Kenta Nakai
Orcid: 0000-0002-8721-8883
According to our database1,
Kenta Nakai
authored at least 68 papers
between 1994 and 2024.
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Bibliography
2024
HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.
Briefings Bioinform., 2024
2023
CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides.
Briefings Bioinform., September, 2023
2022
Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics.
Frontiers Bioinform., 2022
Bioinform., 2022
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.
BMC Bioinform., 2021
OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data.
Bioinform., 2021
2019
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019
2018
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
TimeXNet Web: identifying cellular response networks from diverse omics time-course data.
Bioinform., 2018
2016
Nucleic Acids Res., 2016
BMC Bioinform., 2016
2015
DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
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
Proceedings of the Bioinformatics and Biomedical Engineering, 2015
2014
TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles.
BMC Syst. Biol., 2014
2013
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
2012
Nucleic Acids Res., 2012
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
2011
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
2010
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
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
2007
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
2006
Nucleic Acids Res., 2006
Nucleic Acids Res., 2006
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.
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
Proceedings of the Biocomputing 2005, 2005
2004
IEEE ACM Trans. Comput. Biol. Bioinform., 2004
Nucleic Acids Res., 2004
BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.
Nucleic Acids Res., 2004
Silico Biol., 2004
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004
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
Proceedings of the Discovery Science, 7th International Conference, 2004
2003
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria.
Nucleic Acids Res., 2003
Bioinform., 2003
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
2002
Nucleic Acids Res., 2002
2001
Nucleic Acids Res., 2001
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.
Bioinform., 1999
1998
Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.
Bioinform., 1998
1997
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
1996
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
1994