Kenta Nakai

According to our database1, Kenta Nakai authored at least 62 papers between 1994 and 2022.

Collaborative distances:



In proceedings 
PhD thesis 




Predicting protein-peptide binding residues via interpretable deep learning.
Bioinform., 2022

Protein design via deep learning.
Briefings Bioinform., 2022

A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations.
BMC Bioinform., 2021

OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data.
Bioinform., 2021

Prediction of Protein Localization.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

Prediction of Protein-Binding Sites in DNA Sequences.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019

DBTSS/DBKERO for integrated analysis of transcriptional regulation.
Nucleic Acids Res., 2018

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.
Nucleic Acids Res., 2018

Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers.
J. Bioinform. Comput. Biol., 2018

Introduction to Selected Papers from GIW2018.
J. Bioinform. Comput. Biol., 2018

TimeXNet Web: identifying cellular response networks from diverse omics time-course data.
Bioinform., 2018

OpenTein: a database of digital whole-slide images of stem cell-derived teratomas.
Nucleic Acids Res., 2016

A study on the application of topic models to motif finding algorithms.
BMC Bioinform., 2016

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
Nucleic Acids Res., 2015

DBTMEE: a database of transcriptome in mouse early embryos.
Nucleic Acids Res., 2015

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.
Database J. Biol. Databases Curation, 2015

A Genetic Algorithm for Motif Finding Based on Statistical Significance.
Proceedings of the Bioinformatics and Biomedical Engineering, 2015

TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles.
BMC Syst. Biol., 2014

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response.
PLoS Comput. Biol., 2013

Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana.
BMC Syst. Biol., 2013

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012.
Nucleic Acids Res., 2012

A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment.
J. Bioinform. Comput. Biol., 2012

Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

HitPredict: a database of quality assessed protein-protein interactions in nine species.
Nucleic Acids Res., 2011

A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns.
BMC Bioinform., 2011

Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping.
Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.
Nucleic Acids Res., 2010

InCoB2010 - 9<sup>th </sup>International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010.
BMC Bioinform., 2010

Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution.
BMC Bioinform., 2010

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

DBTBS: a database of transcriptional regulation in <i>Bacillus subtilis</i> containing upstream intergenic conservation information.
Nucleic Acids Res., 2008

Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.
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>.
Nucleic Acids Res., 2007

WoLF PSORT: protein localization predictor.
Nucleic Acids Res., 2007

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

DBTGR: a database of tunicate promoters and their regulatory elements.
Nucleic Acids Res., 2006

Protein Subcellular Localisation Prediction with WoLF PSORT.
Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

Prediction of Transcriptional Terminators in <i>Bacillus subtilis</i> and Related Species.
PLoS Comput. Biol., 2005

Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues.
Nucleic Acids Res., 2005

Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis.
Proceedings of the Biocomputing 2005, 2005

An O(N<sup>2</sup>) Algorithm for Discovering Optimal Boolean Pattern Pairs.
IEEE ACM Trans. Comput. Biol. Bioinform., 2004

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

BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.
Nucleic Acids Res., 2004

Large-scale collection and characterization of promoters of human and mouse genes.
Silico Biol., 2004

Finding Optimal Pairs of Patterns.
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Parameter Landscape Analysis for Common Motif Discovery Programs.
Proceedings of the Regulatory Genomics, 2004

Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.
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.
Proceedings of the Discovery Science, 7th International Conference, 2004

PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria.
Nucleic Acids Res., 2003

MELINA: motif extraction from promoter regions of potentially co-regulated genes.
Bioinform., 2003

Intrasplicing - Analysis of Long Intron Sequences.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.
Nucleic Acids Res., 2002

Extensive feature detection of N-terminal protein sorting signals.
Bioinform., 2002

DBTBS: a database of Bacillus subtilis promoters and transcription factors.
Nucleic Acids Res., 2001

ORI-GENE: gene classification based on the evolutionary tree.
Bioinform., 2001

Views: Fundamental Building Blocks in the Process of Knowledge Discovery.
Proceedings of the Fourteenth International Florida Artificial Intelligence Research Society Conference, 2001

Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov models.
Bioinform., 1999

Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.
Bioinform., 1998

Functional Prediction of B. subtilis Genes from Their Regulatory Sequences.
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.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins.
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

Gnome - an Internet-based sequence analysis tool.
Comput. Appl. Biosci., 1994