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Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.
Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI, Brand D, Vandervalk BP, Kirk H, Pandoh P, Moore RA, Zhao Y, Mungall AJ, Jaquish B, Yanchuk A, Ritland C, Boyle B, Bousquet J, Ritland K, Mackay J, Bohlmann J, Jones SJ. Birol I, et al. Among authors: jackman sd. Bioinformatics. 2013 Jun 15;29(12):1492-7. doi: 10.1093/bioinformatics/btt178. Epub 2013 May 22. Bioinformatics. 2013. PMID: 23698863 Free PMC article.
Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.
Warren RL, Keeling CI, Yuen MM, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJ, MacKay J, Birol I, Bohlmann J. Warren RL, et al. Among authors: jackman sd. Plant J. 2015 Jul;83(2):189-212. doi: 10.1111/tpj.12886. Epub 2015 Jun 19. Plant J. 2015. PMID: 26017574 Free article.
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.
Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, Ritland CE, Bousquet J, Jones SJ, Bohlmann J, Birol I. Jackman SD, et al. Genome Biol Evol. 2015 Dec 8;8(1):29-41. doi: 10.1093/gbe/evv244. Genome Biol Evol. 2015. PMID: 26645680 Free PMC article.
ABySS: a parallel assembler for short read sequence data.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Simpson JT, et al. Among authors: jackman sd. Genome Res. 2009 Jun;19(6):1117-23. doi: 10.1101/gr.089532.108. Epub 2009 Feb 27. Genome Res. 2009. PMID: 19251739 Free PMC article.
ABySS-Explorer: visualizing genome sequence assemblies.
Nielsen CB, Jackman SD, Birol I, Jones SJ. Nielsen CB, et al. Among authors: jackman sd. IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):881-8. doi: 10.1109/TVCG.2009.116. IEEE Trans Vis Comput Graph. 2009. PMID: 19834150
De novo assembly and analysis of RNA-seq data.
Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I. Robertson G, et al. Among authors: jackman sd. Nat Methods. 2010 Nov;7(11):909-12. doi: 10.1038/nmeth.1517. Epub 2010 Oct 10. Nat Methods. 2010. PMID: 20935650
DIDA: Distributed Indexing Dispatched Alignment.
Mohamadi H, Vandervalk BP, Raymond A, Jackman SD, Chu J, Breshears CP, Birol I. Mohamadi H, et al. Among authors: jackman sd. PLoS One. 2015 Apr 29;10(4):e0126409. doi: 10.1371/journal.pone.0126409. eCollection 2015. PLoS One. 2015. PMID: 25923767 Free PMC article.
43 results