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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
2009 1
2010 4
2011 15
2012 9
2013 6
2014 3
2015 5
2017 2
2019 1
2020 0
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43 results
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Page 1
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Kim D, et al. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. Nat Biotechnol. 2019. PMID: 31375807
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. Pertea M, et al. Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. Nat Biotechnol. 2015. PMID: 25690850 Free PMC article.
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Trapnell C, et al. Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. Nat Protoc. 2012. PMID: 22383036 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.
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.
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Trapnell C, et al. Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2. Nat Biotechnol. 2010. PMID: 20436464 Free PMC article.
Genome-guided transcriptome assembly in the age of next-generation sequencing.
Florea LD, Salzberg SL. Florea LD, et al. IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1234-40. doi: 10.1109/tcbb.2013.140. IEEE/ACM Trans Comput Biol Bioinform. 2013. PMID: 24524156 Free PMC article. Review.
Short Read Mapping: An Algorithmic Tour.
Canzar S, Salzberg SL. Canzar S, et al. Proc IEEE Inst Electr Electron Eng. 2017 Mar;105(3):436-458. doi: 10.1109/JPROC.2015.2455551. Epub 2015 Sep 7. Proc IEEE Inst Electr Electron Eng. 2017. PMID: 28502990 Free PMC article.
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