Kenta Nakai

发表

Parameter Landscape Analysis for Common Motif Discovery Programs

Natalia Polouliakh, Michiko Konno, Paul Horton, 2004, Regulatory Genomics.

Gnome - an Internet-based sequence analysis tool

Kenta Nakai, T. Tokimori, A. Ogiwara, 1994, Comput. Appl. Biosci..

Computational prediction of subcellular localization.

Kenta Nakai, Paul Horton, K. Nakai, 2007, Methods in molecular biology.

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

Kenta Nakai, Yutaka Suzuki, Sumio Sugano, 2005, Nucleic Acids Res..

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

Masato Ishikawa, Kenta Nakai, Kiyoshi Asai, 1998, Bioinform..

Extensive feature detection of N-terminal protein sorting signals

Satoru Miyano, Kenta Nakai, Hideo Bannai, 2002, Bioinform..

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

Yosvany López, Kenta Nakai, Ashwini Patil, 2018, Bioinform..

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

Kenta Nakai, Ashwini Patil, Yutaka Suzuki, 2013, PLoS Comput. Biol..

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

Kenta Nakai, Tetsushi Yada, Yasushi Totoki, 1999, Bioinform..

Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species

Satoru Miyano, Kenta Nakai, Yuko Makita, 2005, PLoS Comput. Biol..

Gnome: Recent Developments

Kenta Nakai, Ikuo Uchiyama, Toshiyuki Niiyama, 1994 .

DBTMEE: a database of transcriptome in mouse early embryos

Kenta Nakai, Sung-Joon Park, Katsuhiko Shirahige, 2014, Nucleic Acids Res..

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

Shinzaburo Noguchi, Kenta Nakai, Toshihisa Takagi, 2004, Nucleic Acids Res..

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

Kenta Nakai, Sung-Joon Park, K. Nakai, 2011, BMC Bioinformatics.

An assessment of prediction algorithms for nucleosome positioning.

Kenta Nakai, Yoshiaki Tanaka, K. Nakai, 2009, Genome informatics. International Conference on Genome Informatics.

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

Yosvany López, Kenta Nakai, Ashwini Patil, 2013, BMC Systems Biology.

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

Kenta Nakai, Toshihisa Takagi, Natalia V. Poluliakh, 2003, Bioinform..

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

Kenta Nakai, Yutaka Suzuki, Sumio Sugano, 2014, Nucleic Acids Res..

A Genetic Algorithm for Motif Finding Based on Statistical Significance

Kenta Nakai, Martin C. Frith, Josep Basha Gutierrez, 2015, IWBBIO.

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

Kenta Nakai, Ashwini Patil, Shunsuke Teraguchi, 2012, Pacific Symposium on Biocomputing.

PROTEIN SUBCELLULAR LOCALIZATION PREDICTION WITH WOLF PSORT

Paul Horton, Kenta Nakai, Keun-Joon Park, 2005 .

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

Kenta Nakai, Yuko Makita, Naotake Ogasawara, 2004, Nucleic Acids Res..

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

Kenta Nakai, Josep Basha Gutierrez, 2016, BMC Bioinformatics.

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

Paul Horton, Kenta Nakai, K. Nakai, 1996, ISMB.

Introduction to Selected Papers from GIW2018

Limsoon Wong, Yun Zheng, Kenta Nakai, 2018, J. Bioinform. Comput. Biol..

Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis

Satoru Miyano, Kenta Nakai, Yuko Makita, 2005, Pacific Symposium on Biocomputing.

Views: Fundamental Building Blocks in the Process of Knowledge Discovery

Satoru Miyano, Kenta Nakai, Hideo Bannai, 2001, FLAIRS.

Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance

Ayumi Shinohara, Satoru Miyano, Kenta Nakai, 2004, Discovery Science.

DBTSS: database of transcription start sites, progress report 2008

Kenta Nakai, Yutaka Suzuki, Sumio Sugano, 2007, Nucleic Acids Res..

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

Kenta Nakai, Myungjin Moon, K. Nakai, 2018, J. Bioinform. Comput. Biol..

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

Kenta Nakai, Yuko Makita, Riu Yamashita, 1996, Nucleic Acids Res..

Finding Optimal Pairs of Patterns

Ayumi Shinohara, Satoru Miyano, Kenta Nakai, 2004, WABI.

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

Kengo Kinoshita, Kenta Nakai, Shinpei Hayashi, 2006, Nucleic Acids Res..

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

Kenta Nakai, Asako Koike, Kouichi Kimura, 2011, WABI.

Functional Prediction of B. subtilis Genes from Their Regulatory Sequences

Kenta Nakai, Tetsushi Yada, Yasushi Totoki, 1997, ISMB.

"Melina" - Novel Tool for Elucidation of Consensus Motif in the Promoter Regions of Functionally Related DNA Sequences

Kenta Nakai, Toshihisa Takagi, Natalia Poluliakh, 2001 .

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

Yosvany López, Kenta Nakai, Ashwini Patil, 2015, Database J. Biol. Databases Curation.

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012

Kenta Nakai, Yutaka Suzuki, Sumio Sugano, 2011, Nucleic Acids Res..

USING SIMPLE RULES ON PRESENCE AND POSITIONING OF MOTIFS FOR PROMOTER STRUCTURE MODELING AND TISSUE-SPECIFIC EXPRESSION PREDICTION

Kenta Nakai, Alexis Vandenbon, 2008 .

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

Satoru Miyano, Kenta Nakai, Seiya Imoto, 2004, ISMB/ECCB.

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

Paul Horton, Kenta Nakai, K. Nakai, 1997, ISMB.

DBTGR: a database of tunicate promoters and their regulatory elements

Kengo Kinoshita, Kenta Nakai, Keun-Joon Park, 2006, Nucleic Acids Res..

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

Kenta Nakai, Kohji Okamura, Kazuaki A. Matsumoto, 2010, BMC Bioinformatics.

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

Kenta Nakai, Asako Koike, Kouichi Kimura, 2012, J. Bioinform. Comput. Biol..

InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010

Tin Wee Tan, Kenta Nakai, Shoba Ranganathan, 2010, BMC Bioinformatics.

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

Kenta Nakai, Yuko Makita, Michiel J. L. de Hoon, 2007, Nucleic Acids Res..

BTSS, DataBase of Transcriptional Start Sites: progress report 2004

Kenta Nakai, Yutaka Suzuki, Sumio Sugano, 2004, Nucleic Acids Res..

DBTSS/DBKERO for integrated analysis of transcriptional regulation

Kenta Nakai, Yutaka Suzuki, Sumio Sugano, 2017, Nucleic Acids Res..

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

Alexander E. Kel, Kenta Nakai, Toshihisa Takagi, 2004, Silico Biol..

Nucleic Acids Research Advance Access published May 21, 2007 WoLF PSORT: protein localization predictor

Paul Horton, Kenta Nakai, Keun-Joon Park, 2007 .

Intrasplicing - Analysis of Long Intron Sequences

Satoru Miyano, Kenta Nakai, Hideo Bannai, 2002, Pacific Symposium on Biocomputing.

Biochemistry and Internet's utilization. 3. Sequence analysis by network.

Kenta Nakai, 1996 .

DBTSS provides a tissue specific dynamic view of Transcription Start Sites

Kenta Nakai, Yutaka Suzuki, Sumio Sugano, 2009, Nucleic Acids Res..

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

Kenta Nakai, Yutaka Suzuki, Sumio Sugano, 2002, Nucleic Acids Res..

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

Ke Wang, Christophe G. Lambert, Martin Ester, 2003, Nucleic Acids Res..

ORI-GENE: gene classification based on the evolutionary tree

Kenta Nakai, Akinori Sarai, Yoshimasa Tanaka, 2001, Bioinform..

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

Kenta Nakai, Ashwini Patil, K. Nakai, 2014, BMC Systems Biology.

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

Haruki Nakamura, Kenta Nakai, Ashwini Patil, 2010, Nucleic Acids Res..

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

Frédéric Delsuc, Patrick Lemaire, Kenta Nakai, 2017, Nucleic Acids Res..

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

Ayumi Shinohara, Satoru Miyano, Kenta Nakai, 2004, IEEE ACM Trans. Comput. Biol. Bioinform..

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

Kenta Nakai, Sung-Joon Park, K. Nakai, 2021, Bioinform..

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

Kenta Nakai, Sung-Joon Park, Hao Jia, 2021, BMC Bioinformatics.

Genome Structure, Functional Genomics, and Proteomics in Ascidians

Kenta Nakai, Kazuo Inaba, Yasunori Sasakura, 2012 .

Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)

Tin Wee Tan, Kenta Nakai, Shoba Ranganathan, 2010, BMC Genomics.

Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus integration sites

Yosvany López, Kenta Nakai, Sumio Sugano, 2014, Genome Medicine.

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.

Kenta Nakai, Sumio Sugano, Riu Yamashita, 2011, Genome research.

PrognoScan: a new database for meta-analysis of the prognostic value of genes

Kenta Nakai, Hideaki Mizuno, Akinori Sarai, 2009, BMC Medical Genomics.

Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes.

Kenta Nakai, Sumio Sugano, Hiroyuki Wakaguri, 2007, Genome research.

Pseudocounts for transcription factor binding sites

Kenta Nakai, Martin C. Frith, K. Nakai, 2008, Nucleic acids research.

Evaluation of Sequence Features from Intrinsically Disordered Regions for the Estimation of Protein Function

Satoru Miyano, Abdollah Dehzangi, Kenta Nakai, 2014, PloS one.

Biomarker discovery by integrated joint non-negative matrix factorization and pathway signature analyses

Kenta Nakai, Naoya Fujita, K. Nakai, 2018, Scientific Reports.

Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst

Kenta Nakai, Fahong Yu, Miki Sakatani, 2012, BMC Developmental Biology.

Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks

Kengo Kinoshita, Kenta Nakai, Ashwini Patil, 2011, BMC Genomics.

Genome informatics for data-driven biology

Kenta Nakai, Jean-Philippe Vert, 2002, Genome Biology.

Computational Promoter Modeling Identifies the Modes of Transcriptional Regulation in Hematopoietic Stem Cells

Kenta Nakai, Masayuki Yamato, Sung-Joon Park, 2014, PloS one.

Retrotransposition as a Source of New Promoters

Kenta Nakai, Kohji Okamura, K. Okamura, 2008, Molecular biology and evolution.

Refinement of The Prediction Methods of Signal Peptides for The Genome Analyses of Saccharomyces cerevisiae and Bacillus subtilis

Kenta Nakai, K. Nakai, 1996 .

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals

Kenta Nakai, Makiko Suwa, Chie Motono, 2005, Nucleic acids research.

Clonality of HTLV-1-infected T cells as a risk indicator for development and progression of adult T-cell leukemia.

Kenta Nakai, K. Nakai, Yutaka Suzuki, 2017, Blood advances.

Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species

Kenta Nakai, Toshihisa Takagi, Goro Terai, 2001, Genome Biology.

Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis

Kenta Nakai, Rui Yokomori, K. Nakai, 2016, Genome research.

Genomic cis-regulatory networks in the early Ciona intestinalis embryo

Kenta Nakai, Nobuhiro Suzuki, Yutaka Satou, 2010, Development.

Stable feature selection based on the ensemble L1-norm support vector machine for biomarker discovery

Kenta Nakai, Myungjin Moon, K. Nakai, 2016, BMC Genomics.

Modeling tissue-specific structural patterns in human and mouse promoters

Kenta Nakai, Alexis Vandenbon, K. Nakai, 2009, Nucleic acids research.

Inferring clonal structure in HTLV-1-infected individuals: towards bridging the gap between analysis and visualization

Kenta Nakai, Wojciech Makałowski, K. Nakai, 2017, Human Genomics.

Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues

Kenta Nakai, Ashwini Patil, Tarjei S. Mikkelsen, 2017, Cell.

DBTSS: DataBase of Human Transcriptional Start Sites and Full-Length cDNA

Kenta Nakai, Sumio Sugano, Riu Yamashita, 2001 .