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

Year Number of Results
2010 3
2011 11
2012 7
2013 1
2020 0
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19 results
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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.
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.
Repetitive DNA and next-generation sequencing: computational challenges and solutions.
Treangen TJ, Salzberg SL. Treangen TJ, et al. Nat Rev Genet. 2011 Nov 29;13(1):36-46. doi: 10.1038/nrg3117. Nat Rev Genet. 2011. PMID: 22124482 Free PMC article. Review.
Current challenges in de novo plant genome sequencing and assembly.
Schatz MC, Witkowski J, McCombie WR. Schatz MC, et al. Genome Biol. 2012;13(4):243. doi: 10.1186/gb4015. Genome Biol. 2012. PMID: 22546054 Free PMC article. Review.
FLASH: fast length adjustment of short reads to improve genome assemblies.
Magoč T, Salzberg SL. Magoč T, et al. Bioinformatics. 2011 Nov 1;27(21):2957-63. doi: 10.1093/bioinformatics/btr507. Epub 2011 Sep 7. Bioinformatics. 2011. PMID: 21903629 Free PMC article.
Genotyping in the cloud with Crossbow.
Gurtowski J, Schatz MC, Langmead B. Gurtowski J, et al. Curr Protoc Bioinformatics. 2012 Sep;Chapter 15:Unit15.3. doi: 10.1002/0471250953.bi1503s39. Curr Protoc Bioinformatics. 2012. PMID: 22948728 Free PMC article.
The genome of woodland strawberry (Fragaria vesca).
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM. Shulaev V, et al. Nat Genet. 2011 Feb;43(2):109-16. doi: 10.1038/ng.740. Epub 2010 Dec 26. Nat Genet. 2011. PMID: 21186353 Free PMC article.
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. Salzberg SL, et al. Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Genome Res. 2012. PMID: 22147368 Free PMC article.
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
Kim D, Salzberg SL. Kim D, et al. Genome Biol. 2011 Aug 11;12(8):R72. doi: 10.1186/gb-2011-12-8-r72. Genome Biol. 2011. PMID: 21835007 Free PMC article.
Improving pan-genome annotation using whole genome multiple alignment.
Angiuoli SV, Dunning Hotopp JC, Salzberg SL, Tettelin H. Angiuoli SV, et al. BMC Bioinformatics. 2011 Jun 30;12:272. doi: 10.1186/1471-2105-12-272. BMC Bioinformatics. 2011. PMID: 21718539 Free PMC article.
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