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For: Ma J, Cáceres M, Salmela L, Mäkinen V, Tomescu AI. Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. Bioinformatics 2023;39:btad460. [PMID: 37494467 PMCID: PMC10423031 DOI: 10.1093/bioinformatics/btad460] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/08/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]  Open
Number Cited by Other Article(s)
1
Chandra G, Gibney D, Jain C. Haplotype-aware sequence alignment to pangenome graphs. Genome Res 2024;34:1265-1275. [PMID: 39013594 PMCID: PMC11529843 DOI: 10.1101/gr.279143.124] [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: 02/15/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024]
2
Brejová B, Gagie T, Herencsárová E, Vinař T. Maximum-scoring path sets on pangenome graphs of constant treewidth. FRONTIERS IN BIOINFORMATICS 2024;4:1391086. [PMID: 39011297 PMCID: PMC11246863 DOI: 10.3389/fbinf.2024.1391086] [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: 02/24/2024] [Accepted: 06/03/2024] [Indexed: 07/17/2024]  Open
3
Mustafa H, Karasikov M, Mansouri Ghiasi N, Rätsch G, Kahles A. Label-guided seed-chain-extend alignment on annotated De Bruijn graphs. Bioinformatics 2024;40:i337-i346. [PMID: 38940164 PMCID: PMC11211850 DOI: 10.1093/bioinformatics/btae226] [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] [Indexed: 06/29/2024]  Open
4
Hu H, Li R, Zhao J, Batley J, Edwards D. Technological Development and Advances for Constructing and Analyzing Plant Pangenomes. Genome Biol Evol 2024;16:evae081. [PMID: 38669452 PMCID: PMC11058698 DOI: 10.1093/gbe/evae081] [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: 11/06/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]  Open
5
Rizzo N, Cáceres M, Mäkinen V. Finding maximal exact matches in graphs. Algorithms Mol Biol 2024;19:10. [PMID: 38468275 DOI: 10.1186/s13015-024-00255-5] [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: 11/08/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]  Open
6
Rajput J, Chandra G, Jain C. Co-linear chaining on pangenome graphs. Algorithms Mol Biol 2024;19:4. [PMID: 38279113 PMCID: PMC11288099 DOI: 10.1186/s13015-024-00250-w] [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: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 01/28/2024]  Open
7
Chandra G, Jain C. Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs. J Comput Biol 2023;30:1182-1197. [PMID: 37902967 DOI: 10.1089/cmb.2023.0186] [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] [Indexed: 11/01/2023]  Open
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