Works by Nakai, Kenta

Results: 124

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

Published in:

Human Genomics, 2017, v. 11, p. 1, doi. 10.1186/s40246-017-0112-8

By:

Farmanbar, Amir;
Firouzi, Sanaz;
Makałowski, Wojciech;
Masako Iwanaga;
Kaoru Uchimaru;
Utsunomiya, Atae;
Toshiki Watanabe;
Kenta Nakai

Publication type:

Article

The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection.

Published in:

Nature Immunology, 2010, v. 11, n. 10, p. 936, doi. 10.1038/ni.1920

By:

Satoh, Takashi;
Takeuchi, Osamu;
Vandenbon, Alexis;
Yasuda, Koubun;
Tanaka, Yoshiaki;
Kumagai, Yutaro;
Miyake, Tohru;
Matsushita, Kazufumi;
Okazaki, Toshihiko;
Saitoh, Tatsuya;
Honma, Kiri;
Matsuyama, Toshifumi;
Yui, Katsuyuki;
Tsujimura, Tohru;
Standley, Daron M.;
Nakanishi, Kenji;
Nakai, Kenta;
Akira, Shizuo

Publication type:

Article

Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization.

Published in:

Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2023.1304778

By:

Yubo Zhang;
Wenbo Yang;
Yutaro Kumagai;
Loza, Martin;
Weihang Zhang;
Sung-Joon Park;
Kenta Nakai

Publication type:

Article

Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences.

Published in:

Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.607812

By:

Imai, Kenichiro;
Nakai, Kenta

Publication type:

Article

STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning for domain exploration and alignment-free integration.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-56276-0

By:

Yang, Yitao;
Cui, Yang;
Zeng, Xin;
Zhang, Yubo;
Loza, Martin;
Park, Sung-Joon;
Nakai, Kenta

Publication type:

Article

Predicting protein–peptide binding residues via interpretable deep learning.

Published in:

Bioinformatics, 2022, v. 38, n. 13, p. 3351, doi. 10.1093/bioinformatics/btac352

By:

Wang, Ruheng;
Jin, Junru;
Zou, Quan;
Nakai, Kenta;
Wei, Leyi

Publication type:

Article

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

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3021, doi. 10.1093/bioinformatics/btab101

By:

Park, Sung-Joon;
Nakai, Kenta

Publication type:

Article

Genomic analysis of pancreatic juice DNA assesses malignant risk of intraductal papillary mucinous neoplasm of pancreas.

Published in:

Cancer Medicine, 2019, v. 8, n. 10, p. 4565, doi. 10.1002/cam4.2340

By:

Mateos, Raúl N.;
Nakagawa, Hidewaki;
Hirono, Seiko;
Takano, Shinichi;
Fukasawa, Mitsuharu;
Yanagisawa, Akio;
Yasukawa, Satoru;
Maejima, Kazuhiro;
Oku‐Sasaki, Aya;
Nakano, Kaoru;
Dutta, Munmee;
Tanaka, Hiroko;
Miyano, Satoru;
Enomoto, Nobuyuki;
Yamaue, Hiroki;
Nakai, Kenta;
Fujita, Masashi

Publication type:

Article

Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells.

Published in:

Journal of Human Genetics, 2008, v. 53, n. 2, p. 185, doi. 10.1007/s10038-007-0228-0

By:

Hatada, Izuho;
Morita, Sumiyo;
Kimura, Mika;
Horii, Takuro;
Yamashita, Riu;
Nakai, Kenta

Publication type:

Article

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012.

Published in:

Nucleic Acids Research, 2012, p. D150, doi. 10.1093/nar/gkr1005

By:

Yamashita, Riu;
Sugano, Sumio;
Suzuki, Yutaka;
Nakai, Kenta

Publication type:

Article

Predicting promoter activities of primary human DNA sequences.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 11, p. e75, doi. 10.1093/nar/gkr173

By:

Irie, Takuma;
Park, Sung-Joon;
Yamashita, Riu;
Seki, Masahide;
Yada, Tetsushi;
Sugano, Sumio;
Nakai, Kenta;
Suzuki, Yutaka

Publication type:

Article

Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 7, p. 2638, doi. 10.1093/nar/gkq1151

By:

Khare, Parul;
Mortimer, Sandra I.;
Cleto, Cynthia L.;
Okamura, Kohji;
Suzuki, Yutaka;
Kusakabe, Takehiro;
Nakai, Kenta;
Meedel, Thomas H.;
Hastings, Kenneth E. M.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D744, doi. 10.1093/nar/gkq897

By:

Patil, Ashwini;
Nakai, Kenta;
Nakamura, Haruki

Publication type:

Article

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

Published in:

Nucleic Acids Research, 2010, v. 38, p. D98, doi. 10.1093/nar/gkp1017

By:

Riu Yamashita;
Hiroyuki Wakaguri;
Sumio Sugano;
Yutaka Suzuki;
Kenta Nakai

Publication type:

Article

Modeling tissue-specific structural patterns in human and mouse promoters.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 1, p. 17, doi. 10.1093/nar/gkp866

By:

Vandenbon, Alexis;
Nakai, Kenta

Publication type:

Article

Massive transcriptional start site analysis of human genes in hypoxia cells.

Published in:

Nucleic Acids Research, 2009, v. 37, n. 7, p. 2249, doi. 10.1093/nar/gkp066

By:

Tsuchihara, Katsuya;
Suzuki, Yutaka;
Wakaguri, Hiroyuki;
Irie, Takuma;
Tanimoto, Kousuke;
Hashimoto, Shin-ichi;
Matsushima, Kouji;
Mizushima-Sugano, Junko;
Yamashita, Riu;
Nakai, Kenta;
Bentley, David;
Esumi, Hiroyasu;
Sugano, Sumio

Publication type:

Article

Pseudocounts for transcription factor binding sites.

Published in:

Nucleic Acids Research, 2009, v. 37, n. 3, p. 939, doi. 10.1093/nar/gkn1019

By:

Nishida, Keishin;
Frith, Martin C.;
Nakai, Kenta

Publication type:

Article

Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 11, p. 3707, doi. 10.1093/nar/gkn248

By:

Yamashita, Riu;
Suzuki, Yutaka;
Takeuchi, Nono;
Wakaguri, Hiroyuki;
Ueda, Takuya;
Sugano, Sumio;
Nakai, Kenta

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2008, v. 36, p. D93, doi. 10.1093/nar/gkm910

By:

Sierro, Nicolas;
Makita, Yuko;
de Hoon, Michiel;
Nakai, Kenta

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2008, v. 36, p. D97

By:

Wakaguri, Hiroyuki;
Yamashita, Riu;
Suzuki, Yutaka;
Sugano, Sumio;
Nakai, Kenta

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W227, doi. 10.1093/nar/gkm362

By:

Okumura, Toshiyuki;
Makiguchi, Hiroki;
Makita, Yuko;
Yamashita, Riu;
Nakai, Kenta

Publication type:

Article

WoLF PSORT: protein localization predictor.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W585, doi. 10.1093/nar/gkm259

By:

Horton, Paul;
Park, Keun-Joon;
Obayashi, Takeshi;
Fujita, Naoya;
Harada, Hajime;
Adams-Collier, C.J.;
Nakai, Kenta

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2007, v. 35, p. d863, doi. 10.1093/nar/gkl783

By:

Obayashi, Takeshi;
Kinoshita, Kengo;
Nakai, Kenta;
Shibaoka, Masayuki;
Hayashi, Shinpei;
Saeki, Motoshi;
Shibata, Daisuke;
Saito, Kazuki;
Ohta, Hiroyuki

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d86, doi. 10.1093/nar/gkj129

By:

Yamashita, Riu;
Suzuki, Yutaka;
Wakaguri, Hiroyuki;
Tsuritani, Katsuki;
Nakai, Kenta;
Sugano, Sumio

Publication type:

Article

DBTGR: a database of tunicate promoters and their regulatory elements.

Published in:

Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d552, doi. 10.1093/nar/gkj064

By:

Sierro, Nicolas;
Kusakabe, Takehiro;
Park, Keun-Joon;
Yamashita, Riu;
Kinoshita, Kengo;
Nakai, Kenta

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2005, v. 33, n. 8, p. 2355, doi. 10.1093/nar/gki520

By:

Nakao, Mitsuteru;
Barrero, Roberto A.;
Mukai, Yuri;
Motono, Chie;
Suwa, Makiko;
Nakai, Kenta

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d533

By:

Kato, Kikuya;
Yamashita, Riu;
Matoba, Ryo;
Monden, Morito;
Noguchi, Shinzaburo;
Takagi, Toshihisa;
Nakai, Kenta

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d75

By:

Makita, Yuko;
Nakao, Mitsuteru;
Ogasawara, Naotake;
Nakai, Kenta

Publication type:

Article

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d78

By:

Suzuki, Yutaka;
Yamashita, Riu;
Sugano, Sumio;
Nakai, Kenta

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2003, v. 31, n. 13, p. 3613, doi. 10.1093/nar/gkg602

By:

Gardy, Jennifer L.;
Spencer, Cory;
Wang, Ke;
Ester, Martin;
Tusnády, Gábor E.;
Simon, István;
Hua, Sujun;
deFays, Katalin;
Lambert, Christophe;
Nakai, Kenta;
Brinkman, Fiona S.L.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2002, v. 30, n. 1, p. 328, doi. 10.1093/nar/30.1.328

By:

Suzuki, Yutaka;
Yamashita, Riu;
Nakai, Kenta;
Sugano, Sumio

Publication type:

Article

Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation.

Published in:

Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1524-z

By:

Vandenbon, Alexis;
Kumagai, Yutaro;
Lin, Mengjie;
Suzuki, Yutaka;
Nakai, Kenta

Publication type:

Article

A hypothetical trivalent epigenetic code that affects the nature of human ESCs.

Published in:

PLoS ONE, 2020, v. 15, n. 9, p. 1, doi. 10.1371/journal.pone.0238742

By:

Ishikawa, Yasuhisa;
Nakai, Kenta

Publication type:

Article

Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma.

Published in:

BMC Medical Genomics, 2019, v. 11, n. 7, p. N.PAG, doi. 10.1186/s12920-018-0437-8

By:

Nagai, Luis Augusto Eijy;
Park, Sung-Joon;
Nakai, Kenta

Publication type:

Article

Assessment of prediction accuracy of protein function from protein-protein interaction data.

Published in:

Yeast, 2001, v. 18, n. 6, p. 523, doi. 10.1002/yea.706

By:

Hishigaki, Haretsugu;
Nakai, Kenta;
Ono, Toshihide;
Tanigami, Akira;
Takagi, Toshihisa

Publication type:

Article

Expert system for predicting protein localization sites in gram-negative bacteria.

Published in:

Proteins, 1991, v. 11, n. 2, p. 95, doi. 10.1002/prot.340110203

By:

Nakai, Kenta;
Kanehisa, Minoru

Publication type:

Article

An Alternative-Exon Database and Its Statistical Analysis.

Published in:

DNA & Cell Biology, 2000, v. 19, n. 12, p. 739, doi. 10.1089/104454900750058107

By:

Stamm, Stefan;
Zhu, Jian;
Nakai, Kenta;
Stoilov, Peter;
Stoss, Oliver;
Zhang, Michael Q.

Publication type:

Article

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

Published in:

Bioinformatics, 2003, v. 19, n. 3, p. 423, doi. 10.1093/bioinformatics/btf872

By:

Poluliakh, Natalia;
Takagi, Toshihisa;
Nakai, Kenta

Publication type:

Article

Extensive feature detection of N-terminal protein sorting signals.

Published in:

Bioinformatics, 2002, v. 18, n. 2, p. 298, doi. 10.1093/bioinformatics/18.2.298

By:

Bannai, Hideo;
Tamada, Yoshinori;
Maruyama, Osamu;
Nakai, Kenta;
Miyano, Satoru

Publication type:

Article

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

Published in:

Bioinformatics, 2001, v. 17, n. 2, p. 167, doi. 10.1093/bioinformatics/17.2.167

By:

Mizuno, Hideaki;
Tanaka, Yoshimasa;
Nakai, Kenta;
Sarai, Akinori

Publication type:

Article

Modeling and predicting transcriptional units of Escherichia coligenes using hidden Markov models.

Published in:

Bioinformatics, 1999, v. 15, n. 12, p. 987, doi. 10.1093/bioinformatics/15.12.987

By:

Yada, Tetsushi;
Nakao, Mitsuteru;
Totoki, Yasushi;
Nakai, Kenta

Publication type:

Article

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

Published in:

Bioinformatics, 1998, v. 14, n. 4, p. 317, doi. 10.1093/bioinformatics/14.4.317

By:

Yada, Tetsushi;
Totoki, Yasushi;
Ishikawa, Masato;
Asai, Kiyoshi;
Nakai, Kenta

Publication type:

Article

Signaling Pathway of Taurine-Induced Upregulation of TXNIP.

Published in:

Metabolites (2218-1989), 2022, v. 12, n. 7, p. N.PAG, doi. 10.3390/metabo12070636

By:

Satsu, Hideo;
Gondo, Yusuke;
Shimanaka, Hana;
Imae, Masato;
Murakami, Shigeru;
Watari, Kenji;
Wakabayashi, Shunichi;
Park, Sung-Joon;
Nakai, Kenta;
Shimizu, Makoto

Publication type:

Article

The Exon Junction Complex Controls the Efficient and Faithful Splicing of a Subset of Transcripts Involved in Mitotic Cell-Cycle Progression.

Published in:

International Journal of Molecular Sciences, 2016, v. 17, n. 8, p. 1153, doi. 10.3390/ijms17081153

By:

Kazuhiro Fukumura;
Shunichi Wakabayashi;
Naoyuki Kataoka;
Hiroshi Sakamoto;
Yutaka Suzuki;
Kenta Nakai;
Akila Mayeda;
Kunio Inoue

Publication type:

Article

Genome-Wide Analysis of DNA Methylation and Expression of MicroRNAs in Breast Cancer Cells.

Published in:

International Journal of Molecular Sciences, 2012, v. 13, n. 7, p. 8259, doi. 10.3390/ijms13078259

By:

Morita, Sumiyo;
Takahashi, Ryou-u;
Yamashita, Riu;
Toyoda, Atsushi;
Horii, Takuro;
Kimura, Mika;
Fujiyama, Asao;
Nakai, Kenta;
Tajima, Shoji;
Matoba, Ryo;
Ochiya, Takahiro;
Hatada, Izuho

Publication type:

Article

Prediction of subcellular locations of proteins: Where to proceed?

Published in:

Proteomics, 2010, v. 10, n. 22, p. 3970, doi. 10.1002/pmic.201000274

By:

Imai, Kenichiro;
Nakai, Kenta

Publication type:

Article

HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing data.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae152

By:

Zhang, Weihang;
Cui, Yang;
Liu, Bowen;
Loza, Martin;
Park, Sung-Joon;
Nakai, Kenta

Publication type:

Article

CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad352

By:

Li, Zhongshen;
Jin, Junru;
He, Wenjia;
Long, Wentao;
Yu, Haoqing;
Gao, Xin;
Nakai, Kenta;
Zou, Quan;
Wei, Leyi

Publication type:

Article

Protein design via deep learning.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac102

By:

Ding, Wenze;
Nakai, Kenta;
Gong, Haipeng

Publication type:

Article

Characterizing Promoter and Enhancer Sequences by a Deep Learning Method.

Published in:

Frontiers in Genetics, 2021, v. 11, p. 1, doi. 10.3389/fgene.2021.681259

By:

Zeng, Xin;
Park, Sung-Joon;
Nakai, Kenta

Publication type:

Article