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2020 – today
- 2024
[j49]Weihang Zhang, Yang Cui
, Bowen Liu, Martin Loza, Sung-Joon Park, Kenta Nakai:
HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data. Briefings Bioinform. 25(3) (2024)- 2023
- [j48]Zhongshen Li, Junru Jin, Wenjia He, Wentao Long, Haoqing Yu, Xin Gao, Kenta Nakai, Quan Zou, Leyi Wei:
CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. Briefings Bioinform. 24(6) (2023) - 2022
- [j47]Wenze Ding, Kenta Nakai, Haipeng Gong:
Protein design via deep learning. Briefings Bioinform. 23(3) (2022) - [j46]Ruheng Wang, Junru Jin, Quan Zou, Kenta Nakai, Leyi Wei:
Predicting protein-peptide binding residues via interpretable deep learning. Bioinform. 38(13): 3351-3360 (2022) - [j45]Kenta Nakai, Leyi Wei:
Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. Frontiers Bioinform. 2 (2022) - [c15]Shu Liu, Fujio Toriumi, Xin Zeng, Mao Nishiguchi, Kenta Nakai:
SignedS2V: Structural Embedding Method for Signed Networks. COMPLEX NETWORKS (1) 2022: 337-349 - 2021
- [j44]Sung-Joon Park, Kenta Nakai:
OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data. Bioinform. 37(18): 3021-3022 (2021) - [j43]Hao Jia, Sung-Joon Park, Kenta Nakai:
A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations. BMC Bioinform. 22-S(6): 128 (2021)
2010 – 2019
- 2019
- [e3]Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 1. Elsevier 2019, ISBN 978-0-12-811432-2 [contents] - [e2]Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 2. Elsevier 2019, ISBN 978-0-12-811432-2 [contents] - [e1]Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 3. Elsevier 2019, ISBN 978-0-12-811432-2 [contents] - [r2]Kenta Nakai, Kenichiro Imai:
Prediction of Protein Localization. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 53-59 - [r1]Kenta Nakai:
Prediction of Protein-Binding Sites in DNA Sequences. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 447-451 - 2018
- [j42]Phit Ling Tan, Yosvany López, Kenta Nakai, Ashwini Patil:
TimeXNet Web: identifying cellular response networks from diverse omics time-course data. Bioinform. 34(21): 3764-3765 (2018) - [j41]Myungjin Moon, Kenta Nakai:
Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers. J. Bioinform. Comput. Biol. 16(2): 1850006:1-1850006:20 (2018) - [j40]Jinyan Li, Kenta Nakai, Yun Zheng, Kengo Sato, Limsoon Wong:
Introduction to Selected Papers from GIW2018. J. Bioinform. Comput. Biol. 16(6): 1802005:1-1802005:2 (2018) - [j39]Ayako Suzuki, Shin Kawano, Toutai Mituyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki:
DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucleic Acids Res. 46(Database-Issue): D229-D238 (2018) - [j38]Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Magali Naville, Kazuhiro R. Nitta, Jacques Piette, Wendy Reeves, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin Jacox, Elijah K. Lowe, Mickaël Mendez, Alexis Roberge, Alberto Stolfi, Rui Yokomori, C. Titus Brown, Christian Cambillau, Lionel A. Christiaen, Frédéric Delsuc, Emmanuel J. P. Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie J. Swalla, Michael Veeman, Jean-Nicolas Volff, Patrick Lemaire:
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res. 46(Database-Issue): D718-D725 (2018) - 2016
- [j37]Josep Basha Gutierrez, Kenta Nakai:
A study on the application of topic models to motif finding algorithms. BMC Bioinform. 17(S-19): 129-138 (2016) - [j36]Sung-Joon Park, Yusuke Komiyama, Hirofumi Suemori, Akihiro Umezawa, Kenta Nakai:
OpenTein: a database of digital whole-slide images of stem cell-derived teratomas. Nucleic Acids Res. 44(Database-Issue): 1000-1004 (2016) - 2015
- [j35]Yosvany López, Kenta Nakai, Ashwini Patil:
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. Database J. Biol. Databases Curation 2015 (2015) - [j34]Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. Nucleic Acids Res. 43(Database-Issue): 87-91 (2015) - [j33]Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi, Kenta Nakai:
DBTMEE: a database of transcriptome in mouse early embryos. Nucleic Acids Res. 43(Database-Issue): 771-776 (2015) - [c14]Josep Basha Gutierrez, Martin C. Frith, Kenta Nakai:
A Genetic Algorithm for Motif Finding Based on Statistical Significance. IWBBIO (1) 2015: 438-449 - 2014
- [j32]Ashwini Patil, Kenta Nakai:
TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles. BMC Syst. Biol. 8(S-4): S2 (2014) - 2013
- [j31]Yosvany López, Ashwini Patil, Kenta Nakai:
Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana. BMC Syst. Biol. 7(S-3): S10 (2013) - [j30]Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai:
Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response. PLoS Comput. Biol. 9(11) (2013) - 2012
- [j29]Kouichi Kimura, Asako Koike, Kenta Nakai:
A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment. J. Bioinform. Comput. Biol. 10(4) (2012) - [j28]Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Res. 40(Database-Issue): 150-154 (2012) - [c13]Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, Daron M. Standley:
Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator. Pacific Symposium on Biocomputing 2012: 164-175 - 2011
- [j27]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 Bioinform. 12(S-1): S50 (2011) - [j26]Ashwini Patil, Kenta Nakai, Haruki Nakamura:
HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res. 39(Database-Issue): 744-749 (2011) - [c12]Kouichi Kimura, Asako Koike, Kenta Nakai:
Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping. WABI 2011: 151-162 - 2010
- [j25]Christian Schönbach, Kenta Nakai, Tin Wee Tan, Shoba Ranganathan:
InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. BMC Bioinform. 11(S-7): S1 (2010) - [j24]Kohji Okamura, Kazuaki A. Matsumoto, Kenta Nakai:
Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution. BMC Bioinform. 11(S-7): S2 (2010) - [j23]Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Res. 38(Database-Issue): 98-104 (2010)
2000 – 2009
- 2008
- [j22]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 Res. 36(Database-Issue): 93-96 (2008) - [j21]Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai:
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res. 36(Database-Issue): 97-101 (2008) - 2007
- [j20]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 Res. 35(Database-Issue): 863-869 (2007) - [j19]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 Res. 35(Web-Server-Issue): 227-231 (2007) - [j18]Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C. J. Adams-Collier, Kenta Nakai:
WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35(Web-Server-Issue): 585-587 (2007) - 2006
- [j17]Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano:
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res. 34(Database-Issue): 86-89 (2006) - [j16]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 Res. 34(Database-Issue): 552-555 (2006) - [c11]Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai:
Protein Subcellular Localisation Prediction with WoLF PSORT. APBC 2006: 39-48 - 2005
- [j15]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 Res. 33(Database-Issue): 533-536 (2005) - [j14]Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano:
Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. PLoS Comput. Biol. 1(3) (2005) - [c10]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 - 2004
- [j13]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. Silico Biol. 4(4): 429-444 (2004) - [j12]Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, Kenta Nakai:
BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 32(Database-Issue): 75-77 (2004) - [j11]Yutaka Suzuki, Riu Yamashita, Sumio Sugano, Kenta Nakai:
BTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res. 32(Database-Issue): 78-81 (2004) - [j10]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. Biol. Bioinform. 1(4): 159-170 (2004) - [c9]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 - [c8]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 - [c7]Natalia Polouliakh, Michiko Konno, Paul Horton, Kenta Nakai:
Parameter Landscape Analysis for Common Motif Discovery Programs. Regulatory Genomics 2004: 79-87 - [c6]Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano:
Finding Optimal Pairs of Patterns. WABI 2004: 450-462 - 2003
- [j9]Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai:
MELINA: motif extraction from promoter regions of potentially co-regulated genes. Bioinform. 19(3): 423-424 (2003) - [j8]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 Res. 31(13): 3613-3617 (2003) - [c5]Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano:
Intrasplicing - Analysis of Long Intron Sequences. Pacific Symposium on Biocomputing 2003: 339-350 - 2002
- [j7]Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano:
Extensive feature detection of N-terminal protein sorting signals. Bioinform. 18(2): 298-305 (2002) - [j6]Yutaka Suzuki, Riu Yamashita, Kenta Nakai, Sumio Sugano:
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res. 30(1): 328-331 (2002) - 2001
- [j5]Hideaki Mizuno, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai:
ORI-GENE: gene classification based on the evolutionary tree. Bioinform. 17(1): 167-173 (2001) - [j4]Takahiro Ishii, Ken-ichi Yoshida, Goro Terai, Yasutaro Fujita, Kenta Nakai:
DBTBS: a database of Bacillus subtilis promoters and transcription factors. Nucleic Acids Res. 29(1): 278-280 (2001) - [c4]Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano:
Views: Fundamental Building Blocks in the Process of Knowledge Discovery. FLAIRS 2001: 233-238
1990 – 1999
- 1999
- [j3]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. Bioinform. 15(12): 987-993 (1999) - 1998
- [j2]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. Bioinform. 14(4): 317-325 (1998) - 1997
- [c3]Paul Horton, Kenta Nakai:
Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier. ISMB 1997: 147-152 - [c2]Tetsushi Yada, Yasushi Totoki, Takahiro Ishii, Kenta Nakai:
Functional Prediction of B. subtilis Genes from Their Regulatory Sequences. ISMB 1997: 354-357 - 1996
- [c1]Paul Horton, Kenta Nakai:
A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins. ISMB 1996: 109-115 - [d2]Kenta Nakai:
Yeast. UCI Machine Learning Repository, 1996
- [d1]Kenta Nakai:
Ecoli. UCI Machine Learning Repository, 1996 - 1994
- [j1]Kenta Nakai, T. Tokimori, A. Ogiwara, Ikuo Uchiyama, T. Niiyama:
Gnome - an Internet-based sequence analysis tool. Comput. Appl. Biosci. 10(5): 547-550 (1994)
Coauthor Index
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