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Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.

Okumura T, Makiguchi H, Makita Y, Yamashita R, Nakai K. Okumura T, et al. Among authors: makita y. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W227-31. doi: 10.1093/nar/gkm362. Epub 2007 May 30. Nucleic Acids Res. 2007. PMID: 17537821 Free PMC article.

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DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.

Makita Y, Nakao M, Ogasawara N, Nakai K. Makita Y, et al. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D75-7. doi: 10.1093/nar/gkh074. Nucleic Acids Res. 2004. PMID: 14681362 Free PMC article.

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PromoterCAD: Data-driven design of plant regulatory DNA.

Cox RS 3rd, Nishikata K, Shimoyama S, Yoshida Y, Matsui M, Makita Y, Toyoda T. Cox RS 3rd, et al. Among authors: makita y. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W569-74. doi: 10.1093/nar/gkt518. Epub 2013 Jun 12. Nucleic Acids Res. 2013. PMID: 23766287 Free PMC article.

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PosMed: Ranking genes and bioresources based on Semantic Web Association Study.

Makita Y, Kobayashi N, Yoshida Y, Doi K, Mochizuki Y, Nishikata K, Matsushima A, Takahashi S, Ishii M, Takatsuki T, Bhatia R, Khadbaatar Z, Watabe H, Masuya H, Toyoda T. Makita Y, et al. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W109-14. doi: 10.1093/nar/gkt474. Epub 2013 Jun 12. Nucleic Acids Res. 2013. PMID: 23761449 Free PMC article.

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OmicBrowse: a Flash-based high-performance graphics interface for genomic resources.

Matsushima A, Kobayashi N, Mochizuki Y, Ishii M, Kawaguchi S, Endo TA, Umetsu R, Makita Y, Toyoda T. Matsushima A, et al. Among authors: makita y. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W57-62. doi: 10.1093/nar/gkp404. Epub 2009 Jun 15. Nucleic Acids Res. 2009. PMID: 19528066 Free PMC article.

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PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning.

Yoshida Y, Makita Y, Heida N, Asano S, Matsushima A, Ishii M, Mochizuki Y, Masuya H, Wakana S, Kobayashi N, Toyoda T. Yoshida Y, et al. Among authors: makita y. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W147-52. doi: 10.1093/nar/gkp384. Epub 2009 May 25. Nucleic Acids Res. 2009. PMID: 19468046 Free PMC article.

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DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.

Sierro N, Makita Y, de Hoon M, Nakai K. Sierro N, et al. Among authors: makita y. Nucleic Acids Res. 2008 Jan;36(Database issue):D93-6. doi: 10.1093/nar/gkm910. Epub 2007 Oct 25. Nucleic Acids Res. 2008. PMID: 17962296 Free PMC article.

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Database construction for PromoterCAD: synthetic promoter design for mammals and plants.

Nishikata K, Cox RS 3rd, Shimoyama S, Yoshida Y, Matsui M, Makita Y, Toyoda T. Nishikata K, et al. Among authors: makita y. ACS Synth Biol. 2014 Mar 21;3(3):192-6. doi: 10.1021/sb400178c. Epub 2014 Jan 6. ACS Synth Biol. 2014. PMID: 24364365

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The RIKEN integrated database of mammals.

Masuya H, Makita Y, Kobayashi N, Nishikata K, Yoshida Y, Mochizuki Y, Doi K, Takatsuki T, Waki K, Tanaka N, Ishii M, Matsushima A, Takahashi S, Hijikata A, Kozaki K, Furuichi T, Kawaji H, Wakana S, Nakamura Y, Yoshiki A, Murata T, Fukami-Kobayashi K, Mohan S, Ohara O, Hayashizaki Y, Mizoguchi R, Obata Y, Toyoda T. Masuya H, et al. Among authors: makita y. Nucleic Acids Res. 2011 Jan;39(Database issue):D861-70. doi: 10.1093/nar/gkq1078. Epub 2010 Nov 13. Nucleic Acids Res. 2011. PMID: 21076152 Free PMC article.

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PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants.

Makita Y, Kobayashi N, Mochizuki Y, Yoshida Y, Asano S, Heida N, Deshpande M, Bhatia R, Matsushima A, Ishii M, Kawaguchi S, Iida K, Hanada K, Kuromori T, Seki M, Shinozaki K, Toyoda T. Makita Y, et al. Plant Cell Physiol. 2009 Jul;50(7):1249-59. doi: 10.1093/pcp/pcp086. Epub 2009 Jun 15. Plant Cell Physiol. 2009. PMID: 19528193 Free PMC article.

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