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For: Kallenborn F, Cascitti J, Schmidt B. CARE 2.0: reducing false-positive sequencing error corrections using machine learning. BMC Bioinformatics 2022;23:227. [PMID: 35698033 PMCID: PMC9195321 DOI: 10.1186/s12859-022-04754-3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/30/2022] [Indexed: 11/10/2022]  Open
Number Cited by Other Article(s)
1
Moon Y, Hong CH, Kim YH, Kim JK, Ye SH, Kang EK, Choi HW, Cho H, Choi H, Lee DE, Choi Y, Kim TM, Heo SG, Han N, Hong KM. Enhancing Clinical Applications by Evaluation of Sensitivity and Specificity in Whole Exome Sequencing. Int J Mol Sci 2024;25:13250. [PMID: 39769013 PMCID: PMC11678496 DOI: 10.3390/ijms252413250] [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: 10/31/2024] [Revised: 12/04/2024] [Accepted: 12/06/2024] [Indexed: 01/11/2025]  Open
2
Moeckel C, Mareboina M, Konnaris MA, Chan CS, Mouratidis I, Montgomery A, Chantzi N, Pavlopoulos GA, Georgakopoulos-Soares I. A survey of k-mer methods and applications in bioinformatics. Comput Struct Biotechnol J 2024;23:2289-2303. [PMID: 38840832 PMCID: PMC11152613 DOI: 10.1016/j.csbj.2024.05.025] [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: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024]  Open
3
Schmidt B, Hildebrandt A. From GPUs to AI and quantum: three waves of acceleration in bioinformatics. Drug Discov Today 2024;29:103990. [PMID: 38663581 DOI: 10.1016/j.drudis.2024.103990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/05/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
4
Tang T, Liu Y, Zheng B, Li R, Zhang X, Liu Y. Integration of hybrid and self-correction method improves the quality of long-read sequencing data. Brief Funct Genomics 2024;23:249-255. [PMID: 37340778 DOI: 10.1093/bfgp/elad026] [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: 02/16/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]  Open
5
Kallenborn F, Schmidt B. CAREx: context-aware read extension of paired-end sequencing data. BMC Bioinformatics 2024;25:186. [PMID: 38730374 PMCID: PMC11088031 DOI: 10.1186/s12859-024-05802-w] [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: 06/23/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024]  Open
6
Sami A, El-Metwally S, Rashad MZ. MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads. BMC Bioinformatics 2024;25:61. [PMID: 38321434 PMCID: PMC10848413 DOI: 10.1186/s12859-024-05681-1] [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: 09/12/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024]  Open
7
Długosz M, Deorowicz S. Illumina reads correction: evaluation and improvements. Sci Rep 2024;14:2232. [PMID: 38278837 PMCID: PMC11222498 DOI: 10.1038/s41598-024-52386-9] [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: 03/20/2023] [Accepted: 01/18/2024] [Indexed: 01/28/2024]  Open
8
Yan L, Yin Z, Zhang H, Zhao Z, Wang M, Müller A, Kallenborn F, Wichmann A, Wei Y, Niu B, Schmidt B, Liu W. RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data. Methods 2023;216:39-50. [PMID: 37330158 DOI: 10.1016/j.ymeth.2023.06.007] [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: 03/27/2023] [Revised: 05/26/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]  Open
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