Detailed list of publications is available at Google Scholar

Early Release Manuscripts

Trouern-Trend, A. J., Falk, T. A., Zaman, S., Caballero, M., Neale, D. B., Langley, C. H., Dandekar, A., Stevens, K., & Wegrzyn, J. (2019). Comparative Genomics of Six Juglans Species Reveals Patterns of Disease-associated Gene Family Contractions. BioRxiv, 561738. https://doi.org/10.1101/561738

Caballero, M., & Wegrzyn, J. (2019). gFACs: Filtering, analysis, and conversion to unify genome annotations across alignment and gene prediction frameworks. Genomics, Proteomics, & Bioinformatics. In Press. https://doi.org/10.1016/j.gpb.2019.04.002

Hart, A. J., Ginzburg, S., Xu, M. (Sam), Fisher, C. R., Rahmatpour, N., Mitton, J. B., Paul, R., and Wegrzyn, J. L. (2018). EnTAP: Bringing Faster and Smarter Functional Annotation to Non-Model Eukaryotic Transcriptomes. BioRxiv, 307868. https://doi.org/10.1101/307868

Published Works

Spoor, S., Cheng, C.-H., Sanderson, L.-A., Condon, B., Almsaeed, A., Chen, M., Bretaudeau, A., Rasche, H., Jung, S., Main, D., Bett, K., Staton, M., Wegrzyn, J.L., Feltus, F.A., and Ficklin, S. P. (2019). Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. Database, 2019. https://doi.org/10.1093/database/baz077

Wegrzyn, J.L., Staton, M.A., Street, N.R., Main, D., Grau, E., Herndon, N., Buehler, S., Falk, T., Zaman, S., Ramnath, R., Richter, P., Sun, L., Condon, B., Almsaeed, A., Chen, M., Mannapperuma, C., Jung, S. and Ficklin, S. (2019) Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. Front. Plant Sci. 10:813. doi: https://doi.org/10.3389/fpls.2019.00813

Visser, E. A., Wegrzyn, J. L., Myburg, A. A., & Naidoo, S. (2018). Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation). BMC Genomics, 19(1), 632. https://doi.org/10.1186/s12864-018-5015-0

Jung, S., Lee, T., Cheng, C.-H., Buble, K., Zheng, P., Yu, J., Humann, J., Ficklin, S. P., Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Evans, K., Peace, C., Olmstead, M., DeVetter, L. W., McFerson, J., Coe, M., Wegrzyn, J. L., Staton, M. E., Abbott, A. G., & Main, D. (2018). 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Research, 47(D1), D1137–D1145. https://doi.org/10.1093/nar/gky1000

Falk, T., Herndon, N., Grau, E., Buehler, S., Richter, P., Zaman, S., Baker, E.M., Ramnath, R., Ficklin, S., Staton, M., Feltus, F.A., Jung, S., Main, D., and Wegrzyn, J. L. (2018). Growing and cultivating the forest genomics database, TreeGenes. Database, 2018, bay084-bay084. Retrieved from http://dx.doi.org/10.1093/database/bay084

Baker, E. A.G., Wegrzyn, J. L., Sezen, U. U., Falk, T., Maloney, P. E,.Vogler, D. R., Delfino-Mix, A., Jensen, C., Mitton, J., Wright, J., Knaus, B., Rai, H., Cronn, R., Gonzalez-Ibeas, D., Vasquez-Gross, H. A., Famula, R. A., Liu, J., Kueppers, L. M., & Neale, D. B. (2018). Comparative Transcriptomics Among Four White Pine Species. G3: Genes, Genomes, Genetics, g3. 200257.2018. https://doi.org/10.1534/g3.118.200257

Vangestel, C., Eckert, A. J., Wegrzyn, J. L., St Clair, J. B., & Neale, D. B. (2018). Linking phenotype, genotype and environment to unravel genetic components underlying cold hardiness in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii) Tree Genetics & Genomes, 14(1), 10. https://doi.org/10.1007/s11295-017-1225-x

Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T.Z., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C.G., Farmer, A., Ficklin, S.P., Grant, D., Grau, E., Herndon, N., Hu, Z., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C., Munoz-Torres, M.C., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L., Sen, T.Z., Staton, M., Subramaniam, S., Tello-Ruiz, M.K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M., Yu, J., and Main, D. (2018). AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database, 2018, bay088-bay088. http://dx.doi.org/10.1093/database/bay088

Vázquez-Lobo, A., De La Torre, A. R., Martínez-García, P. J., Vangestel, C., Wegrzyn, J. L., Ćalić, I., Burton, D., Davis, D., Kinloch, B., Vogler, D., & Neale, D.B B. (2017). Finding loci associated to partial resistance to white pine blister rust in sugar pine (Pinus lambertiana Dougl.). Tree Genetics & Genomes, 13: 108. https://doi.org/10.1007/s11295-017-1190-4

Sablok, G., Chen, T.-W., Lee, C.-C., Yang, C., Gan, R.-C., Wegrzyn, J. L., … Tang, P. (2017). ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications. DNA Research, dsw044. https://doi.org/10.1093/dnares/dsw044

Lind, B. M., Friedline, C. J., Wegrzyn, J. L., Maloney, P. E., Vogler, D. R., Neale, D. B., & Eckert, A. J. (2017). Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA. Molecular Ecology, 26(12), 3168-3185. https://doi.org/10.1111/mec.14106

Neale, D. B., McGuire, P. E., Wheeler, N. C., Stevens, K. A., Crepeau, M. W., Cardeno, C., … Wegrzyn, J. L. (2017). The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3: Genes|Genomes|Genetics, 7(9), 3157-3167. https://doi.org/10.1534/g3.117.300078

Li, W., Katin-Grazzini, L., Gu, X., Wang, X., El-tanbouly, R., Yer, H., Thammina, C., Inguagiato, J., Guillard, K., McAvoy, R., Wegrzyn, J. L., Gu, T., & Li, Y. (2017). Transcriptome Analysis Reveals Differential Gene Expression and a Possible Role of Gibberellins in a Shade-Tolerant Mutant of Perennial Ryegrass. Frontiers in Plant Science, 8, 868. https://doi.org/10.3389/fpls.2017.00868

Carrasco, A., Wegrzyn, J. L., Durán, R., Fernández, M., Donoso, A., Rodriguez, V., … Valenzuela, S. (2017). Expression profiling in Pinus radiata infected with Fusarium circinatum. Tree Genetics & Genomes, 13(2), 46. https://doi.org/10.1007/s11295-017-1125-0

Frelin, O., Dervinis, C., Wegrzyn, J. L., Davis, J. M., & Hanson, A. D. (2017). Drought stress in Pinus taeda L. induces coordinated transcript accumulation of genes involved in the homogentisate pathway. Tree Genetics & Genomes, 13(1), 27. https://doi.org/10.1007/s11295-017-1115-2

Velotta, J. P., Wegrzyn, J. L., Ginzburg, S., Kang, L., Czesny, S., O’Neill, R. J., … Schultz, E. T. (2017). Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife. Molecular Ecology, 26(3), 831–848. https://doi.org/10.1111/mec.13983

Zimin, A. V., Stevens, K. A., Crepeau, M. W., Puiu, D., Wegrzyn, J. L., Yorke, J. A., … Salzberg, S. L. (2017). An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. GigaScience, 6(1), 1–4. https://doi.org/10.1093/gigascience/giw016

Chen, M., Henry, N., Almsaeed, A., Zhou, X., Wegrzyn, J. L., Ficklin, S., & Staton, M. (2017). New extension software modules to enhance searching and display of transcriptome data in Tripal databases. Database, 2017, bax052. https://doi.org/10.1093/database/bax052

Cronn, R., Dolan, P. C., Jogdeo, S., Wegrzyn, J. L., Neale, D. B., Clair, J. S., & Denver, D. R. (2017). Transcription Through The Eye Of A Needle: Daily And Annual Cyclic Gene Expression Variation In Douglas-Fir Needles. BMC Genomics, 18(1), 558. https://doi.org/10.1186/s12864-017-3916-y

Stevens, K. A., Wegrzyn, J. L., Zimin, A., Puiu, D., Crepeau, M., Cardeno, C., Paul, R., Gonzalez-Ibeas, D., Koriabine, M., Holtz-Morris, A. E., Martínez-García, P. J., Sezen, U. U., Marçais, G., Jermstad, K., McGuire, P. E., Loopstra, C. A., Davis, J. M., Eckert, A., de Jong, P., Yorke, J. A., Salzberg, S. L., Neale, D. B., & Langley, C. H. (2016). Sequence of the sugar pine megagenome. Genetics, 204(4), 1613-1626. https://doi.org/10.1534/genetics.116.193227

Gonzalez-Ibeas, D., Martinez-Garcia, P. J., Famula, R. A., Delfino-Mix, A., Stevens, K. A., Loopstra, C. A., Langley, C. H., Neale, D. B., & Wegrzyn, J. L. (2016). Assessing the gene content of the megagenome: Sugar pine (Pinus lambertiana). G3: Genes, Genomes, Genetics 6(12), 3787-3802. https://doi.org/10.1534/g3.116.032805

Xiong, J. S., McKeand, S. E., Isik, F., Wegrzyn, J. L., Neale, D. B., Zeng, Z., da Costa e Silva, L., & Whetten, R. W. (2016). Quantitative trait loci influencing forking defects in an outbred pedigree of loblolly pine. BMC Genetics, 17(1), 138. https://doi.org/10.1186/s12863-016-0446-6

Martínez-García, P. J., Crepeau, M. W., Puiu, D., Gonzalez-Ibeas, D., Whalen, J., Stevens, K. A., Paul, R., Butterfield, T. S., Britton, M. T., Reagan, R. L., Chakraborty, S., Walawage, S. L., Vasquez-Gross, H. A., Cardeno, C., Famula, R. A., Pratt, K., Kuruganti, S., Aradhya, M. K., Leslie, C. A., Dandekar, A. M., Salzberg, S. L., Wegrzyn, J. L., Langley, C. H. and Neale, D. B. (2016). The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols. Plant J, 87, 507–532. https://doi.org/10.1111/tpj.13207

Herndon, N., Grau, E. S., Batra, I., Demurjian Jr, S. A., Vasquez-Gross, H. A., Staton, M. E., & Wegrzyn, J. L. (2016). CartograTree: Enabling landscape genomics for forest trees. PeerJ Preprints. https://doi.org/10.7287/peerj.preprints.2345v4

Staton, M., Chen, M., Henry, N., Grau, E., Wytko, C., Soto, B., Jung, S., Wang, K., Watts, N., Cheng, C-H.,  Sanderson, L.A., Wegrzyn, J. L., Main, D., Feltus, F. A., & Ficklin, S. P. (2016). Moving data from the warehouse to the workbench: a bridge to Galaxy from the Tripal community genome database software platform. F1000Research, 5. https://doi.org/10.7490/f1000research.1112734.1

Hoffman, M. L., Peck, K. N., Wegrzyn, J. L., Reed, S. A., Zinn, S. A., & Govoni, K. E. (2016). Poor maternal nutrition during gestation alters the expression of genes involved in muscle development and metabolism in lambs. J. Anim. Sci., 94(7),3093-3099. https://doi.org/10.2527/jas.2016-0570

Vangestel, C., Vázquez-Lobo, A., Martínez-García, P. J., Calic, I., Wegrzyn, J. L., & Neale, D. B. (2016). Patterns of neutral and adaptive genetic diversity across the natural range of sugar pine (Pinus lambertiana Dougl.). Tree Genetics & Genomes, 12(3), 51. https://doi.org/10.1007/s11295-016-0998-7

Wegrzyn, J. L., Whalen, J., Kinlaw, C. S. et al. (2016). Transcriptomic profile of leaf tissue from the leguminous tree, Millettia pinnata. Tree Genetics & Genomes, 12(3), 44. https://doi.org/10.1007/s11295-016-0986-y

Nishiyama, A., Boshans, L., Goncalves, C. M., Wegrzyn, J. L., & Patel, K. D. (2016). Lineage, fate, and fate potential of NG2-glia. Brain research, 1638, 116-128. https://doi.org/10.1016/j.brainres.2015.08.013

G. Hussey, S. G., Wegrzyn, J. L., & Vasquez-Gross, H. A. (2016). Evolutionary histories of gene families in angiosperm trees. Plant Genetics and Genomics: Crops and Models, 1-17. https://doi.org/10.1007/7397_2016_26

Syring, J. V., Tennessen, J. A., Jennings, T. N., Wegrzyn, J. L., Scelfo-Dalbey, C., & Cronn, R. (2016). Targeted capture sequencing in whitebark pine reveals range-wide demographic and adaptive patterns despite challenges of a large, repetitive genome. Frontiers in Plant Science7, 484. https://doi.org/10.3389/fpls.2016.00484

Martínez-García, P. J., Crepeau, M. W., Puiu, D., Gonzalez-Ibeas, D., Whalen, J., Stevens, K. A., Paul, R., Butterfield, T. S., Britton, M. T., Reagan, R. L., Chakraborty, S., Walawage, S. L., Vasquez-Gross, H. A., Cardeno, C., Famula, R. A., Pratt, K., Kuruganti, S., Aradhya, M. K., Leslie, C. A., Dandekar, A. M., Salzberg, S. L., Wegrzyn, J. L., Langley, C. H. and Neale, D. B. (2016). The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols. The Plant Journal, 87(5), 507–532. https://doi.org/10.1111/tpj.13207

Vangestel, C., Vázquez-Lobo, A., Martínez-García, P. J., Calic, I., Wegrzyn, J. L., & Neale, D. B. (2016). Patterns of neutral and adaptive genetic diversity across the natural range of sugar pine (Pinus lambertiana Dougl.). Tree Genetics & Genomes, 12(3), 51. https://doi.org/10.1007/s11295-016-0998-7

Wegrzyn, J. L., Whalen, J., Kinlaw, C. S., Harry, D. E., Puryear, J., Loopstra, C. A., . . . Neale, D. B. (2016). Transcriptomic profile of leaf tissue from the leguminous tree, Millettia pinnata. Tree Genetics & Genomes, 12(3), 44. https://doi.org/10.1007/s11295-016-0986-y

Visser, E. A., Wegrzyn, J. L., Steenkmap, E. T., Myburg, A. A., & Naidoo, S. (2015). Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome. BMC Genomics, 16(1), 1057. https://doi.org/10.1186/s12864-015-2277-7

Chakraborty S., Britton M., Wegrzyn J. L., Butterfield T., Dandekar A. (2015). YeATS – a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut.  F1000 Research, 5:144. https://doi.org/10.12688/f1000research.6617.2

Westbrook, J. W., Walker, A. R., Neves, L. G., Munoz, P., Resende, M. F. R., Neale, D. B., Wegrzyn J. L., Huber, D. A., Kirst, M., Davis, J. M., & Peter, G. F. (2015). Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis across environments, ages, and populations. New Phytol, 205: 627–641. https://doi.org/10.1111/nph.13074

Eckert, A. J., van Heerwaarden, J., Wegrzyn J. L.Nelson, C. D., Ross-Ibarra, J., González-Martínez, S. C., & Neale, D. B. (2014). Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae). 

Munoz P.R., Resende M.F., Huber D.A., Quesada T., Resende M.D., Neale D.B., Wegrzyn J. L., & Peter G.F. (2014). Genomic relationship matrix for correcting pedigree errors in breeding populations: Impact on genetic parameters and genomic selection accuracy. Crop Science, 54(3), 1115-1123. https://doi.org/10.2135/cropsci2012.12.0673

Neale D.B., Wegrzyn J. L., Stevens K.A., Zimin A.V., Puiu D., Crepeau M.W., . . . Liechty J.D. (2014). Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome biology, 15(3), R59. https://doi.org/10.1186/gb-2014-15-3-r59

Quesada T., Resende Jr, M.F., Muñoz P., Wegrzyn J. L., Neale D.B., Kirst M., . . . Davis, J. M. (2014). Mapping fusiform rust resistance genes within a complex mating design of loblolly pine. Forests, 5(2), 347-362. https://doi.org/10.3390/f5020347

Wegrzyn J. L., Liechty J.D., Stevens K. A., Wu L.-S., Loopstra C.A., Vasquez-Gross, H. A., . . . Martínez-García, P. J. (2014). Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation. Genetics, 196(3), 891-909. https://doi.org/10.1534/genetics.113.159996

Zimin A., Stevens K. A., Crepeau M.W., Holtz-Morris A., Koriabine M., Marçais G., Wegrzyn J. L. . . de Jong, P. J. (2014). Sequencing and Assembly of the 22-Gb Loblolly Pine Genome. Genetics, 196(3), 875-890. https://doi.org/10.1534/genetics.113.159715

Eckert A.J., Wegrzyn J. L., Liechty J.D., Lee J.M., Cumbie W.P., Davis J.M., Goldfarb B., Loopstra C.A., Palle S.R., Quesada T., Langley C.H., and Neale D.B. (2013). The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda Pinaceae). Genetics, 195(4), 1353-1372. https://doi.org/10.1534/genetics.113.157198

Eckert A.J., Bower A.D., Jermstad K.D., Wegrzyn J. L., Knaus B.J., Syring J.V., Neale D.B. (2013). Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus strobus). Molecular Ecology, 22, 5635-5650. https://doi.org/10.1111/mec.12514

Mann I.K., Wegrzyn J. L., Rajora O.P. (2013). Generation, functional annotation, and comparative analysis of black spruce ESTs: an important conifer genomic resource. BMC Genomics, 14(1), 702. https://doi.org/10.1186/1471-2164-14-702

Martinez-Garcia P.J., Stevens K.A., Wegrzyn J. L., Liechty J., Crepeau M., Langley C.H., Neale D.B. (2013). Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high density genetic linkage map for loblolly pine (Pinus taeda L.). Tree Genetics and Genomes, 9(6), 1529-1535. https://doi.org/10.1007/s11295-013-0646-4

Chhatre, V.E., Byram, T.D., Neale, D.B., Wegrzyn J. L., & Krutovsky, K. V. (2013). Genetic structure and association mapping of adaptive and selective traits in the east Texas loblolly pine (Pinus taeda L.) breeding populations. Tree Genetics & Genomes, 9: 1161. https://doi.org/10.1007/s11295-013-0624-x

Wegrzyn J. L., Lin B., Zieve J., Dougherty M., Garcia-Martinez P.J., Koriabine M., Holtz-Morris A., deJong P., Crepeau M., Langley C.H., Puiu D., Salzberg S.L., Neale D.B., Stevens K.A. (2013). Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. PLoS ONE, 8(9), e72439. https://doi.org/10.1371/journal.pone.0072439

Palle S., Seeve C., Eckert A.J., Wegrzyn J. L., Neale D.B., Loopstra C. (2013). Association of loblolly pine xylem development gene expression with single nucleotide polymorphisms. Tree Physiology, 33(7), 763-774. https://doi.org/10.1093/treephys/tpt054

Westbrook J.R., Resende M.F.R., Munoz P., Walker A.R., Wegrzyn J. L., Nelson C.D., Neale D.B., Kirst M., Huber D.A., Gezan S.A., Peter G.F., Davis J.M. (2013). Association genetics of oleoresin flow in loblolly pine: discovering genes and predicting phenotype for improved resistance to bark beetles and bioenergy potential. New Phytologist, 199(1), 89-100. https://doi.org/10.1111/nph.12240

Neale D.B., Langley C.H., Salzberg S.L., Wegrzyn J. L. (2013). Open access to tree genomes, the path to a better forest. Genome Biology (Opinion), 14(6), 120. https://dx.doi.org/10.1186%2Fgb-2013-14-6-120

Vasquez-Gross H.A., Yu J.J., Figueroa B., Gessler D.G., Neale D.B., Wegrzyn J. L. (2013). CartograTree: connecting tree genomes, phenotypes, and environment. Molecular Ecology Resources, 13(3), 528-537. https://doi.org/10.1111/1755-0998.12067

Guerra, F. P., Wegrzyn J. L., Sykes, R., Davis, M. F., Stanton, B. J. and Neale, D. B. (2013). Association genetics of chemical wood properties in black poplar (Populus nigra). New Phytol, 197: 162–176. https://doi.org/10.1111/nph.12003

Chen J., Kallman T., Ma X., Gyllenstrand N., Zaina G., Morgante M., Bousquet J., Eckert A., Wegrzyn J. L., Neale D., Lagercrantz U., Lascoux M. (2012). Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies). Genetics, 191(3), 865-881. https://doi.org/10.1534/genetics.112.140749

Wegrzyn J. L., Bark S.J., Taupenot L., Ziegler M., O’Connor D.T., Ma Q., Smoot M., Ideker T., Hook, V. (2012). The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases. PLoS ONE, 7(8), e41134. https://doi.org/10.1371/journal.pone.0041134

Lens F., Cooper L., Gandolfo M.A., Groover A., Jaiswal P., Lachenbruch B., Spicer R., Staton M.E., Stevenson D.W., Walls R.L., Wegrzyn J. L. (2012). An extension of the plant ontology project supporting wood anatomy and development research. IAWA Journal, 33(2), 113-117. https://doi.org/10.1163/22941932-90000083

Eckert A.J., Wegrzyn J. L., Cumbie W.P., Goldfarb B., Huber D.A., Tolstikoc V., Fiehn O., Neale D.B. (2012). Association genetics of the loblolly pine (Pinus taeda Pinaceae) metabolome. New Phytologist, 193(4), 890-902. https://doi.org/10.1111/j.1469-8137.2011.03976.x

Guerra F., Wegrzyn J. L., Sykes R., Davis M., Stanton B., Neale D.B. (2012). Association genetics of chemical wood properties in black poplar (Populus nigra L.). New Phytologist, 197(1), 162-176. https://doi.org/10.1111/nph.12003

Mosca E., Eckert A.J., Liechty J.D., Wegrzyn J. L., La Porta N., Vendramin G.G., Neale D.B. (2012). Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests. Evolutionary Applications, 1(1), 1-14. https://doi.org/10.1111/j.1752-4571.2012.00256.x

Wegrzyn J. L., Main D., Figueroa B., Choi M., Yu J., Neale D.B., Stanton M., Zheng P., Ficklin S., Cho I., Peace C., Evans K., Volk G., Oraguzie N., Chen C., Jr. F.G., Abbott A.G. (2012). Uniform standards for genome databases in forest and fruit trees. Tree Genetics and Genomes, 8(3), 549-557. https://doi.org/10.1007/s11295-012-0494-7

Zapata-Valenzuela J., Isik F., Maltecca C., Wegrzyn J. L., Neale D., McKeand S., Whetten R. (2012). SNP markers trace familial linkages in a cloned population of Pinus taeda – prospects for genomic selection. Tree Genetics and Genomes, 8(6), 1307-1318. https://doi.org/10.1007/s11295-012-0516-5

Chancerel E., Lepoittevin C., Le Provost G., Lin Y., Jaramillo-Correa J.P., Eckert A.J., Wegrzyn J. L., Zelenika D., Boland A., Frigerio J., Chaumeil P., Garnier-Gere P., Boury C., Grivet D., Gonzalez-Martinez S.C., Rouze P., Van de Peer Y., Neale D.B., Cervera M.T., Kremer A., Plomion C. (2011). Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC Genomics, 12(368), 1-14. https://doi.org/10.1186/1471-2164-12-368

Hook V., Funkelstein L., Wegrzyn J. L., Bark S., Kindy M., Hook G. (2011). Cysteine Cathepsins in the secretory vesicle produce active peptides: Cathepsin L generates peptide neurotransmitters and cathepsin B produces beta-amyloid of Alzheimer’s disease. Biochimica et Biophysica Acta, 89-104. https://doi.org/10.1016/j.bbapap.2011.08.015

Cumbie W.P., Eckert A.J., Wegrzyn J. L., Whetten R., Neale D.B., Goldfarb B. (2011). Association genetics of carbon isotope discrimination, height and foliar nitrogen in a natural population of Pinus taeda L. Heredity, 107, 105-114. https://doi.org/10.1038/hdy.2010.168

Jermstad K.D., Eckert A.J., Wegrzyn J. L., Delfino-Mix A., Davis D.A., Burton D.C., Neale D.B. (2010). Comparative mapping in Pinus: sugar pine (Pinus lambertiana Dougl.) and loblolly pine (Pinus taeda L.). Tree Genetics and Genomes, 7(3), 457-468. https://doi.org/10.1007/s11295-010-0347-1

Wegrzyn J. L., Bark S.J., Yap A., O’Connor D.T. and Hook V.H. (2010). Proteomics of dense core secretory vesicles reveal distinct protein categories for secretion of neurotransmitters and neurohumoral molecules for cell-cell communication. Journal of Proteome Research, 9(10), 5002-5024. https://doi.org/10.1021/pr1003104

Quesada T., Gopal V., Cumbie W.P., Eckert A.J., Wegrzyn J. L., Neale D.B., Goldfarb B., Huber D.A., Casella G., Davis J.M. (2010). Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.). Genetics, 186, 677-686. https://doi.org/10.1534/genetics.110.117549

Hook V.H., Bark S., Gupta N., Lortie M., Lu W.D. Bandeira N., Funkelstein L., Wegrzyn J. L. (2010). Neuropeptidomic components generated by proteomic functions in secretory vesicles for neuroendocrine cell-cell communication.  AAPS, 12(4), 635-645. https://doi.org/10.1208/s12248-010-9223-z

Wegrzyn J. L., Eckert, A.J., Choi M., Lee J.M., Stanton B.J., Davis M., Tsai C.J., Neale D.B. (2010). Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (populus trichocarpa, salicaceae) secondary xylem.  New Phytologist, 188, 969-982. https://doi.org/10.1111/j.1469-8137.2010.03415.x

Kovach A.S., Wegrzyn J. L., Parra G., Holt C., Bruening G.E., Loopstra C.A., Hartigan J., Yandell M., Langley C.H., Korf I., Neale D.B. (2010). The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics, 11, 420-429. https://doi.org/10.1186/1471-2164-11-420

Eckert A.J., Gonzalez-Martinez S.C., Bower A.D., Wegrzyn J. L., Coop G., Neale D.B. (2010). Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Molecular Ecology, 19, 3789-3805. https://doi.org/10.1111/j.1365-294X.2010.04698.x

Eckert A.J., Van Heerwaarden J., Wegrzyn J. L., Nelson D.D., Ross-Ibarra J., Gonzalez-Martinez S.C., Neale D.B. (2010). Patterns of population structure and environmental associations with aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics, 185, 969-982. https://doi.org/10.1534/genetics.110.115543

Wegrzyn J. L., Lee J.M., Liechty J. and Neale D.B. (2009). PineSAP – Pine sequence alignment and SNP identification pipeline. Bioinformatics, 25, 2609-2610. https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtp477

Eckert A., Wegrzyn J. L., Pande B., Jermstad K.D., Lee J.M., Liechty J.D., Tearse B.R., Krutovsky K.V., Neale D.B. (2009). 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). Genetics, 183, 289-298. https://doi.org/10.1534/genetics.109.103895

Eckert A.J., Bower A.D., Wegrzyn J. L., Pande B., Jermstad K.D., Krutovsky K.V., St Clair J.B., Neale, D.B. (2009). Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). Genetics, 182, 1289-1302. https://doi.org/10.1534/genetics.109.102350

Wegrzyn J. L., Lee J.M., Tearse B.R., Neale D.B. (2008). TreeGenes: A forest tree genome database. International Journal of Plant Genomics, 2008, 412875. https://dx.doi.org/10.1155%2F2008%2F412875

Hook V., Funkelstein L., Lu D., Bark S., Wegrzyn J. L., Hwang S.R. (2008). Proteases for processing proneuropeptides into peptide neurotransmitters and hormones, Annu Rev Pharmacol Toxicol, 48, 393-423. https://doi.org/10.1146/annurev.pharmtox.48.113006.094812

Wegrzyn J. L., Drudge T.M., Valafar F., Hook V. (2008). Bioinformatic analyses of mammalian 5′-UTR sequence properties of mRNAs predicts alternative translation initiation sites. BMC Bioinformatics, 9, 232. https://dx.doi.org/10.1186%2F1471-2105-9-232

Wegrzyn J. L., Lee J., Neveu J.M., Lane W.S., Hook V. (2007). Proteomics of neuroendocrine secretory vesicles reveal distinct functional systems for biosynthesis and exocytosis of peptide hormones and neurotransmitters. J Proteome Res, 6, 1652-1665. https://doi.org/10.1021/pr060503p

Hwang S.R., Garza C.Z., Wegrzyn J. L., Hook V. (2005). Demonstration of GTG as an alternative initiation codon for the serpin endopin 2B-2. Biochem Biophys Res Commun, 327, 837-844. https://doi.org/10.1016/j.bbrc.2004.12.053

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