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For: Cheng H, Rao B, Liu L, Cui L, Xiao G, Su R, Wei L. PepFormer: End-to-End Transformer-Based Siamese Network to Predict and Enhance Peptide Detectability Based on Sequence Only. Anal Chem 2021;93:6481-6490. [DOI: 10.1021/acs.analchem.1c00354] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Number Cited by Other Article(s)
1
Zuo Y, Fang X, Wan J, He W, Liu X, Zeng X, Deng Z. PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites. PLoS Comput Biol 2024;20:e1012544. [PMID: 39436947 DOI: 10.1371/journal.pcbi.1012544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 10/09/2024] [Indexed: 10/25/2024]  Open
2
Zhang X, Zhao S, Su X, Xu L. From docking to dynamics: Unveiling the potential non-peptide and non-covalent inhibitors of Mpro from natural products. Comput Biol Med 2024;181:108963. [PMID: 39216402 DOI: 10.1016/j.compbiomed.2024.108963] [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: 04/24/2024] [Revised: 07/05/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
3
Ahmed Z, Shahzadi K, Temesgen SA, Ahmad B, Chen X, Ning L, Zulfiqar H, Lin H, Jin YT. A protein pre-trained model-based approach for the identification of the liquid-liquid phase separation (LLPS) proteins. Int J Biol Macromol 2024;277:134146. [PMID: 39067723 DOI: 10.1016/j.ijbiomac.2024.134146] [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: 05/02/2024] [Revised: 07/06/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
4
Liu YX, Song JL, Li XM, Lin H, Cao YN. Identification of target genes co-regulated by four key histone modifications of five key regions in hepatocellular carcinoma. Methods 2024;231:165-177. [PMID: 39349287 DOI: 10.1016/j.ymeth.2024.09.017] [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: 06/27/2024] [Revised: 08/27/2024] [Accepted: 09/27/2024] [Indexed: 10/02/2024]  Open
5
Zhang W, Ding Y, Wei L, Guo X, Ni F. Therapeutic peptides identification via kernel risk sensitive loss-based k-nearest neighbor model and multi-Laplacian regularization. Brief Bioinform 2024;25:bbae534. [PMID: 39438076 PMCID: PMC11495874 DOI: 10.1093/bib/bbae534] [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: 07/14/2024] [Revised: 08/30/2024] [Accepted: 10/08/2024] [Indexed: 10/25/2024]  Open
6
Zuo Y, Zhang B, He W, Bi Y, Liu X, Zeng X, Deng Z. MSlocPRED: deep transfer learning-based identification of multi-label mRNA subcellular localization. Brief Bioinform 2024;25:bbae504. [PMID: 39401145 PMCID: PMC11472759 DOI: 10.1093/bib/bbae504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/19/2024] [Accepted: 09/30/2024] [Indexed: 10/17/2024]  Open
7
Zuo Y, Wan M, Shen Y, Wang X, He W, Bi Y, Liu X, Deng Z. ILYCROsite: Identification of lysine crotonylation sites based on FCM-GRNN undersampling technique. Comput Biol Chem 2024;113:108212. [PMID: 39277959 DOI: 10.1016/j.compbiolchem.2024.108212] [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: 07/08/2024] [Revised: 09/02/2024] [Accepted: 09/12/2024] [Indexed: 09/17/2024]
8
Wu CY, Xu ZX, Li N, Qi DY, Hao ZH, Wu HY, Gao R, Jin YT. Accurately identifying positive and negative regulation of apoptosis using fusion features and machine learning methods. Comput Biol Chem 2024;113:108207. [PMID: 39265463 DOI: 10.1016/j.compbiolchem.2024.108207] [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: 06/28/2024] [Revised: 08/20/2024] [Accepted: 09/06/2024] [Indexed: 09/14/2024]
9
Zuo Y, Zhang B, Dong Y, He W, Bi Y, Liu X, Zeng X, Deng Z. Glypred: Lysine Glycation Site Prediction via CCU-LightGBM-BiLSTM Framework with Multi-Head Attention Mechanism. J Chem Inf Model 2024;64:6699-6711. [PMID: 39121059 DOI: 10.1021/acs.jcim.4c01034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
10
Meng C, Pei Y, Bu Y, Liu Q, Li Q, Zou Q, Zhang Y. IIFS2.0: An Improved Incremental Feature Selection Method for Protein Sequence Processing Based on a Caching Strategy. J Mol Biol 2024:168741. [PMID: 39122168 DOI: 10.1016/j.jmb.2024.168741] [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: 06/05/2024] [Revised: 07/08/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
11
Petrovskiy DV, Nikolsky KS, Kulikova LI, Rudnev VR, Butkova TV, Malsagova KA, Kopylov AT, Kaysheva AL. PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models. Sci Rep 2024;14:15000. [PMID: 38951578 PMCID: PMC11217302 DOI: 10.1038/s41598-024-65861-0] [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: 04/05/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024]  Open
12
Li H, Jiang L, Yang K, Shang S, Li M, Lv Z. iNP_ESM: Neuropeptide Identification Based on Evolutionary Scale Modeling and Unified Representation Embedding Features. Int J Mol Sci 2024;25:7049. [PMID: 39000158 PMCID: PMC11240975 DOI: 10.3390/ijms25137049] [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: 05/25/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024]  Open
13
Feng C, Wei H, Li X, Feng B, Xu C, Zhu X, Liu R. A stacking-based algorithm for antifreeze protein identification using combined physicochemical, pseudo amino acid composition, and reduction property features. Comput Biol Med 2024;176:108534. [PMID: 38754217 DOI: 10.1016/j.compbiomed.2024.108534] [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: 02/04/2024] [Revised: 04/03/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024]
14
Jiao S, Ye X, Sakurai T, Zou Q, Liu R. Integrated convolution and self-attention for improving peptide toxicity prediction. BIOINFORMATICS (OXFORD, ENGLAND) 2024;40:btae297. [PMID: 38696758 DOI: 10.1093/bioinformatics/btae297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/02/2024] [Accepted: 04/30/2024] [Indexed: 05/04/2024]
15
Lou R, Shui W. Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023. Mol Cell Proteomics 2024;23:100712. [PMID: 38182042 PMCID: PMC10847697 DOI: 10.1016/j.mcpro.2024.100712] [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: 10/31/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]  Open
16
Wu J, Liu B, Zhang J, Wang Z, Li J. DL-PPI: a method on prediction of sequenced protein-protein interaction based on deep learning. BMC Bioinformatics 2023;24:473. [PMID: 38097937 PMCID: PMC10722729 DOI: 10.1186/s12859-023-05594-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]  Open
17
Le NQK. Leveraging transformers-based language models in proteome bioinformatics. Proteomics 2023;23:e2300011. [PMID: 37381841 DOI: 10.1002/pmic.202300011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/30/2023]
18
Yu X, Hu J, Zhang Y. SNN6mA: Improved DNA N6-methyladenine site prediction using Siamese network-based feature embedding. Comput Biol Med 2023;166:107533. [PMID: 37793205 DOI: 10.1016/j.compbiomed.2023.107533] [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: 08/13/2023] [Revised: 09/01/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023]
19
Bustillo L, Laino T, Rodrigues T. The rise of automated curiosity-driven discoveries in chemistry. Chem Sci 2023;14:10378-10384. [PMID: 37799997 PMCID: PMC10548516 DOI: 10.1039/d3sc03367h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/07/2023] [Indexed: 10/07/2023]  Open
20
Son J, Na S, Paek E. DbyDeep: Exploration of MS-Detectable Peptides via Deep Learning. Anal Chem 2023;95:11193-11200. [PMID: 37459568 PMCID: PMC10401496 DOI: 10.1021/acs.analchem.3c00460] [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: 01/31/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023]
21
PD-BertEDL: An Ensemble Deep Learning Method Using BERT and Multivariate Representation to Predict Peptide Detectability. Int J Mol Sci 2022;23:ijms232012385. [PMID: 36293242 PMCID: PMC9604182 DOI: 10.3390/ijms232012385] [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: 09/01/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 12/03/2022]  Open
22
Ekvall M, Truong P, Gabriel W, Wilhelm M, Käll L. Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities. J Proteome Res 2022;21:1359-1364. [PMID: 35413196 PMCID: PMC9087333 DOI: 10.1021/acs.jproteome.1c00870] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
23
Yang Y, Lin L, Qiao L. Deep learning approaches for data-independent acquisition proteomics. Expert Rev Proteomics 2021;18:1031-1043. [PMID: 34918987 DOI: 10.1080/14789450.2021.2020654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
24
Zhu Y, Yin S, Zheng J, Shi Y, Jia C. O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine. J Bioinform Comput Biol 2021;20:2150029. [PMID: 34806952 DOI: 10.1142/s0219720021500293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
25
Prediction of Peptide Detectability Based on CapsNet and Convolutional Block Attention Module. Int J Mol Sci 2021;22:ijms222112080. [PMID: 34769509 PMCID: PMC8584443 DOI: 10.3390/ijms222112080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022]  Open
26
Sun B, Smialowski P, Straub T, Imhof A. Investigation and Highly Accurate Prediction of Missed Tryptic Cleavages by Deep Learning. J Proteome Res 2021;20:3749-3757. [PMID: 34137619 DOI: 10.1021/acs.jproteome.1c00346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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