This is old site. The new site is here. †
Kana Shimizu †
Senior Research Scientist of National Institute of Advanced Industrial Science and Technology (AIST)
Postal Address: 135-0064, 2-4-7 Aomi Koto-ku Tokyo Japan
Contact: shimizu-kana at aist.go.jp †
Key words †
Biological sequence analyses, Next-generation sequencing data analyses, Algorithm, Machine learning, Privacy-preserving data-mining
清水 佳奈 †
産業技術総合研究所 主任研究員
住所: 〒135-0064, 東京都江東区青海2-4-7
Upcoming Events †
We will organize Privacy-aware computational genomics (PRIVAGEN 2015)
: An official satellite workshop of GIW/InCoB 2015 focusing on privacy-aware technologies that assist computational genomics, aiming to facilitate discussion among researchers in diverse fields including bioinformatics, genome ethics, machine learning, data-mining and cryptography.
Softwares †
SLIDESORT †

Link †
Home site
Executable binaries and C++ libraries: †
For Windows PC, Linux PC with intel 64bit
Reference †
Shimizu K, Tsuda K, SlideSort: All pairs similarity search for short reads. Bioinformatics (2011) 27 (4): 464-470. (pubmed link)
ANGLE †

Download †
The following programs are used under BSD lisence.
Reference †
- 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
POODLE †

Link †
Web server
Reference †
- 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, 2337-8
- 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
- Shimizu, K., Hirose, S., Inoue, N., Kanai, S., and Noguchi, T. (2006) POODLE: predicting protein disorder using machine-learning approaches. In Proceedings of CASP7 pp. 22-23
(Our team was invited to CASP7 meeting as a discussion panelist of disorder prediction.)