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For: Mehrab Z, Mobin J, Tahmid IA, Rahman A. Efficient association mapping from k-mers-An application in finding sex-specific sequences. PLoS One 2021;16:e0245058. [PMID: 33411830 PMCID: PMC7790365 DOI: 10.1371/journal.pone.0245058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]  Open
Number Cited by Other Article(s)
1
Yang Q, Wang X, Han M, Sheng H, Sun Y, Su L, Lu W, Li M, Wang S, Chen J, Cui S, Yang BW. Bacterial genome-wide association studies: exploring the genetic variation underlying bacterial phenotypes. Appl Environ Microbiol 2025:e0251224. [PMID: 40377303 DOI: 10.1128/aem.02512-24] [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: 05/18/2025]  Open
2
Roberts MD, Davis O, Josephs EB, Williamson RJ. K-mer-based Approaches to Bridging Pangenomics and Population Genetics. Mol Biol Evol 2025;42:msaf047. [PMID: 40111256 PMCID: PMC11925024 DOI: 10.1093/molbev/msaf047] [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: 09/18/2024] [Revised: 01/10/2025] [Accepted: 02/04/2025] [Indexed: 03/12/2025]  Open
3
Roberts M, Josephs EB. Previously unmeasured genetic diversity explains part of Lewontin's paradox in a k -mer-based meta-analysis of 112 plant species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594778. [PMID: 38798362 PMCID: PMC11118579 DOI: 10.1101/2024.05.17.594778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
4
Corut AK, Wallace JG. kGWASflow: a modular, flexible, and reproducible Snakemake workflow for k-mers-based GWAS. G3 (BETHESDA, MD.) 2023;14:jkad246. [PMID: 37976215 PMCID: PMC10755180 DOI: 10.1093/g3journal/jkad246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/15/2023] [Indexed: 11/19/2023]
5
Lemane T, Chikhi R, Peterlongo P. k mdiff, large-scale and user-friendly differential k-mer analyses. Bioinformatics 2022;38:5443-5445. [PMID: 36315078 PMCID: PMC9750116 DOI: 10.1093/bioinformatics/btac689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/23/2022] [Accepted: 10/28/2022] [Indexed: 12/25/2022]  Open
6
Gupta PK. GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers. Bioessays 2021;43:e2100109. [PMID: 34486143 DOI: 10.1002/bies.202100109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/22/2022]
7
Mehrab Z, Mobin J, Tahmid IA, Pachter L, Rahman A. Reference-free Association Mapping from Sequencing Reads Using k-mers. Bio Protoc 2020;10:e3815. [PMID: 33659468 PMCID: PMC7842384 DOI: 10.21769/bioprotoc.3815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/21/2020] [Accepted: 10/14/2020] [Indexed: 11/02/2022]  Open
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