Gnome - an Internet-based sequence analysis tool. - Kenta Nakai; T. Tokimori; A. Ogiwara; Ikuo Uchiyama; T. Niiyama (Comput. Appl. Biosci., 1994)

A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins. - Paul Horton; Kenta Nakai (ISMB, 1996)

Yeast. - Kenta Nakai (UCI Machine Learning Repository, 1996)

Ecoli. - Kenta Nakai (UCI Machine Learning Repository, 1996)

Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier. - Paul Horton; Kenta Nakai (ISMB, 1997)

Functional Prediction of B. subtilis Genes from Their Regulatory Sequences. - Tetsushi Yada; Yasushi Totoki; Takahiro Ishii; Kenta Nakai (ISMB, 1997)

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)

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)

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

ORI-GENE: gene classification based on the evolutionary tree. - Hideaki Mizuno; Yoshimasa Tanaka; Kenta Nakai; Akinori Sarai (Bioinform., 2001)

DBTBS: a database of Bacillus subtilis promoters and transcription factors. - Takahiro Ishii; Ken-ichi Yoshida 002; Goro Terai; Yasutaro Fujita; Kenta Nakai (Nucleic Acids Res., 2001)

Extensive feature detection of N-terminal protein sorting signals. - Hideo Bannai; Yoshinori Tamada; Osamu Maruyama; Kenta Nakai; Satoru Miyano (Bioinform., 2002)

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

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

MELINA: motif extraction from promoter regions of potentially co-regulated genes. - Natalia V. Poluliakh; Toshihisa Takagi; Kenta Nakai (Bioinform., 2003)

PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. - Jennifer L. Gardy; Cory Spencer; Ke Wang 001; 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)

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 (Discovery Science, 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 (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Parameter Landscape Analysis for Common Motif Discovery Programs. - Natalia Polouliakh; Michiko Konno; Paul Horton; Kenta Nakai (Regulatory Genomics, 2004)

Finding Optimal Pairs of Patterns. - Hideo Bannai; Heikki Hyyrö; Ayumi Shinohara; Masayuki Takeda; Kenta Nakai; Satoru Miyano (WABI, 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; et al. (Silico Biol., 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)

BTSS, DataBase of Transcriptional Start Sites: progress report 2004. - Yutaka Suzuki; Riu Yamashita; Sumio Sugano; Kenta Nakai (Nucleic Acids Res., 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)

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

Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. - Michiel J. L. de Hoon; Yuko Makita; Kenta Nakai; Satoru Miyano (PLoS Comput. Biol., 2005)

Protein Subcellular Localisation Prediction with WoLF PSORT. - Paul Horton; Keun-Joon Park; Takeshi Obayashi; Kenta Nakai (APBC, 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)

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)

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)

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

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

DBTSS: database of transcription start sites, progress report 2008. - Hiroyuki Wakaguri; Riu Yamashita; Yutaka Suzuki; Sumio Sugano; Kenta Nakai (Nucleic Acids Res., 2008)

Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution. - Kohji Okamura; Kazuaki A. Matsumoto; Kenta Nakai (BMC Bioinform., 2010)

InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. - Christian Schönbach; Kenta Nakai; Tin Wee Tan; Shoba Ranganathan (BMC Bioinform., 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)

Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping. - Kouichi Kimura; Asako Koike; Kenta Nakai (WABI, 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)

HitPredict: a database of quality assessed protein-protein interactions in nine species. - Ashwini Patil; Kenta Nakai; Haruki Nakamura (Nucleic Acids Res., 2011)

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 (Pacific Symposium on Biocomputing, 2012)

A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment. - Kouichi Kimura; Asako Koike; Kenta Nakai (J. Bioinform. Comput. Biol., 2012)

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. - Riu Yamashita; Sumio Sugano; Yutaka Suzuki; Kenta Nakai (Nucleic Acids Res., 2012)

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)

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)

TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles. - Ashwini Patil; Kenta Nakai (BMC Syst. Biol., 2014)

A Genetic Algorithm for Motif Finding Based on Statistical Significance. - Josep Basha Gutierrez; Martin C. Frith; Kenta Nakai (IWBBIO (1), 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)

DBTMEE: a database of transcriptome in mouse early embryos. - Sung-Joon Park; Katsuhiko Shirahige; Miho Ohsugi; Kenta Nakai (Nucleic Acids Res., 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)

A study on the application of topic models to motif finding algorithms. - Josep Basha Gutierrez; Kenta Nakai (BMC Bioinform., 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)

TimeXNet Web: identifying cellular response networks from diverse omics time-course data. - Phit Ling Tan; Yosvany López; Kenta Nakai; Ashwini Patil (Bioinform., 2018)

Introduction to Selected Papers from GIW2018. - Jinyan Li 001; Kenta Nakai; Yun Zheng; Kengo Sato; Limsoon Wong (J. Bioinform. Comput. Biol., 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)

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; et al. (Nucleic Acids Res., 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)

Prediction of Protein-Binding Sites in DNA Sequences. - Kenta Nakai (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Prediction of Protein Localization. - Kenta Nakai; Kenichiro Imai (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data. - Sung-Joon Park; Kenta Nakai (Bioinform., 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)

SignedS2V: Structural Embedding Method for Signed Networks. - Shu Liu; Fujio Toriumi; Xin Zeng; Mao Nishiguchi; Kenta Nakai (COMPLEX NETWORKS (1), 2022)

Protein design via deep learning. - Wenze Ding; Kenta Nakai; Haipeng Gong (Briefings Bioinform., 2022)

Predicting protein-peptide binding residues via interpretable deep learning. - Ruheng Wang; Junru Jin; Quan Zou 001; Kenta Nakai; Leyi Wei (Bioinform., 2022)

Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. - Kenta Nakai; Leyi Wei (Frontiers Bioinform., 2022)

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 001; Kenta Nakai; Quan Zou 001; Leyi Wei (Briefings Bioinform., 2023)

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)

Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks. - Xin Zeng; Shu Liu; Bowen Liu; Weihang Zhang; Wanzhe Xu; Fujio Toriumi; Kenta Nakai (BMC Bioinform., 2025)