Kenta Nakai

72 papers A 3B 2C 2Misc 4Journal 52Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
Establishing the Asia & Pacific Bioinformatics Joint Congress: a historic milestone in regional bioinformatics collaboration.
Briefings Bioinform.
Asif M. Khan, Susumu Goto, Kenta Nakai, Limsoon Wong, Diane E. Kovats, Yuki Saito, Shinya Ikematsu, Yoshihiro Yamanishi, Nurul Salwanie Che Wahid, Harpreet Singh, Pradeep Eranti, Yi-Ping Phoebe Chen, Tae-Min Kim, Shinn-Ying Ho, Jessica Cara Mar, Wataru Iwasaki, Jayaraman Valadi, Prashanth Suravajhala, Christian Schönbach, Tin Wee Tan, Shoba Ranganathan, Kiyoko F. Aoki-Kinoshita
2025 J jnl
Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks.
BMC Bioinform.
Xin Zeng, Shu Liu, Bowen Liu, Weihang Zhang, Wanzhe Xu, Fujio Toriumi, Kenta Nakai
2025 J jnl
OmniTFT: Omni Target Forecasting for Vital Signs and Laboratory Result Trajectories in Multi Center ICU Data.
CoRR
Wanzhe Xu, Yutong Dai, Yitao Yang, Martin Loza, Weihang Zhang, Yang Cui, Xin Zeng, Sung Joon Park, Kenta Nakai
2024 J jnl
HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.
Briefings Bioinform.
Weihang Zhang, Yang Cui, Bowen Liu, Martin Loza, Sung-Joon Park, Kenta Nakai
2023 J jnl
CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides.
Briefings Bioinform.
Zhongshen Li, Junru Jin, Wenjia He, Wentao Long, Haoqing Yu, Xin Gao, Kenta Nakai, Quan Zou, Leyi Wei
2022 J jnl
Predicting protein-peptide binding residues via interpretable deep learning.
Bioinform.
Ruheng Wang, Junru Jin, Quan Zou, Kenta Nakai, Leyi Wei
2022 J jnl
Protein design via deep learning.
Briefings Bioinform.
Wenze Ding, Kenta Nakai, Haipeng Gong
2022 J jnl
Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics.
Frontiers Bioinform.
Kenta Nakai, Leyi Wei
2022 — conf
SignedS2V: Structural Embedding Method for Signed Networks.
COMPLEX NETWORKS (1)
Shu Liu, Fujio Toriumi, Xin Zeng, Mao Nishiguchi, Kenta Nakai
2021 J jnl
A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations.
BMC Bioinform.
Hao Jia, Sung-Joon Park, Kenta Nakai
2021 J jnl
OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data.
Bioinform.
Sung-Joon Park, Kenta Nakai
2019 — book
Encyclopedia of Bioinformatics and Computational Biology - Volume 1
Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach
2019 — book
Encyclopedia of Bioinformatics and Computational Biology - Volume 2
Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach
2019 — book
Encyclopedia of Bioinformatics and Computational Biology - Volume 3
Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach
2019 — ch.
Prediction of Protein Localization.
Encyclopedia of Bioinformatics and Computational Biology (2)
Kenta Nakai, Kenichiro Imai
2019 — ch.
Prediction of Protein-Binding Sites in DNA Sequences.
Encyclopedia of Bioinformatics and Computational Biology (3)
Kenta Nakai
2018 J jnl
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.
Nucleic Acids Res.
Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Magali Naville, Kazuhiro R. Nitta, Jacques Piette, Wendy Reeves, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin Jacox, Elijah K. Lowe, Mickaël Mendez, Alexis Roberge, Alberto Stolfi, Rui Yokomori, C. Titus Brown, Christian Cambillau, Lionel A. Christiaen, Frédéric Delsuc, Emmanuel J. P. Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie J. Swalla, Michael Veeman, Jean-Nicolas Volff, Patrick Lemaire
2018 J jnl
DBTSS/DBKERO for integrated analysis of transcriptional regulation.
Nucleic Acids Res.
Ayako Suzuki, Shin Kawano, Toutai Mituyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki
2018 J jnl
Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers.
J. Bioinform. Comput. Biol.
Myungjin Moon, Kenta Nakai
2018 J jnl
Introduction to Selected Papers from GIW2018.
J. Bioinform. Comput. Biol.
Jinyan Li, Kenta Nakai, Yun Zheng, Kengo Sato, Limsoon Wong
2018 J jnl
TimeXNet Web: identifying cellular response networks from diverse omics time-course data.
Bioinform.
Phit Ling Tan, Yosvany López, Kenta Nakai, Ashwini Patil
2016 J jnl
A study on the application of topic models to motif finding algorithms.
BMC Bioinform.
Josep Basha Gutierrez, Kenta Nakai
2016 J jnl
OpenTein: a database of digital whole-slide images of stem cell-derived teratomas.
Nucleic Acids Res.
Sung-Joon Park, Yusuke Komiyama, Hirofumi Suemori, Akihiro Umezawa, Kenta Nakai
2015 — conf
A Genetic Algorithm for Motif Finding Based on Statistical Significance.
IWBBIO (1)
Josep Basha Gutierrez, Martin C. Frith, Kenta Nakai
2015 J jnl
DBTMEE: a database of transcriptome in mouse early embryos.
Nucleic Acids Res.
Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi, Kenta Nakai
2015 J jnl
DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
Nucleic Acids Res.
Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, Kenta Nakai
2015 J jnl
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.
Database J. Biol. Databases Curation
Yosvany López, Kenta Nakai, Ashwini Patil
2014 J jnl
TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles.
BMC Syst. Biol.
Ashwini Patil, Kenta Nakai
2013 J jnl
Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana.
BMC Syst. Biol.
Yosvany López, Ashwini Patil, Kenta Nakai
2013 J jnl
Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response.
PLoS Comput. Biol.
Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai
2012 J jnl
A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment.
J. Bioinform. Comput. Biol.
Kouichi Kimura, Asako Koike, Kenta Nakai
2012 J jnl
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012.
Nucleic Acids Res.
Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai
2012 Misc conf
Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator.
Pacific Symposium on Biocomputing
Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, Daron M. Standley
2011 J jnl
A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns.
BMC Bioinform.
Sung-Joon Park, Kenta Nakai
2011 J jnl
HitPredict: a database of quality assessed protein-protein interactions in nine species.
Nucleic Acids Res.
Ashwini Patil, Kenta Nakai, Haruki Nakamura
2011 C conf
Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping.
WABI
Kouichi Kimura, Asako Koike, Kenta Nakai
2010 J jnl
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.
Nucleic Acids Res.
Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, Kenta Nakai
2010 J jnl
Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution.
BMC Bioinform.
Kohji Okamura, Kazuaki A. Matsumoto, Kenta Nakai
2010 J jnl
InCoB2010 - 9
BMC Bioinform.
Christian Schönbach, Kenta Nakai, Tin Wee Tan, Shoba Ranganathan
2008 J jnl
DBTBS: a database of transcriptional regulation in
Nucleic Acids Res.
Nicolas Sierro, Yuko Makita, Michiel J. L. de Hoon, Kenta Nakai
2008 J jnl
DBTSS: database of transcription start sites, progress report 2008.
Nucleic Acids Res.
Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai
2007 J jnl
ATTED-II: a database of co-expressed genes and
Nucleic Acids Res.
Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta
2007 J jnl
Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.
Nucleic Acids Res.
Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, Kenta Nakai
2007 J jnl
WoLF PSORT: protein localization predictor.
Nucleic Acids Res.
Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C. J. Adams-Collier, Kenta Nakai
2006 J jnl
DBTGR: a database of tunicate promoters and their regulatory elements.
Nucleic Acids Res.
Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
2006 J jnl
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006.
Nucleic Acids Res.
Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano
2006 B conf
Protein Subcellular Localisation Prediction with WoLF PSORT.
APBC
Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai
2005 Misc conf
Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis.
Pacific Symposium on Biocomputing
Yuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai
2005 J jnl
Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues.
Nucleic Acids Res.
Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai
2005 J jnl
Prediction of Transcriptional Terminators in
PLoS Comput. Biol.
Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano
2004 J jnl
An O(N
IEEE ACM Trans. Comput. Biol. Bioinform.
Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
2004 J jnl
BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.
Nucleic Acids Res.
Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, Kenta Nakai
2004 J jnl
BTSS, DataBase of Transcriptional Start Sites: progress report 2004.
Nucleic Acids Res.
Yutaka Suzuki, Riu Yamashita, Sumio Sugano, Kenta Nakai
2004 B conf
Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance.
Discovery Science
Shunsuke Inenaga, Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
2004 C conf
Finding Optimal Pairs of Patterns.
WABI
Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
2004 J jnl
Large-scale collection and characterization of promoters of human and mouse genes.
Silico Biol.
Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Alexander E. Kel, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Toshihisa Takagi, Kenta Nakai, Sumio Sugano
2004 — conf
Parameter Landscape Analysis for Common Motif Discovery Programs.
Regulatory Genomics
Natalia Polouliakh, Michiko Konno, Paul Horton, Kenta Nakai
2004 — conf
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.
ISMB/ECCB (Supplement of Bioinformatics)
Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano
2003 Misc conf
Intrasplicing - Analysis of Long Intron Sequences.
Pacific Symposium on Biocomputing
Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano
2003 J jnl
MELINA: motif extraction from promoter regions of potentially co-regulated genes.
Bioinform.
Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai
2003 J jnl
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria.
Nucleic Acids Res.
Jennifer L. Gardy, Cory Spencer, Ke Wang, Martin Ester, Gábor E. Tusnády, István Simon, Sujun Hua, Katalin de Fays, Christophe G. Lambert, Kenta Nakai, Fiona S. L. Brinkman
2002 J jnl
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.
Nucleic Acids Res.
Yutaka Suzuki, Riu Yamashita, Kenta Nakai, Sumio Sugano
2002 J jnl
Extensive feature detection of N-terminal protein sorting signals.
Bioinform.
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano
2001 J jnl
DBTBS: a database of Bacillus subtilis promoters and transcription factors.
Nucleic Acids Res.
Takahiro Ishii, Ken-ichi Yoshida, Goro Terai, Yasutaro Fujita, Kenta Nakai
2001 J jnl
ORI-GENE: gene classification based on the evolutionary tree.
Bioinform.
Hideaki Mizuno, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai
2001 Misc conf
Views: Fundamental Building Blocks in the Process of Knowledge Discovery.
FLAIRS
Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano
1999 J jnl
Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov models.
Bioinform.
Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Kenta Nakai
1998 J jnl
Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.
Bioinform.
Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai, Kenta Nakai
1997 A conf
Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier.
ISMB
Paul Horton, Kenta Nakai
1997 A conf
Functional Prediction of B. subtilis Genes from Their Regulatory Sequences.
ISMB
Tetsushi Yada, Yasushi Totoki, Takahiro Ishii, Kenta Nakai
1996 A conf
A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins.
ISMB
Paul Horton, Kenta Nakai
1994 J jnl
Gnome - an Internet-based sequence analysis tool.
Comput. Appl. Biosci.
Kenta Nakai, T. Tokimori, A. Ogiwara, Ikuo Uchiyama, T. Niiyama