomoakira Kawai, Hideaki Sugawara
    P123[PDF file]

    Reclassification of Oxidoreductase Subclasses Based on the Relationships of Reductants and Oxidants
    Masaaki Kotera, Toshiaki Tokimatsu, Zen-ichi Nakagawa, Yuki Moriya, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
    P124[PDF file]

    INOH Pathway Database
    Noriko Sakai, Satoko Sakai, Hiromi Nakamura, KenIchiro Fukuda, Toshihisa Takagi
    P125[PDF file]

    The New Version of MutationView : Enhanced Search Function and Significant Increase in the Number of Gene Entries
    Masafumi Ohtsubo, Kouichi Kawaguchi, Katsue Adachi, Tomoyoshi Horisawa, Nobuyoshi Shimizu, Shinsei Minoshima
    P126[PDF file]

    Structural Clustering of Plant Secondary Metabolite to Estimate Compound Classes Reflecting their Biosynthetic Pathway
    Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto, Shigehiko Kanaya, Minoru Kanehisa
    P127[PDF file]

    A Trial to Develop a Integrative Database of Mouse Phenotype Related Information
    Hiroshi Masuya, Norio Kobayashi, Nobuhiko Tanaka, Kazunori Waki, Kouji Kozaki, Shigeharu Wakana, Riichiro Mizoguchi, Tetsuro Toyoda
    P128[PDF file]

    The Ontology-Based Data Processing System for International Integration, Ontology and Data Mining of Mouse Phenome Information
    Kazunori Waki, Hiroshi Masuya
    P129[PDF file]

    DMPD: Dynamic Macrophage Pathway Database
    Ayumu Saito, Masao Nagasaki, Andre Fujita, Kazuko Ueno, Emi Ikeda, Satoru Miyano
    P130[PDF file]

    ♦Chemoinformatics and Chemical Biology

    An Automatic Glyco-Work ow Generator in RINGS
    Daisuke Shinmachi, Kiyoko F. Aoki-Kinoshita
    P131[PDF file]

    Constrained Clustering for Discovering High Binding Affinity Glycan Substructures
    Haruna Terai, Jun Sese
    P132[PDF file]

    A Method for Extraction of the Active Compound Groups which Have Strong Relationship between Structure and Activity
    Takahiro Kishimoto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    P133[PDF file]

    Extracting Common Substructures of GPCR Ligands
    Bekir Erguner, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
    P134[PDF file]

    Chemical Continuity of Reaction Centers along Successive Metabolic Reactions
    Masahiro Hattori, Masaaki Kotera, Ai Muto, Susumu Goto, Minoru Kanehisa
    P135[PDF file]

    Applied Method of Extending Van Krevelen Diagrams for Exhaustive Analysis of Metabolites
    Kaori Matsuda, Md Altaf-Ul-Amin, Kensuke Nakamura, Hiroki Takahashi, Daisaku Ohta, Shigehiko Kanaya
    P136[PDF file]

    Structural Similarity-Based Approach to Characterize Crude Drug Components
    Ai Muto, Minoru Kanehisa
    P137[PDF file]

    ♦Biomedical Informatics

    Constructing Database of Epilepsy Genes and Mutations for Development of Genetic Diagnosis System
    Shuichi Yoshida, Kazuaki Kanai, Toshio Shimizu, Sunao Kaneko
    P138[PDF file]

    Molecular Evolutionary Origins of the Adaptive Immune System in Gnathostomata
    Jun-Ichi Kaneta, Masumi Itoh, Kanako O. Koyanagi, Hidemi Watanabe
    P139[PDF file]

    Spatiotemporal Sequence Analysis of Influenza Virus Sequences
    Chih-Jen Tai ,Tzu-Wen Chen, Po-An Cheng, Chen-hsiung Chan
    P140[PDF file]