Kenta Nakai

According to our database1, Kenta Nakai authored at least 58 papers between 1994 and 2019.

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Bibliography

2019
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

2018
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

2016
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

2015
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

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
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

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
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

2008
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

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

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

2006
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

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

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

2004
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

2003
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

2002
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

2001
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

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
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

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


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