Kenta Nakai

According to our database, Kenta Nakai authored at least 68 papers between 1994 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.

Weihang Zhang, Yang Cui, Bowen Liu, Martin Loza, Sung-Joon Park, Kenta Nakai

Briefings Bioinform., 2024

2023

CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides.

Zhongshen Li, Junru Jin, Wenjia He, Wentao Long, Haoqing Yu, Xin Gao, Kenta Nakai, Quan Zou, Leyi Wei

Briefings Bioinform., September, 2023

2022

Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics.

Kenta Nakai, Leyi Wei

Frontiers Bioinform., 2022

Predicting protein-peptide binding residues via interpretable deep learning.

Ruheng Wang, Junru Jin, Quan Zou, Kenta Nakai, Leyi Wei

Bioinform., 2022

Protein design via deep learning.

Wenze Ding, Kenta Nakai, Haipeng Gong

Briefings Bioinform., 2022

SignedS2V: Structural Embedding Method for Signed Networks.

Shu Liu, Fujio Toriumi, Xin Zeng, Mao Nishiguchi, Kenta Nakai

Proceedings of the Complex Networks and Their Applications XI, 2022

2021

A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations.

Hao Jia, Sung-Joon Park, Kenta Nakai

BMC Bioinform., 2021

OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data.

Sung-Joon Park, Kenta Nakai

Bioinform., 2021

2019

Prediction of Protein Localization.

Kenta Nakai, Kenichiro Imai

Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

Prediction of Protein-Binding Sites in DNA Sequences.

Kenta Nakai

Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019

2018

DBTSS/DBKERO for integrated analysis of transcriptional regulation.

Ayako Suzuki, Shin Kawano, Toutai Mituyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki

Nucleic Acids Res., 2018

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

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

Nucleic Acids Res., 2018

Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers.

Myungjin Moon, Kenta Nakai

J. Bioinform. Comput. Biol., 2018

Introduction to Selected Papers from GIW2018.

Jinyan Li, Kenta Nakai, Yun Zheng, Kengo Sato, Limsoon Wong

J. Bioinform. Comput. Biol., 2018

TimeXNet Web: identifying cellular response networks from diverse omics time-course data.

Phit Ling Tan, Yosvany López, Kenta Nakai, Ashwini Patil

Bioinform., 2018

2016

OpenTein: a database of digital whole-slide images of stem cell-derived teratomas.

Sung-Joon Park, Yusuke Komiyama, Hirofumi Suemori, Akihiro Umezawa, Kenta Nakai

Nucleic Acids Res., 2016

A study on the application of topic models to motif finding algorithms.

Josep Basha Gutierrez, Kenta Nakai

BMC Bioinform., 2016

2015

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.

Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, Kenta Nakai

Nucleic Acids Res., 2015

DBTMEE: a database of transcriptome in mouse early embryos.

Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi, Kenta Nakai

Nucleic Acids Res., 2015

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.

Yosvany López, Kenta Nakai, Ashwini Patil

Database J. Biol. Databases Curation, 2015

A Genetic Algorithm for Motif Finding Based on Statistical Significance.

Josep Basha Gutierrez, Martin C. Frith, Kenta Nakai

Proceedings of the Bioinformatics and Biomedical Engineering, 2015

2014

TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles.

Ashwini Patil, Kenta Nakai

BMC Syst. Biol., 2014

2013

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response.

Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai

PLoS Comput. Biol., 2013

Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana.

Yosvany López, Ashwini Patil, Kenta Nakai

BMC Syst. Biol., 2013

2012

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012.

Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai

Nucleic Acids Res., 2012

A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment.

Kouichi Kimura, Asako Koike, Kenta Nakai

J. Bioinform. Comput. Biol., 2012

Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator.

Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, Daron M. Standley

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

2011

HitPredict: a database of quality assessed protein-protein interactions in nine species.

Ashwini Patil, Kenta Nakai, Haruki Nakamura

Nucleic Acids Res., 2011

A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns.

Sung-Joon Park, Kenta Nakai

BMC Bioinform., 2011

Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping.

Kouichi Kimura, Asako Koike, Kenta Nakai

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

2010

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, Kenta Nakai

Nucleic Acids Res., 2010

InCoB2010 - 9^thInternational Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010.

Christian Schönbach, Kenta Nakai, Tin Wee Tan, Shoba Ranganathan

BMC Bioinform., 2010

Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution.

Kohji Okamura, Kazuaki A. Matsumoto, Kenta Nakai

BMC Bioinform., 2010

2008

DBTSS: database of transcription start sites, progress report 2008.

Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai

Nucleic Acids Res., 2008

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

Nicolas Sierro, Yuko Makita, Michiel J. L. de Hoon, Kenta Nakai

Nucleic Acids Res., 2008

2007

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

Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, Kenta Nakai

Nucleic Acids Res., 2007

ATTED-II: a database of co-expressed genes and <i>cis</i> elements for identifying co-regulated gene groups in <i>Arabidopsis</i>.

Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta

Nucleic Acids Res., 2007

WoLF PSORT: protein localization predictor.

Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C. J. Adams-Collier, Kenta Nakai

Nucleic Acids Res., 2007

2006

DBTSS: DataBase of Human Transcription Start Sites, progress report 2006.

Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano

Nucleic Acids Res., 2006

DBTGR: a database of tunicate promoters and their regulatory elements.

Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai

Nucleic Acids Res., 2006

Protein Subcellular Localisation Prediction with WoLF PSORT.

Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai

Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

2005

Prediction of Transcriptional Terminators in <i>Bacillus subtilis</i> and Related Species.

Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano

PLoS Comput. Biol., 2005

Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues.

Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai

Nucleic Acids Res., 2005

Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis.

Yuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai

Proceedings of the Biocomputing 2005, 2005

2004

An O(N²) Algorithm for Discovering Optimal Boolean Pattern Pairs.

Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano

IEEE ACM Trans. Comput. Biol. Bioinform., 2004

BTSS, DataBase of Transcriptional Start Sites: progress report 2004.

Yutaka Suzuki, Riu Yamashita, Sumio Sugano, Kenta Nakai

Nucleic Acids Res., 2004

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

Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, Kenta Nakai

Nucleic Acids Res., 2004

Large-scale collection and characterization of promoters of human and mouse genes.

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

Silico Biol., 2004

Finding Optimal Pairs of Patterns.

Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano

Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Parameter Landscape Analysis for Common Motif Discovery Programs.

Natalia Polouliakh, Michiko Konno, Paul Horton, Kenta Nakai

Proceedings of the Regulatory Genomics, 2004

Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.

Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance.

Shunsuke Inenaga, Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano

Proceedings of the Discovery Science, 7th International Conference, 2004

2003

PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria.

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

Nucleic Acids Res., 2003

MELINA: motif extraction from promoter regions of potentially co-regulated genes.

Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai

Bioinform., 2003

Intrasplicing - Analysis of Long Intron Sequences.

Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

2002

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.

Yutaka Suzuki, Riu Yamashita, Kenta Nakai, Sumio Sugano

Nucleic Acids Res., 2002

Extensive feature detection of N-terminal protein sorting signals.

Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano

Bioinform., 2002

2001

DBTBS: a database of Bacillus subtilis promoters and transcription factors.

Takahiro Ishii, Ken-ichi Yoshida, Goro Terai, Yasutaro Fujita, Kenta Nakai

Nucleic Acids Res., 2001

ORI-GENE: gene classification based on the evolutionary tree.

Hideaki Mizuno, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai

Bioinform., 2001

Views: Fundamental Building Blocks in the Process of Knowledge Discovery.

Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano

Proceedings of the Fourteenth International Florida Artificial Intelligence Research Society Conference, 2001

1999

Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov models.

Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Kenta Nakai

Bioinform., 1999

1998

Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.

Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai, Kenta Nakai

Bioinform., 1998

1997

Functional Prediction of B. subtilis Genes from Their Regulatory Sequences.

Tetsushi Yada, Yasushi Totoki, Takahiro Ishii, Kenta Nakai

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier.

Paul Horton, Kenta Nakai

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

1996

Ecoli.

Kenta Nakai

Dataset, August, 1996

Yeast.

Kenta Nakai

Dataset, August, 1996

A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins.

Paul Horton, Kenta Nakai

Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

1994

Gnome - an Internet-based sequence analysis tool.

Kenta Nakai, T. Tokimori, A. Ogiwara, Ikuo Uchiyama, T. Niiyama

Comput. Appl. Biosci., 1994