update　2013.10.28
Chem-Bio Informatics Society(CBI) Annual Meeting 2013
＜Poster List＞

（１）分子認識と分子計算 (Molecular recognition and molecular modeling)
（２）インシリコ創薬認識と分子計算 (In silico drug discovery)　
（３）バイオインフォマティクスとその医学応用 (Bioinformatics and its applications in medicine)
（４）医薬品研究とADMET (Information and computing approach for drug design and ADMET study)
（５）上記に属さない先進的研究 (Emerging new technology)

Poster No.　＝　C-Area-Id No.
Poster No. Title First Author Affiliation
（１）分子認識と分子計算 (Molecular recognition and molecular modeling)

C-1-01

 A random-forest based method that can predict detailed enzyme functions and also identify specificity determining residues Chioko Nagao National Institute of Biomedical Innovation

C-1-02

 Large-Scale Fragment Molecular Orbital Calculations toward Evaluating the Drug Effects of AIDS Agents Yoichiro Yagi Okayama University of Science

C-1-03

 FMO calculations for nano-biotechnology Yuji Mochizuki Rikkyo University

C-1-04

 A practical procedure to calculate intermolecular interactions including statistical information between a protein and a large ligand Hiroyuki Sato Fujitsu Laboratories Ltd.

C-1-05

 Analysis of antibody-antigen interactions and prediction of their complex structures Yuko Tsuchiya National institute of biomedical innovation

C-1-06

 Screening and Design of Small Molecules that Reversibly Bind to Streptavidin Moe Kohno Graduate School of The University of Tokyo

C-1-07

 Standard binding free energy calculation for theophylline-RNA aptamer system: alchemical transformation and metadynamics Yoshiaki Tanida Fujitsu Laboratories Ltd.

C-1-08

 Molecular Dynamics Simulation of Shiga Toxin Kazumi Omata National Center for Global Health and Medicine

C-1-09

 Random Matrix Theory Analysis of Molecular Dynamics Simulation Masanori Yamanaka CST, Nihon University

C-1-10

 Binding Mechanism of KNI-272 with HIV-1 Protease Takahisa Hayashi The University of Tokushima

C-1-11

 LERE-QSAR Analysis of Binding of γ-Lactum Hydroxamic Acid Derivatives with Tumor Necrosis Factor-Alpha Converting Enzyme Koh Nonoshita University of Tokushima

C-1-12

 Spatial distribution of QM based interaction energy between amino-acids and probe molecules Hirofumi Watanabe RIKEN, Center for Life Science Technologies

C-1-13

 Estimation of Non-covalent Interactions with a New Efficient Dispersion Corrected HF Approach Tatsusada Yoshida The University of Tokushima

C-1-14

 Refinement of Crystal Structures Using Partial Geometry Optimization and Electron Density Calculations Based on the Fragment Molecular Orbital Method Kaori Fukuzawa Mizuho Information ＆ Research Institute Inc.

C-1-15

 FMO calculations with ABINIT-MP on K-computer Yoshio Okiyama The University of Tokyo

C-1-16

 Molecular Simulation Analysis of Glucuronidation of UDP-glucuronosyltransferase 1A7 and 1A10 Kenji Miura Kobe University Hospital

C-1-17

 FMO-based cluster analysis for drug design by multi-dimensional scaling Ryo Kurauchi Kobe University

C-1-18

 Statistical analysis of 3D distribution of ligand atoms in Protein Data Bank using kernel density estimation Tomohiro Sato Center for Life Science Technology, RIKEN

C-1-19

 FMO-based electron density analysis to protein structure refinement Chiduru Watanabe The University of Tokyo

C-1-20

 Development of molecular modeling software for protein complex animations Shuntaro Itou Nara Institute of Science and Technology

C-1-21

 Prediction of Protein-ligand Binding Affinities Using Molecular Simulations Noriaki Okimoto RIKEN

C-1-22

 A proposal for peptide inhibitors to block the ligand-binding pocket of urokinase receptor: ab initio molecular simulations Noriyuki Kurita Toyohashi University of Technology
（２）インシリコ創薬 (In silico drug discovery)

C-2-01

 Protein-Ligand Docking Using Artificial Bee Colony Algorithm Shota Uehara Kobe university

C-2-02

 A new approach for constructing CYP2C9 pKi estimation scheme with ligand-receptor interaction effects Sumie Tajima Hulinks Inc.

C-2-03

 Electronic Similarity of Molecules for Evaluation, Classification, and Discovery Manabu Sugimoto Kumamoto University

C-2-04

 Understanding polypharmacology and promiscuous chemotypes on LSKB Atsushi Midorikawa World Fusion

C-2-05

 Ensemble Docking Simulation for β-２ Adrenergic Receptor Using Elastic Network Model Tomoyuki Iwamoto Institute for Protein Research, Osaka University

C-2-06

 Investigation of protein-ligand interactions Yoshinori Hirano RIKEN

C-2-07

 Predicting bioactivity of compound-drug target protein pairs using support vector regression models reflecting ligand efficiency Nobuyoshi Sugaya PharmaDesign, Inc.

C-2-08

 CzeekD: Fragment-based de novo Drug Design System for Drug Discovery Tatsuya Yoshikawa Kyoto Constella Technologies Co., Ltd.

C-2-09

 Mixed Fragment-based screening of WNK1 inhibitor Nae Saito The University of Tokyo

C-2-10

 Identification of novel chemical agents with antibacterial activity against Mycobacterium by in silico structure-based drug screening Yuji Koseki Kyushu Institute of Technology

C-2-11

 Identification of novel potential antibiotics for Staphylococcus by Structure-Based Drug Screening Maiko Kobayashi Kyushu Institute of Techonology

C-2-12

 Design of transfection reagents in RNAi therapeutics by chemoinformatics approach Yu Sakai The University of Tokyo

C-2-13

 Toward Crowdsourcing Evaluation of Synthetic Accessibility Yukino Baba The University of Tokyo
（３）バイオインフォマティクスとその医学応用 (Bioinformatics and its applications in medicine)

C-3-01

 Identification of genes and pathways involved in DNA methylation in hepatocellular carcinoma Sufeiya Subati Dept. of System Biology, TMDU

C-3-02

 1H NMR-based metabolomics of plasma and dialysate from hemodialysis patients Masako Fujiwara Tohoku University

C-3-03

 Epigenome-wide discovery of ovarian and breast cancer specific DNA methylation markers Hitomi Hasegawa Genedata

C-3-04

 Analysis of Human Immunodeficiency Virus Type 1 (HIV-1) CRF07_BC in China Using BEAST Asiya Hapaer Tokyo Medical and Dental University

C-3-05

 Computational approach to validate long-range chromatin association between estrogen receptor alpha proteins and candidate genes of breast cancer MCF-7 within different human reference genomes Vutha Phav Tokyo Institute of Technology

C-3-06

 Association of CDKN2A/B, ADTRP and PDGFD　polymorphisms with coronary atherosclerosis in Japan  Sariya Dechamethakun Tokyo Medical and Dental University

C-3-07

 PoSSuM Updates and Integration With ChEMBL For Application of Drug Reuse Kazuyoshi Ikeda LEVEL FIVE Co.,Ltd.

C-3-08

 Phasing haplotypes of HLA genes from Next Generation Sequencing data at individual level Chenxi Zhao Tokyo Medical and Dental University

C-3-09

 Dynamic evolution of forkhead transcription factors and changes in their DNA-binding sites So Nakagawa Tokai University School of Medicine

C-3-10

 Applications of an integrated data warehouse system to investigate complex biological systems Yi-An Chen National Institute of Biomedical Innovation

C-3-11

 Exploring Development Origin of Health and Disease (DOHaD) hypothesis employing publicly available data Tay Zar Kyaw Research Student

C-3-12

 Correlation of annotation terms in heterogeneous databases and its application to Gene Set Enrichment Analysis (GSEA) and ontology construction katsuhiko murakami National Institute of Advanced Industrial Science

C-3-13

 Analysis of abnormalities in gene expression and splicing patterns of spinocerebellar ataxia type 6 knockin mice using RNA-seq Junya Hagiwara Dept. of Comput. Biol., Tokyo Med. Dent. Univ.

C-3-14

 Comprehensive transcriptome and proteome analysis revealed Wolfberry (Lycium barbarum) as a novel dietary intervention in optimal IBD management Wanping Aw Tokyo Medical and Dental University

C-3-15

 PathAct: a novel method for pathway analysis using gene expression profiles Kaoru Mogushi Dept. of Bioinformatics, Tokyo Med. Dent. Univ.

C-3-16

 RNA-Sequencing-Based Screening of Long Non-Coding RNAs Targeted by Steroid and Xenobiotic Receptor Kuniko Horie-Inoue Res Cntr for Genomic Med, Saitama Med Univ

C-3-17

 The Inferring Method of the large scale regulatory network for omics studies Asako Komori Kyushu University

C-3-18

 Development of an Ontology for Periodontitis Asami Suzuki The Nippon Dental University Hospital at Tokyo

C-3-19

 Improving the visual interpretation of experimental data by a more informative display of confidence intervals Daniel Berrar Tokyo Institute of Technology

C-3-20

 A comprehensive selection of single nucleotide polymorphisms to predict genetic risks of developing common chronic diseases in Japanese Akio Ametani InfoBio Co., Ltd.
（４）医薬品研究とADMET (Information and computing approach for drug design and ADMET study)

C-4-01

 Precise estimation of the contribution of CYP enzymes to overall metabolism from in vivo information: application of Cluster Newton Method Kenta Yoshida The University of Tokyo

C-4-02

 Development of the Discriminant KY-methods for Toxicity Screening Kohtaro Yuta In Silico Data, Ltd.

C-4-03

 Quantitative Structure-Pharmacokinetic Relationship (QSPkR) Analyses of Opioids Yoshihiro Uesawa Meiji Pharmaceutical Universithy

C-4-04

 Proposal of Toxicity Risk Index (TRI) for Warning Idiosyncratic Drug Toxicity Takashi Mizuma Matsuyama University

C-4-05

 Improvements to the Cluster Newton Method for Underdetermined Inverse Problems - Parameter Identification for Pharmacokinetics- Khin Moh Moh Latt Asian Institute of Technology
（５）上記に属さない先進的研究 (Emerging new technology)

C-5-01

 New Tools for HT Engineering, Cloning &Expression of Multispecific Next-generation Antibodies Futoshi Hashino Genedata KK, Tokyo, Japan

C-5-02

 Installation of orthogonality to the interface that assembles two modular domains in the Tetrahymena group I ribozyme Yoshiya Ikawa Kyushu University

C-5-03

 Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning Yasuhiro Fujino Mitsubishi Tanabe Pharma Corporation

C-5-04

 In silico analysis of interactions between the ingredient molecules contained in cold medicines and HLA-A*02:06 Noriaki Hirayama Tokai University School of Medicine

C-5-05

 Analysis of the Drug Prescribing Patterns of Physicians in Patients with both Cardiac and Renal Failure Mizuki Morita AIST

C-5-06

 Biophysical Approach of Fragment Screening to inhibit the heme transfer system of Pathogenic bacteria Satoru Nagatoishi The University of Tokyo

C-5-07

 Inhibitor Screening of Capsular Polysaccharide Synthesizing Enzyme CapF from Staphylococcus aureus Koichiro Nakano Grad. Sch. of Frontier Sci. , Univ. of Tokyo

C-5-08

 Functional analysis of Liposome binding peptide selected by cDNA display Yuki Yoshikawa Grad. Sch. Sci.＆ Eng., Saitama Univ.

C-5-09

 The CADU Alliance N3 Project Tsuguchika Kaminuma Institute for Cyber Associates

C-5-10

 Light-induced membrane potential regulates bone cell function; development of the light-responsive bone cells Takuya Notomi Tokyo Medical and Dental University

C-5-11

 E. coli host engineering for efficient enzyme discovery Miyuki Tsukuda Dep. Med. Gen. Sci., Univ. Tokyo

C-5-12

 Methylome diversification through changes in the sequence specificity of DNA methyltransferases Yoshikazu Furuta Grad. Sch. of Frontier Sci, U Tokyo

C-5-13

 Site-specific Cellular Modification by Cre-incorporating Integrase-defective Retroviral Vectors Takuya Shimomura Kyushu University

C-5-14

 Construction of artificial sensor to regulate gene　expression in the cyanobacterium Synechocystis sp. PCC 6803 Misaki Kawaguchi Graduate School of Life and Environmental Sciences

C-5-15

 Development of an ON/OFF-transcriptional control system for plural genes to express sequentially Yuri Samata Saitama University

C-5-16

 Which has a better chemotaxis controller, E. coli or Paramecium? Shun-ichi Azuma Kyoto University

C-5-17

 t-Riboregulator: Regulation of Nonsense Suppression by Modulating 3’ Processing of Suppressor tRNA Yasunori Doi Proteo-Science Center, Ehime University

C-5-18

 DNA Modification Enzymes Utilizing Sequence-Specificity of Zinc Finger Domains Wataru Nomura Tokyo Medical and Dental University

C-5-19

 Discovery of a Potent and Selective FLT3 Kinase Inhibitor by Fragment Evolution Hirofumi Nakano The University of Tokyo

C-5-20

 An approach to reconstruction of cell cycle oscillation of DnaA activity for replication initiation and transcription regulation Masayuki Suetsugu Dept. of Life Sci., Col. of Sci. Rikkyo Univ.

C-5-21

 Photodynamic Effect of Single-walled Carbon Nanotubes and its potential for cancer phototherapy Tatsuya Murakami Kyoto University

C-5-22

 Probabilistic Model Based Error Correction of Various Mutant Sequences Analyzed by the Single-Molecule Real-Time Sequencing Takuyo Aita Japan Science and Technology Agency

C-5-23

 Meta-synthetic metabolism: Identification of critical intermediates for synthetic amino acid derivative production Robert Sidney Cox III Kobe Univeristy

C-5-24

 A Cellular Automaton Approach for Modeling Chemical Reactions in Protein Synthesis Daichi Takata University of Hyogo

C-5-25

 Dynamical control of protein concentration using synthetic two-component system Akifumi Nishida Tokyo Institute of Technology

C-5-26

 Synthetic cellular membrane systems Tsutomu Hamada Japan Advanced Institute of Science ＆ Technology

C-5-27

 Molecular Evolution of a TALE Protein to Change DNA Binding Manner Miki Imanishi Institute for Chemical Research, Kyoto University

C-5-28

 A Magnetically Triggered Gene Expression System Mediated by Heating of Nanoparticles Masaki Yamaguchi Kyushu University

C-5-29

 A combinatorial library of enzymes for anthocyanin biosynthesis toward designing of an artificial anthocyanin operon Takeshi Yoshizumi Institute for Advanced Biosciences, Keio University

C-5-30

 Mathematical modeling and theoretical analysis for the quantitative control of the target gene expression of synthetic genetic circuit Yuki Soma Kyushu University

C-5-31

 Synthetic analysis of the effect of parameter balance on phenotypic stabilities in a synthetic mutual inhibitory network Ryoji Sekine Tokyo Institute of Technology

C-5-32

 Theophylline-dependent Riboswitch as a Useful Genetic Tool for Synthetic Biology in Cyanobacteria Yoichi Nakahira Venture Business Laboratory, Ehime University

C-5-33

 Automatic Design with Frequency Characteristics for Synthetic Gene Oscillators Takafumi Hayashi Tokyo Institute of Technology

C-5-34

 RNA-protein complexes for designing functional nanostructured molecules Yoshihiko Fujita Graduate School of Biostudies, Kyoto University

C-5-35

 Construction of a computational platform for metabolic pathway design Michihiro Araki Kobe University

C-5-36

 Highly parallel and sensitive method for analyzing　gene expression kinetics  Maasa Yokomori Dept. of Life Sci., Univ. of Tokyo

C-5-37

 A development of molecular sensor that delivers environmental information to inside of vesicle-based molecular robots Koh-ichiroh Shohda University of Tokyo

C-5-38

DNA computer-based rational construction of artificial genetic circuits in cell model vesicles containing cell-free protein synthesis system Takamasa Hasegawa Univ Tokyo, Dept Phys, Grad Sch Sci

C-5-39

 New Bottom-up Construction Strategy of Biomolecular Circuits Based on Dynamic Robustness Measure Masaki Inoue JST and Tokyo Institute of Technology

C-5-40

 iGEM 2013 Team Tokyo Tech Project: Mutant Ninja Coli Daisuke Kiga Tokyo Institute of Technology

C-5-41

 Construction and functional analysis of DNA origami base DNA-RNAP hybrid nanomachine Takeya Masubuchi Grad. Sch. Frontier Sci., Univ. Tokyo

C-5-42

 Heat-induced Morphological Transformation of Supramolecular Nanostructures Masato Ikeda Gifu University

C-5-43

 Towards an Automatic Recognition of DNA Nanostructures on AFM images Yuexing Han Tokyo Institute of Technology

C-5-44

 Simple Local-information-based Self-optimizing Algorithms in Grid Networks Fukuhito Ooshita Osaka University

C-5-45

 A Study on pH-Responsive Photosensitizers for Potential Applications in Molecular Robotics Takuya Terai The University of Tokyo

C-5-46

 Acceleration of DNA strand exchange reaction by cationic comb-type copolymers Naohiko Shimada Tokyo Institute of Technology

C-5-47

 A study on controller structure of biochemical reaction networks Takashi Nakakuki Kyushu Institute of Technology

C-5-48

 Toward Spatial and Temporal Gel-Sol Transition of Hydrogel Driven by DNA Hybridization Reaction Ibuki Kawamata The University of Tokyo

C-5-49

 Science Communication in DNA nano-engineering Satoru Yoshizawa Graduate school of Engineering, Tohoku University

C-5-50

 Spatio-temporal change of BZ gel Hiroyuki Mayama Asahikawa Medical University

C-5-51

 Construction of Giant Vesicle Containing Microspheres at High Volume Fraction and Its Transformation Taro Toyota The University of Tokyo

C-5-52

 Reversible Gel-Sol Transition of DNA Gel Daisuke Kandatsu Tohoku University

C-5-53

 Smart Lenses Created with Transparent Shape Memory Gels Jin Gong Yamagata University

C-5-54

 Chain-Reactive Molecular Releasing System BIOMOD TeamSendai School of Engineering, Tohoku University

C-5-55

 Dynamic biomolecular computing system for artificial genetic network Takashi Nukada Department of Life Sciences, The Univ. of Tokyo

C-5-56

 Towards Persistent Molecular Computers for Molecular Robots Masami Hagiya University of Tokyo

C-5-57

 A Computing Model for Biochemical Reactions Fumiya Okubo Waseda University

C-5-58

 Progress in the Enumeration Approach to Computing Equilibrium of Interacting Nucleic Acid Strands Satoshi Kobayashi University of Electro-Communications

C-5-59

 Modeling and Simulation of self oscillating gel - toward a molecular gel robot Hiroshi Morita AIST

C-5-60

 Numerical studies of protein-induced shape changes of liposomes Tamiki Umeda Kobe University

C-5-61

 Robustness Criteria of Hybridization of double-stranded DNA Sequences Hirotaka Ono Kyushu University

C-5-62

 Recapitulation of the hepatic function using in vitro liver model from murine ES/iPS cells Miho Tamai Tokyo Institute of Technology

C-5-63

 A Design Method of Artificial Genetic Circuits on Effective Search of These Logical Structures Manabu Sugii Yamaguchi University

C-5-64

 Identification of Key Regulators in Glycogen Utilization in E. coli Based on the Simulations from a Hybrid Functional Petri Net Model Zhongyuan Tian Yamaguchi University

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