Shimizu K - Search Results

1

Efficient privacy-preserving variable-length substring match for genome sequence.

Nakagawa Y, Ohata S, Shimizu K. Nakagawa Y, et al. Among authors: shimizu k. Algorithms Mol Biol. 2022 Apr 26;17(1):9. doi: 10.1186/s13015-022-00211-1. Algorithms Mol Biol. 2022. PMID: 35473587 Free PMC article.

2

Efficient privacy-preserving string search and an application in genomics.

Shimizu K, Nuida K, Rätsch G. Shimizu K, et al. Bioinformatics. 2016 Jun 1;32(11):1652-61. doi: 10.1093/bioinformatics/btw050. Epub 2016 Mar 2. Bioinformatics. 2016. PMID: 27153731 Free PMC article.

3

Interaction between intrinsically disordered proteins frequently occurs in a human protein-protein interaction network.

Shimizu K, Toh H. Shimizu K, et al. J Mol Biol. 2009 Oct 9;392(5):1253-65. doi: 10.1016/j.jmb.2009.07.088. Epub 2009 Aug 3. J Mol Biol. 2009. PMID: 19660471

4

POODLE: tools predicting intrinsically disordered regions of amino acid sequence.

Shimizu K. Shimizu K. Methods Mol Biol. 2014;1137:131-45. doi: 10.1007/978-1-4939-0366-5_10. Methods Mol Biol. 2014. PMID: 24573479

5

Discovery of Cryoprotective Activity in Human Genome-Derived Intrinsically Disordered Proteins.

Matsuo N, Goda N, Shimizu K, Fukuchi S, Ota M, Hiroaki H. Matsuo N, et al. Among authors: shimizu k. Int J Mol Sci. 2018 Jan 30;19(2):401. doi: 10.3390/ijms19020401. Int J Mol Sci. 2018. PMID: 29385704 Free PMC article.

6

SlideSort: all pairs similarity search for short reads.

Shimizu K, Tsuda K. Shimizu K, et al. Bioinformatics. 2011 Feb 15;27(4):464-70. doi: 10.1093/bioinformatics/btq677. Epub 2010 Dec 9. Bioinformatics. 2011. PMID: 21148542 Free PMC article.

Using an efficient pattern growth algorithm, SlideSort discovers chains of common k-mers to narrow down the search. Compared to existing methods based on single k-mers, our method is more effective in reducing the number of edit distance calculations. ...AVAILABILIT …

Using an efficient pattern growth algorithm, SlideSort discovers chains of common k-mers to narrow down the search. Compared to exist …

7

ANGLE: a sequencing errors resistant program for predicting protein coding regions in unfinished cDNA.

Shimizu K, Adachi J, Muraoka Y. Shimizu K, et al. J Bioinform Comput Biol. 2006 Jun;4(3):649-64. doi: 10.1142/s0219720006002260. J Bioinform Comput Biol. 2006. PMID: 16960968

8

A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR.

Goda N, Shimizu K, Kuwahara Y, Tenno T, Noguchi T, Ikegami T, Ota M, Hiroaki H. Goda N, et al. Among authors: shimizu k. Int J Mol Sci. 2015 Jul 10;16(7):15743-60. doi: 10.3390/ijms160715743. Int J Mol Sci. 2015. PMID: 26184172 Free PMC article.

9

Reference-free prediction of rearrangement breakpoint reads.

Wijaya E, Shimizu K, Asai K, Hamada M. Wijaya E, et al. Among authors: shimizu k. Bioinformatics. 2014 Sep 15;30(18):2559-67. doi: 10.1093/bioinformatics/btu360. Epub 2014 May 29. Bioinformatics. 2014. PMID: 24876376

10

Predicting mostly disordered proteins by using structure-unknown protein data.

Shimizu K, Muraoka Y, Hirose S, Tomii K, Noguchi T. Shimizu K, et al. BMC Bioinformatics. 2007 Mar 6;8:78. doi: 10.1186/1471-2105-8-78. BMC Bioinformatics. 2007. PMID: 17338828 Free PMC article.

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