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For: Knyazev S, Tsyvina V, Shankar A, Melnyk A, Artyomenko A, Malygina T, Porozov YB, Campbell EM, Switzer WM, Skums P, Mangul S, Zelikovsky A. Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction. Nucleic Acids Res 2021:gkab576. [PMID: 34214168 DOI: 10.1093/nar/gkab576] [Cited by in Crossref: 17] [Cited by in F6Publishing: 18] [Article Influence: 8.5] [Reference Citation Analysis]
Number Citing Articles
1 Koh JX, Masomian M, Anasir MI, Ong S, Poh CL. Insights into In Vitro Adaptation of EV71 and Analysis of Reduced Virulence by In Silico Predictions. Vaccines 2023;11:629. [DOI: 10.3390/vaccines11030629] [Reference Citation Analysis]
2 Wagner J, Yuen L, Littlejohn M, Sozzi V, Jackson K, Martin R, Aeschbacher T, Suri V, Tan SK, Feierbach B, Gaggar A, Marcellin P, Buti Ferret M, Janssen HLA, Gane E, Meagher N, Price DJ, Wong D, Thompson AT, Revill PA. Hepatitis B virus haplotype number at baseline is a predictive marker of functional cure during antiviral therapy for patients with genotypes A and D HBeAg-positive chronic hepatitis B. Aliment Pharmacol Ther 2023;57:509-23. [PMID: 36427857 DOI: 10.1111/apt.17299] [Reference Citation Analysis]
3 Belser JA, Sun X, Kieran TJ, Brock N, Pulit-Penaloza JA, Pappas C, Basu Thakur P, Jones J, Wentworth DE, Zhou B, Tumpey TM, Maines TR. Detection of Airborne Influenza A and SARS-CoV-2 Virus Shedding following Ocular Inoculation of Ferrets. J Virol 2022;96:e0140322. [PMID: 36448801 DOI: 10.1128/jvi.01403-22] [Reference Citation Analysis]
4 Shakola F, Palejev D, Ivanov I. A Framework for Comparison and Assessment of Synthetic RNA-Seq Data. Genes (Basel) 2022;13. [PMID: 36553629 DOI: 10.3390/genes13122362] [Reference Citation Analysis]
5 Baaijens JA, Zulli A, Ott IM, Nika I, van der Lugt MJ, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy KA, Ghaeli N, Imakaev M, Mckenzie-Bennett MF, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer ML, Simen BB, Hanage WP, Grubaugh ND, Peccia J, Baym M; Yale SARS-CoV-2 Genomic Surveillance Initiative. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biol 2022;23:236. [PMID: 36348471 DOI: 10.1186/s13059-022-02805-9] [Cited by in Crossref: 4] [Cited by in F6Publishing: 1] [Article Influence: 4.0] [Reference Citation Analysis]
6 Venturini C, Pang J, Tamuri AU, Roy S, Atkinson C, Griffiths P, Breuer J, Goldstein RA. Haplotype assignment of longitudinal viral deep sequencing data using covariation of variant frequencies. Virus Evol 2022;8:veac093. [PMID: 36478783 DOI: 10.1093/ve/veac093] [Reference Citation Analysis]
7 Borutzki S, Richter B, Proemmel M, Fabianska I, Tran HQ, Hundt B, Mayer D, Kaiser C, Neubert A, Vos A. Oral Rabies Vaccine Strain SPBN GASGAS: Genetic Stability after Serial In Vitro and In Vivo Passaging. Viruses 2022;14. [PMID: 36298691 DOI: 10.3390/v14102136] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
8 Legnardi M, Cecchinato M, Homonnay Z, Dauphin G, Koutoulis KC, Tucciarone CM, Franzo G. Viral subpopulation variability in different batches of Infectious bronchitis virus (IBV) vaccines based on GI-23 lineage: Implications for the field. Virus Res 2022;319:198877. [PMID: 35872282 DOI: 10.1016/j.virusres.2022.198877] [Reference Citation Analysis]
9 Link RW, De Souza DR, Spector C, Mele AR, Chung C, Nonnemacher MR, Wigdahl B, Dampier W. HIV-Quasipore: A Suite of HIV-1-Specific Nanopore Basecallers Designed to Enhance Viral Quasispecies Detection. Front Virol 2022;2. [DOI: 10.3389/fviro.2022.858375] [Reference Citation Analysis]
10 Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK. HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy. mBio 2022;:e0026922. [PMID: 35446121 DOI: 10.1128/mbio.00269-22] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
11 Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nat Methods 2022. [PMID: 35396471 DOI: 10.1038/s41592-022-01444-z] [Cited by in Crossref: 2] [Cited by in F6Publishing: 4] [Article Influence: 2.0] [Reference Citation Analysis]
12 Seoane P, Díaz-martínez L, Viguera E, Claros MG, Grande-pérez A. QuasiFlow: a bioinformatic tool for genetic variability analysis from next generation sequencing data.. [DOI: 10.1101/2022.04.05.487169] [Reference Citation Analysis]
13 Liu Y, Kearney J, Mahmoud M, Kille B, Sedlazeck FJ, Treangen TJ. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data. Nat Commun 2022;13. [DOI: 10.1038/s41467-022-28852-1] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 2.0] [Reference Citation Analysis]
14 Ringlander J, Fingal J, Kann H, Prakash K, Rydell G, Andersson M, Martner A, Lindh M, Horal P, Hellstrand K, Kann M. Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2. Proc Natl Acad Sci U S A 2022;119:e2112663119. [PMID: 35064076 DOI: 10.1073/pnas.2112663119] [Cited by in Crossref: 4] [Cited by in F6Publishing: 7] [Article Influence: 4.0] [Reference Citation Analysis]
15 Liao H, Cai D, Sun Y. VirStrain: a strain identification tool for RNA viruses. Genome Biol 2022;23. [DOI: 10.1186/s13059-022-02609-x] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
16 Luo X, Kang X, Schönhuth A. Strainline: full-length de novo viral haplotype reconstruction from noisy long reads. Genome Biol 2022;23. [DOI: 10.1186/s13059-021-02587-6] [Reference Citation Analysis]
17 Joussef-Piña S, Nankya I, Nalukwago S, Baseke J, Rwambuya S, Winner D, Kyeyune F, Chervenak K, Thiel B, Asaad R, Dobrowolski C, Luttge B, Lawley B, Kityo CM, Boom WH, Karn J, Quiñones-Mateu ME. Reduced and highly diverse peripheral HIV-1 reservoir in virally suppressed patients infected with non-B HIV-1 strains in Uganda. Retrovirology 2022;19:1. [PMID: 35033105 DOI: 10.1186/s12977-022-00587-3] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
18 Wang S, Sotcheff SL, Gallardo CM, Jaworski E, Torbett BE, Routh AL. Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa. Nucleic Acids Res 2022:gkab1259. [PMID: 35018461 DOI: 10.1093/nar/gkab1259] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 3.0] [Reference Citation Analysis]
19 Juyal A, Hosseini R, Novikov D, Grinshpon M, Zelikovsky A. Entropy Based Clustering of Viral Sequences. Bioinformatics Research and Applications 2022. [DOI: 10.1007/978-3-031-23198-8_33] [Reference Citation Analysis]
20 Chen Q, Jia H, Wang X, Shi Y, Zhang L, Hu L, Wang C, He X, Harrison TJ, Jackson JB, Wu L, Fang Z. Analysis of entire hepatitis B virus genomes reveals reversion of mutations to wild type in natural infection, a 15 year follow-up study. Infection, Genetics and Evolution 2022;97:105184. [DOI: 10.1016/j.meegid.2021.105184] [Reference Citation Analysis]
21 Knyazev S, Novikov D, Grinshpon M, Singh H, Ayyala R, Sarwal V, Hosseini R, Baykal PI, Skums P, Campbell E, Mangul S, Zelikovsky A. A Novel Network Representation of SARS-CoV-2 Sequencing Data. Bioinformatics Research and Applications 2021. [DOI: 10.1007/978-3-030-91415-8_15] [Cited by in Crossref: 1] [Article Influence: 0.5] [Reference Citation Analysis]