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For: De Waele G, Clauwaert J, Menschaert G, Waegeman W. CpG Transformer for imputation of single-cell methylomes. Bioinformatics 2021;38:597-603. [PMID: 34718418 PMCID: PMC8756163 DOI: 10.1093/bioinformatics/btab746] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 02/03/2023]  Open
Number Cited by Other Article(s)
1
Chen SF, Steele RJ, Hocky GM, Lemeneh B, Lad SP, Oermann EK. Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions. ARXIV 2025:arXiv:2408.16245v3. [PMID: 40236839 PMCID: PMC11998858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
2
Zhou J, Luo C, Liu H, Heffel MG, Straub RE, Kleinman JE, Hyde TM, Ecker JR, Weinberger DR, Han S. Deep learning imputes DNA methylation states in single cells and enhances the detection of epigenetic alterations in schizophrenia. CELL GENOMICS 2025;5:100774. [PMID: 39986279 PMCID: PMC11960545 DOI: 10.1016/j.xgen.2025.100774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 11/13/2024] [Accepted: 01/24/2025] [Indexed: 02/24/2025]
3
Luo S, Peng H, Shi Y, Cai J, Zhang S, Shao N, Li J. Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey. Brief Bioinform 2025;26:bbaf087. [PMID: 40052441 PMCID: PMC11886573 DOI: 10.1093/bib/bbaf087] [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: 10/17/2024] [Revised: 12/29/2024] [Accepted: 02/19/2025] [Indexed: 03/10/2025]  Open
4
Zeng R, Li Z, Li J, Zhang Q. DNA promoter task-oriented dictionary mining and prediction model based on natural language technology. Sci Rep 2025;15:153. [PMID: 39747934 PMCID: PMC11697570 DOI: 10.1038/s41598-024-84105-9] [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: 09/07/2024] [Accepted: 12/19/2024] [Indexed: 01/04/2025]  Open
5
Park S, To Chong K, Tayara H. CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites. Brief Bioinform 2024;26:bbaf063. [PMID: 39968737 PMCID: PMC11836533 DOI: 10.1093/bib/bbaf063] [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: 01/30/2024] [Revised: 12/27/2024] [Accepted: 02/07/2025] [Indexed: 02/20/2025]  Open
6
Zhou J, Luo C, Liu H, Heffel MG, Straub RE, Kleinman JE, Hyde TM, Ecker JR, Weinberger DR, Han S. scMeFormer: a transformer-based deep learning model for imputing DNA methylation states in single cells enhances the detection of epigenetic alterations in schizophrenia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577200. [PMID: 38328094 PMCID: PMC10849713 DOI: 10.1101/2024.01.25.577200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
7
Qu S, Gong M, Deng Y, Xiang Y, Ye D. Research progress and application of single-cell sequencing in head and neck malignant tumors. Cancer Gene Ther 2024;31:18-27. [PMID: 37968342 PMCID: PMC10794142 DOI: 10.1038/s41417-023-00691-2] [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: 06/06/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023]
8
Huang L, Song M, Shen H, Hong H, Gong P, Deng HW, Zhang C. Deep Learning Methods for Omics Data Imputation. BIOLOGY 2023;12:1313. [PMID: 37887023 PMCID: PMC10604785 DOI: 10.3390/biology12101313] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
9
Yassi M, Chatterjee A, Parry M. Application of deep learning in cancer epigenetics through DNA methylation analysis. Brief Bioinform 2023;24:bbad411. [PMID: 37985455 PMCID: PMC10661960 DOI: 10.1093/bib/bbad411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/08/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023]  Open
10
Deng Y, Tang J, Zhang J, Zou J, Zhu Q, Fan S. GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs. Bioinformatics 2023;39:btad533. [PMID: 37647650 PMCID: PMC10516632 DOI: 10.1093/bioinformatics/btad533] [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: 03/21/2023] [Revised: 07/24/2023] [Accepted: 08/28/2023] [Indexed: 09/01/2023]  Open
11
Wichmann A, Buschong E, Müller A, Jünger D, Hildebrandt A, Hankeln T, Schmidt B. MetaTransformer: deep metagenomic sequencing read classification using self-attention models. NAR Genom Bioinform 2023;5:lqad082. [PMID: 37705831 PMCID: PMC10495543 DOI: 10.1093/nargab/lqad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/14/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]  Open
12
Sereshki S, Lee N, Omirou M, Fasoula D, Lonardi S. On the prediction of non-CG DNA methylation using machine learning. NAR Genom Bioinform 2023;5:lqad045. [PMID: 37206627 PMCID: PMC10189801 DOI: 10.1093/nargab/lqad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/06/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023]  Open
13
Luo X, Wang Y, Zou Q, Xu L. Recall DNA methylation levels at low coverage sites using a CNN model in WGBS. PLoS Comput Biol 2023;19:e1011205. [PMID: 37315069 DOI: 10.1371/journal.pcbi.1011205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/22/2023] [Indexed: 06/16/2023]  Open
14
Dodlapati S, Jiang Z, Sun J. Completing Single-Cell DNA Methylome Profiles via Transfer Learning Together With KL-Divergence. Front Genet 2022;13:910439. [PMID: 35938031 PMCID: PMC9353187 DOI: 10.3389/fgene.2022.910439] [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: 04/01/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022]  Open
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