Kenta Nakai

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 14

Top Topics

Predicting Protein

Gene Expression

Subcellular Localization

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

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)
Shu Liu, Fujio Toriumi, Xin Zeng, Mao Nishiguchi, Kenta Nakai
SignedS2V: Structural Embedding Method for Signed Networks. COMPLEX NETWORKS (1) (2022)
Kenta Nakai, Leyi Wei
Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. Frontiers Bioinform. 2 (2022)
Ruheng Wang, Junru Jin, Quan Zou, Kenta Nakai, Leyi Wei
Predicting protein-peptide binding residues via interpretable deep learning. Bioinform. 38 (13) (2022)
Wenze Ding, Kenta Nakai, Haipeng Gong
Protein design via deep learning. Briefings Bioinform. 23 (3) (2022)
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. (6) (2021)
Sung-Joon Park, Kenta Nakai
OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data. Bioinform. 37 (18) (2021)
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) (2018)
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) (2018)
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) (2018)
Jinyan Li, Kenta Nakai, Yun Zheng, Kengo Sato, Limsoon Wong
Introduction to Selected Papers from GIW2018. J. Bioinform. Comput. Biol. 16 (6) (2018)
Phit Ling Tan, Yosvany López, Kenta Nakai, Ashwini Patil
TimeXNet Web: identifying cellular response networks from diverse omics time-course data. Bioinform. 34 (21) (2018)
Josep Basha Gutierrez, Kenta Nakai
A study on the application of topic models to motif finding algorithms. BMC Bioinform. 17 (S-19) (2016)
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) (2016)
Josep Basha Gutierrez, Martin C. Frith, Kenta Nakai
A Genetic Algorithm for Motif Finding Based on Statistical Significance. IWBBIO (1) (2015)
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)
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) (2015)
Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi, Kenta Nakai
DBTMEE: a database of transcriptome in mouse early embryos. Nucleic Acids Res. 43 (Database-Issue) (2015)
Ashwini Patil, Kenta Nakai
TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles. BMC Syst. Biol. 8 (S-4) (2014)
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) (2013)
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)
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)
Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Res. 40 (Database-Issue) (2012)
Kouichi Kimura, Asako Koike, Kenta Nakai
A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment. J. Bioinform. Comput. Biol. 10 (4) (2012)
Ashwini Patil, Kenta Nakai, Haruki Nakamura
HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res. 39 (Database-Issue) (2011)
Kouichi Kimura, Asako Koike, Kenta Nakai
Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping. WABI (2011)
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) (2011)
Christian Schönbach, Kenta Nakai, Tin Wee Tan, Shoba Ranganathan
International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. BMC Bioinform. 11 (S-7) (2010)
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) (2010)
Kohji Okamura, Kazuaki A. Matsumoto, Kenta Nakai
Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution. BMC Bioinform. 11 (S-7) (2010)
Nicolas Sierro, Yuko Makita, Michiel J. L. de Hoon, Kenta Nakai
containing upstream intergenic conservation information. Nucleic Acids Res. 36 (Database-Issue) (2008)
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) (2008)
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) (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 Res. 35 (Web-Server-Issue) (2007)
Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta
. Nucleic Acids Res. 35 (Database-Issue) (2007)
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) (2006)
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) (2006)
Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai
Protein Subcellular Localisation Prediction with WoLF PSORT. APBC (2006)
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)
Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano
and Related Species. PLoS Comput. Biol. 1 (3) (2005)
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) (2005)
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)
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)
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) (2004)
Natalia Polouliakh, Michiko Konno, Paul Horton, Kenta Nakai
Parameter Landscape Analysis for Common Motif Discovery Programs. Regulatory Genomics (2004)
Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
Finding Optimal Pairs of Patterns. WABI (2004)
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) (2004)
Yutaka Suzuki, Riu Yamashita, Sumio Sugano, Kenta Nakai
BTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res. 32 (Database-Issue) (2004)
Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
) Algorithm for Discovering Optimal Boolean Pattern Pairs. IEEE ACM Trans. Comput. Biol. Bioinform. 1 (4) (2004)
Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai
MELINA: motif extraction from promoter regions of potentially co-regulated genes. Bioinform. 19 (3) (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 Res. 31 (13) (2003)
Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano
Intrasplicing - Analysis of Long Intron Sequences. Pacific Symposium on Biocomputing (2003)
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano
Extensive feature detection of N-terminal protein sorting signals. Bioinform. 18 (2) (2002)
Yutaka Suzuki, Riu Yamashita, Kenta Nakai, Sumio Sugano
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res. 30 (1) (2002)
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano
Views: Fundamental Building Blocks in the Process of Knowledge Discovery. FLAIRS Conference (2001)
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) (2001)
Hideaki Mizuno, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai
ORI-GENE: gene classification based on the evolutionary tree. Bioinform. 17 (1) (2001)
Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Kenta Nakai
Modeling and predicting transcriptional units of Escherichia coligenes using hidden Markov models. Bioinform. 15 (12) (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. Bioinform. 14 (4) (1998)
Paul Horton, Kenta Nakai
Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier. ISMB (1997)
Tetsushi Yada, Yasushi Totoki, Takahiro Ishii, Kenta Nakai
Functional Prediction of B. subtilis Genes from Their Regulatory Sequences. ISMB (1997)
Paul Horton, Kenta Nakai
A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins. ISMB (1996)
Kenta Nakai, T. Tokimori, A. Ogiwara, Ikuo Uchiyama, T. Niiyama
Gnome - an Internet-based sequence analysis tool. Comput. Appl. Biosci. 10 (5) (1994)