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MetaQUAST: evaluation of metagenome assemblies.
Mikheenko A, Saveliev V, Gurevich A. Mikheenko A, et al. Bioinformatics. 2016 Apr 1;32(7):1088-90. doi: 10.1093/bioinformatics/btv697. Epub 2015 Nov 26. Bioinformatics. 2016. PMID: 26614127
Icarus: visualizer for de novo assembly evaluation.
Mikheenko A, Valin G, Prjibelski A, Saveliev V, Gurevich A. Mikheenko A, et al. Bioinformatics. 2016 Nov 1;32(21):3321-3323. doi: 10.1093/bioinformatics/btw379. Epub 2016 Jul 4. Bioinformatics. 2016. PMID: 27378299
Versatile genome assembly evaluation with QUAST-LG.
Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A. Mikheenko A, et al. Bioinformatics. 2018 Jul 1;34(13):i142-i150. doi: 10.1093/bioinformatics/bty266. Bioinformatics. 2018. PMID: 29949969 Free PMC article.
Dereplication of microbial metabolites through database search of mass spectra.
Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA. Mohimani H, et al. Among authors: mikheenko a. Nat Commun. 2018 Oct 2;9(1):4035. doi: 10.1038/s41467-018-06082-8. Nat Commun. 2018. PMID: 30279420 Free PMC article.
MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.
Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H. Cao L, et al. Among authors: mikheenko a. Cell Syst. 2019 Dec 18;9(6):600-608.e4. doi: 10.1016/j.cels.2019.09.004. Epub 2019 Oct 16. Cell Syst. 2019. PMID: 31629686 Free PMC article.
Complete genomic and epigenetic maps of human centromeres.
Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. Altemose N, et al. Among authors: mikheenko a. Science. 2022 Apr;376(6588):eabl4178. doi: 10.1126/science.abl4178. Epub 2022 Apr 1. Science. 2022. PMID: 35357911 Free PMC article.
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