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Results: 1 to 20 of 110

1.

Sequencing and assembly of the 22-gb loblolly pine genome.

Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH.

Genetics. 2014 Mar;196(3):875-90. doi: 10.1534/genetics.113.159715.

PMID:
24653210
[PubMed - in process]
2.

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH.

Genome Biol. 2014 Mar 4;15(3):R59. doi: 10.1186/gb-2014-15-3-r59.

PMID:
24647006
[PubMed - in process]
Free PMC Article
3.

Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, Dejong PJ, Mockaitis K, Main D, Langley CH, Neale DB.

Genetics. 2014 Mar;196(3):891-909. doi: 10.1534/genetics.113.159996.

PMID:
24653211
[PubMed - in process]
4.

Whole-exome targeted sequencing of the uncharacterized pine genome.

Neves LG, Davis JM, Barbazuk WB, Kirst M.

Plant J. 2013 Jul;75(1):146-56. doi: 10.1111/tpj.12193. Epub 2013 May 7.

PMID:
23551702
[PubMed - indexed for MEDLINE]
5.

Insights into the loblolly pine genome: characterization of BAC and fosmid sequences.

Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA.

PLoS One. 2013 Sep 4;8(9):e72439. doi: 10.1371/journal.pone.0072439. eCollection 2013.

PMID:
24023741
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.

Alexeyenko A, Nystedt B, Vezzi F, Sherwood E, Ye R, Knudsen B, Simonsen M, Turner B, de Jong P, Wu CC, Lundeberg J.

BMC Genomics. 2014 Jun 6;15:439. doi: 10.1186/1471-2164-15-439.

PMID:
24906298
[PubMed - in process]
Free PMC Article
7.

De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Pöggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kück U, Freitag M.

PLoS Genet. 2010 Apr 8;6(4):e1000891. doi: 10.1371/journal.pgen.1000891.

PMID:
20386741
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping.

Neves LG, Davis JM, Barbazuk WB, Kirst M.

G3 (Bethesda). 2014 Jan 10;4(1):29-37. doi: 10.1534/g3.113.008714.

PMID:
24192835
[PubMed - in process]
Free PMC Article
9.

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences.

Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB.

BMC Genomics. 2010 Jul 7;11:420. doi: 10.1186/1471-2164-11-420.

PMID:
20609256
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine.

Magbanua ZV, Ozkan S, Bartlett BD, Chouvarine P, Saski CA, Liston A, Cronn RC, Nelson CD, Peterson DG.

PLoS One. 2011 Jan 21;6(1):e16214. doi: 10.1371/journal.pone.0016214.

PMID:
21283709
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems.

Tulin S, Aguiar D, Istrail S, Smith J.

Evodevo. 2013 Jun 3;4:16. doi: 10.1186/2041-9139-4-16. eCollection 2013.

PMID:
23731568
[PubMed]
Free PMC Article
12.

SOPRA: Scaffolding algorithm for paired reads via statistical optimization.

Dayarian A, Michael TP, Sengupta AM.

BMC Bioinformatics. 2010 Jun 24;11:345. doi: 10.1186/1471-2105-11-345.

PMID:
20576136
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
23698863
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.

Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS.

BMC Genomics. 2008 Aug 28;9:404. doi: 10.1186/1471-2164-9-404.

PMID:
18755037
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Timber! Felling the loblolly pine genome.

Hamilton JP, Buell CR.

Genome Biol. 2014 Mar 31;15(3):111. doi: 10.1186/gb4170.

PMID:
25000971
[PubMed - in process]
16.

Paired-end sequencing of Fosmid libraries by Illumina.

Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK, Jaffe DB, Nusbaum C, Gnirke A.

Genome Res. 2012 Nov;22(11):2241-9. doi: 10.1101/gr.138925.112. Epub 2012 Jul 16.

PMID:
22800726
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Regulation of loblolly pine (Pinus taeda L.) arginase in developing seedling tissue during germination and post-germinative growth.

Todd CD, Cooke JE, Mullen RT, Gifford DJ.

Plant Mol Biol. 2001 Mar;45(5):555-65.

PMID:
11414614
[PubMed - indexed for MEDLINE]
18.

Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly.

Liu T, Tsai CH, Lee WB, Chiang JH.

PLoS One. 2013 Jul 29;8(7):e69503. doi: 10.1371/journal.pone.0069503. Print 2013.

PMID:
23922726
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis.

Cairney J, Zheng L, Cowels A, Hsiao J, Zismann V, Liu J, Ouyang S, Thibaud-Nissen F, Hamilton J, Childs K, Pullman GS, Zhang Y, Oh T, Buell CR.

Plant Mol Biol. 2006 Nov;62(4-5):485-501. Epub 2006 Sep 26.

PMID:
17001497
[PubMed - indexed for MEDLINE]
20.

Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat.

Belova T, Zhan B, Wright J, Caccamo M, Asp T, Simková H, Kent M, Bendixen C, Panitz F, Lien S, Doležel J, Olsen OA, Sandve SR.

BMC Genomics. 2013 Apr 4;14:222. doi: 10.1186/1471-2164-14-222.

PMID:
23557231
[PubMed - indexed for MEDLINE]
Free PMC Article

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