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  • 誌上発表・査読有り：2007年

論　文（誌上発表・査読有り：2007年）

  • Shimizu, K., Noguchi, T.: "Analysis of intrinsic protein disorder in human genome", The proceedings of the 2007 annual conference of the japanese society for bioinformatics, (2007).
  • Motono, C., Gromiha, MM., Kumar, S.: "A Structural and Dynamic Analysis of Hyperthermophilic Cold Shock Protein Stability", The proceedings of the 2007 annual conference of the Japanese society for bioinformatics, pp.P091-2(2007).
  • Gromiha MM, Suwa M.: "Computational analysis on beta-barrel Membrane Protein Sequences and Structures: Genome-wide Applications", Proc. Annual Meeting of CBRC, pp.12-15(2007).
  • Steinke, F., Seeger, M., Tsuda, K.: "Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models", BMC Systems Biology, 1(51), pp.1-15(2009). ■PubMed ■Full Text Paper(PDF) on the Journal Website.
  • Frith MC, Carninci P, Kai C, Kawai J, Bailey TL, Hayashizaki Y, Mattick JS.: "Splicing bypasses 3' end formation signals to allow complex gene architectures.", GENE, 403(1-2), pp.188-193(2007). ■PubMed
  • Nowozin, S., Bakir, G., Tsuda, K.: "Discriminative Subsequence Mining for Action Classification". Proceedings of the 2007 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, (2007). ■PDF
  • Okada, Y., Ohkubo, K., Horton, P., Fujibuchi, W.: "Exhaustive Search Method of Gene Expression Modules and Its Application to Human Tissue Data, IAENG International Journal of Computer Science, 34(1) , pp.119-126(2007).
  • Iwaya,N., Akiyama,K., Unzai,S., Tomii,K.,Goda,N., Tochio,H., Shirakawa,M.,Hiroaki,H.: "Structure and function of the MIT-domain variant isolated from katanin p60, a microtubule severing enzyme", FEBS workshop: the biology of modular protein domains abstract book, p.81(2007).
  • Hirose S, Shimizu K, Kanai S, Kuroda Y, Noguchi T.: "POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions.", Bioinformatics, 23(16), pp.2046-2053(2007).
    ■PubMed
  • Saigo, H., Uno, T., Tsuda, K.: "Mining complex genotypic features for predicting HIV-1 drug resistance", Bioinformatics, 23, Issue 18, pp.2455-2462(2007). ■Full Text Paper on the Journal Website.
  • Kiryu, H., Tabei, Y., Kin, T., Asai, K.: "Murlet: a practical multiple alignment tool for structural RNA sequences.", BIOINFORMATICS, 23(13), pp.1588-1598(2007). ■PubMed
  • Tominaga, D., Horimoto, K.: "Judgment algorithm for detection of periodicity and its application", Proceedings of the 3rd Moscow Conference on Computational Molecular Biology, pp.p.296(2007).
  • Fujibuchi W, Kato T.: "Classification of heterogeneous microarray data by maximum entropy kernel.", BMC BIOINFORMATICS, 8(267), (2007). ■ジャーナルサイトのFull Text Paper(PDF)/閲覧にはオンラインジャーナルの契約等が必要です。
  • Nowozin, S., Tsuda, K., Uno, T., Kudo, T., Bakir, G.: "Weighted Substructure Mining for Image Analysis", Proceedings of the 2007 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. (2007). ■Abstract on the Journal Website.■PDF
  • Tsuda, K.: "Entire Regularization Paths for Graph Data", Proceedings of the 24th International Conference on Machine Learning, pp.919-926(2007). ■Full Text Paper on The International Machine Learning Society Website.
  • Horton, P., Park, K. J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier CJ, Nakai, K.: "WoLF PSORT: Protein Localization Predictor", Nucleic Acids Research, 35, pp.585-587(2007). ■PubMed ■Full Text Paper on the Journal Website.
  • Ide, T., Tsuda, K.: "Change-Point Detection using Krylov Subspace Learning", Proceedings of the SIAM International Conference on Data Mining, pp.515-520(2007). ■Full Text Paper(PDF) on the Conference Website.
  • Seeger, M., Steinke, F., Tsuda, K.: "Bayesian Inference and Optimal Design in the Sparse Linear Model", Proceedings of the 11th International Conference on Artificial Intelligence and Statistics, pp.444-451(2007). ■Full Text Paper(PDF) on the Journal Website.
  • Kin, T., Yamada, K., Terai, G., Okida, H., Yoshinari, Y., Ono, Y., Kojima, A., Kimura, Y., Komori, T., Asai, K.: "fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences" NUCLEIC ACIDS RESEARCH, 35（Database Issue ）, pp.D145-148(2007). ■PubMed
  • Okada, Y., Horton, P., Fujibuchi, W.: "SAMURAI: a tool for gene expression module mining", The Proc. of the 2007 Annual Conference of the Japanese Society for Bioinformatics, (2007).
  • Gromiha, M.M.: "Prediction of protein stability upon point mutation", Proc. 2007 Annual Conf. JSBi, 35(6), pp.1569-73(2007).
  • Gromiha, M.M., Motono. C., Kumar, S.: "A structural and dynamic analysis of hyperthermophilic cold shock protein stability", Proc. Annual conference on JSBi, (2007).
  • Hourai, Y.: "Upgrade of 3D-Convolution Library CONV3D for Faster Docking", JSBi2007, (2007).
  • 広川 貴次: "膜タンパク質と低分子有機化合物のドッキング", YAKUGAKU ZASSHI, 127(1), pp.123-131(2007). ■ジャーナルサイトのFull Text Paper(PDF)
  • Nukada, A., Hourai, Y., Nishida, A., Akiyama, A.: "High Performance 3D Convolution for Protein Docking on IBM Blue Gene", Lecture Notes in Computer Science, 4742, pp.958-969(2007). ■ジャーナルサイトのFull Text Paper(PDF)/閲覧にはオンラインジャーナルの契約等が必要です。
  • Nakazawa, M., Takada, M., Yokota, K., Sekijima, M., Noguchi, M., Joe, K.: "Development of SVM based Prediction System for Metalbinding Sites in Protein", Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007) , CSREA Press, 135, pp.157-164(2007).
  • Nagano, N., Nakagawa, Y., Arita, M., Ttsukamoto, H., Noguchi, N.: "EzCatDB", Nucleic Acids Research, 613, (2007). ■Nucleic Acids Research
  • 澤井 政宏, 岡田 吉史, 長島 知正: "Web上の評価文書を用いた嗜好記述システムと構築手法の提案", 日本感性工学会研究論文集, 7(1), pp.127-135(2007).
  • Gromiha, M.M., Yabuki, Y., Suwa,: "TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences", Journal of Chemical Information and Modeling, 47, pp.2456-2461(2007). ■PubMed
  • Gromiha, M.M., Kumar, M., Raghava, PG.: "Identification of DNA-binding proteins using support vector machines and evolutionary profiles", BMC BIOINFORMATICS, 8(463), pp.1-10(2007). ■ジャーナルサイトのFull Text Paper(PDF)
  • Gromiha, M.M., Taguchi, Y.: "Protein Fold Recongnition based upon the Amino Acid Occurrence", Lecture notes in Bioinformatics, 4774, pp.120-131(2007).
  • Usui, T., Ban, HS., Kawada, J., Hirokawa, T., Nakamura, H.: "Discovery of indenopyrazoles as EGFR and VEGFR-2 tyrosine kinase inhibitors by in silico high-throughput screening.", BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 18, pp.285-288(2007). ■PubMed
  • Tominaga, D., Iguchi, F., Akiyama, Y., Horimoto, K.: "Development of automated image processing procedure for cell-arrays", The 11th World Multi-Conference on Systemics, Cybernetics and Informatics Proceedings, 4, pp.19-24(2007).
  • Tominaga, D., Horimoto, K.: "Symbolic approach for dynamical analysis of biological network modules", The 11th World Multi-Conference on Systemics, Cybernetics and Informatics Proceedings, 4, pp.25-29(2007).
  • Tominaga, D., Iguchi, F., Akiyama, Y., Horimoto, K.: "High-throughput Automated Image Processing System for Cell Array Observations", IPSJ Transactions on Bioinformatics, 48(17-3), pp.1-7(2007).
  • Gromiha, MM.,Suwa, M.: "Current developments on beta-barrel membrane proteins: sequence and structure analysis, discrimination and prediction", CURRENT PROTEIN & PEPTIDE SCIENCE, 8(6), pp.580-599(2007).
  • Gromiha, M.M.: "Prediction of protein stability upon point mutations", BIOCHEMICAL SOCIETY TRANSACTIONS, 35(6), pp.1569-1573 (2007). ■PubMed
  • Okada, Y., Okubo, K., Horton, P., Fujibuchi, W.: "Exhaustive Search Method of Gene Expression Modules and Its Application to Human Tissue Data", IAENG International Journal of Computer Science, 34(1), pp.119-126(2007). ■Full Text Paper(PDF)
  • Terai, G., Komori, T., Asai, K., Kin, T.: "miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity.", RNA-A PUBLICATION OF THE RNA SOCIETY, 13(12), pp.2081-2090(2007). ■ジャーナルサイトのFull Text Paper(PDF)
  • 藤 博幸, 富井 健太郎: "タンパク質の配列および立体構造の類似性を解析するための手法の概説", 生物物理学ハンドブック,
  • Horton, P., Park, KJ., Obayashi, T., Nakai, K.: "Protein Subcellular Localization Prediction with WoLF PSORT", Proceedings Asian Pacific Bioinformatics Conference APBC06, pp.39-48(2007). ■Full text paper(PDF)
  • Shimizu, K., Hirose, S., Noguchi, T.: "POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.", Bioinformatics, 23(17), pp.2337-2338(2007). ■PubMed
  • 野口 保: "タンパク質disorder領域予測法の最前線", 生物物理, 47(4), pp.248-252, (2007).
  • Fujibuchi, W., Kiseleva, L., Taniguchi, T., Harada, H., Horton, P.: "CellMontage: similar expression profile search server.", BIOINFORMATICS, 23(22), pp.3103-3104(2007). ■ジャーナルサイトのFull Text Paper(PDF)
  • Kin, T., Ono, Y:. "Idiographica: a general-purpose web application to build idio-grams on-demand for human, mouse and rat ", BIOINFORMATICS, 23(21), pp.2945-2946(2007). ■ジャーナルサイトのFull Text Paper(PDF)
  • 関嶋 政和, 本田 真也, 野口 保: "超並列計算機を用いた生体分子解析　─疾病関連蛋白質解析と世界最小蛋白質設計への応用─", 次世代スーパーコンピューティング・シンポジウム2007予稿集, pp.31-32(2007). ■PDF(248KB)
  • Gromiha, MM.: "Bioinformatics on beta-barrel Membrane Proteins: Sequence and Structural Analysis, Discrimination and Prediction", LECTURE NOTES IN COMPUTER SCIENCE, 4774, pp.148-157(2007).
  • Huang, LT., Gromiha, MM., Ho, SY.: "Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model.", JOURNAL OF MOLECULAR MODELING, 13(8), pp.879-890(2007).
  • Parthiban, V., Gromiha, MM., Abhinandan M, Schomburg D.: "Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development.", BMC STRUCTURAL BIOLOGY, 7(54), pp.54(2007). ■ジャーナルサイトのFull Text Paper(PDF)
  • 長野 希美: "酵素触媒機構データベース：EzCatDB　−加水分解反応、転移反応機構の系統的な比較について", 生物物理, 47(5), pp.323-327(2007).
  • Taguchi, YH., Gromiha, MM.: "Application of amino acid occurrence for discriminating different folding types of globular proteins", BMC BIOINFORMATICS, 8(1), pp.404(2007). ■Full Text Paper on Journal Site(PDF)
  • Sakakibara, Y., Popendorf, K., Ogawa, N., Asai, K., Sato, K.: "Stem kernels for RNA sequence analyses.", JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5(5), pp.1103-1122(2007). ■PubMed
  • Osato, N., Suzuki, Y., Ikeo, K., Gojobori, T.: "Transcriptional interferences in cis natural antisense transcripts of humans and mice", The Proceedings of the 2007 Annual Conference of the Japanese Society for Bioinformatics, 176(2), pp.1299-1306(2007). ■PubMed
  • Fujibuchi, W., Okada, Y., Horton, P.: "Global and Local Similarity Searches of Gene Expression Data", The Proceedings of the 2007 Annual Conference of the Japanese Society for Bioinformatics, pp.33-34(2007).
  • Okada, Y., Fujibuchi, W.: "Mining a Large-scale Microarray Database for Similar Gene Expression Modules to Find Distant Relationships between Down Syndrome and Huntington's Disease", Critical Assessment of Microarray Analysis Conference, Valencia, Proceedings, (2007).
  • Sekijima, M., Doi, A., Honda, S., Nogudhi, T., Shimizu, K., Akiyama, Y.: "Development of Free Energy Landscape Analysis System based on Parallel Molecular Dynamics Simulation", IPSJ Transactions on Bioinformatics, 48(17), pp.30-39(2007).
  • Okada, Y., fujibuchi, W., Horton, P.: "A Biclustering Method for Gene Expression Module Discovery Using a Closed Itemset Enumeration Algorithm". IPSJ Transactions on Bioinformatics, 48(SIG5), pp.183-192(2007). ■ジャーナルサイトのFull Text Paper(PDF)
  • 榊原 康文, 佐藤 健吾: "機能性RNAの配列解析と構造解析". 人工知能学会誌, 22(1), pp.54-62(2007)
  • Mukai, Y., Hirokawa, T., Tomii, K., Asai, K., Akiyama, Y., Suwa, M.: "Identification of glycosyltransferases focusing on Golgi transmembrane region", Trends In Glycoscience And Glycotechnology, 19(105), pp.41-47(2007).
  • Hirokawa, T.: "Receptor-ligand docking simulation for membrane proteins", Yakugaku Zasshi-Journal Of The Pharmaceutical Society Of Japan, 127(1), pp.123-131(2007). ■PubMed
  • Kimura, S., Sekijima, M., Takada, M., Noguchi, M., Joe, K.: "Development of Molecular Dynamics Simulation based Flexible Docking System", Proceedings of the 2007 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007), pp.732-745(2007).
  • Sasaki, M., Sekijima, M., Takada, M., Joe, K.: "Optimization of Molecular Dynamics Simulation on Cell Processor", Proceedings of the 2007 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007), pp.780-783(2007).
  • Sakakibara, Y., Asai, K., Sato, K.: "Stem Kernels for RNA Sequence Analyses", Lecture Notes in Bioinformatics, 4414, pp.278-291(2007).
  • Okada, Y., Fujibuchi, W., Horton, P.: "Exhaustive search of maximal biclusters in gene expression data", Proceedings of IAENG International Conference on Computer Science (ICCS'07), Lecture Notes in Engineering and Computer Science, 2(1), pp.307-312(2007). ■ジャーナルサイトのFull Text Paper(PDF)
  • 小野田 崇, 村田 博士, 山名 美智子:"腕金再利用自動判定システムの開発". 人工知能学会全国大会(第21回)論文集, 1E1-1, pp.1-2(2007).
  • 村田 博士, 山名 美智子, 小野田 崇:"計算機と人間との協調作業による事例データベース構築の省力化", 人工知能学会全国大会(第21回)論文集, 1E1-5, pp. 1-4(2007).
  • Doi, J., Shimizu, K., Sekijima, M.: "High-Density Surface Reconstruction of Fine Arts and Documents for Complete Reproduction and Counterfeit Detection", Proceedings of the 2007 IEEE International Conference on Networking, Sensing and Control (ICNSC2007), pp.392-397(2007). ■ジャーナルサイトのFull Text Paper(PDF)/閲覧にはオンラインジャーナルの契約等が必要です。
  • Huang, LT., Gromiha, MM, Ho, SY.: "iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations", Bioinformatics, 23(10), pp.1292-1293(2007). ■ジャーナルサイトのFull Text Paper(PDF)
  • Tashiro, T., Nakagawa, R., Hirokawa, T., Inoue, H., Watarai, H., Taniguchi, M., Mori, K.: "RCAI-56, a carbocyclic analogue of KRN7000: its synthesis and potent activity for natural killer (NK) T cells to preferentially produce interferon-γ", Tetrahedron Letters, 48(19), pp.3343-3347(2007). ■ジャーナルのFull Text Paper(PDF)／閲覧にはオンラインジャーナルの契約等が必要です。
  • 福田 賢一郎: "BioPAX: パスウェイデータフォーマットの標準化とオントロジー ", 生物物理, 47(3), pp.179-84(2007). ■ジャーナルのFull Text Paper(PDF)／どなたでもご覧になれます。
  • 富井 健太郎: "膜タンパク質のホモロジーモデリング", ファルマシア, 43(4), pp.353-354(2007).
  • 廣明 秀一, 塩澤 久美子, 富井 健太郎: "ペルオキシソーム因子PEX1 ATPaseのN末端ドメインの立体構造が示したAAA ATPase間の進化的類縁関係", 日本生物物理学会, 46(3), pp.159-163(2007). ■CiNiiのFull Text Paper(PDF)／どなたでもご覧になれます。
  • 富井 健太郎: "プロファイル比較に基づくタンパク質立体構造類似性検索技術とその立体構造予測への応用", 日本物理學會誌, 62(1), pp.39-42(2007). ■CiNiiのFull Text Paper(PDF)／閲覧にはオンラインジャーナルの契約等が必要です。
  • Shimizu, K., Muraoka, Y., Hirose, S., Tomii, K., Noguchi, T.: "Predicting mostly disordered proteins by using structure-unknown protein data Predicting mostly", BMC Bioinformatics, 8(78), (2007). ■ジャーナルサイトのFull Text Paper(PDF)/どなたでもご覧になれます。 ■PubMed
  • Kin, T., Yamada, K., Terai, G., Okida, H., Yoshinari, Y., Ono, Y., Kojima, A., Kimura, Y., Komori, T., Asai, K.: "fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences", Nucleic Acids Res, 35(Database issue), pp.D145-D148(2007). ■ジャーナルサイトのFull Text Paper(PDF)／どなたでもご覧になれます。 ■PubMed
  • 福田 賢一郎: "生命科学におけるオントロジーとその利用", 人工知能学会誌, 22(1), pp.70-76(2007).
  • Iwaya, N., Goda, N., Unzai, S., Fujiwara, K., Tanaka, T., Tomii, K., Tochio, H., Shirakawa, M., Hiroaki, H.: "Fine-tuning of protein domain boundary by minimizing potential coiled coil regions", Journal of Biomolecular NMR, 37(1), pp.53-63(2007). ■ジャーナルサイトのFull Text Paper(PDF)／どなたでもご覧になれます。 ■PubMed
  • Sekijima, M., Doi, J., Noguchi, T., Akiyama, Y., Shimizu, S.: "Optimization and Evaluation of Parallel Molecular Dynamics Simulation on Blue Gene/L", Proceedings of the 25th IASTED International Conference on Parallel and Distributed Computing and Networks, pp.257-262(2007).
  • Gromiha, M.M., Yabuki, Y., Kundu, S., Suharnan, S., Suwa, M.: "TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences", Nucleic Acids Research, 35(Database issue), pp.D314-D316(2007). ■ジャーナルサイトのFull Text Paper(PDF)／どなたでもご覧になれます。 ■PubMed
  • Huang, L.T., Saraboji, K., Ho, S.Y., Hwang, S.F., Ponnuswamy, M.N., Gromiha, M.M.: "Prediction of protein mutant stability using classification and regression tool", Biophysical Chemistry, 125(2-3), pp.462-470(2007). ■ジャーナルサイトのFull Text Paper(PDF)/閲覧にはオンラインジャーナルの契約等が必要です。 ■PubMed
  • Parthiban, V., Gromiha, M.M., Hoppe, C., Schomburg, D.: "Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility", Proteins: Structure, Function, and Bioinformatics, 66(1), pp.41-52(2007). ■ジャーナルサイトのFull Text Paper(PDF)／どなたでもご覧になれます。 ■PubMed
  • Nagano, N., Noguchi, N., Akiyama, Y.: "Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database", PROTEINS: Structure, Function, and Bioinformatics, 66(1), pp.147-159(2007). ■ジャーナルサイトのFull Text Paper(PDF)／どなたでもご覧になれます。 ■PubMed
  • Fukuda, K., Yamamoto, S., Sakai, N., Nakanishi, Y., Nakamura, H., Takagi, T.: "Graphical Syntax and Query for Pathway Database", The 10th World Multi-Conference on Systemics, Cybernetics and Infrmatics, pp.7-10(2007).
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