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Items: 30

1.

The Genome of the Steller Sea Lion (Eumetopias jubatus).

Kwan HH, Culibrk L, Taylor GA, Leelakumari S, Tan R, Jackman SD, Tse K, MacLeod T, Cheng D, Chuah E, Kirk H, Pandoh P, Carlsen R, Zhao Y, Mungall AJ, Moore R, Birol I, Marra MA, Rosen DAS, Haulena M, Jones SJM.

Genes (Basel). 2019 Jun 26;10(7). pii: E486. doi: 10.3390/genes10070486.

2.

Complete Chloroplast Genome Sequence of an Engelmann Spruce (Picea engelmannii, Genotype Se404-851) from Western Canada.

Lin D, Coombe L, Jackman SD, Gagalova KK, Warren RL, Hammond SA, McDonald H, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Doerksen T, Jaquish B, Bousquet J, Jones SJM, Bohlmann J, Birol I.

Microbiol Resour Announc. 2019 Jun 13;8(24). pii: e00382-19. doi: 10.1128/MRA.00382-19.

3.

Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada.

Lin D, Coombe L, Jackman SD, Gagalova KK, Warren RL, Hammond SA, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Jaquish B, Isabel N, Bousquet J, Jones SJM, Bohlmann J, Birol I.

Microbiol Resour Announc. 2019 Jun 6;8(23). pii: e00381-19. doi: 10.1128/MRA.00381-19.

4.

De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries.

Berner D, Roesti M, Bilobram S, Chan SK, Kirk H, Pandoh P, Taylor GA, Zhao Y, Jones SJM, DeFaveri J.

Genes (Basel). 2019 Jun 3;10(6). pii: E426. doi: 10.3390/genes10060426.

5.

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.

Biotechniques. 2019 Feb;66(2):85-92. doi: 10.2144/btn-2018-0148.

6.

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.

Genes (Basel). 2018 Nov 30;9(12). pii: E598. doi: 10.3390/genes9120598.

7.

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.

Nucleic Acids Res. 2019 Jan 25;47(2):e12. doi: 10.1093/nar/gky1142.

8.

A case report on a novel MT-ATP6 gene variation in atypical mitochondrial Leigh syndrome associated with bilateral basal ganglia calcifications.

Angural A, Sharma I, Pandoh P, Sharma V, Spolia A, Rai E, Singh V, Razdan S, Pandita KK, Sharma S.

Mitochondrion. 2019 May;46:209-213. doi: 10.1016/j.mito.2018.06.005. Epub 2018 Jun 19.

PMID:
29929013
9.

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.

Genes (Basel). 2017 Dec 11;8(12). pii: E378. doi: 10.3390/genes8120378.

10.

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.

Genes (Basel). 2017 Dec 11;8(12). pii: E379. doi: 10.3390/genes8120379.

11.

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.

Nat Commun. 2017 Nov 10;8(1):1433. doi: 10.1038/s41467-017-01316-7.

12.

A variation in PANK2 gene is causing Pantothenate kinase-associated Neurodegeneration in a family from Jammu and Kashmir - India.

Angural A, Singh I, Mahajan A, Pandoh P, Dhar MK, Kaul S, Verma V, Rai E, Razdan S, Kishore Pandita K, Sharma S.

Sci Rep. 2017 Jul 5;7(1):4834. doi: 10.1038/s41598-017-05388-9.

13.

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.

BMC Genomics. 2017 Jul 5;18(1):515. doi: 10.1186/s12864-017-3900-6.

14.

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.

PLoS One. 2017 Jun 1;12(6):e0178706. doi: 10.1371/journal.pone.0178706. eCollection 2017.

15.

Diagnostic value of next-generation sequencing in an unusual sphenoid tumor.

Jamshidi F, Pleasance E, Li Y, Shen Y, Kasaian K, Corbett R, Eirew P, Lum A, Pandoh P, Zhao Y, Schein JE, Moore RA, Rassekh R, Huntsman DG, Knowling M, Lim H, Renouf DJ, Jones SJ, Marra MA, Nielsen TO, Laskin J, Yip S.

Oncologist. 2014 Jun;19(6):623-30. doi: 10.1634/theoncologist.2013-0390. Epub 2014 May 7.

16.

Clonal analysis via barcoding reveals diverse growth and differentiation of transplanted mouse and human mammary stem cells.

Nguyen LV, Makarem M, Carles A, Moksa M, Kannan N, Pandoh P, Eirew P, Osako T, Kardel M, Cheung AM, Kennedy W, Tse K, Zeng T, Zhao Y, Humphries RK, Aparicio S, Eaves CJ, Hirst M.

Cell Stem Cell. 2014 Feb 6;14(2):253-63. doi: 10.1016/j.stem.2013.12.011. Epub 2014 Jan 16.

17.

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.

Bioinformatics. 2013 Jun 15;29(12):1492-7. doi: 10.1093/bioinformatics/btt178. Epub 2013 May 22.

18.

Complete genomic landscape of a recurring sporadic parathyroid carcinoma.

Kasaian K, Wiseman SM, Thiessen N, Mungall KL, Corbett RD, Qian JQ, Nip KM, He A, Tse K, Chuah E, Varhol RJ, Pandoh P, McDonald H, Zeng T, Tam A, Schein J, Birol I, Mungall AJ, Moore RA, Zhao Y, Hirst M, Marra MA, Walker BA, Jones SJ.

J Pathol. 2013 Jul;230(3):249-60. doi: 10.1002/path.4203.

PMID:
23616356
19.

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest.

Keeling CI, Yuen MM, Liao NY, Docking TR, Chan SK, Taylor GA, Palmquist DL, Jackman SD, Nguyen A, Li M, Henderson H, Janes JK, Zhao Y, Pandoh P, Moore R, Sperling FA, Huber DP, Birol I, Jones SJ, Bohlmann J.

Genome Biol. 2013 Mar 27;14(3):R27. doi: 10.1186/gb-2013-14-3-r27.

20.

Preparation and analysis of microRNA libraries using the Illumina massively parallel sequencing technology.

Morin RD, Zhao Y, Prabhu AL, Dhalla N, McDonald H, Pandoh P, Tam A, Zeng T, Hirst M, Marra M.

Methods Mol Biol. 2010;650:173-99. doi: 10.1007/978-1-60761-769-3_14.

PMID:
20686952
21.

Digital gene expression by tag sequencing on the illumina genome analyzer.

Morrissy S, Zhao Y, Delaney A, Asano J, Dhalla N, Li I, McDonald H, Pandoh P, Prabhu AL, Tam A, Hirst M, Marra M.

Curr Protoc Hum Genet. 2010 Apr;Chapter 11:Unit 11.11.1-36. doi: 10.1002/0471142905.hg1111s65.

PMID:
20373513
22.

LongSAGE profiling of nine human embryonic stem cell lines.

Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O'Connor MD, Zeng T, Moksa M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, Prabhu AL, Pandoh P, McDonald H, Asano J, Dhalla N, Ma K, Lee S, Ally A, Chahal N, Menzies S, Siddiqui A, Holt R, Jones S, Gerhard DS, Thomson JA, Eaves CJ, Marra MA.

Genome Biol. 2007;8(6):R113.

23.

Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.

Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Eaves C, Jones S, Holt R, Hirst M, Hoodless PA, Marra MA.

Genome Res. 2007 Jan;17(1):108-16. Epub 2006 Nov 29.

24.

A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells.

Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BY, Lee LL, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu AL, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie YY, Yang G, Zhang I, Hirst M, Jones SJ, Helgason CD, Simpson EM, Hoodless PA, Marra MA.

Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18485-90. Epub 2005 Dec 13.

25.

A set of BAC clones spanning the human genome.

Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Girn N, Lee D, Masson A, Mayo M, Olson T, Pandoh P, Prabhu AL, Schoenmakers E, Tsai M, Albertson D, Lam W, Choy CO, Osoegawa K, Zhao S, de Jong PJ, Schein J, Jones S, Marra MA.

Nucleic Acids Res. 2004 Jul 9;32(12):3651-60. Print 2004.

26.

Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome.

Krzywinski M, Wallis J, Gösele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu AL, Shin H, Tänzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong PJ, Warren W, Mardis E, McPherson JD, Wilson R, Hübner N, Jones S, Marra M, Schein J.

Genome Res. 2004 Apr;14(4):766-79.

27.

The Genome sequence of the SARS-associated coronavirus.

Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, Czub M, Drebot M, Fernando L, Flick R, Garbutt M, Gray M, Grolla A, Jones S, Feldmann H, Meyers A, Kabani A, Li Y, Normand S, Stroher U, Tipples GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL.

Science. 2003 May 30;300(5624):1399-404. Epub 2003 May 1.

28.

Resuspension of DNA sequencing reaction products in agarose increases sequence quality on an automated sequencer.

Vatcher G, Smailus D, Krzywinski M, Guin R, Stott J, Tsai M, Chan S, Pandoh P, Yang G, Asano J, Olson T, Prabhu AL, Coope R, Marziali A, Schein J, Jones S, Marra M.

Biotechniques. 2002 Sep;33(3):532-4, 536, 538-9.

29.

A physical map of the mouse genome.

Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR.

Nature. 2002 Aug 15;418(6899):743-50. Epub 2002 Aug 4.

PMID:
12181558
30.

An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones.

Butterfield YS, Marra MA, Asano JK, Chan SY, Guin R, Krzywinski MI, Lee SS, MacDonald KW, Mathewson CA, Olson TE, Pandoh PK, Prabhu AL, Schnerch A, Skalska U, Smailus DE, Stott JM, Tsai MI, Yang GS, Zuyderduyn SD, Schein JE, Jones SJ.

Nucleic Acids Res. 2002 Jun 1;30(11):2460-8.

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