196 related articles for article (PubMed ID: 37389439)
1. Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data.
Roder AE; Johnson KEE; Knoll M; Khalfan M; Wang B; Schultz-Cherry S; Banakis S; Kreitman A; Mederos C; Youn JH; Mercado R; Wang W; Chung M; Ruchnewitz D; Samanovic MI; Mulligan MJ; Lässig M; Luksza M; Das S; Gresham D; Ghedin E
mBio; 2023 Aug; 14(4):e0104623. PubMed ID: 37389439
[TBL] [Abstract][Full Text] [Related]
2. Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data.
Roder AE; Johnson K; Knoll M; Khalfan M; Wang B; Schultz-Cherry S; Banakis S; Kreitman A; Mederos C; Youn JH; Mercado R; Wang W; Ruchnewitz D; Samanovic MI; Mulligan MJ; Lassig M; Åuksza M; Das S; Gresham D; Ghedin E
bioRxiv; 2022 Aug; ():. PubMed ID: 36656775
[TBL] [Abstract][Full Text] [Related]
3. Patterns of within-host genetic diversity in SARS-CoV-2.
Tonkin-Hill G; Martincorena I; Amato R; Lawson ARJ; Gerstung M; Johnston I; Jackson DK; Park N; Lensing SV; Quail MA; Gonçalves S; Ariani C; Spencer Chapman M; Hamilton WL; Meredith LW; Hall G; Jahun AS; Chaudhry Y; Hosmillo M; Pinckert ML; Georgana I; Yakovleva A; Caller LG; Caddy SL; Feltwell T; Khokhar FA; Houldcroft CJ; Curran MD; Parmar S; ; Alderton A; Nelson R; Harrison EM; Sillitoe J; Bentley SD; Barrett JC; Torok ME; Goodfellow IG; Langford C; Kwiatkowski D;
Elife; 2021 Aug; 10():. PubMed ID: 34387545
[TBL] [Abstract][Full Text] [Related]
4. Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling.
McCrone JT; Lauring AS
J Virol; 2016 Aug; 90(15):6884-95. PubMed ID: 27194763
[TBL] [Abstract][Full Text] [Related]
5. Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients.
Wang Y; Wang D; Zhang L; Sun W; Zhang Z; Chen W; Zhu A; Huang Y; Xiao F; Yao J; Gan M; Li F; Luo L; Huang X; Zhang Y; Wong SS; Cheng X; Ji J; Ou Z; Xiao M; Li M; Li J; Ren P; Deng Z; Zhong H; Xu X; Song T; Mok CKP; Peiris M; Zhong N; Zhao J; Li Y; Li J; Zhao J
Genome Med; 2021 Feb; 13(1):30. PubMed ID: 33618765
[TBL] [Abstract][Full Text] [Related]
6. Identification of a High-Frequency Intrahost SARS-CoV-2 Spike Variant with Enhanced Cytopathic and Fusogenic Effects.
Rocheleau L; Laroche G; Fu K; Stewart CM; Mohamud AO; Côté M; Giguère PM; Langlois MA; Pelchat M
mBio; 2021 Jun; 12(3):e0078821. PubMed ID: 34182784
[TBL] [Abstract][Full Text] [Related]
7. RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants.
Rothman JA; Loveless TB; Kapcia J; Adams ED; Steele JA; Zimmer-Faust AG; Langlois K; Wanless D; Griffith M; Mao L; Chokry J; Griffith JF; Whiteson KL
Appl Environ Microbiol; 2021 Nov; 87(23):e0144821. PubMed ID: 34550753
[TBL] [Abstract][Full Text] [Related]
8. TaME-seq2: tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling.
Hesselberg Løvestad A; Stosic MS; Costanzi JM; Christiansen IK; Aamot HV; Ambur OH; Rounge TB
Virol J; 2023 Mar; 20(1):44. PubMed ID: 36890572
[TBL] [Abstract][Full Text] [Related]
9. Evaluating the performance of tools used to call minority variants from whole genome short-read data.
Said Mohammed K; Kibinge N; Prins P; Agoti CN; Cotten M; Nokes DJ; Brand S; Githinji G
Wellcome Open Res; 2018; 3():21. PubMed ID: 30483597
[No Abstract] [Full Text] [Related]
10. SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants.
Sun F; Wang X; Tan S; Dan Y; Lu Y; Zhang J; Xu J; Tan Z; Xiang X; Zhou Y; He W; Wan X; Zhang W; Chen Y; Tan W; Deng G
Microbiol Spectr; 2021 Sep; 9(1):e0026121. PubMed ID: 34346744
[TBL] [Abstract][Full Text] [Related]
11. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data.
Liu Y; Kearney J; Mahmoud M; Kille B; Sedlazeck FJ; Treangen TJ
Nat Commun; 2022 Mar; 13(1):1321. PubMed ID: 35288552
[TBL] [Abstract][Full Text] [Related]
12. Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.
Gibson KM; Steiner MC; Rentia U; Bendall ML; Pérez-Losada M; Crandall KA
Viruses; 2020 Jul; 12(7):. PubMed ID: 32674515
[TBL] [Abstract][Full Text] [Related]
13. Sequencing Framework for the Sensitive Detection and Precise Mapping of Defective Interfering Particle-Associated Deletions across Influenza A and B Viruses.
Alnaji FG; Holmes JR; Rendon G; Vera JC; Fields CJ; Martin BE; Brooke CB
J Virol; 2019 Jun; 93(11):. PubMed ID: 30867305
[TBL] [Abstract][Full Text] [Related]
14. Evaluation of haplotype callers for next-generation sequencing of viruses.
Eliseev A; Gibson KM; Avdeyev P; Novik D; Bendall ML; Pérez-Losada M; Alexeev N; Crandall KA
Infect Genet Evol; 2020 Aug; 82():104277. PubMed ID: 32151775
[TBL] [Abstract][Full Text] [Related]
15. Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data.
Karimnezhad A; Palidwor GA; Thavorn K; Stewart DJ; Campbell PA; Lo B; Perkins TJ
BMC Med Genomics; 2020 Oct; 13(1):156. PubMed ID: 33059707
[TBL] [Abstract][Full Text] [Related]
16. A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome.
Arana C; Liang C; Brock M; Zhang B; Zhou J; Chen L; Cantarel B; SoRelle J; Hooper LV; Raj P
PLoS One; 2022; 17(1):e0261014. PubMed ID: 35025877
[TBL] [Abstract][Full Text] [Related]
17. Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants.
Blanquart F; Hozé N; Cowling BJ; Débarre F; Cauchemez S
Elife; 2022 May; 11():. PubMed ID: 35587653
[TBL] [Abstract][Full Text] [Related]
18. ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections.
Marcolungo L; Beltrami C; Degli Esposti C; Lopatriello G; Piubelli C; Mori A; Pomari E; Deiana M; Scarso S; Bisoffi Z; Grosso V; Cosentino E; Maestri S; Lavezzari D; Iadarola B; Paterno M; Segala E; Giovannone B; Gallinaro M; Rossato M; Delledonne M
Genomics; 2021 Jul; 113(4):1628-1638. PubMed ID: 33839270
[TBL] [Abstract][Full Text] [Related]
19. A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations.
King DJ; Freimanis G; Lasecka-Dykes L; Asfor A; Ribeca P; Waters R; King DP; Laing E
Viruses; 2020 Oct; 12(10):. PubMed ID: 33092085
[TBL] [Abstract][Full Text] [Related]
20. Assessing the hidden diversity underlying consensus sequences of SARS-CoV-2 using VICOS, a novel bioinformatic pipeline for identification of mixed viral populations.
Goya S; Sosa E; Nabaes Jodar M; Torres C; König G; Acuña D; Ceballos S; Distéfano AJ; Dopazo H; Dus Santos M; Fass M; Fernández Do Porto D; Fernández A; Gallego F; Gismondi MI; Gramundi I; Lusso S; Martí M; Mazzeo M; Mistchenko AS; Muñoz Hidalgo M; Natale M; Nardi C; Ousset J; Peralta AV; Pintos C; Puebla AF; Pianciola L; Rivarola M; Turjanski A; Valinotto L; Vera PA; Zaiat J; Zubrycki J; ; Aulicino P; Viegas M
Virus Res; 2023 Feb; 325():199035. PubMed ID: 36586487
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
