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QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.
Skums P, Zelikovsky A, Singh R, Gussler W, Dimitrova Z, Knyazev S, Mandric I, Ramachandran S, Campo D, Jha D, Bunimovich L, Costenbader E, Sexton C, O'Connor S, Xia GL, Khudyakov Y. Skums P, et al. Among authors: zelikovsky a. Bioinformatics. 2018 Jan 1;34(1):163-170. doi: 10.1093/bioinformatics/btx402. Bioinformatics. 2018. PMID: 29304222 Free PMC article.
2SNP: scalable phasing based on 2-SNP haplotypes.
Brinza D, Zelikovsky A. Brinza D, et al. Among authors: zelikovsky a. Bioinformatics. 2006 Feb 1;22(3):371-3. doi: 10.1093/bioinformatics/bti785. Epub 2005 Nov 15. Bioinformatics. 2006. PMID: 16287933
Inferring viral quasispecies spectra from 454 pyrosequencing reads.
Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A. Astrovskaya I, et al. Among authors: zelikovsky a. BMC Bioinformatics. 2011;12 Suppl 6(Suppl 6):S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28. BMC Bioinformatics. 2011. PMID: 21989211 Free PMC article.
Efficient error correction for next-generation sequencing of viral amplicons.
Skums P, Dimitrova Z, Campo DS, Vaughan G, Rossi L, Forbi JC, Yokosawa J, Zelikovsky A, Khudyakov Y. Skums P, et al. Among authors: zelikovsky a. BMC Bioinformatics. 2012 Jun 25;13 Suppl 10(Suppl 10):S6. doi: 10.1186/1471-2105-13-S10-S6. BMC Bioinformatics. 2012. PMID: 22759430 Free PMC article.
Reconstructing viral quasispecies from NGS amplicon reads.
Mancuso N, Tork B, Skums P, Ganova-Raeva L, Măndoiu I, Zelikovsky A. Mancuso N, et al. Among authors: zelikovsky a. In Silico Biol. 2011-2012;11(5-6):237-49. doi: 10.3233/ISB-2012-0458. In Silico Biol. 2011. PMID: 23202425
Accurate viral population assembly from ultra-deep sequencing data.
Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E. Mangul S, et al. Among authors: zelikovsky a. Bioinformatics. 2014 Jun 15;30(12):i329-37. doi: 10.1093/bioinformatics/btu295. Bioinformatics. 2014. PMID: 24932001 Free PMC article.
103 results