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Items: 44

1.

15 years of GDR: New data and functionality in the Genome Database for Rosaceae.

Jung S, Lee T, Cheng CH, Buble K, Zheng P, Yu J, Humann J, Ficklin SP, Gasic K, Scott K, Frank M, Ru S, Hough H, Evans K, Peace C, Olmstead M, DeVetter LW, McFerson J, Coe M, Wegrzyn JL, Staton ME, Abbott AG, Main D.

Nucleic Acids Res. 2018 Oct 24. doi: 10.1093/nar/gky1000. [Epub ahead of print]

PMID:
30357347
2.

Growing and cultivating the forest genomics database, TreeGenes.

Falk T, Herndon N, Grau E, Buehler S, Richter P, Zaman S, Baker EM, Ramnath R, Ficklin S, Staton M, Feltus FA, Jung S, Main D, Wegrzyn JL.

Database (Oxford). 2018 Jan 1;2018:1-11. doi: 10.1093/database/bay084.

3.

Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation).

Visser EA, Wegrzyn JL, Myburg AA, Naidoo S.

BMC Genomics. 2018 Aug 23;19(1):632. doi: 10.1186/s12864-018-5015-0.

4.

Comparative Transcriptomics Among Four White Pine Species.

Baker EAG, Wegrzyn JL, Sezen UU, Falk T, Maloney PE, Vogler DR, Delfino-Mix A, Jensen C, Mitton J, Wright J, Knaus B, Rai H, Cronn R, Gonzalez-Ibeas D, Vasquez-Gross HA, Famula RA, Liu JJ, Kueppers LM, Neale DB.

G3 (Bethesda). 2018 May 4;8(5):1461-1474. doi: 10.1534/g3.118.200257.

5.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Oct 1;6(10):1. doi: 10.1093/gigascience/gix072.

6.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL.

G3 (Bethesda). 2017 Sep 7;7(9):3157-3167. doi: 10.1534/g3.117.300078.

7.

Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles.

Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St Clair JB, Denver DR.

BMC Genomics. 2017 Jul 24;18(1):558. doi: 10.1186/s12864-017-3916-y.

8.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

Sablok G, Chen TW, Lee CC, Yang C, Gan RC, Wegrzyn JL, Porta NL, Nayak KC, Huang PJ, Varotto C, Tang P.

DNA Res. 2017 Jun 1;24(3):327-332. doi: 10.1093/dnares/dsw044.

9.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Jan 1;6(1):1-4. doi: 10.1093/gigascience/giw016. Erratum in: Gigascience. 2017 Oct 1;6(10):1.

10.

Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA.

Lind BM, Friedline CJ, Wegrzyn JL, Maloney PE, Vogler DR, Neale DB, Eckert AJ.

Mol Ecol. 2017 Jun;26(12):3168-3185. doi: 10.1111/mec.14106. Epub 2017 May 6.

PMID:
28316116
11.

Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife.

Velotta JP, Wegrzyn JL, Ginzburg S, Kang L, Czesny S, O'Neill RJ, McCormick SD, Michalak P, Schultz ET.

Mol Ecol. 2017 Feb;26(3):831-848. doi: 10.1111/mec.13983. Epub 2017 Jan 27.

PMID:
28012221
12.

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

Gonzalez-Ibeas D, Martinez-Garcia PJ, Famula RA, Delfino-Mix A, Stevens KA, Loopstra CA, Langley CH, Neale DB, Wegrzyn JL.

G3 (Bethesda). 2016 Dec 7;6(12):3787-3802. doi: 10.1534/g3.116.032805.

13.

Sequence of the Sugar Pine Megagenome.

Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeas D, Koriabine M, Holtz-Morris AE, Martínez-García PJ, Sezen UU, Marçais G, Jermstad K, McGuire PE, Loopstra CA, Davis JM, Eckert A, de Jong P, Yorke JA, Salzberg SL, Neale DB, Langley CH.

Genetics. 2016 Dec;204(4):1613-1626. Epub 2016 Oct 28.

14.

Poor maternal nutrition during gestation alters the expression of genes involved in muscle development and metabolism in lambs.

Hoffman ML, Peck KN, Wegrzyn JL, Reed SA, Zinn SA, Govoni KE.

J Anim Sci. 2016 Jul;94(7):3093-9. doi: 10.2527/jas.2016-0570.

PMID:
27482696
15.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.

Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB.

Plant J. 2016 Sep;87(5):507-32. doi: 10.1111/tpj.13207. Epub 2016 Jul 18.

16.

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome.

Visser EA, Wegrzyn JL, Steenkmap ET, Myburg AA, Naidoo S.

BMC Genomics. 2015 Dec 12;16:1057. doi: 10.1186/s12864-015-2277-7.

17.

Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis across environments, ages, and populations.

Westbrook JW, Walker AR, Neves LG, Munoz P, Resende MF Jr, Neale DB, Wegrzyn JL, Huber DA, Kirst M, Davis JM, Peter GF.

New Phytol. 2015 Jan;205(2):627-41. doi: 10.1111/nph.13074. Epub 2014 Sep 30.

18.

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.

19.

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.

20.

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.

21.

Multilocus analyses reveal little evidence for lineage-wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus).

Eckert AJ, Bower AD, Jermstad KD, Wegrzyn JL, Knaus BJ, Syring JV, Neale DB.

Mol Ecol. 2013 Nov;22(22):5635-50. doi: 10.1111/mec.12514. Epub 2013 Oct 18.

PMID:
24134614
22.

The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae).

Eckert AJ, Wegrzyn JL, Liechty JD, Lee JM, Cumbie WP, Davis JM, Goldfarb B, Loopstra CA, Palle SR, Quesada T, Langley CH, Neale DB.

Genetics. 2013 Dec;195(4):1353-72. doi: 10.1534/genetics.113.157198. Epub 2013 Oct 11.

23.
24.

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.

25.

Association of loblolly pine xylem development gene expression with single-nucleotide polymorphisms.

Palle SR, Seeve CM, Eckert AJ, Wegrzyn JL, Neale DB, Loopstra CA.

Tree Physiol. 2013 Jul;33(7):763-74. doi: 10.1093/treephys/tpt054.

PMID:
23933831
26.

Open access to tree genomes: the path to a better forest.

Neale DB, Langley CH, Salzberg SL, Wegrzyn JL.

Genome Biol. 2013 Jun 24;14(6):120. doi: 10.1186/gb-2013-14-6-120.

27.

Association genetics of oleoresin flow in loblolly pine: discovering genes and predicting phenotype for improved resistance to bark beetles and bioenergy potential.

Westbrook JW, Resende MF Jr, Munoz P, Walker AR, Wegrzyn JL, Nelson CD, Neale DB, Kirst M, Huber DA, Gezan SA, Peter GF, Davis JM.

New Phytol. 2013 Jul;199(1):89-100. doi: 10.1111/nph.12240. Epub 2013 Mar 28.

28.

CartograTree: connecting tree genomes, phenotypes and environment.

Vasquez-Gross HA, Yu JJ, Figueroa B, Gessler DD, Neale DB, Wegrzyn JL.

Mol Ecol Resour. 2013 May;13(3):528-37. doi: 10.1111/1755-0998.12067. Epub 2013 Feb 25.

PMID:
23433187
29.

Association genetics of chemical wood properties in black poplar (Populus nigra).

Guerra FP, Wegrzyn JL, Sykes R, Davis MF, Stanton BJ, Neale DB.

New Phytol. 2013 Jan;197(1):162-76. doi: 10.1111/nph.12003. Epub 2012 Nov 16.

30.

Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests.

Mosca E, Eckert AJ, Liechty JD, Wegrzyn JL, La Porta N, Vendramin GG, Neale DB.

Evol Appl. 2012 Nov;5(7):762-75. doi: 10.1111/j.1752-4571.2012.00256.x.

31.

Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome.

Eckert AJ, Wegrzyn JL, Cumbie WP, Goldfarb B, Huber DA, Tolstikov V, Fiehn O, Neale DB.

New Phytol. 2012 Mar;193(4):890-902. doi: 10.1111/j.1469-8137.2011.03976.x. Epub 2011 Nov 30.

32.

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine.

Chancerel E, Lepoittevin C, Le Provost G, Lin YC, Jaramillo-Correa JP, Eckert AJ, Wegrzyn JL, Zelenika D, Boland A, Frigerio JM, Chaumeil P, Garnier-Géré P, Boury C, Grivet D, González-Martínez SC, Rouzé P, Van de Peer Y, Neale DB, Cervera MT, Kremer A, Plomion C.

BMC Genomics. 2011 Jul 18;12:368. doi: 10.1186/1471-2164-12-368.

33.

Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem.

Wegrzyn JL, Eckert AJ, Choi M, Lee JM, Stanton BJ, Sykes R, Davis MF, Tsai CJ, Neale DB.

New Phytol. 2010 Oct;188(2):515-32. doi: 10.1111/j.1469-8137.2010.03415.x. Epub 2010 Sep 10.

34.

Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae).

Eckert AJ, Bower AD, González-Martínez SC, Wegrzyn JL, Coop G, Neale DB.

Mol Ecol. 2010 Sep;19(17):3789-805. doi: 10.1111/j.1365-294X.2010.04698.x. Epub 2010 Aug 13.

PMID:
20723060
35.

Proteomics of dense core secretory vesicles reveal distinct protein categories for secretion of neuroeffectors for cell-cell communication.

Wegrzyn JL, Bark SJ, Funkelstein L, Mosier C, Yap A, Kazemi-Esfarjani P, La Spada AR, Sigurdson C, O'Connor DT, Hook V.

J Proteome Res. 2010 Oct 1;9(10):5002-24. doi: 10.1021/pr1003104.

36.

Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.).

Quesada T, Gopal V, Cumbie WP, Eckert AJ, Wegrzyn JL, Neale DB, Goldfarb B, Huber DA, Casella G, Davis JM.

Genetics. 2010 Oct;186(2):677-86. doi: 10.1534/genetics.110.117549. Epub 2010 Jul 13.

37.

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.

38.

Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae).

Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, González-Martínez SC, Neale DB.

Genetics. 2010 Jul;185(3):969-82. doi: 10.1534/genetics.110.115543. Epub 2010 May 3. Erratum in: Genetics. 2014 May;197(1):433.

39.

PineSAP--sequence alignment and SNP identification pipeline.

Wegrzyn JL, Lee JM, Liechty J, Neale DB.

Bioinformatics. 2009 Oct 1;25(19):2609-10. doi: 10.1093/bioinformatics/btp477. Epub 2009 Aug 10.

40.

Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas Fir (Pseudotsuga menziesii var. menziesii).

Eckert AJ, Wegrzyn JL, Pande B, Jermstad KD, Lee JM, Liechty JD, Tearse BR, Krutovsky KV, Neale DB.

Genetics. 2009 Sep;183(1):289-98. doi: 10.1534/genetics.109.103895. Epub 2009 Jul 13.

41.

Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits.

Eckert AJ, Bower AD, Wegrzyn JL, Pande B, Jermstad KD, Krutovsky KV, St Clair JB, Neale DB.

Genetics. 2009 Aug;182(4):1289-302. doi: 10.1534/genetics.109.102350. Epub 2009 Jun 1.

42.

TreeGenes: A forest tree genome database.

Wegrzyn JL, Lee JM, Tearse BR, Neale DB.

Int J Plant Genomics. 2008;2008:412875. doi: 10.1155/2008/412875.

43.

Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites.

Wegrzyn JL, Drudge TM, Valafar F, Hook V.

BMC Bioinformatics. 2008 May 8;9:232. doi: 10.1186/1471-2105-9-232.

44.

Demonstration of GTG as an alternative initiation codon for the serpin endopin 2B-2.

Hwang SR, Garza CZ, Wegrzyn JL, Hook VY.

Biochem Biophys Res Commun. 2005 Feb 18;327(3):837-44.

PMID:
15649421

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