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** Kana Shimizu [#l679ade8]
Research Scientist of Computational Biology Research Center [[(CBRC):http://www.cbrc.jp]], National Institute of Advanced Industrial Science and Technology [[(AIST):http://www.aist.go.jp]], RNA informatics Team
Visiting Associate Professor of [[Waseda University:http://www.waseda.ac.jp]] (Additional Post)
Postal Address: 135-0064, 2-4-7 Aomi Koto-ku Tokyo Japan
*** Contact: shimizu-kana at aist.go.jp [#d8d8836b]
***[[Publication List]] , [[CV:http://www.cbrc.jp/~shimizu/CV.html]], [[Research Interests]] [#ta578ee3]
*** Key words [#va126907]
Biological sequence analyses, Next-generation sequencing data analyses, Algorithm,Machine learning, Privacy-preserving data-mining
-----------
**清水 佳奈 [#b333d17d]
産業技術総合研究所 生命情報工学研究センター RNA情報工学チーム 研究員
早稲田大学理工学術院 客員准教授 （併任）
住所: 〒135-0064, 東京都江東区青海2-4-7
~
~
**Softwares [#h9073c4d]
*SLIDESORT [#s3e415b3]
[[&ref(sslogo.png,,20%);>http://www.cbrc.jp/~shimizu/slidesort]]
***Link [#h413666e]
[[Home site:http://www.cbrc.jp/~shimizu/slidesort/]]
***Executable binaries and C++ libraries: [#ja622f69]
[[For Windows PC, Linux PC with intel 64bit :http://www.cbrc.jp/~shimizu/slidesort/index.php?Download]]
***Reference [#v9d77969]
Shimizu K, Tsuda K, SlideSort: All pairs similarity search for short reads. Bioinformatics (2011) 27 (4): 464-470. [[(pubmed link):http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035798/]]
*ANGLE [#t11a427e]
&ref(angle.jpg,,100%);
***Download [#zddbe95d]
-[[For Linux PC 64bit:http://www.cbrc.jp/~shimizu/soft/ANGLE-UNIX-STATIC.TGZ]]
-For windows PC (Comming soon)
***Reference [#dbb89f98]
-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 [#p629a4dd]
[[&ref(poodle.png,,100%);>http://mbs.cbrc.jp/poodle/]]
***Link [#u132646d]
[[Web server:http://mbs.cbrc.jp/poodle/]]
***Reference [#e23c8930]
-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.)
End:
** Kana Shimizu [#l679ade8]
Research Scientist of Computational Biology Research Center [[(CBRC):http://www.cbrc.jp]], National Institute of Advanced Industrial Science and Technology [[(AIST):http://www.aist.go.jp]], RNA informatics Team
Visiting Associate Professor of [[Waseda University:http://www.waseda.ac.jp]] (Additional Post)
Postal Address: 135-0064, 2-4-7 Aomi Koto-ku Tokyo Japan
*** Contact: shimizu-kana at aist.go.jp [#d8d8836b]
***[[Publication List]] , [[CV:http://www.cbrc.jp/~shimizu/CV.html]], [[Research Interests]] [#ta578ee3]
*** Key words [#va126907]
Biological sequence analyses, Next-generation sequencing data analyses, Algorithm,Machine learning, Privacy-preserving data-mining
-----------
**清水 佳奈 [#b333d17d]
産業技術総合研究所 生命情報工学研究センター RNA情報工学チーム 研究員
早稲田大学理工学術院 客員准教授 （併任）
住所: 〒135-0064, 東京都江東区青海2-4-7
~
~
**Softwares [#h9073c4d]
*SLIDESORT [#s3e415b3]
[[&ref(sslogo.png,,20%);>http://www.cbrc.jp/~shimizu/slidesort]]
***Link [#h413666e]
[[Home site:http://www.cbrc.jp/~shimizu/slidesort/]]
***Executable binaries and C++ libraries: [#ja622f69]
[[For Windows PC, Linux PC with intel 64bit :http://www.cbrc.jp/~shimizu/slidesort/index.php?Download]]
***Reference [#v9d77969]
Shimizu K, Tsuda K, SlideSort: All pairs similarity search for short reads. Bioinformatics (2011) 27 (4): 464-470. [[(pubmed link):http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035798/]]
*ANGLE [#t11a427e]
&ref(angle.jpg,,100%);
***Download [#zddbe95d]
-[[For Linux PC 64bit:http://www.cbrc.jp/~shimizu/soft/ANGLE-UNIX-STATIC.TGZ]]
-For windows PC (Comming soon)
***Reference [#dbb89f98]
-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 [#p629a4dd]
[[&ref(poodle.png,,100%);>http://mbs.cbrc.jp/poodle/]]
***Link [#u132646d]
[[Web server:http://mbs.cbrc.jp/poodle/]]
***Reference [#e23c8930]
-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.)
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