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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: ma y. Genes (Basel). 2017 Dec 11;8(12):378. doi: 10.3390/genes8120378. Genes (Basel). 2017. PMID: 29232881 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: ma y. Genes (Basel). 2017 Dec 11;8(12):379. doi: 10.3390/genes8120379. Genes (Basel). 2017. PMID: 29232880 Free PMC article.
Large-scale profiling of microRNAs for The Cancer Genome Atlas.
Chu A, Robertson G, Brooks D, Mungall AJ, Birol I, Coope R, Ma Y, Jones S, Marra MA. Chu A, et al. Among authors: ma y. Nucleic Acids Res. 2016 Jan 8;44(1):e3. doi: 10.1093/nar/gkv808. Epub 2015 Aug 13. Nucleic Acids Res. 2016. PMID: 26271990 Free PMC article.
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: ma y. PLoS One. 2017 Jun 1;12(6):e0178706. doi: 10.1371/journal.pone.0178706. eCollection 2017. PLoS One. 2017. PMID: 28570594 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: ma y. BMC Genomics. 2017 Jul 5;18(1):515. doi: 10.1186/s12864-017-3900-6. BMC Genomics. 2017. PMID: 28679365 Free PMC article.
MAVIS: merging, annotation, validation, and illustration of structural variants.
Reisle C, Mungall KL, Choo C, Paulino D, Bleile DW, Muhammadzadeh A, Mungall AJ, Moore RA, Shlafman I, Coope R, Pleasance S, Ma Y, Jones SJM. Reisle C, et al. Among authors: ma y. Bioinformatics. 2019 Feb 1;35(3):515-517. doi: 10.1093/bioinformatics/bty621. Bioinformatics. 2019. PMID: 30016509
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: ma y. Nucleic Acids Res. 2019 Jan 25;47(2):e12. doi: 10.1093/nar/gky1142. Nucleic Acids Res. 2019. PMID: 30418619 Free PMC article.
Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision-making.
Chahal M, Pleasance E, Grewal J, Zhao E, Ng T, Chapman E, Jones MR, Shen Y, Mungall KL, Bonakdar M, Taylor GA, Ma Y, Mungall AJ, Moore RA, Lim H, Renouf D, Yip S, Jones SJM, Marra MA, Laskin J. Chahal M, et al. Among authors: ma y. Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2):a002626. doi: 10.1101/mcs.a002626. Print 2018 Apr. Cold Spring Harb Mol Case Stud. 2018. PMID: 29610392 Free PMC article.
Clinical outcomes after whole-genome sequencing in patients with metastatic non-small-cell lung cancer.
Tsang ES, Shen Y, Chooback N, Ho C, Jones M, Renouf DJ, Lim H, Sun S, Yip S, Pleasance E, Ionescu DN, Mungall K, Kasaian K, Ma Y, Zhao Y, Mungall A, Moore R, Jones SJM, Marra M, Laskin J. Tsang ES, et al. Among authors: ma y. Cold Spring Harb Mol Case Stud. 2019 Feb 1;5(1):a002659. doi: 10.1101/mcs.a002659. Print 2019 Feb. Cold Spring Harb Mol Case Stud. 2019. PMID: 30514790 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: ma y. Biotechniques. 2019 Feb;66(2):85-92. doi: 10.2144/btn-2018-0148. Biotechniques. 2019. PMID: 30744412 Free article.
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