• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4828845)   Today's Articles (157)
For: Wang H, Liu H, Huang T, Li G, Zhang L, Sun Y. EMDLP: Ensemble multiscale deep learning model for RNA methylation site prediction. BMC Bioinformatics 2022;23:221. [PMID: 35676633 DOI: 10.1186/s12859-022-04756-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/27/2022] [Indexed: 01/27/2023]  Open
Number Cited by Other Article(s)
1
Han B, Bai S, Liu Y, Wu J, Feng X, Xin R. Definer: A computational method for accurate identification of RNA pseudouridine sites based on deep learning. PLoS One 2025;20:e0320077. [PMID: 40273178 PMCID: PMC12021131 DOI: 10.1371/journal.pone.0320077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 02/12/2025] [Indexed: 04/26/2025]  Open
2
Sheng N, Qiao J, Wei L, Shi H, Guo H, Yang C. Computational models for prediction of m6A sites using deep learning. Methods 2025;240:113-124. [PMID: 40268153 DOI: 10.1016/j.ymeth.2025.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 04/02/2025] [Accepted: 04/07/2025] [Indexed: 04/25/2025]  Open
3
Asim MN, Asif T, Mehmood F, Dengel A. Peptide classification landscape: An in-depth systematic literature review on peptide types, databases, datasets, predictors architectures and performance. Comput Biol Med 2025;188:109821. [PMID: 39987697 DOI: 10.1016/j.compbiomed.2025.109821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Revised: 02/03/2025] [Accepted: 02/05/2025] [Indexed: 02/25/2025]
4
Tyagi N, Vahab N, Tyagi S. Genome language modeling (GLM): a beginner's cheat sheet. Biol Methods Protoc 2025;10:bpaf022. [PMID: 40370585 PMCID: PMC12077296 DOI: 10.1093/biomethods/bpaf022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 02/17/2025] [Accepted: 03/23/2025] [Indexed: 05/16/2025]  Open
5
Asim MN, Ibrahim MA, Asif T, Dengel A. RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models. Heliyon 2025;11:e41488. [PMID: 39897847 PMCID: PMC11783440 DOI: 10.1016/j.heliyon.2024.e41488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Revised: 12/23/2024] [Accepted: 12/24/2024] [Indexed: 02/04/2025]  Open
6
Zhao J, Chen Z, Zhang M, Zou L, He S, Liu J, Wang Q, Song X, Wu J. DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs. Brief Bioinform 2024;25:bbae439. [PMID: 39234953 PMCID: PMC11375421 DOI: 10.1093/bib/bbae439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/03/2024] [Accepted: 08/21/2024] [Indexed: 09/06/2024]  Open
7
Yang S, Kim SH, Yang E, Kang M, Joo JY. Molecular insights into regulatory RNAs in the cellular machinery. Exp Mol Med 2024;56:1235-1249. [PMID: 38871819 PMCID: PMC11263585 DOI: 10.1038/s12276-024-01239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024]  Open
8
Li F, Zhang J, Li K, Peng Y, Zhang H, Xu Y, Yu Y, Zhang Y, Liu Z, Wang Y, Huang L, Zhou F. GANSamples-ac4C: Enhancing ac4C site prediction via generative adversarial networks and transfer learning. Anal Biochem 2024;689:115495. [PMID: 38431142 DOI: 10.1016/j.ab.2024.115495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024]
9
Wang X, Li P, Wang R, Gao X. PseUpred-ELPSO Is an Ensemble Learning Predictor with Particle Swarm Optimizer for Improving the Prediction of RNA Pseudouridine Sites. BIOLOGY 2024;13:248. [PMID: 38666860 PMCID: PMC11048358 DOI: 10.3390/biology13040248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024]
10
Di Liegro CM, Schiera G, Schirò G, Di Liegro I. Role of Post-Transcriptional Regulation in Learning and Memory in Mammals. Genes (Basel) 2024;15:337. [PMID: 38540396 PMCID: PMC10970538 DOI: 10.3390/genes15030337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 06/14/2024]  Open
11
Jia J, Wu G, Li M. iGly-IDN: Identifying Lysine Glycation Sites in Proteins Based on Improved DenseNet. J Comput Biol 2024;31:161-174. [PMID: 38016151 DOI: 10.1089/cmb.2023.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]  Open
12
Yan W, Tan L, Mengshan L, Weihong Z, Sheng S, Jun W, Fu-An W. Time series-based hybrid ensemble learning model with multivariate multidimensional feature coding for DNA methylation prediction. BMC Genomics 2023;24:758. [PMID: 38082253 PMCID: PMC10712061 DOI: 10.1186/s12864-023-09866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023]  Open
13
Yang Y, Liu Z, Lu J, Sun Y, Fu Y, Pan M, Xie X, Ge Q. Analysis approaches for the identification and prediction of N6-methyladenosine sites. Epigenetics 2023;18:2158284. [PMID: 36562485 PMCID: PMC9980620 DOI: 10.1080/15592294.2022.2158284] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
14
Yu L, Zhang Y, Xue L, Liu F, Jing R, Luo J. EnsembleDL-ATG: Identifying autophagy proteins by integrating their sequence and evolutionary information using an ensemble deep learning framework. Comput Struct Biotechnol J 2023;21:4836-4848. [PMID: 37854634 PMCID: PMC10579870 DOI: 10.1016/j.csbj.2023.09.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023]  Open
15
Wang Z, Xiang S, Zhou C, Xu Q. DeepMethylation: a deep learning based framework with GloVe and Transformer encoder for DNA methylation prediction. PeerJ 2023;11:e16125. [PMID: 37780374 PMCID: PMC10538282 DOI: 10.7717/peerj.16125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/27/2023] [Indexed: 10/03/2023]  Open
16
Hu W, Guan L, Li M. Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network. PLoS Comput Biol 2023;19:e1011370. [PMID: 37639434 PMCID: PMC10461834 DOI: 10.1371/journal.pcbi.1011370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]  Open
17
Soylu NN, Sefer E. BERT2OME: Prediction of 2'-O-Methylation Modifications From RNA Sequence by Transformer Architecture Based on BERT. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:2177-2189. [PMID: 37819796 DOI: 10.1109/tcbb.2023.3237769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
18
Zou J, Liu H, Tan W, Chen YQ, Dong J, Bai SY, Wu ZX, Zeng Y. Dynamic regulation and key roles of ribonucleic acid methylation. Front Cell Neurosci 2022;16:1058083. [PMID: 36601431 PMCID: PMC9806184 DOI: 10.3389/fncel.2022.1058083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]  Open
19
Ma L, He LN, Kang S, Gu B, Gao S, Zuo Z. Advances in detecting N6-methyladenosine modification in circRNAs. Methods 2022;205:234-246. [PMID: 35878749 DOI: 10.1016/j.ymeth.2022.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022]  Open
PrevPage 1 of 1 1Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA