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Provider: Schloss Dagstuhl - Leibniz Center for Informatics Database: dblp computer science bibliography Content:text/plain; charset="utf-8" TY - JOUR ID - DBLP:journals/bib/ZhangCLLPN24 AU - Zhang, Weihang AU - Cui, Yang AU - Liu, Bowen AU - Loza, Martin AU - Park, Sung-Joon AU - Nakai, Kenta TI - HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data. JO - Briefings Bioinform. VL - 25 IS - 3 PY - 2024// DO - 10.1093/BIB/BBAE152 UR - https://doi.org/10.1093/bib/bbae152 ER - TY - JOUR ID - DBLP:journals/bib/LiJHLYGNZW23 AU - Li, Zhongshen AU - Jin, Junru AU - He, Wenjia AU - Long, Wentao AU - Yu, Haoqing AU - Gao, Xin AU - Nakai, Kenta AU - Zou, Quan AU - Wei, Leyi TI - CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. JO - Briefings Bioinform. VL - 24 IS - 6 PY - 2023/09/ DO - 10.1093/BIB/BBAD352 UR - https://doi.org/10.1093/bib/bbad352 ER - TY - JOUR ID - DBLP:journals/bib/DingNG22 AU - Ding, Wenze AU - Nakai, Kenta AU - Gong, Haipeng TI - Protein design via deep learning. JO - Briefings Bioinform. VL - 23 IS - 3 PY - 2022// DO - 10.1093/BIB/BBAC102 UR - https://doi.org/10.1093/bib/bbac102 UR - https://www.wikidata.org/entity/Q112687941 ER - TY - JOUR ID - DBLP:journals/bioinformatics/WangJZNW22 AU - Wang, Ruheng AU - Jin, Junru AU - Zou, Quan AU - Nakai, Kenta AU - Wei, Leyi TI - Predicting protein-peptide binding residues via interpretable deep learning. JO - Bioinform. VL - 38 IS - 13 SP - 3351 EP - 3360 PY - 2022// DO - 10.1093/BIOINFORMATICS/BTAC352 UR - https://doi.org/10.1093/bioinformatics/btac352 ER - TY - JOUR ID - DBLP:journals/fbinf/NakaiW22 AU - Nakai, Kenta AU - Wei, Leyi TI - Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. JO - Frontiers Bioinform. VL - 2 PY - 2022// DO - 10.3389/FBINF.2022.910531 UR - https://doi.org/10.3389/fbinf.2022.910531 ER - TY - CPAPER ID - DBLP:conf/complexnetworks/LiuTZNN22 AU - Liu, Shu AU - Toriumi, Fujio AU - Zeng, Xin AU - Nishiguchi, Mao AU - Nakai, Kenta TI - SignedS2V: Structural Embedding Method for Signed Networks. BT - Complex Networks and Their Applications XI - Proceedings of The Eleventh International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2022, Palermo, Italy, 8-10 November, 2022, Volume 1 SP - 337 EP - 349 PY - 2022// DO - 10.1007/978-3-031-21127-0_28 UR - https://doi.org/10.1007/978-3-031-21127-0_28 ER - TY - JOUR ID - DBLP:journals/bioinformatics/ParkN21 AU - Park, Sung-Joon AU - Nakai, Kenta TI - OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data. JO - Bioinform. VL - 37 IS - 18 SP - 3021 EP - 3022 PY - 2021// DO - 10.1093/BIOINFORMATICS/BTAB101 UR - https://doi.org/10.1093/bioinformatics/btab101 ER - TY - JOUR ID - DBLP:journals/bmcbi/JiaPN21 AU - Jia, Hao AU - Park, Sung-Joon AU - Nakai, Kenta TI - A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations. JO - BMC Bioinform. VL - 22-S IS - 6 SP - 128 PY - 2021// DO - 10.1186/S12859-021-03999-8 UR - https://doi.org/10.1186/s12859-021-03999-8 ER - TY - EDBOOK ID - DBLP:reference/bioinf/2019-1 ED - Ranganathan, Shoba ED - Gribskov, Michael ED - Nakai, Kenta ED - Schönbach, Christian TI - Encyclopedia of Bioinformatics and Computational Biology - Volume 1 PY - 2019// PB - Elsevier UR - https://www.sciencedirect.com/referencework/9780128114322/encyclopedia-of-bioinformatics-and-computational-biology#book-description SN - ISBN 978-0-12-811432-2 ER - TY - EDBOOK ID - DBLP:reference/bioinf/2019-2 ED - Ranganathan, Shoba ED - Gribskov, Michael ED - Nakai, Kenta ED - Schönbach, Christian TI - Encyclopedia of Bioinformatics and Computational Biology - Volume 2 PY - 2019// PB - Elsevier UR - https://www.sciencedirect.com/referencework/9780128114322/encyclopedia-of-bioinformatics-and-computational-biology#book-description SN - ISBN 978-0-12-811432-2 ER - TY - EDBOOK ID - DBLP:reference/bioinf/2019-3 ED - Ranganathan, Shoba ED - Gribskov, Michael ED - Nakai, Kenta ED - Schönbach, Christian TI - Encyclopedia of Bioinformatics and Computational Biology - Volume 3 PY - 2019// PB - Elsevier UR - https://www.sciencedirect.com/referencework/9780128114322/encyclopedia-of-bioinformatics-and-computational-biology#book-description SN - ISBN 978-0-12-811432-2 ER - TY - ENCYC ID - DBLP:reference/bioinf/NakaiI19 AU - Nakai, Kenta AU - Imai, Kenichiro TI - Prediction of Protein Localization. BT - Encyclopedia of Bioinformatics and Computational Biology - Volume 2 SP - 53 EP - 59 PY - 2019// DO - 10.1016/B978-0-12-809633-8.20270-7 UR - https://doi.org/10.1016/b978-0-12-809633-8.20270-7 ER - TY - ENCYC ID - DBLP:reference/bioinf/Nakai19 AU - Nakai, Kenta TI - Prediction of Protein-Binding Sites in DNA Sequences. BT - Encyclopedia of Bioinformatics and Computational Biology - Volume 3 SP - 447 EP - 451 PY - 2019// DO - 10.1016/B978-0-12-809633-8.20131-3 UR - https://doi.org/10.1016/b978-0-12-809633-8.20131-3 ER - TY - JOUR ID - DBLP:journals/bioinformatics/TanLNP18 AU - Tan, Phit Ling AU - López, Yosvany AU - Nakai, Kenta AU - Patil, Ashwini TI - TimeXNet Web: identifying cellular response networks from diverse omics time-course data. JO - Bioinform. VL - 34 IS - 21 SP - 3764 EP - 3765 PY - 2018// DO - 10.1093/BIOINFORMATICS/BTY393 UR - https://doi.org/10.1093/bioinformatics/bty393 UR - https://www.wikidata.org/entity/Q88677810 ER - TY - JOUR ID - DBLP:journals/jbcb/MoonN18 AU - Moon, Myungjin AU - Nakai, Kenta TI - Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers. JO - J. Bioinform. Comput. Biol. VL - 16 IS - 2 SP - 1850006:1 EP - 1850006:20 PY - 2018// DO - 10.1142/S0219720018500063 UR - https://doi.org/10.1142/S0219720018500063 UR - https://www.wikidata.org/entity/Q52642430 ER - TY - JOUR ID - DBLP:journals/jbcb/LiNZSWYZZK18 AU - Li, Jinyan AU - Nakai, Kenta AU - Zheng, Yun AU - Sato, Kengo AU - Wong, Limsoon TI - Introduction to Selected Papers from GIW2018. JO - J. Bioinform. Comput. Biol. VL - 16 IS - 6 SP - 1802005:1 EP - 1802005:2 PY - 2018// DO - 10.1142/S0219720018020055 UR - https://doi.org/10.1142/S0219720018020055 UR - https://www.wikidata.org/entity/Q90925875 ER - TY - JOUR ID - DBLP:journals/nar/SuzukiKMSKSSTTS18 AU - Suzuki, Ayako AU - Kawano, Shin AU - Mituyama, Toutai AU - Suyama, Mikita AU - Kanai, Yae AU - Shirahige, Katsuhiko AU - Sasaki, Hiroyuki AU - Tokunaga, Katsushi AU - Tsuchihara, Katsuya AU - Sugano, Sumio AU - Nakai, Kenta AU - Suzuki, Yutaka TI - DBTSS/DBKERO for integrated analysis of transcriptional regulation. JO - Nucleic Acids Res. VL - 46 IS - Database-Issue SP - D229 EP - D238 PY - 2018// DO - 10.1093/NAR/GKX1001 UR - https://doi.org/10.1093/nar/gkx1001 UR - https://www.wikidata.org/entity/Q47160144 ER - TY - JOUR ID - DBLP:journals/nar/BrozovicDDDFGLN18 AU - Brozovic, Matija AU - Dantec, Christelle AU - Dardaillon, Justine AU - Dauga, Delphine AU - Faure, Emmanuel AU - Gineste, Mathieu AU - Louis, Alexandra AU - Naville, Magali AU - Nitta, Kazuhiro R. AU - Piette, Jacques AU - Reeves, Wendy AU - Scornavacca, Céline AU - Simion, Paul AU - Vincentelli, Renaud AU - Bellec, Maelle AU - Aicha, Sameh Ben AU - Fagotto, Marie AU - Guéroult-Bellone, Marion AU - Haeussler, Maximilian AU - Jacox, Edwin AU - Lowe, Elijah K. AU - Mendez, Mickaël AU - Roberge, Alexis AU - Stolfi, Alberto AU - Yokomori, Rui AU - Brown, C. Titus AU - Cambillau, Christian AU - Christiaen, Lionel A. AU - Delsuc, Frédéric AU - Douzery, Emmanuel J. P. AU - Dumollard, Rémi AU - Kusakabe, Takehiro AU - Nakai, Kenta AU - Nishida, Hiroki AU - Satou, Yutaka AU - Swalla, Billie J. AU - Veeman, Michael AU - Volff, Jean-Nicolas AU - Lemaire, Patrick TI - ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. JO - Nucleic Acids Res. VL - 46 IS - Database-Issue SP - D718 EP - D725 PY - 2018// DO - 10.1093/NAR/GKX1108 UR - https://doi.org/10.1093/nar/gkx1108 UR - https://www.wikidata.org/entity/Q46259534 ER - TY - JOUR ID - DBLP:journals/bmcbi/GutierrezN16 AU - Gutierrez, Josep Basha AU - Nakai, Kenta TI - A study on the application of topic models to motif finding algorithms. JO - BMC Bioinform. VL - 17 IS - S-19 SP - 129 EP - 138 PY - 2016// DO - 10.1186/S12859-016-1364-3 UR - https://doi.org/10.1186/s12859-016-1364-3 UR - https://www.wikidata.org/entity/Q36268679 ER - TY - JOUR ID - DBLP:journals/nar/ParkKSUN16 AU - Park, Sung-Joon AU - Komiyama, Yusuke AU - Suemori, Hirofumi AU - Umezawa, Akihiro AU - Nakai, Kenta TI - OpenTein: a database of digital whole-slide images of stem cell-derived teratomas. JO - Nucleic Acids Res. VL - 44 IS - Database-Issue SP - 1000 EP - 1004 PY - 2016// DO - 10.1093/NAR/GKV1096 UR - https://doi.org/10.1093/nar/gkv1096 UR - https://www.wikidata.org/entity/Q35819507 ER - TY - JOUR ID - DBLP:journals/biodb/LopezNP15 AU - López, Yosvany AU - Nakai, Kenta AU - Patil, Ashwini TI - HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. JO - Database J. Biol. Databases Curation VL - 2015 PY - 2015// DO - 10.1093/DATABASE/BAV117 UR - https://doi.org/10.1093/database/bav117 UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691340/ UR - https://www.wikidata.org/entity/Q38398015 ER - TY - JOUR ID - DBLP:journals/nar/SuzukiWYKTSSN15 AU - Suzuki, Ayako AU - Wakaguri, Hiroyuki AU - Yamashita, Riu AU - Kawano, Shin AU - Tsuchihara, Katsuya AU - Sugano, Sumio AU - Suzuki, Yutaka AU - Nakai, Kenta TI - DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. JO - Nucleic Acids Res. VL - 43 IS - Database-Issue SP - 87 EP - 91 PY - 2015// DO - 10.1093/NAR/GKU1080 UR - https://doi.org/10.1093/nar/gku1080 UR - https://www.wikidata.org/entity/Q30868314 ER - TY - JOUR ID - DBLP:journals/nar/ParkSON15 AU - Park, Sung-Joon AU - Shirahige, Katsuhiko AU - Ohsugi, Miho AU - Nakai, Kenta TI - DBTMEE: a database of transcriptome in mouse early embryos. JO - Nucleic Acids Res. 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VL - 8 IS - S-4 SP - S2 PY - 2014// DO - 10.1186/1752-0509-8-S4-S2 UR - https://doi.org/10.1186/1752-0509-8-S4-S2 UR - https://www.wikidata.org/entity/Q35529692 ER - TY - JOUR ID - DBLP:journals/bmcsb/LopezPN13 AU - López, Yosvany AU - Patil, Ashwini AU - Nakai, Kenta TI - Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana. JO - BMC Syst. Biol. VL - 7 IS - S-3 SP - S10 PY - 2013// DO - 10.1186/1752-0509-7-S3-S10 UR - https://doi.org/10.1186/1752-0509-7-S3-S10 UR - https://www.wikidata.org/entity/Q35098935 ER - TY - JOUR ID - DBLP:journals/ploscb/PatilKLSN13 AU - Patil, Ashwini AU - Kumagai, Yutaro AU - Liang, Kuo-ching AU - Suzuki, Yutaka AU - Nakai, Kenta TI - Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response. JO - PLoS Comput. Biol. VL - 9 IS - 11 PY - 2013// DO - 10.1371/JOURNAL.PCBI.1003323 UR - https://doi.org/10.1371/journal.pcbi.1003323 UR - https://www.wikidata.org/entity/Q35045380 ER - TY - JOUR ID - DBLP:journals/jbcb/KimuraKN12 AU - Kimura, Kouichi AU - Koike, Asako AU - Nakai, Kenta TI - A Bit-Parallel Dynamic Programming Algorithm Suitable for DNA Sequence Alignment. JO - J. Bioinform. Comput. Biol. VL - 10 IS - 4 PY - 2012// DO - 10.1142/S0219720012500023 UR - https://doi.org/10.1142/S0219720012500023 UR - https://www.wikidata.org/entity/Q43531571 ER - TY - JOUR ID - DBLP:journals/nar/YamashitaSSN12 AU - Yamashita, Riu AU - Sugano, Sumio AU - Suzuki, Yutaka AU - Nakai, Kenta TI - DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. JO - Nucleic Acids Res. 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