Kenta Nakai

Kouichi Kimura, Asako Koike, Kenta Nakai: A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment. J. Bioinformatics and Computational Biology 10(4) (2012)

Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai: DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Research 40(Database-Issue): 150-154 (2012)

Sung-Joon Park, Kenta Nakai: A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns. BMC Bioinformatics 12(S-1): S50 (2011)

Ashwini Patil, Kenta Nakai, Haruki Nakamura: HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Research 39(Database-Issue): 744-749 (2011)

Kouichi Kimura, Asako Koike, Kenta Nakai: Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping. WABI 2011: 151-162

Christian Schönbach, Kenta Nakai, Tin Wee Tan, Shoba Ranganathan: InCoB2010 - 9^th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. BMC Bioinformatics 11(S-7): S1 (2010)

Kohji Okamura, Kazuaki A. Matsumoto, Kenta Nakai: Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution. BMC Bioinformatics 11(S-7): S2 (2010)

Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, Kenta Nakai: DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Research 38(Database-Issue): 98-104 (2010)

Nicolas Sierro, Yuko Makita, Michiel J. L. de Hoon, Kenta Nakai: DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Research 36(Database-Issue): 93-96 (2008)

Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai: DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Research 36(Database-Issue): 97-101 (2008)

Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta: ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Research 35(Database-Issue): 863-869 (2007)

Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, Kenta Nakai: Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. Nucleic Acids Research 35(Web-Server-Issue): 227-231 (2007)

Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C. J. Adams-Collier, Kenta Nakai: WoLF PSORT: protein localization predictor. Nucleic Acids Research 35(Web-Server-Issue): 585-587 (2007)

Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano: DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Research 34(Database-Issue): 86-89 (2006)

Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai: DBTGR: a database of tunicate promoters and their regulatory elements. Nucleic Acids Research 34(Database-Issue): 552-555 (2006)

Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai: Protein Subcellular Localisation Prediction with WoLF PSORT. APBC 2006: 39-48

Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai: Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Research 33(Database-Issue): 533-536 (2005)

Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano: Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. PLoS Computational Biology 1(3) (2005)

Yuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai: Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis. Pacific Symposium on Biocomputing 2005

Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Alexander E. Kel, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Toshihisa Takagi, Kenta Nakai, Sumio Sugano: Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biology 4 (2004)

Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, Kenta Nakai: BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Research 32(Database-Issue): 75-77 (2004)

Yutaka Suzuki, Riu Yamashita, Sumio Sugano, Kenta Nakai: BTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Research 32(Database-Issue): 78-81 (2004)

Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano: An O(N²) Algorithm for Discovering Optimal Boolean Pattern Pairs. IEEE/ACM Trans. Comput. Biology Bioinform. 1(4): 159-170 (2004)

Shunsuke Inenaga, Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano: Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance. Discovery Science 2004: 32-46

Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano: Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. ISMB/ECCB (Supplement of Bioinformatics) 2004: 101-108

Natalia Polouliakh, Michiko Konno, Paul Horton, Kenta Nakai: Parameter Landscape Analysis for Common Motif Discovery Programs. Regulatory Genomics 2004: 79-87

Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano: Finding Optimal Pairs of Patterns. WABI 2004: 450-462

Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai: MELINA: motif extraction from promoter regions of potentially co-regulated genes. Bioinformatics 19(3): 423-424 (2003)

Jennifer L. Gardy, Cory Spencer, Ke Wang, Martin Ester, Gábor E. Tusnády, István Simon, Sujun Hua, Katalin de Fays, Christophe G. Lambert, Kenta Nakai, Fiona S. L. Brinkman: PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Research 31(13): 3613-3617 (2003)

Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano: Intrasplicing - Analysis of Long Intron Sequences. Pacific Symposium on Biocomputing 2003: 339-350

Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano: Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 18(2): 298-305 (2002)

Yutaka Suzuki, Riu Yamashita, Kenta Nakai, Sumio Sugano: DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Research 30(1): 328-331 (2002)

Hideaki Mizuno, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai: ORI-GENE: gene classification based on the evolutionary tree. Bioinformatics 17(1): 167-173 (2001)

Takahiro Ishii, Ken-ichi Yoshida, Goro Terai, Yasutaro Fujita, Kenta Nakai: DBTBS: a database of Bacillus subtilis promoters and transcription factors. Nucleic Acids Research 29(1): 278-280 (2001)

Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano: Views: Fundamental Building Blocks in the Process of Knowledge Discovery. FLAIRS Conference 2001: 233-238

Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Kenta Nakai: Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov models. Bioinformatics 15(12): 987-993 (1999)

Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai, Kenta Nakai: Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinformatics 14(4): 317-325 (1998)

Paul Horton, Kenta Nakai: Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier. ISMB 1997: 147-152

Tetsushi Yada, Yasushi Totoki, Takahiro Ishii, Kenta Nakai: Functional Prediction of B. subtilis Genes from Their Regulatory Sequences. ISMB 1997: 354-357

Paul Horton, Kenta Nakai: A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins. ISMB 1996: 109-115

Kenta Nakai, T. Tokimori, A. Ogiwara, I. Uchiyama, T. Niiyama: Gnome - an Internet-based sequence analysis tool. Computer Applications in the Biosciences 10(5): 547-550 (1994)