Kana Shimizu's web site

LINKS

• SLIDESORT
• CBRC
• AIST
• YEAR OF CAT

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 †

Publication List , CV †

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.

• For Linux PC 64bit
• For Linux PC source for training
• For Linux PC source
• For windows PC (Comming soon)

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.)