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For: Naseer S, Ali RF, Khan YD, Dominic PDD. iGluK-Deep: computational identification of lysine glutarylation sites using deep neural networks with general pseudo amino acid compositions. J Biomol Struct Dyn 2022;40:11691-11704. [PMID: 34396935 DOI: 10.1080/07391102.2021.1962738] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Number Cited by Other Article(s)
1
Yang S, Xu P. LLM4THP: a computing tool to identify tumor homing peptides by molecular and sequence representation of large language model based on two-layer ensemble model strategy. Amino Acids 2024;56:62. [PMID: 39404804 PMCID: PMC11480143 DOI: 10.1007/s00726-024-03422-5] [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: 06/18/2024] [Accepted: 10/04/2024] [Indexed: 10/19/2024]
2
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
3
Angaitkar P, Ram Janghel R, Prasad Sahu T. An MCDM approach for Reverse vaccinology model to predict bacterial protective antigens. Vaccine 2024;42:3874-3882. [PMID: 38704249 DOI: 10.1016/j.vaccine.2024.04.078] [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: 06/21/2023] [Revised: 01/26/2024] [Accepted: 04/20/2024] [Indexed: 05/06/2024]
4
Suleman MT, Alturise F, Alkhalifah T, Khan YD. m1A-Ensem: accurate identification of 1-methyladenosine sites through ensemble models. BioData Min 2024;17:4. [PMID: 38360720 PMCID: PMC10868122 DOI: 10.1186/s13040-023-00353-x] [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: 06/30/2023] [Accepted: 12/31/2023] [Indexed: 02/17/2024]  Open
5
Guo X, Chen L. From G1 to M: a comparative study of methods for identifying cell cycle phases. Brief Bioinform 2024;25:bbad517. [PMID: 38261342 PMCID: PMC10805071 DOI: 10.1093/bib/bbad517] [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: 08/04/2023] [Revised: 11/08/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024]  Open
6
Liu X, Zhu B, Dai XW, Xu ZA, Li R, Qian Y, Lu YP, Zhang W, Liu Y, Zheng J. GBDT_KgluSite: An improved computational prediction model for lysine glutarylation sites based on feature fusion and GBDT classifier. BMC Genomics 2023;24:765. [PMID: 38082413 PMCID: PMC10712101 DOI: 10.1186/s12864-023-09834-z] [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: 04/02/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023]  Open
7
Gao D, Ren L, Hao YD, Schaduangrat N, Liu XW, Yuan SS, Yang YH, Wang Y, Shoombuatong W, Ding H. The role of ncRNA regulatory mechanisms in diseases-case on gestational diabetes. Brief Bioinform 2023;25:bbad489. [PMID: 38189542 PMCID: PMC10772982 DOI: 10.1093/bib/bbad489] [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: 10/07/2023] [Revised: 11/16/2023] [Accepted: 12/01/2023] [Indexed: 01/09/2024]  Open
8
Alotaibi FM, Khan YD. A Framework for Prediction of Oncogenomic Progression Aiding Personalized Treatment of Gastric Cancer. Diagnostics (Basel) 2023;13:2291. [PMID: 37443684 DOI: 10.3390/diagnostics13132291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]  Open
9
Butt AH, Alkhalifah T, Alturise F, Khan YD. Ensemble Learning for Hormone Binding Protein Prediction: A Promising Approach for Early Diagnosis of Thyroid Hormone Disorders in Serum. Diagnostics (Basel) 2023;13:diagnostics13111940. [PMID: 37296792 DOI: 10.3390/diagnostics13111940] [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: 03/31/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]  Open
10
Lin Y, Sun M, Zhang J, Li M, Yang K, Wu C, Zulfiqar H, Lai H. Computational identification of promoters in Klebsiella aerogenes by using support vector machine. Front Microbiol 2023;14:1200678. [PMID: 37250059 PMCID: PMC10215528 DOI: 10.3389/fmicb.2023.1200678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023]  Open
11
Jia J, Sun M, Wu G, Qiu W. DeepDN_iGlu: prediction of lysine glutarylation sites based on attention residual learning method and DenseNet. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:2815-2830. [PMID: 36899559 DOI: 10.3934/mbe.2023132] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
12
Suleman MT, Alturise F, Alkhalifah T, Khan YD. iDHU-Ensem: Identification of dihydrouridine sites through ensemble learning models. Digit Health 2023;9:20552076231165963. [PMID: 37009307 PMCID: PMC10064468 DOI: 10.1177/20552076231165963] [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: 12/29/2022] [Accepted: 03/09/2023] [Indexed: 04/04/2023]  Open
13
Suleman MT, Khan YD. m1A-pred: Prediction of Modified 1-methyladenosine Sites in RNA Sequences through Artificial Intelligence. Comb Chem High Throughput Screen 2022;25:2473-2484. [PMID: 35718969 DOI: 10.2174/1386207325666220617152743] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 01/27/2023]
14
Ning Q, Qi Z, Wang Y, Deng A, Chen C. FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites. Brief Bioinform 2022;23:6720406. [PMID: 36168700 DOI: 10.1093/bib/bbac421] [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: 06/14/2022] [Revised: 08/15/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022]  Open
15
Akmal MA, Hassan MA, Muhammad S, Khurshid KS, Mohamed A. An analytical study on the identification of N-linked glycosylation sites using machine learning model. PeerJ Comput Sci 2022;8:e1069. [PMID: 36262138 PMCID: PMC9575850 DOI: 10.7717/peerj-cs.1069] [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: 04/19/2022] [Accepted: 07/25/2022] [Indexed: 06/16/2023]
16
Shah AA, Alturise F, Alkhalifah T, Khan YD. Evaluation of deep learning techniques for identification of sarcoma-causing carcinogenic mutations. Digit Health 2022;8:20552076221133703. [PMID: 36312852 PMCID: PMC9597026 DOI: 10.1177/20552076221133703] [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] [Received: 05/31/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]  Open
17
Yu L, Xue L, Liu F, Li Y, Jing R, Luo J. The applications of deep learning algorithms on in silico druggable proteins identification. J Adv Res 2022;41:219-231. [PMID: 36328750 PMCID: PMC9637576 DOI: 10.1016/j.jare.2022.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/21/2021] [Accepted: 01/18/2022] [Indexed: 11/20/2022]  Open
18
Malebary SJ, Alzahrani E, Khan YD. A comprehensive tool for accurate identification of methyl-Glutamine sites. J Mol Graph Model 2021;110:108074. [PMID: 34768228 DOI: 10.1016/j.jmgm.2021.108074] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022]
19
iTAGPred: A Two-Level Prediction Model for Identification of Angiogenesis and Tumor Angiogenesis Biomarkers. Appl Bionics Biomech 2021;2021:2803147. [PMID: 34616486 PMCID: PMC8490072 DOI: 10.1155/2021/2803147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/02/2021] [Indexed: 12/09/2022]  Open
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