Kenta Nakai

2008
32	EE	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)
31	EE	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)
2007
30	EE	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)
29	EE	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)
28	EE	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)
2006
27	EE	Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai: Protein Subcellular Localisation Prediction with WoLF PSORT. APBC 2006: 39-48
26	EE	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)
25	EE	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)
2005
24	EE	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
23	EE	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)
2004
22	EE	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
21	EE	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
20	EE	Natalia Polouliakh, Michiko Konno, Paul Horton, Kenta Nakai: Parameter Landscape Analysis for Common Motif Discovery Programs. Regulatory Genomics 2004: 79-87
19	EE	Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano: Finding Optimal Pairs of Patterns. WABI 2004: 450-462
18	EE	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)
17	EE	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)
16		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)
15		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)
2003
14	EE	Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano: Intrasplicing - Analysis of Long Intron Sequences. Pacific Symposium on Biocomputing 2003: 339-350
13		Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai: MELINA: motif extraction from promoter regions of potentially co-regulated genes. Bioinformatics 19(3): 423-424 (2003)
12		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)
2002
11		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)
10		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)
2001
9		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
8		Hideaki Mizuno, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai: ORI-GENE: gene classification based on the evolutionary tree. Bioinformatics 17(1): 167-173 (2001)
7		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)
1999
6		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)
1998
5		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)
1997
4		Paul Horton, Kenta Nakai: Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier. ISMB 1997: 147-152
3		Tetsushi Yada, Yasushi Totoki, Takahiro Ishii, Kenta Nakai: Functional Prediction of B. subtilis Genes from Their Regulatory Sequences. ISMB 1997: 354-357
1996
2		Paul Horton, Kenta Nakai: A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins. ISMB 1996: 109-115
1994
1		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)

Coauthor Index

1	C. J. Adams-Collier	[28]
2	Takahiro Arakawa	[17]
3	Kiyoshi Asai	[5]
4	Hideo Bannai	[9] [11] [14] [18] [19] [22]
5	Fiona S. L. Brinkman	[12]
6	Piero Carninci	[17]
7	Joe Chiba	[17]
8	Martin Ester	[12]
9	Katalin de Fays	[12]
10	Naoya Fujita	[28]
11	Yasutaro Fujita	[7]
12	Jennifer L. Gardy	[12]
13	Hajime Harada	[28]
14	Shinpei Hayashi	[30]
15	Yoshihide Hayashizaki	[17]
16	Michiel J. L. de Hoon	[21] [24] [32]
17	Paul Horton	[2] [4] [20] [27] [28]
18	Sujun Hua	[12]
19	Heikki Hyyrö	[18] [19] [22]
20	Seiya Imoto	[21]
21	Shunsuke Inenaga	[22]
22	Takahiro Ishii	[3] [7]
23	Masato Ishikawa	[5]
24	Kikuya Kato	[23]
25	Jun Kawai	[17]
26	Alexander E. Kel	[17]
27	Kengo Kinoshita	[26] [30]
28	Kazuo Kobayashi	[21]
29	Michiko Konno	[20]
30	Takehiro Kusakabe	[26]
31	Christophe G. Lambert	[12]
32	Hiroki Makiguchi	[29]
33	Yuko Makita	[16] [21] [24] [29] [32]
34	Osamu Maruyama	[9] [11]
35	Ryo Matoba	[23]
36	Satoru Miyano	[9] [11] [14] [18] [19] [21] [22] [24]
37	Hideaki Mizuno	[8]
38	Junko Mizushima-Sugano	[17]
39	Morito Monden	[23]
40	Mitsuteru Nakao	[6] [16]
41	T. Niiyama	[1]
42	Shinzaburo Noguchi	[23]
43	Takeshi Obayashi	[27] [28] [30]
44	Naotake Ogasawara	[16] [21] [24]
45	A. Ogiwara	[1]
46	Hiroyuki Ohta	[30]
47	Toshiyuki Okumura	[29]
48	Sascha Ott	[14]
49	Keun-Joon Park	[26] [27] [28]
50	Natalia Polouliakh	[20]
51	Natalia V. Poluliakh	[13]
52	Motoshi Saeki	[30]
53	Kazuki Saito	[30]
54	Yuta Sakakibara	[17]
55	Akinori Sarai	[8]
56	Masayuki Shibaoka	[30]
57	Daisuke Shibata	[30]
58	Ayumi Shinohara	[18] [19] [22]
59	Matsuyuki Shirota	[17]
60	Nicolas Sierro	[26] [32]
61	István Simon	[12]
62	Cory Spencer	[12]
63	Sumio Sugano	[10] [15] [17] [25] [31]
64	Yutaka Suzuki	[10] [15] [17] [25] [31]
65	Toshihisa Takagi	[13] [17] [23]
66	Masayuki Takeda	[18] [19] [22]
67	Yoshinori Tamada	[9] [11] [14]
68	Yoshimasa Tanaka	[8]
69	Goro Terai	[7]
70	T. Tokimori	[1]
71	Yasushi Totoki	[3] [5] [6]
72	Katsuki Tsuritani	[25]
73	Gábor E. Tusnády	[12]
74	I. Uchiyama	[1]
75	Hiroyuki Wakaguri	[25] [31]
76	Ke Wang	[12]
77	Tetsushi Yada	[3] [5] [6]
78	Riu Yamashita	[10] [15] [17] [23] [25] [26] [29] [31]
79	Ken-ichi Yoshida	[7]

Colors in the list of coauthors