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For: Malebary SJ, Rehman MSU, Khan YD. iCrotoK-PseAAC: Identify lysine crotonylation sites by blending position relative statistical features according to the Chou's 5-step rule. PLoS One 2019;14:e0223993. [PMID: 31751380 PMCID: PMC6874067 DOI: 10.1371/journal.pone.0223993] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/02/2019] [Indexed: 01/22/2023]  Open
Number Cited by Other Article(s)
1
Yang S, Fan X, Yu W. Regulatory Mechanism of Protein Crotonylation and Its Relationship with Cancer. Cells 2024;13:1812. [PMID: 39513918 PMCID: PMC11545499 DOI: 10.3390/cells13211812] [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: 09/30/2024] [Revised: 10/26/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024]  Open
2
Qin Z, Ren H, Zhao P, Wang K, Liu H, Miao C, Du Y, Li J, Wu L, Chen Z. Current computational tools for protein lysine acylation site prediction. Brief Bioinform 2024;25:bbae469. [PMID: 39316944 PMCID: PMC11421846 DOI: 10.1093/bib/bbae469] [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: 05/31/2024] [Revised: 08/20/2024] [Accepted: 09/07/2024] [Indexed: 09/26/2024]  Open
3
Ansar Khawaja S, Alturise F, Alkhalifah T, Khan SA, Khan YD. Gluconeogenesis unraveled: A proteomic Odyssey with machine learning. Methods 2024;232:29-42. [PMID: 39276958 DOI: 10.1016/j.ymeth.2024.09.002] [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: 05/29/2024] [Revised: 08/05/2024] [Accepted: 09/01/2024] [Indexed: 09/17/2024]  Open
4
Naseem A, Khan YD. An intelligent model for prediction of abiotic stress-responsive microRNAs in plants using statistical moments based features and ensemble approaches. Methods 2024;228:65-79. [PMID: 38768931 DOI: 10.1016/j.ymeth.2024.05.008] [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: 04/04/2024] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024]  Open
5
Gao J, Zhao Y, Chen C, Ning Q. MVNN-HNHC:A multi-view neural network for identification of human non-histone crotonylation sites. Anal Biochem 2024;687:115426. [PMID: 38141798 DOI: 10.1016/j.ab.2023.115426] [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: 08/28/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
6
Jiang Y, Yan R, Wang X. PlantNh-Kcr: a deep learning model for predicting non-histone crotonylation sites in plants. PLANT METHODS 2024;20:28. [PMID: 38360730 PMCID: PMC10870457 DOI: 10.1186/s13007-024-01157-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
7
Perveen G, Alturise F, Alkhalifah T, Daanial Khan Y. Hemolytic-Pred: A machine learning-based predictor for hemolytic proteins using position and composition-based features. Digit Health 2023;9:20552076231180739. [PMID: 37434723 PMCID: PMC10331097 DOI: 10.1177/20552076231180739] [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: 12/30/2022] [Accepted: 05/22/2023] [Indexed: 07/13/2023]  Open
8
Butt AH, Alkhalifah T, Alturise F, Khan YD. A machine learning technique for identifying DNA enhancer regions utilizing CIS-regulatory element patterns. Sci Rep 2022;12:15183. [PMID: 36071071 PMCID: PMC9452539 DOI: 10.1038/s41598-022-19099-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022]  Open
9
Dou L, Zhang Z, Xu L, Zou Q. iKcr_CNN: A novel computational tool for imbalance classification of human nonhistone crotonylation sites based on convolutional neural networks with focal loss. Comput Struct Biotechnol J 2022;20:3268-3279. [PMID: 35832615 PMCID: PMC9251780 DOI: 10.1016/j.csbj.2022.06.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/26/2022]  Open
10
βLact-Pred: A Predictor Developed for Identification of Beta-Lactamases Using Statistical Moments and PseAAC via 5-Step Rule. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2021;2021:8974265. [PMID: 34956358 PMCID: PMC8709780 DOI: 10.1155/2021/8974265] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/22/2021] [Indexed: 12/02/2022]
11
Tng SS, Le NQK, Yeh HY, Chua MCH. Improved Prediction Model of Protein Lysine Crotonylation Sites Using Bidirectional Recurrent Neural Networks. J Proteome Res 2021;21:265-273. [PMID: 34812044 DOI: 10.1021/acs.jproteome.1c00848] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
12
Alzahrani E, Alghamdi W, Ullah MZ, Khan YD. Identification of stress response proteins through fusion of machine learning models and statistical paradigms. Sci Rep 2021;11:21767. [PMID: 34741132 PMCID: PMC8571424 DOI: 10.1038/s41598-021-99083-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022]  Open
13
Sohrawordi M, Hossain MA. Prediction of lysine formylation sites using support vector machine based on the sample selection from majority classes and synthetic minority over-sampling techniques. Biochimie 2021;192:125-135. [PMID: 34627982 DOI: 10.1016/j.biochi.2021.10.001] [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: 05/15/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022]
14
Subba P, Prasad TSK. Protein Crotonylation Expert Review: A New Lens to Take Post-Translational Modifications and Cell Biology to New Heights. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021;25:617-625. [PMID: 34582706 DOI: 10.1089/omi.2021.0132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
15
Islam MKB, Rahman J, Hasan MAM, Ahmad S. predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance. Comput Biol Chem 2021;94:107553. [PMID: 34384997 DOI: 10.1016/j.compbiolchem.2021.107553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 06/22/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
16
Jiang G, Li C, Lu M, Lu K, Li H. Protein lysine crotonylation: past, present, perspective. Cell Death Dis 2021;12:703. [PMID: 34262024 PMCID: PMC8280118 DOI: 10.1038/s41419-021-03987-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 02/08/2023]
17
Chen YZ, Wang ZZ, Wang Y, Ying G, Chen Z, Song J. nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. Brief Bioinform 2021;22:6277413. [PMID: 34002774 DOI: 10.1093/bib/bbab146] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022]  Open
18
Li A, Deng Y, Tan Y, Chen M. A Transfer Learning-Based Approach for Lysine Propionylation Prediction. Front Physiol 2021;12:658633. [PMID: 33967828 PMCID: PMC8096918 DOI: 10.3389/fphys.2021.658633] [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: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022]  Open
19
Dou L, Yang F, Xu L, Zou Q. A comprehensive review of the imbalance classification of protein post-translational modifications. Brief Bioinform 2021;22:6217722. [PMID: 33834199 DOI: 10.1093/bib/bbab089] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/17/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022]  Open
20
Ahmed S, Rahman A, Hasan MAM, Islam MKB, Rahman J, Ahmad S. predPhogly-Site: Predicting phosphoglycerylation sites by incorporating probabilistic sequence-coupling information into PseAAC and addressing data imbalance. PLoS One 2021;16:e0249396. [PMID: 33793659 PMCID: PMC8016359 DOI: 10.1371/journal.pone.0249396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/18/2021] [Indexed: 12/14/2022]  Open
21
Jing XY, Li FM. Predicting Cell Wall Lytic Enzymes Using Combined Features. Front Bioeng Biotechnol 2021;8:627335. [PMID: 33585423 PMCID: PMC7874139 DOI: 10.3389/fbioe.2020.627335] [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: 11/09/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022]  Open
22
Wang R, Wang Z, Wang H, Pang Y, Lee TY. Characterization and identification of lysine crotonylation sites based on machine learning method on both plant and mammalian. Sci Rep 2020;10:20447. [PMID: 33235255 PMCID: PMC7686339 DOI: 10.1038/s41598-020-77173-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022]  Open
23
Mahmood MK, Ehsan A, Khan YD, Chou KC. iHyd-LysSite (EPSV): Identifying Hydroxylysine Sites in Protein Using Statistical Formulation by Extracting Enhanced Position and Sequence Variant Feature Technique. Curr Genomics 2020;21:536-545. [PMID: 33214770 PMCID: PMC7604750 DOI: 10.2174/1389202921999200831142629] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 11/22/2022]  Open
24
Lv H, Dao FY, Guan ZX, Yang H, Li YW, Lin H. Deep-Kcr: accurate detection of lysine crotonylation sites using deep learning method. Brief Bioinform 2020;22:5937175. [PMID: 33099604 DOI: 10.1093/bib/bbaa255] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/23/2022]  Open
25
Some illuminating remarks on molecular genetics and genomics as well as drug development. Mol Genet Genomics 2020;295:261-274. [PMID: 31894399 DOI: 10.1007/s00438-019-01634-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
26
Shao YT, Liu XX, Lu Z, Chou KC. pLoc_Deep-mHum: Predict Subcellular Localization of Human Proteins by Deep Learning. ACTA ACUST UNITED AC 2020. [DOI: 10.4236/ns.2020.127042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
27
Lu Z, Chou KC. pLoc_Deep-mGpos: Predict Subcellular Localization of Gram Positive Bacteria Proteins by Deep Learning. ACTA ACUST UNITED AC 2020. [DOI: 10.4236/jbise.2020.135005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
28
Shao Y, Chou KC. pLoc_Deep-mEuk: Predict Subcellular Localization of Eukaryotic Proteins by Deep Learning. ACTA ACUST UNITED AC 2020. [DOI: 10.4236/ns.2020.126034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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