Publication List

Refereed Journal Articles

Wijaya E, Shimizu K, Asai K, Hamada M, Reference-free Prediction of Rearrangement Breakpoint Reads. Bioinformatics, 2014: 27 (18): 2559-2567. (pubmed)

Ito JI., Tabei Y., Shimizu K., Tsuda K., Tomii K. (2012) PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res 2012 Database issue (pubmed)

Ito JI., Tabei Y., Shimizu K., Tomii K., Tsuda K. (2011) PDB-scale analysis of known and putative ligand-binding sites with structural sketches. Proteins (pubmed)

Shimizu K. and Tsuda K. (2011) SlideSort: All pairs similarity search for short reads. Bioinformatics 27 (4): 464-470 (pubmed)

Motono C., Nakata J., Koike R., Shimizu K., Shirota M., Amemiya T., Tomii K., Nagano N., Sakaya N., Misoo K., Sato M., Kidera A., Hiroaki H., Shirai T., Kinoshita K., Noguchi T., Ota M. (2011) SAHG, a comprehensive database of predicted structures of all human proteins. Nucleic Acids Res 2011 Database issue: D487-93 (pubmed)

Hirose, S., Shimizu, K., Noguchi, T. (2010) POODLE-I: Disordered region prediction by integrating POODLE series and structural information predictors based on a workflow approach. In Silico Biology 10, 0015 (published online)

Shimizu, K., and Toh, H. (2009) Interaction between intrinsically disordered proteins frequently occurs in a human protein-protein interaction network. Journal of Molecular Biology, 392(5), 1253-1265 (Selected by Faculty of 1000 Biology) (pubmed)

Shimizu, K., Hirose, S., and Noguchi, T. (2007) 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, 2337-2338 (pubmed)

Hirose, S., Shimizu, K., Kanai, S., Kuroda, Y., and Noguchi, T. (2007) POODLE-L: A Two-level SVM Prediction System for Reliably Predicting Long Disordered Regions. Bioinformatics, 23, 2046-2053 (pubmed)

Shimizu, K., Muraoka, Y., Hirose, S., Tomii, K., and Noguchi, T. (2007) Predicting mostly disordered proteins by using structure-unknown protein data. BMC Bioinformatics 8, 78 (pubmed)

Shimizu, K., Adachi, J., and Muraoka, Y. (2006) ANGLE: a sequencing errors resistant program for predicting protein coding regions in unfinished cDNA. J Bioinform Comput Biol 4, 649-664 (pubmed)

Refereed Conference Proceedings

Shimizu, K., Muraoka, Y., Hirose, S., and Noguchi, T. (2005) Feature Selection Based on Physicochemical Properties of Redefined N-term Region and C-term Regions for Predicting Disorder. In Proceedings of 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology pp. 262-267

Sonoda, T., Ikenaga, T., Shimizu, K., and Muraoka, Y. (2002) THE DESIGN METHOD OF MELODY RETRIEVAL SYSTEM ON PARALLEL-ZIED COMPUTERS. In Proceedings of Web Delivering of Music 2002 pp. 66-73

Sonoda, T., Ikenaga, T., Shimizu, K., and Muraoka, Y. (2002) A melody retrieval system on parallelized computers. In Proceedings of International Workshop on Entertainment Computing 2002 pp. 265-272

Shimizu, K., Adachi, J., Hayashizaki, Y., and Muraoka, Y. (2002) Using Boosting to predict the protein coding region in cDNA with frame-shift errors. In Proceedings of The 2002 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Science

Preprints

Shimizu K, Nuida K, Arai H, Mitsunari S, Hamada M, Tsuda K, Sakuma J, Hirokawa T, Hanaoka G, Asai K, Privacy-preserving similarity search for chemical compound databases. (link to bioRxiv)

Shimizu K, Nuida K, Rätsch G, Efficient Privacy-Preserving String Search and an Application in Genomics. (link to bioRxiv)

Invited book chapter

Shimizu K, POODLE: tools predicting intrinsically disordered regions of amino acid sequence. Protein Structure Prediction 3rd Edition. Springer, 2014, 1137:131-45

Patents

Shimizu K , Hirokawa T, Tsuda K, Arai H, Sakuma J, Asai K, Hamada M, Hanaoka G, Nuida, K, Search System, Search Method and Program. Priority 2011-9-14, WO Patent 2013038698

Shimizu K, Tsuda, K, Japanese Patent 2010-156342

Invited talks

Shimizu K, Arai H, Nuida K, Hamada M, Tsuda K, Sakuma J, Hirokawa T, Hanaoka G, Asai K, Privacy-preserving search for a chemical compound database. ISMB/ECCB 2013 Oral Poster Presentations Track, Berlin Germany, July 21, 2013

Shimizu K, Next generation sequencing data analyses by using ultra-fast all pairs similarity search. International Symposium on Single Biomolecule Analysis 2013, Kyoto Japan, Nov 2013

Other works (Selected)

Shimizu K, Privacy Preserving Similarity Search in Biomedical Data by Homomorphic encryption, Biological Data Science, Cold Spring Harbor, November 8, 2014

Shimizu K, Privacy-preserving search for a chemical compound database, ISCB-Asia/SCCG 2012, Shenzhen China, Dec 18, 2012

Shimizu, K, Tsuda K, (2011) SlideSort: Fast and exact algorithm for Next Generation Sequencing data analysis, Talk at ISMB 2011 Highlights Track.

Shimizu, K., Fukui, K., and Toh, H. (2009) Estimating the genome-wide preference of interaction between disordered proteins in a human protein-protein interaction network. the 17th International Conference on Intelligent Systems for Molecular Biology (ISMB 2009)

清水 佳奈, 福井 一彦, 藤 博幸 (2009) ヒトのタンパク質間相互作用ネットワークにおいてディスオーダー間の相互作用は頻繁に起きている 第九回日本蛋白質科学会年会 若手奨励賞シンポジウム

Hirose S, Shimizu K, Inoue N, Kanai S, Noguchi T (2008) Disordered region prediction by integrating POODLE series. In: Proceedings of the 8th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP8): 14-15.

清水佳奈 (2007) POODLE:タンパク質のディスオーダー予測. In: 医福研ニュース. vol. 186: 技術研究組合医療福祉機器研究所; 15-16.

Shimizu, K., Hirose, S., Inoue, N., Kanai, S., and Noguchi, T. (2006) POODLE: predicting protein disorder using machine-learning approaches. In Proceedings of the 7th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP7) pp. 22-23 (selected as one of the best methods at CASP7 competition)

Shimizu, K. (2006) Predicting protein disorder by a PSSM based method and a semi-supervised learning based method. In 3rd Student Addendum Conference to Critical Assessment of Techniques for Protein Structure Prediction (sac-CASP7)

Hirose, S., Shimizu, K., Kanai, S., and Noguchi, T. (2005) Prediction of Long Disorder Region Using Two-Step SVM. In Proceedings of the 16th International Conference on Genome Informatics (GIW 2005)

Shimizu, K., and Muraoka, Y. (2004) Predicting protein coding region in cDNA with frame shift errors using boosting based classifier. In Proceedings of the12th International Conference on Intelligent Systems for Molecular Biology (ISMB 2004) p. 165

Shimizu, K., Hirose, S., Noguchi, T., and Muraoka, Y. (2004) Predicting the protein disordered region using modified position specific scoring matrix. In Proceedings of the 15th International Conference on Genome Informatics (GIW 2004) p. 150

Shimizu, K., Hirose, S., and Noguchi, T. (2004) Predicting protein disordered regions using SVMs. In Proceedings of the 6th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP6) pp. 35-36

Noguchi, T., Hirose, S., Shimizu, K., and Kentaro, T. (2004) Prediction of disordered coil regions in proteins by threading and secondary structure prediction. In Proceedings of the 6th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP6) pp. 34-35


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Last-modified: 2015-05-22 (Fri) 05:19:28 (2184d)