Genome Informatics 2009
 |
Genome Informatics 2009 Presented at the 20th International Conference on Genome Informatics Poster and Software Demonstrations |
- Genome Analysis
- Sequence Analysis
- Phylogenetics
- Structural bioinformatics
- Gene Expression
- Genetic and Population Analysis
- Systems Biology
- Data and Text Mining
- Databases and Ontologies
- Chemoinformatics and Chemical Biology
- 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]
