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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. Bankevich A, et al. J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16. J Comput Biol. 2012. PMID: 22506599 Free PMC article.
Scalable heuristics for design of DNA probe arrays.
Kahng AB, Măndoiu II, Pevzner PA, Reda S, Zelikovsky AZ. Kahng AB, et al. J Comput Biol. 2004;11(2-3):429-47. doi: 10.1089/1066527041410391. J Comput Biol. 2004. PMID: 15285900
Correcting base-assignment errors in repeat regions of shotgun assembly.
Zhi D, Keich U, Pevzner P, Heber S, Tang H. Zhi D, et al. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):54-64. doi: 10.1109/TCBB.2007.1005. IEEE/ACM Trans Comput Biol Bioinform. 2007. PMID: 17277413
Whole-genome sequencing and assembly with high-throughput, short-read technologies.
Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Sundquist A, et al. PLoS One. 2007 May 30;2(5):e484. doi: 10.1371/journal.pone.0000484. PLoS One. 2007. PMID: 17534434 Free PMC article.
Short read fragment assembly of bacterial genomes.
Chaisson MJ, Pevzner PA. Chaisson MJ, et al. Genome Res. 2008 Feb;18(2):324-30. doi: 10.1101/gr.7088808. Epub 2007 Dec 14. Genome Res. 2008. PMID: 18083777 Free PMC article.
Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage.
Grindberg RV, Ishoey T, Brinza D, Esquenazi E, Coates RC, Liu WT, Gerwick L, Dorrestein PC, Pevzner P, Lasken R, Gerwick WH. Grindberg RV, et al. PLoS One. 2011 Apr 12;6(4):e18565. doi: 10.1371/journal.pone.0018565. PLoS One. 2011. PMID: 21533272 Free PMC article.
Error correction of high-throughput sequencing datasets with non-uniform coverage.
Medvedev P, Scott E, Kakaradov B, Pevzner P. Medvedev P, et al. Bioinformatics. 2011 Jul 1;27(13):i137-41. doi: 10.1093/bioinformatics/btr208. Bioinformatics. 2011. PMID: 21685062 Free PMC article.
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.
Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS. Chitsaz H, et al. Nat Biotechnol. 2011 Sep 18;29(10):915-21. doi: 10.1038/nbt.1966. Nat Biotechnol. 2011. PMID: 21926975 Free PMC article.
Multiplex de novo sequencing of peptide antibiotics.
Mohimani H, Liu WT, Yang YL, Gaudêncio SP, Fenical W, Dorrestein PC, Pevzner PA. Mohimani H, et al. J Comput Biol. 2011 Nov;18(11):1371-81. doi: 10.1089/cmb.2011.0158. Epub 2011 Oct 28. J Comput Biol. 2011. PMID: 22035290 Free PMC article.
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