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For: Oliva A, Tobler R, Cooper A, Llamas B, Souilmi Y. Systematic benchmark of ancient DNA read mapping. Brief Bioinform 2021;22:6217726. [PMID: 33834210 DOI: 10.1093/bib/bbab076] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
Wood JR, Zhou C, Cole TL, Coleman M, Anderson DP, Lyver PO, Tan S, Xiang X, Long X, Luo S, Lou M, Southon JR, Li Q, Zhang G. Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica. Nat Commun 2025;16:1798. [PMID: 40044673 PMCID: PMC11883008 DOI: 10.1038/s41467-025-56925-4] [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: 08/14/2024] [Accepted: 02/05/2025] [Indexed: 03/09/2025]  Open
2
Koptekin D, Yapar E, Vural KB, Sağlıcan E, Altınışık NE, Malaspinas AS, Alkan C, Somel M. Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data. Genome Biol 2025;26:6. [PMID: 39789608 PMCID: PMC11721506 DOI: 10.1186/s13059-024-03462-w] [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: 11/26/2023] [Accepted: 12/16/2024] [Indexed: 01/12/2025]  Open
3
Haarkötter C, Roca-Rada X, Saiz M, Vinueza-Espinosa DC, Gálvez X, Medina-Lozano MI, Díaz-Ruiz D, Álvarez JC, Llamas B, Lorente JA, Austin J. Exploring the Potential of Genome-Wide Hybridization Capture Enrichment for Forensic DNA Profiling of Degraded Bones. Genes (Basel) 2024;16:23. [PMID: 39858570 PMCID: PMC11764906 DOI: 10.3390/genes16010023] [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: 11/18/2024] [Revised: 12/17/2024] [Accepted: 12/24/2024] [Indexed: 01/27/2025]  Open
4
Ravishankar S, Perez V, Davidson R, Roca-Rada X, Lan D, Souilmi Y, Llamas B. Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping. Brief Bioinform 2024;26:bbae646. [PMID: 39674265 DOI: 10.1093/bib/bbae646] [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: 07/18/2024] [Revised: 11/03/2024] [Accepted: 11/28/2024] [Indexed: 12/16/2024]  Open
5
Souilmi Y, Wasef S, Williams MP, Conroy G, Bar I, Bover P, Dann J, Heiniger H, Llamas B, Ogbourne S, Archer M, Ballard JWO, Reed E, Tobler R, Koungoulos L, Walshe K, Wright JL, Balme J, O’Connor S, Cooper A, Mitchell KJ. Ancient genomes reveal over two thousand years of dingo population structure. Proc Natl Acad Sci U S A 2024;121:e2407584121. [PMID: 38976766 PMCID: PMC11287250 DOI: 10.1073/pnas.2407584121] [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: 04/17/2024] [Accepted: 06/04/2024] [Indexed: 07/10/2024]  Open
6
Psonis N, Vassou D, Nafplioti A, Tabakaki E, Pavlidis P, Stamatakis A, Poulakakis N. Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes. Forensic Sci Int Genet 2024;71:103060. [PMID: 38796876 DOI: 10.1016/j.fsigen.2024.103060] [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: 11/07/2023] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/29/2024]
7
Dolenz S, van der Valk T, Jin C, Oppenheimer J, Sharif MB, Orlando L, Shapiro B, Dalén L, Heintzman PD. Unravelling reference bias in ancient DNA datasets. Bioinformatics 2024;40:btae436. [PMID: 38960861 PMCID: PMC11254355 DOI: 10.1093/bioinformatics/btae436] [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: 07/24/2023] [Revised: 03/22/2024] [Accepted: 07/02/2024] [Indexed: 07/05/2024]  Open
8
Almeida da Paz M, Warger S, Taher L. Disregarding multimappers leads to biases in the functional assessment of NGS data. BMC Genomics 2024;25:455. [PMID: 38720252 PMCID: PMC11078754 DOI: 10.1186/s12864-024-10344-9] [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: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024]  Open
9
Hempel E, Faith JT, Preick M, de Jager D, Barish S, Hartmann S, Grau JH, Moodley Y, Gedman G, Pirovich KM, Bibi F, Kalthoff DC, Bocklandt S, Lamm B, Dalén L, Westbury MV, Hofreiter M. Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size. Curr Biol 2024;34:2020-2029.e6. [PMID: 38614080 DOI: 10.1016/j.cub.2024.03.051] [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: 12/20/2023] [Revised: 02/09/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
10
Yin PK, Xiao H, Yang ZB, Yang DS, Yang YH. Shotgun metagenomics reveals the gut microbial diversity and functions in Vespa mandarinia (Hymenoptera: Vespidae) at multiple life stages. Front Microbiol 2024;15:1288051. [PMID: 38529182 PMCID: PMC10961340 DOI: 10.3389/fmicb.2024.1288051] [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: 09/03/2023] [Accepted: 02/12/2024] [Indexed: 03/27/2024]  Open
11
Eisenhofer R, Wright S, Weyrich L. Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities. PeerJ 2024;12:e16770. [PMID: 38440408 PMCID: PMC10911074 DOI: 10.7717/peerj.16770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/16/2023] [Indexed: 03/06/2024]  Open
12
Davidson R, Williams MP, Roca-Rada X, Kassadjikova K, Tobler R, Fehren-Schmitz L, Llamas B. Allelic bias when performing in-solution enrichment of ancient human DNA. Mol Ecol Resour 2023;23:1823-1840. [PMID: 37712846 DOI: 10.1111/1755-0998.13869] [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: 05/09/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
13
Ma H, Lao Y, Liu S, Ai J, Sun X, Zhang W, Kang M, Li J, Sun Y. The diurnal salivary glands transcriptome of Dermacentor nuttalli from the first four days of blood feeding. Ticks Tick Borne Dis 2023;14:102178. [PMID: 37001418 DOI: 10.1016/j.ttbdis.2023.102178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 02/25/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023]
14
Westbury MV, Lorenzen ED. Iteratively mapping ancient DNA to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
15
Oliva A, Tobler R, Llamas B, Souilmi Y. Additional evaluations show that specific BWA-aln settings still outperform BWA-mem for ancient DNA data alignment. Ecol Evol 2022;11:18743-18748. [PMID: 35003706 PMCID: PMC8717315 DOI: 10.1002/ece3.8297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022]  Open
16
Mining museums for historical DNA: advances and challenges in museomics. Trends Ecol Evol 2021;36:1049-1060. [PMID: 34456066 DOI: 10.1016/j.tree.2021.07.009] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/22/2023]
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