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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.
Searching for SNPs with cloud computing.
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Langmead B, et al. Genome Biol. 2009;10(11):R134. doi: 10.1186/gb-2009-10-11-r134. Epub 2009 Nov 20. Genome Biol. 2009. PMID: 19930550 Free PMC article.
Cloud computing and the DNA data race.
Schatz MC, Langmead B, Salzberg SL. Schatz MC, et al. Nat Biotechnol. 2010 Jul;28(7):691-3. doi: 10.1038/nbt0710-691. Nat Biotechnol. 2010. PMID: 20622843 Free PMC article. No abstract available.
Aligning short sequencing reads with Bowtie.
Langmead B. Langmead B. Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.7. doi: 10.1002/0471250953.bi1107s32. Curr Protoc Bioinformatics. 2010. PMID: 21154709 Free PMC article.
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL. Langmead B, et al. Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923. Nat Methods. 2012. PMID: 22388286 Free PMC article.
HISAT: a fast spliced aligner with low memory requirements.
Kim D, Langmead B, Salzberg SL. Kim D, et al. Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317. Epub 2015 Mar 9. Nat Methods. 2015. PMID: 25751142 Free PMC article.
Alignment of Next-Generation Sequencing Reads.
Reinert K, Langmead B, Weese D, Evers DJ. Reinert K, et al. Annu Rev Genomics Hum Genet. 2015;16:133-51. doi: 10.1146/annurev-genom-090413-025358. Epub 2015 May 4. Annu Rev Genomics Hum Genet. 2015. PMID: 25939052 Review.
Boiler: lossy compression of RNA-seq alignments using coverage vectors.
Pritt J, Langmead B. Pritt J, et al. Nucleic Acids Res. 2016 Sep 19;44(16):e133. doi: 10.1093/nar/gkw540. Epub 2016 Jun 13. Nucleic Acids Res. 2016. PMID: 27298258 Free PMC article.
Rail-RNA: scalable analysis of RNA-seq splicing and coverage.
Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B. Nellore A, et al. Bioinformatics. 2017 Dec 15;33(24):4033-4040. doi: 10.1093/bioinformatics/btw575. Bioinformatics. 2017. PMID: 27592709 Free PMC article.
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