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For: Wilton R, Szalay AS. Performance optimization in DNA short-read alignment. Bioinformatics 2022;38:2081-2087. [PMID: 35139149 DOI: 10.1093/bioinformatics/btac066] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/03/2022] [Accepted: 02/01/2022] [Indexed: 02/03/2023]  Open
Number Cited by Other Article(s)
1
Cheng W, Wang Y, Wang Y, Hong L, Qiu M, Luo Y, Zhang Q, Wang T, Jia X, Wang H, Ye J. Aerospace Mutagenized Tea Tree Increases Rhizospheric Microorganisms, Enhances Nutrient Conversion Capacity and Promotes Growth. PLANTS (BASEL, SWITZERLAND) 2025;14:981. [PMID: 40219049 PMCID: PMC11990241 DOI: 10.3390/plants14070981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2025] [Revised: 03/18/2025] [Accepted: 03/19/2025] [Indexed: 04/14/2025]
2
He L, Li C, Chen Z, Huo Y, Zhou B, Xie F. Combined metabolome and transcriptome analysis reveal the mechanism of water stress in Ophiocordyceps sinensis. BMC Genomics 2024;25:1014. [PMID: 39472792 PMCID: PMC11523607 DOI: 10.1186/s12864-024-10785-2] [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: 04/17/2024] [Accepted: 09/09/2024] [Indexed: 11/02/2024]  Open
3
Gong X, Liu Y, Wu G, Xu Z, Zeng L, Tian M, Zhang R, Zeng C, Chen Y. An updated resource for the detection of protein-coding circRNA with CircProPlus. Sci Rep 2024;14:19040. [PMID: 39152148 PMCID: PMC11329775 DOI: 10.1038/s41598-024-69744-2] [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: 05/06/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024]  Open
4
Banović Đeri B, Nešić S, Vićić I, Samardžić J, Nikolić D. Benchmarking of five NGS mapping tools for the reference alignment of bacterial outer membrane vesicles-associated small RNAs. Front Microbiol 2024;15:1401985. [PMID: 39101033 PMCID: PMC11294920 DOI: 10.3389/fmicb.2024.1401985] [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: 03/16/2024] [Accepted: 07/01/2024] [Indexed: 08/06/2024]  Open
5
Choudalakis M, Bashtrykov P, Jeltsch A. RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats. Mob DNA 2024;15:6. [PMID: 38570859 PMCID: PMC10988844 DOI: 10.1186/s13100-024-00315-y] [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: 11/03/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]  Open
6
Ji F, Zhou Q, Ruan J, Zhu Z, Liu X. A compressive seeding algorithm in conjunction with reordering-based compression. Bioinformatics 2024;40:btae100. [PMID: 38377404 PMCID: PMC10955252 DOI: 10.1093/bioinformatics/btae100] [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: 09/18/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 02/22/2024]  Open
7
Varsamis GD, Karafyllidis IG, Gilkes KM, Arranz U, Martin-Cuevas R, Calleja G, Dimitrakis P, Kolovos P, Sandaltzopoulos R, Jessen HC, Wong J. Quantum gate algorithm for reference-guided DNA sequence alignment. Comput Biol Chem 2023;107:107959. [PMID: 37717360 DOI: 10.1016/j.compbiolchem.2023.107959] [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: 08/08/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
8
Wang XY, Xu YM, Lau ATY. Proteogenomics in Cancer: Then and Now. J Proteome Res 2023;22:3103-3122. [PMID: 37725793 DOI: 10.1021/acs.jproteome.3c00196] [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: 09/21/2023]
9
Ling X, Wang Q, Wu P, Zhou K, Zhang J, Zhang G. Exploration of Potential Target Genes of miR-24-3p in Chicken Myoblasts by Transcriptome Sequencing Analysis. Genes (Basel) 2023;14:1764. [PMID: 37761904 PMCID: PMC10530709 DOI: 10.3390/genes14091764] [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: 07/20/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]  Open
10
Wilton R, Szalay AS. Short-read aligner performance in germline variant identification. Bioinformatics 2023;39:btad480. [PMID: 37527006 PMCID: PMC10421969 DOI: 10.1093/bioinformatics/btad480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/01/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023]  Open
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