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Kenta Nakai
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2020 – today
- 2024
- [j48]Weihang Zhang, Yang Cui
, Bowen Liu, Martin Loza, Sung-Joon Park
, Kenta Nakai
:
HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data. Briefings Bioinform. 25(3) (2024) - 2022
- [j47]Wenze Ding
, Kenta Nakai
, Haipeng Gong
:
Protein design via deep learning. Briefings Bioinform. 23(3) (2022) - [j46]Ruheng Wang, Junru Jin, Quan Zou
, Kenta Nakai
, Leyi Wei
:
Predicting protein-peptide binding residues via interpretable deep learning. Bioinform. 38(13): 3351-3360 (2022) - [j45]Kenta Nakai, Leyi Wei:
Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. Frontiers Bioinform. 2 (2022) - [c15]Shu Liu
, Fujio Toriumi, Xin Zeng, Mao Nishiguchi, Kenta Nakai:
SignedS2V: Structural Embedding Method for Signed Networks. COMPLEX NETWORKS (1) 2022: 337-349 - 2021
- [j44]Sung-Joon Park
, Kenta Nakai:
OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data. Bioinform. 37(18): 3021-3022 (2021) - [j43]Hao Jia, Sung-Joon Park
, Kenta Nakai
:
A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations. BMC Bioinform. 22-S(6): 128 (2021)
2010 – 2019
- 2019
- [e3]Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 1. Elsevier 2019, ISBN 978-0-12-811432-2 [contents] - [e2]Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 2. Elsevier 2019, ISBN 978-0-12-811432-2 [contents] - [e1]Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 3. Elsevier 2019, ISBN 978-0-12-811432-2 [contents] - [r2]Kenta Nakai, Kenichiro Imai:
Prediction of Protein Localization. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 53-59 - [r1]Kenta Nakai:
Prediction of Protein-Binding Sites in DNA Sequences. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 447-451 - 2018
- [j42]Phit Ling Tan, Yosvany López, Kenta Nakai, Ashwini Patil
:
TimeXNet Web: identifying cellular response networks from diverse omics time-course data. Bioinform. 34(21): 3764-3765 (2018) - [j41]Myungjin Moon, Kenta Nakai:
Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers. J. Bioinform. Comput. Biol. 16(2): 1850006:1-1850006:20 (2018) - [j40]Jinyan Li, Kenta Nakai, Yun Zheng
, Kengo Sato, Limsoon Wong
:
Introduction to Selected Papers from GIW2018. J. Bioinform. Comput. Biol. 16(6): 1802005:1-1802005:2 (2018) - [j39]Ayako Suzuki, Shin Kawano, Toutai Mituyama
, Mikita Suyama
, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki:
DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucleic Acids Res. 46(Database-Issue): D229-D238 (2018) - [j38]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
:
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res. 46(Database-Issue): D718-D725 (2018) - 2016
- [j37]Josep Basha Gutierrez, Kenta Nakai:
A study on the application of topic models to motif finding algorithms. BMC Bioinform. 17(S-19): 129-138 (2016) - [j36]Sung-Joon Park
, Yusuke Komiyama
, Hirofumi Suemori, Akihiro Umezawa, Kenta Nakai:
OpenTein: a database of digital whole-slide images of stem cell-derived teratomas. Nucleic Acids Res. 44(Database-Issue): 1000-1004 (2016) - 2015
- [j35]Yosvany López
, Kenta Nakai, Ashwini Patil
:
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. Database J. Biol. Databases Curation 2015 (2015) - [j34]Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano
, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. Nucleic Acids Res. 43(Database-Issue): 87-91 (2015) - [j33]Sung-Joon Park
, Katsuhiko Shirahige, Miho Ohsugi
, Kenta Nakai:
DBTMEE: a database of transcriptome in mouse early embryos. Nucleic Acids Res. 43(Database-Issue): 771-776 (2015) - [c14]Josep Basha Gutierrez, Martin C. Frith
, Kenta Nakai:
A Genetic Algorithm for Motif Finding Based on Statistical Significance. IWBBIO (1) 2015: 438-449 - 2014
- [j32]Ashwini Patil
, Kenta Nakai:
TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles. BMC Syst. Biol. 8(S-4): S2 (2014) - 2013
- [j31]Yosvany López
, Ashwini Patil
, Kenta Nakai:
Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana. BMC Syst. Biol. 7(S-3): S10 (2013) - [j30]Ashwini Patil
, Yutaro Kumagai
, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai:
Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response. PLoS Comput. Biol. 9(11) (2013) - 2012
- [j29]Kouichi Kimura, Asako Koike, Kenta Nakai:
A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment. J. Bioinform. Comput. Biol. 10(4) (2012) - [j28]Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Res. 40(Database-Issue): 150-154 (2012) - [c13]Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, Daron M. Standley:
Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator. Pacific Symposium on Biocomputing 2012: 164-175 - 2011
- [j27]Sung-Joon Park
, Kenta Nakai:
A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns. BMC Bioinform. 12(S-1): S50 (2011) - [j26]Ashwini Patil
, Kenta Nakai, Haruki Nakamura:
HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res. 39(Database-Issue): 744-749 (2011) - [c12]Kouichi Kimura, Asako Koike, Kenta Nakai:
Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping. WABI 2011: 151-162 - 2010
- [j25]Christian Schönbach
, Kenta Nakai, Tin Wee Tan, Shoba Ranganathan
:
InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. BMC Bioinform. 11(S-7): S1 (2010) - [j24]Kohji Okamura, Kazuaki A. Matsumoto, Kenta Nakai:
Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution. BMC Bioinform. 11(S-7): S2 (2010) - [j23]Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, Kenta Nakai:
DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Res. 38(Database-Issue): 98-104 (2010)
2000 – 2009
- 2008
- [j22]Nicolas Sierro, Yuko Makita, Michiel J. L. de Hoon
, Kenta Nakai:
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 36(Database-Issue): 93-96 (2008) - [j21]Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai:
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res. 36(Database-Issue): 97-101 (2008) - 2007
- [j20]Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi
, Motoshi Saeki, Daisuke Shibata, Kazuki Saito
, Hiroyuki Ohta
:
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res. 35(Database-Issue): 863-869 (2007) - [j19]Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita
, Riu Yamashita, Kenta Nakai:
Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. Nucleic Acids Res. 35(Web-Server-Issue): 227-231 (2007) - [j18]Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C. J. Adams-Collier, Kenta Nakai:
WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35(Web-Server-Issue): 585-587 (2007) - 2006
- [j17]Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano:
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res. 34(Database-Issue): 86-89 (2006) - [j16]Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai:
DBTGR: a database of tunicate promoters and their regulatory elements. Nucleic Acids Res. 34(Database-Issue): 552-555 (2006) - [c11]Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai:
Protein Subcellular Localisation Prediction with WoLF PSORT. APBC 2006: 39-48 - 2005
- [j15]Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai:
Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res. 33(Database-Issue): 533-536 (2005) - [j14]Michiel J. L. de Hoon, Yuko Makita, Kenta Nakai, Satoru Miyano
:
Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. PLoS Comput. Biol. 1(3) (2005) - [c10]Yuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai:
Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis. Pacific Symposium on Biocomputing 2005 - 2004
- [j13]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:
Large-scale collection and characterization of promoters of human and mouse genes. Silico Biol. 4(4): 429-444 (2004) - [j12]Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, Kenta Nakai:
BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 32(Database-Issue): 75-77 (2004) - [j11]Yutaka Suzuki, Riu Yamashita, Sumio Sugano, Kenta Nakai:
BTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res. 32(Database-Issue): 78-81 (2004) - [j10]Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara
, Masayuki Takeda, Kenta Nakai, Satoru Miyano
:
An O(N2) Algorithm for Discovering Optimal Boolean Pattern Pairs. IEEE ACM Trans. Comput. Biol. Bioinform. 1(4): 159-170 (2004) - [c9]Shunsuke Inenaga, Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara
, Masayuki Takeda, Kenta Nakai, Satoru Miyano:
Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance. Discovery Science 2004: 32-46 - [c8]Michiel J. L. de Hoon
, Yuko Makita
, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano
:
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. ISMB/ECCB (Supplement of Bioinformatics) 2004: 101-108 - [c7]Natalia Polouliakh, Michiko Konno, Paul Horton, Kenta Nakai:
Parameter Landscape Analysis for Common Motif Discovery Programs. Regulatory Genomics 2004: 79-87 - [c6]Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara
, Masayuki Takeda, Kenta Nakai, Satoru Miyano:
Finding Optimal Pairs of Patterns. WABI 2004: 450-462 - 2003
- [j9]Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai:
MELINA: motif extraction from promoter regions of potentially co-regulated genes. Bioinform. 19(3): 423-424 (2003) - [j8]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
:
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res. 31(13): 3613-3617 (2003) - [c5]Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano:
Intrasplicing - Analysis of Long Intron Sequences. Pacific Symposium on Biocomputing 2003: 339-350 - 2002
- [j7]Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano
:
Extensive feature detection of N-terminal protein sorting signals. Bioinform. 18(2): 298-305 (2002) - [j6]Yutaka Suzuki, Riu Yamashita, Kenta Nakai, Sumio Sugano:
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res. 30(1): 328-331 (2002) - 2001
- [j5]Hideaki Mizuno
, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai:
ORI-GENE: gene classification based on the evolutionary tree. Bioinform. 17(1): 167-173 (2001) - [j4]Takahiro Ishii, Ken-ichi Yoshida
, Goro Terai, Yasutaro Fujita, Kenta Nakai:
DBTBS: a database of Bacillus subtilis promoters and transcription factors. Nucleic Acids Res. 29(1): 278-280 (2001) - [c4]Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano:
Views: Fundamental Building Blocks in the Process of Knowledge Discovery. FLAIRS 2001: 233-238
1990 – 1999
- 1999
- [j3]Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Kenta Nakai:
Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov models. Bioinform. 15(12): 987-993 (1999) - 1998
- [j2]Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai, Kenta Nakai:
Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinform. 14(4): 317-325 (1998) - 1997
- [c3]Paul Horton, Kenta Nakai:
Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier. ISMB 1997: 147-152 - [c2]Tetsushi Yada, Yasushi Totoki, Takahiro Ishii, Kenta Nakai:
Functional Prediction of B. subtilis Genes from Their Regulatory Sequences. ISMB 1997: 354-357 - 1996
- [c1]Paul Horton, Kenta Nakai:
A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins. ISMB 1996: 109-115 - [d2]Kenta Nakai:
Yeast. UCI Machine Learning Repository, 1996 - [d1]Kenta Nakai:
Ecoli. UCI Machine Learning Repository, 1996 - 1994
- [j1]Kenta Nakai, T. Tokimori, A. Ogiwara, Ikuo Uchiyama
, T. Niiyama:
Gnome - an Internet-based sequence analysis tool. Comput. Appl. Biosci. 10(5): 547-550 (1994)
Coauthor Index
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last updated on 2024-06-19 21:00 CEST by the dblp team
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