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For: Lemoine F, Gascuel O. Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows. NAR Genom Bioinform 2021;3:lqab075. [PMID: 34396097 PMCID: PMC8356961 DOI: 10.1093/nargab/lqab075] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/09/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022]  Open
Number Cited by Other Article(s)
1
Lucotte EA, Jay P, Rougemont Q, Boyer L, Cornille A, Snirc A, Labat A, Chahine E, Duhamel M, Namias A, Gendelman J, Ma WJ, Hayes RK, Baruri S, Ham JP, Perlin MH, Hood ME, Rodríguez de la Vega RC, Giraud T. Repeated loss of function at HD mating-type genes and of recombination in anther-smut fungi. Nat Commun 2025;16:4962. [PMID: 40436846 PMCID: PMC12119880 DOI: 10.1038/s41467-025-60222-5] [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: 04/11/2024] [Accepted: 05/14/2025] [Indexed: 06/01/2025]  Open
2
Feng B, Li Y, Xu B, Liu H, Steenwyk JL, David KT, Tian X, Gonçalves C, Opulente DA, LaBella AL, Harrison MC, Wolters JF, Shao S, Chen Z, Fisher KJ, Groenewald M, Hittinger CT, Shen XX, Li S, Rokas A, Zhou X, Li Y. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage. Mol Syst Biol 2025:10.1038/s44320-025-00118-0. [PMID: 40425814 DOI: 10.1038/s44320-025-00118-0] [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: 10/16/2024] [Revised: 04/11/2025] [Accepted: 04/30/2025] [Indexed: 05/29/2025]  Open
3
Giulieri SG, Leroi M, Daniel D, Chean R, Bond K, Walker H, Holmes NE, Mothobi N, Alexander A, Jenney A, Beckett C, Mahony A, Stevens K, Sherry NL, Howden BP. A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections. Nat Commun 2025;16:4869. [PMID: 40419483 DOI: 10.1038/s41467-025-60045-4] [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: 11/26/2024] [Accepted: 05/13/2025] [Indexed: 05/28/2025]  Open
4
Lemarcis T, Blin A, Cariou M, Derzelle A, Farhat S, Fedosov A, Zaharias P, Zuccon D, Puillandre N. Too Far From Relatives? Impact of the Genetic Distance on the Success of Exon Capture in Phylogenomics. Mol Ecol Resour 2025;25:e14064. [PMID: 39780767 DOI: 10.1111/1755-0998.14064] [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: 07/08/2024] [Revised: 12/11/2024] [Accepted: 12/20/2024] [Indexed: 01/11/2025]
5
Ma J, Bechsgaard J, Aagaard A, Villesen P, Bilde T, Schierup MH. The genomic consequences and persistence of sociality in spiders. Genome Res 2025;35:499-511. [PMID: 39978820 PMCID: PMC11960701 DOI: 10.1101/gr.279503.124] [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: 04/22/2024] [Accepted: 02/04/2025] [Indexed: 02/22/2025]
6
Hu Y, Gan Y, Chen Y, Wang H, Cui X, Shen Y, Shen X. Molecular characterization and prevalence assessment of Durettenema sp. (Nematoda: Trichostrongyloidea) in the great leaf-nosed bats (Hipposideros armiger) in South China. J Helminthol 2025;99:e41. [PMID: 40045704 DOI: 10.1017/s0022149x25000227] [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: 05/13/2025]
7
Olagoke O, Aziz A, Zhu L, Read T, Dean D. Whole-genome automated assembly pipeline for Chlamydia trachomatis strains from reference, in vitro and clinical samples using the integrated CtGAP pipeline. NAR Genom Bioinform 2025;7:lqae187. [PMID: 39781511 PMCID: PMC11704784 DOI: 10.1093/nargab/lqae187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 12/10/2024] [Accepted: 12/18/2024] [Indexed: 01/12/2025]  Open
8
Miller EC, Faucher R, Hart PB, Rincón-Sandoval M, Santaquiteria A, White WT, Baldwin CC, Miya M, Betancur-R R, Tornabene L, Evans K, Arcila D. Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes. Nat Ecol Evol 2025;9:474-490. [PMID: 39604701 DOI: 10.1038/s41559-024-02586-3] [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: 11/03/2023] [Accepted: 10/18/2024] [Indexed: 11/29/2024]
9
Levy S, Jiang AK, Grant MR, Arp G, Minabou Ndjite G, Jiang X, Hall B. Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut. Nat Commun 2025;16:1121. [PMID: 39875389 PMCID: PMC11775122 DOI: 10.1038/s41467-025-56332-9] [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: 06/07/2024] [Accepted: 01/14/2025] [Indexed: 01/30/2025]  Open
10
Cerqueira de Araujo A, Noel B, Bretaudeau A, Labadie K, Boudet M, Tadrent N, Istace B, Kritli S, Cruaud C, Olaso R, Deleuze JF, Voordouw MJ, Hervet C, Plantard O, Zamoto-Niikura A, Chertemps T, Maïbèche M, Hilliou F, Le Goff G, Chmelař J, Mazák V, Jmel MA, Kotsyfakis M, Medina JM, Hackenberg M, Šimo L, Koutroumpa FA, Wincker P, Kopáček P, Perner J, Aury JM, Rispe C. Genome sequences of four Ixodes species expands understanding of tick evolution. BMC Biol 2025;23:17. [PMID: 39838418 PMCID: PMC11752866 DOI: 10.1186/s12915-025-02121-1] [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: 06/03/2024] [Accepted: 01/07/2025] [Indexed: 01/23/2025]  Open
11
Hounmanou YMG, Hougbenou BGJ, Dougnon VT, Hammerl JA, Dalsgaard A. Vibrio cidicii genomes recovered from Baltic Sea samples in Denmark. Microbiol Resour Announc 2025;14:e0112124. [PMID: 39665568 PMCID: PMC11737143 DOI: 10.1128/mra.01121-24] [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: 10/17/2024] [Accepted: 11/25/2024] [Indexed: 12/13/2024]  Open
12
Taouk ML, Featherstone LA, Taiaroa G, Seemann T, Ingle DJ, Stinear TP, Wick RR. Exploring SNP filtering strategies: the influence of strict vs soft core. Microb Genom 2025;11:001346. [PMID: 39812553 PMCID: PMC11734701 DOI: 10.1099/mgen.0.001346] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 12/13/2024] [Indexed: 01/16/2025]  Open
13
Pitot TM, Girard C, Rapp JZ, Somerville V, Culley AI, Vincent WF, Moineau S, Roux S. Viral niche-partitioning: comparative genomics of giant viruses across environmental gradients in a high Arctic freshwater-saltwater lake. ISME COMMUNICATIONS 2025;5:ycae155. [PMID: 39834781 PMCID: PMC11745019 DOI: 10.1093/ismeco/ycae155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 11/20/2024] [Accepted: 12/04/2024] [Indexed: 01/22/2025]
14
Tyrrell GJ, Croxen M, McCullough E, Li V, Golden AR, Martin I. Group A streptococcal infections in Alberta, Canada 2018-2023. Epidemiol Infect 2024;153:e35. [PMID: 39711024 PMCID: PMC11869071 DOI: 10.1017/s0950268824001857] [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: 08/21/2024] [Revised: 11/06/2024] [Accepted: 12/18/2024] [Indexed: 12/24/2024]  Open
15
Rice AM, Troendle EP, Bridgett SJ, Firoozi Nejad B, McKinley JM, Bradley DT, Fairley DJ, Bamford CGG, Skvortsov T, Simpson DA. SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics. Genome Med 2024;16:150. [PMID: 39702217 DOI: 10.1186/s13073-024-01409-1] [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] [Accepted: 11/07/2024] [Indexed: 12/21/2024]  Open
16
Mao B, Zheng Y, Xiao Y, Yang K, Shangguan J, Shen M, Sun H, Fang X, Fu Y. Genome-wide phylogenetic analysis and expansion of gene families involved in detoxification in Smittia aterrima (Meigen)and Smittia pratorum (Goetghebuer) (Diptera, Chironomidae). BMC Genom Data 2024;25:106. [PMID: 39695974 DOI: 10.1186/s12863-024-01289-9] [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: 10/13/2024] [Accepted: 12/10/2024] [Indexed: 12/20/2024]  Open
17
Jagadeesh J, Vembar SS. Evolution of sequence, structural and functional diversity of the ubiquitous DNA/RNA-binding Alba domain. Sci Rep 2024;14:30363. [PMID: 39638848 PMCID: PMC11621453 DOI: 10.1038/s41598-024-79937-4] [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: 06/20/2024] [Accepted: 11/13/2024] [Indexed: 12/07/2024]  Open
18
Boyd JM, Ryan Kaler K, Esquilín-Lebrón K, Pall A, Campbell CJ, Foley ME, Rios-Delgado G, Mustor EM, Stephens TG, Bovermann H, Greco TM, Cristea IM, Carabetta VJ, Beavers WN, Bhattacharya D, Skaar EP, Shaw LN, Stemmler TL. Fpa (YlaN) is an iron(II) binding protein that functions to relieve Fur-mediated repression of gene expression in Staphylococcus aureus. mBio 2024;15:e0231024. [PMID: 39440976 PMCID: PMC11559061 DOI: 10.1128/mbio.02310-24] [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: 08/01/2024] [Accepted: 09/30/2024] [Indexed: 10/25/2024]  Open
19
Ndjite GM, Jiang A, Ravel C, Grant M, Jiang X, Hall B. Gut Microbial Utilization of the Alternative Sweetener, D-Allulose, via AlsE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.07.622513. [PMID: 39574671 PMCID: PMC11580995 DOI: 10.1101/2024.11.07.622513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2024]
20
Thomy J, Schvarcz CR, McBeain KA, Edwards KF, Steward GF. Eukaryotic viruses encode the ribosomal protein eL40. NPJ VIRUSES 2024;2:51. [PMID: 39464202 PMCID: PMC11499249 DOI: 10.1038/s44298-024-00060-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 09/20/2024] [Indexed: 10/29/2024]
21
Rey Redondo E, Leung SKK, Yung CCM. Genomic and biogeographic characterisation of the novel prasinovirus Mantoniella tinhauana virus 1. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024;16:e70020. [PMID: 39392286 PMCID: PMC11467894 DOI: 10.1111/1758-2229.70020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 09/10/2024] [Indexed: 10/12/2024]
22
Chan KO. Next-generation bioinformatics: An ultrafast and user-friendly tool for phylogenomic data exploration. Mol Ecol Resour 2024;24:e13993. [PMID: 38970356 DOI: 10.1111/1755-0998.13993] [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: 05/28/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024]
23
Handika H, Esselstyn JA. SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic datasets. Mol Ecol Resour 2024;24:e13964. [PMID: 38666432 DOI: 10.1111/1755-0998.13964] [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: 04/19/2022] [Revised: 03/18/2024] [Accepted: 04/15/2024] [Indexed: 10/10/2024]
24
Vakirlis N, Acar O, Cherupally V, Carvunis AR. Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence. Genome Biol Evol 2024;16:evae151. [PMID: 39004885 PMCID: PMC11299112 DOI: 10.1093/gbe/evae151] [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: 01/03/2024] [Revised: 06/17/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024]  Open
25
Zhang J, Schneller NM, Field MA, Chan CX, Miller DJ, Strugnell JM, Riginos C, Bay L, Cooke I. Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef. Mol Ecol 2024;33:e17468. [PMID: 39046252 DOI: 10.1111/mec.17468] [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: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024]
26
Vakirlis N, Kupczok A. Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins. Genome Res 2024;34:888-903. [PMID: 38977308 PMCID: PMC11293555 DOI: 10.1101/gr.278977.124] [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: 01/11/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024]
27
Efimenko B, Popadin K, Gunbin K. NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data. Nucleic Acids Res 2024;52:W108-W115. [PMID: 38795067 PMCID: PMC11223800 DOI: 10.1093/nar/gkae438] [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: 03/07/2024] [Revised: 04/23/2024] [Accepted: 05/09/2024] [Indexed: 05/27/2024]  Open
28
Feng B, Li Y, Liu H, Steenwyk JL, David KT, Tian X, Xu B, Gonçalves C, Opulente DA, LaBella AL, Harrison MC, Wolters JF, Shao S, Chen Z, Fisher KJ, Groenewald M, Hittinger CT, Shen XX, Rokas A, Zhou X, Li Y. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597512. [PMID: 38895429 PMCID: PMC11185758 DOI: 10.1101/2024.06.05.597512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
29
Paremskaia AI, Volchkov PY, Deviatkin AA. IAVCP (Influenza A Virus Consensus and Phylogeny): Automatic Identification of the Genomic Sequence of the Influenza A Virus from High-Throughput Sequencing Data. Viruses 2024;16:873. [PMID: 38932165 PMCID: PMC11209090 DOI: 10.3390/v16060873] [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: 03/18/2024] [Revised: 04/27/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024]  Open
30
Thompson A, Liebeskind BJ, Scully EJ, Landis MJ. Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong. Syst Biol 2024;73:183-206. [PMID: 38189575 PMCID: PMC11249978 DOI: 10.1093/sysbio/syad074] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 11/22/2023] [Accepted: 01/05/2024] [Indexed: 01/09/2024]  Open
31
Rey Redondo E, Xu Y, Yung CCM. Genomic characterisation and ecological distribution of Mantoniella tinhauana: a novel Mamiellophycean green alga from the Western Pacific. Front Microbiol 2024;15:1358574. [PMID: 38774501 PMCID: PMC11106453 DOI: 10.3389/fmicb.2024.1358574] [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: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 05/24/2024]  Open
32
Tominaga K, Ozaki S, Sato S, Katayama T, Nishimura Y, Omae K, Iwasaki W. Frequent nonhomologous replacement of replicative helicase loaders by viruses in Vibrionaceae. Proc Natl Acad Sci U S A 2024;121:e2317954121. [PMID: 38683976 PMCID: PMC11087808 DOI: 10.1073/pnas.2317954121] [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: 10/18/2023] [Accepted: 03/14/2024] [Indexed: 05/02/2024]  Open
33
Morel-Letelier I, Yuen B, Kück AC, Camacho-García YE, Petersen JM, Lara M, Leray M, Eisen JA, Osvatic JT, Gros O, Wilkins LGE. Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts. PLoS Genet 2024;20:e1011295. [PMID: 38820540 PMCID: PMC11168628 DOI: 10.1371/journal.pgen.1011295] [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: 11/17/2023] [Revised: 06/12/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024]  Open
34
Morel M, Zhukova A, Lemoine F, Gascuel O. Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor. Genome Biol Evol 2024;16:evae040. [PMID: 38451738 PMCID: PMC10986858 DOI: 10.1093/gbe/evae040] [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: 05/09/2023] [Revised: 01/30/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024]  Open
35
Ngou BPM, Wyler M, Schmid MW, Kadota Y, Shirasu K. Evolutionary trajectory of pattern recognition receptors in plants. Nat Commun 2024;15:308. [PMID: 38302456 PMCID: PMC10834447 DOI: 10.1038/s41467-023-44408-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/12/2023] [Indexed: 02/03/2024]  Open
36
Rosani U, De Felice S, Frizzo R, Kawato S, Wegner KM. FicD genes in invertebrates: A tale of transposons, pathogenic and integrated viruses. Gene 2024;893:147895. [PMID: 37832807 DOI: 10.1016/j.gene.2023.147895] [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: 03/04/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
37
Thomy J, Sanchez F, Prioux C, Yau S, Xu Y, Mak J, Sun R, Piganeau G, Yung CCM. Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea. ISME COMMUNICATIONS 2024;4:ycae109. [PMID: 39296779 PMCID: PMC11408933 DOI: 10.1093/ismeco/ycae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/16/2024] [Accepted: 08/27/2024] [Indexed: 09/21/2024]
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Zaharias P, Lemoine F, Gascuel O. Robustness of Felsenstein's Versus Transfer Bootstrap Supports With Respect to Taxon Sampling. Syst Biol 2023;72:1280-1295. [PMID: 37756489 PMCID: PMC10939309 DOI: 10.1093/sysbio/syad052] [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: 02/24/2022] [Revised: 06/26/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023]  Open
39
Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, et alMatteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 2023;186:5690-5704.e20. [PMID: 38101407 PMCID: PMC10795731 DOI: 10.1016/j.cell.2023.11.024] [Show More Authors] [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: 03/12/2023] [Revised: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
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Suspène R, Raymond KA, Boutin L, Guillier S, Lemoine F, Ferraris O, Tournier JN, Iseni F, Simon-Lorière E, Vartanian JP. APOBEC3F Is a Mutational Driver of the Human Monkeypox Virus Identified in the 2022 Outbreak. J Infect Dis 2023;228:1421-1429. [PMID: 37224627 PMCID: PMC11009509 DOI: 10.1093/infdis/jiad165] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/24/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023]  Open
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Zufan SE, Lau KA, Donald A, Hoang T, Foster CSP, Sikazwe C, Theis T, Rawlinson WD, Ballard SA, Stinear TP, Howden BP, Jennison AV, Seemann T. Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance. Microb Genom 2023;9. [PMID: 38019123 DOI: 10.1099/mgen.0.001146] [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: 11/30/2023]  Open
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Caro H, Dollin S, Biton A, Brancotte B, Desvillechabrol D, Dufresne Y, Li B, Kornobis E, Lemoine F, Maillet N, Perrin A, Traut N, Néron B, Cokelaer T. BioConvert: a comprehensive format converter for life sciences. NAR Genom Bioinform 2023;5:lqad074. [PMID: 37608802 PMCID: PMC10440784 DOI: 10.1093/nargab/lqad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/18/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023]  Open
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Stockdale JE, Susvitasari K, Tupper P, Sobkowiak B, Mulberry N, Gonçalves da Silva A, Watt AE, Sherry NL, Minko C, Howden BP, Lane CR, Colijn C. Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19. Nat Commun 2023;14:4830. [PMID: 37563113 PMCID: PMC10415581 DOI: 10.1038/s41467-023-40544-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/31/2023] [Indexed: 08/12/2023]  Open
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Liu B, Warnow T. Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol Biol 2023;18:6. [PMID: 37468904 PMCID: PMC10355063 DOI: 10.1186/s13015-023-00230-6] [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: 03/29/2023] [Accepted: 06/10/2023] [Indexed: 07/21/2023]  Open
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Holtz A, Baele G, Bourhy H, Zhukova A. Integrating full and partial genome sequences to decipher the global spread of canine rabies virus. Nat Commun 2023;14:4247. [PMID: 37460566 DOI: 10.1038/s41467-023-39847-x] [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: 03/02/2023] [Accepted: 06/30/2023] [Indexed: 07/20/2023]  Open
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Zhukova A, Dunn D, Gascuel O. Modeling Drug Resistance Emergence and Transmission in HIV-1 in the UK. Viruses 2023;15:1244. [PMID: 37376544 DOI: 10.3390/v15061244] [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: 04/17/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023]  Open
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Touret F, Giraud E, Bourret J, Donati F, Tran-Rajau J, Chiaravalli J, Lemoine F, Agou F, Simon-Lorière E, van der Werf S, de Lamballerie X. Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 omicron sub-lineages. iScience 2023;26:106413. [PMID: 36968074 PMCID: PMC10015083 DOI: 10.1016/j.isci.2023.106413] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]  Open
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In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control. Microbiol Spectr 2023;11:e0326722. [PMID: 36692300 PMCID: PMC9927157 DOI: 10.1128/spectrum.03267-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
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Vakirlis N, Vance Z, Duggan KM, McLysaght A. De novo birth of functional microproteins in the human lineage. Cell Rep 2022;41:111808. [PMID: 36543139 PMCID: PMC10073203 DOI: 10.1016/j.celrep.2022.111808] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 06/21/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]  Open
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Díaz-Escandón D, Tagirdzhanova G, Vanderpool D, Allen CCG, Aptroot A, Češka O, Hawksworth DL, Huereca A, Knudsen K, Kocourková J, Lücking R, Resl P, Spribille T. Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes. Curr Biol 2022;32:5209-5218.e5. [PMID: 36423639 DOI: 10.1016/j.cub.2022.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/30/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022]
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