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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL. Langmead B, et al. Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4. Genome Biol. 2009. PMID: 19261174 Free PMC article.
The dog genome: survey sequencing and comparative analysis.
Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM, Venter JC. Kirkness EF, et al. Science. 2003 Sep 26;301(5641):1898-903. doi: 10.1126/science.1086432. Science. 2003. PMID: 14512627
Hierarchical scaffolding with Bambus.
Pop M, Kosack DS, Salzberg SL. Pop M, et al. Genome Res. 2004 Jan;14(1):149-59. doi: 10.1101/gr.1536204. Genome Res. 2004. PMID: 14707177 Free PMC article.
Comparative genome assembly.
Pop M, Phillippy A, Delcher AL, Salzberg SL. Pop M, et al. Brief Bioinform. 2004 Sep;5(3):237-48. doi: 10.1093/bib/5.3.237. Brief Bioinform. 2004. PMID: 15383210
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.
Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. Salzberg SL, et al. Genome Biol. 2005;6(3):R23. doi: 10.1186/gb-2005-6-3-r23. Epub 2005 Feb 22. Genome Biol. 2005. PMID: 15774024 Free PMC article.
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.
Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. Salzberg SL, et al. Genome Biol. 2005;6(7):402. doi: 10.1186/gb-2005-6-7-402. Epub 2005 Jun 24. Genome Biol. 2005. PMID: 15998463 Free PMC article.
A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. ...
A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, …
Minimus: a fast, lightweight genome assembler.
Sommer DD, Delcher AL, Salzberg SL, Pop M. Sommer DD, et al. BMC Bioinformatics. 2007 Feb 26;8:64. doi: 10.1186/1471-2105-8-64. BMC Bioinformatics. 2007. PMID: 17324286 Free PMC article.
Figaro: a novel statistical method for vector sequence removal.
White JR, Roberts M, Yorke JA, Pop M. White JR, et al. Bioinformatics. 2008 Feb 15;24(4):462-7. doi: 10.1093/bioinformatics/btm632. Epub 2008 Jan 17. Bioinformatics. 2008. PMID: 18202027 Free PMC article.
Bioinformatics challenges of new sequencing technology.
Pop M, Salzberg SL. Pop M, et al. Trends Genet. 2008 Mar;24(3):142-9. doi: 10.1016/j.tig.2007.12.006. Epub 2008 Feb 11. Trends Genet. 2008. PMID: 18262676 Free PMC article. Review.
Genome assembly forensics: finding the elusive mis-assembly.
Phillippy AM, Schatz MC, Pop M. Phillippy AM, et al. Genome Biol. 2008;9(3):R55. doi: 10.1186/gb-2008-9-3-r55. Epub 2008 Mar 14. Genome Biol. 2008. PMID: 18341692 Free PMC article.
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