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Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis.
Haile S, Pandoh P, McDonald H, Corbett RD, Tsao P, Kirk H, MacLeod T, Jones M, Bilobram S, Brooks D, Smailus D, Steidl C, Scott DW, Bala M, Hirst M, Miller D, Moore RA, Mungall AJ, Coope RJ, Ma Y, Zhao Y, Holt RA, Jones SJ, Marra MA. Haile S, et al. Among authors: kirk h. PLoS One. 2017 Jun 1;12(6):e0178706. doi: 10.1371/journal.pone.0178706. eCollection 2017. PLoS One. 2017. PMID: 28570594 Free PMC article.
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: kirk h. Bioinformatics. 2013 Jun 15;29(12):1492-7. doi: 10.1093/bioinformatics/btt178. Epub 2013 May 22. Bioinformatics. 2013. PMID: 23698863 Free PMC article.
Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing.
Haile S, Corbett RD, MacLeod T, Bilobram S, Smailus D, Tsao P, Kirk H, McDonald H, Pandoh P, Bala M, Hirst M, Miller D, Moore RA, Mungall AJ, Schein J, Coope RJ, Ma Y, Zhao Y, Holt RA, Jones SJ, Marra MA. Haile S, et al. Among authors: kirk h. BMC Genomics. 2017 Jul 5;18(1):515. doi: 10.1186/s12864-017-3900-6. BMC Genomics. 2017. PMID: 28679365 Free PMC article.
The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.
Hammond SA, Warren RL, Vandervalk BP, Kucuk E, Khan H, Gibb EA, Pandoh P, Kirk H, Zhao Y, Jones M, Mungall AJ, Coope R, Pleasance S, Moore RA, Holt RA, Round JM, Ohora S, Walle BV, Veldhoen N, Helbing CC, Birol I. Hammond SA, et al. Among authors: kirk h. Nat Commun. 2017 Nov 10;8(1):1433. doi: 10.1038/s41467-017-01316-7. Nat Commun. 2017. PMID: 29127278 Free PMC article.
The Genome of the Northern Sea Otter (Enhydra lutris kenyoni).
Jones SJ, Haulena M, Taylor GA, Chan S, Bilobram S, Warren RL, Hammond SA, Mungall KL, Choo C, Kirk H, Pandoh P, Ally A, Dhalla N, Tam AKY, Troussard A, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Jones SJM. Jones SJ, et al. Among authors: kirk h. Genes (Basel). 2017 Dec 11;8(12):379. doi: 10.3390/genes8120379. Genes (Basel). 2017. PMID: 29232880 Free PMC article.
The Genome of the Beluga Whale (Delphinapterus leucas).
Jones SJM, Taylor GA, Chan S, Warren RL, Hammond SA, Bilobram S, Mordecai G, Suttle CA, Miller KM, Schulze A, Chan AM, Jones SJ, Tse K, Li I, Cheung D, Mungall KL, Choo C, Ally A, Dhalla N, Tam AKY, Troussard A, Kirk H, Pandoh P, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Haulena M. Jones SJM, et al. Among authors: kirk h. Genes (Basel). 2017 Dec 11;8(12):378. doi: 10.3390/genes8120378. Genes (Basel). 2017. PMID: 29232881 Free PMC article.
Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples.
Haile S, Corbett RD, Bilobram S, Bye MH, Kirk H, Pandoh P, Trinh E, MacLeod T, McDonald H, Bala M, Miller D, Novik K, Coope RJ, Moore RA, Zhao Y, Mungall AJ, Ma Y, Holt RA, Jones SJ, Marra MA. Haile S, et al. Among authors: kirk h. Nucleic Acids Res. 2019 Jan 25;47(2):e12. doi: 10.1093/nar/gky1142. Nucleic Acids Res. 2019. PMID: 30418619 Free PMC article.
The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis.
Taylor GA, Kirk H, Coombe L, Jackman SD, Chu J, Tse K, Cheng D, Chuah E, Pandoh P, Carlsen R, Zhao Y, Mungall AJ, Moore R, Birol I, Franke M, Marra MA, Dutton C, Jones SJM. Taylor GA, et al. Among authors: kirk h. Genes (Basel). 2018 Nov 30;9(12):598. doi: 10.3390/genes9120598. Genes (Basel). 2018. PMID: 30513700 Free PMC article.
A high-throughput protocol for isolating cell-free circulating tumor DNA from peripheral blood.
Pandoh PK, Corbett RD, McDonald H, Alcaide M, Kirk H, Trinh E, Haile S, MacLeod T, Smailus D, Bilobram S, Mungall AJ, Ma Y, Moore RA, Coope R, Zhao Y, Jones SJ, Holt RA, Karsan A, Morin RD, Marra MA. Pandoh PK, et al. Among authors: kirk h. Biotechniques. 2019 Feb;66(2):85-92. doi: 10.2144/btn-2018-0148. Biotechniques. 2019. PMID: 30744412 Free article.
213 results