Detailed list of publications is available at Google Scholar

Published Works

Guzman-Torres, C.R., Trybulec, E., LeVasseur, H., Akella, H., Amee, M., Strickland, E., Pauloski, N., Williams, M., Romero-Severson, J., Hoban, S., Wegrzyn, J.L., and Woeste, K., In Press. Conserving a threatened North American walnut: a chromosome-scale reference genome for butternut (Juglans cinerea). bioRxiv, pp.2023-05. In Press.

Knutie, S.A., Webster, C.N., Vaziri, G.J., Albert, L., Harvey, J.A., LaRue, M., Verrett, T.B., Soldo, A., Koop, J.A., Chaves, J.A. and Wegrzyn, J.L., In Press. Urban living can rescue Darwin’s finches from the lethal effects of invasive vampire flies. bioRxiv, pp.2023-03. In Press.

Vuruputoor, V.S., Monyak, D., Fetter, K.C., Webster, C., Bhattarai, A., Shrestha, B., Zaman, S., Bennett, J., McEvoy, S.L., Caballero, M. and Wegrzyn, J.L., In Press. Welcome to the big leaves: best practices for improving genome annotation in non-model plant genomes. bioRxiv, pp.2022-10. In Press.

McEvoy, S.L., Grady, P.G., Pauloski, N., O’Neill, R.J. and Wegrzyn, J.L., In Press. Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology. bioRxiv, pp.2022-08. In Press.

Visser, E.A.,  Kampmann, T.P.,  Wegrzyn, J.L., Naidoo, S., 2023. Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms. Plant, Cell & Environment, 45 (12).

Cobo-Simón, I., Maloof, J., Li, R., Amini, H., Méndez-Cea, B., García-García, I., Gómez-Garrido, J., Esteve-Codina, A., Dabad, M., Alioto, T., Wegrzyn, J.L., Seco, J.I., Linares, J.C., Gallego, F.J., 2023. Contrasting transcriptomic patterns reveal a genomic basis for drought resilience in the relict fir Abies pinsapo Boiss. Tree Physiology, 43 (2), pp. 315–334.

Velasco, V.M., Ferreira, A., Zaman, S., Noordermeer, D., Ensminger, I., Wegrzyn, J.L., 2023. A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir). G3, jkac304, pp.2160-1836.

Mahoney, J.D., Wang, S., Iorio, L.A., Wegrzyn J.L., Dorris, M., Martin, D., Bolling, B.W., Brand, M.H. and Wang, H., 2022. De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa. BMC plant biology, 22(1), pp.1-16.

Martínez-García, P.J., Mas-Gómez, J., Wegrzyn J., and Botía, J.A., 2022. Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.). Scientific reports, 12(1), pp.1-10.

McEvoy, S.L., Sezen, U.U., Trouern‐Trend, A., McMahon, S.M., Schaberg, P.G., Yang, J., Wegrzyn J.L., and Swenson, N.G. (2022) Strategies of tolerance reflected in two North American maple genomes. The Plant Journal.

Liu, Y., Wang, S., Li, L., Yang, T., Dong, S., Wei, T., Wu, S., Liu, Y., Gong, Y., Feng, X., Wegrzyn J.L., and Ma, J., 2022. The Cycas genome and the early evolution of seed plants. Nature Plants, pp.1-13.

Webster, C., Figueroa‐Corona, L., Méndez‐González, I., Álvarez‐Soto, L., Neale, D., Jaramillo‐Correa, J., Wegrzyn J.L., Vázquez‐Lobo, A. (2022). Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera. Ecology and Evolution 12(2), e8611.

Ence, D., Smith, K.,Fan, S., Neves, L.G, Paul, R., Wegrzyn J.L., Peter, G., Kirst, M., Brawner, J., Nelson, C., Davis, J. (2022). NLR diversity and candidate fusiform rust resistance genes in loblolly pine. Oxford University Press, G3 12(2), jkab421.

Jackson, C., Christie, N., Reynolds, S.M., Marais, G.C., Tii‐kuzu, Y., Caballero, M., Kampman, T., Visser, E.A., Naidoo, S., Kain, D., Whetten, R.W., Isik, F., Wegrzyn J.L., Hodge,G.R., Acosta, J.J., Myburg, A.A. (2022). A genome‐wide SNP genotyping resource for tropical pine tree species. Molecular Ecology Resources, 22(2), 695-710.

Lawniczak, M.K., Durbin, R., Flicek, P., Lindblad-Toh, K., Wei, X., Archibald, J.M., Baker, W.J., Belov, K., Blaxter, M.L., Bonet, T.M., Childers, A.K., Coddington, J.A, Crandall, K.A., Crawford, A.J., Davey, R.P., Palma, F.D., Fang, Q., Haerty, W., Hall, N., … Wegrzyn J.L.. (2022). Standards recommendations for the Earth BioGenome Project. Proceedings of the National Academy of Sciences, 119(4).

Kress, W.J., Soltis, D.E., Kersey, P.J., Wegrzyn J.L., Leebens-Mack, J.H., Gostel, M.R., Liu, X. and Soltis, P.S. (2022) Green plant genomes: What we know in an era of rapidly expanding opportunities. Proceedings of the National Academy of Sciences, 119(4).

Staton M., Cannon, E., Sanderson, L., Wegrzyn J.L., Anderson T., Buehler S., Cobo-Simón, I., Faaberg, K., Grau, E., Guignon, V., Gunoskey, J., Inderski, B., Jung, S., Lager, K., Main, D., Poelchau, M., Ramnath, R., Richter, P., West, J., Ficklin, S. (2021) Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. Briefings in Bioinformatics, bbab238. 17 p.

Urban, M.C., Merow, C., Wegrzyn J.L., Maitner, B.S. and Corcoran, D., 2021. How to Publish at Pandemic Speed. BioScience, 71(10), pp.1001-1003.

Cobo-Simón, I., Méndez-Cea, B., Seco, J.I., Wegrzyn J., Linares, J.C. and Gallego, F.J., 2021. Gene Frequency Shift in Relict Abies pinsapo Forests Associated with Drought-Induced Mortality: Preliminary Evidence of Local-Scale Divergent Selection. Forests, 12(9), p.1220.

Figueroa-Corona, L., Delgado Valerio, P., Wegrzyn J.L., Piñero, D. (2021) Transcriptome of weeping pinyon pine, Pinus pinceana, shows differences across heterogeneous habitats. Trees. 35, 1351-1365.

Caballero, M., Lauer, E., Bennett, J., Zaman, S., McEvoy, S., Acosta, J., Jackson, C., Townsend, L., Eckert, A., Whetten, R. W., Loopstra C., Holliday J., Mandal, M., Wegrzyn, J. L., Isik, F. (2021) Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome. Applications in Plant Sciences.

Scott, A., Zimin, A., Puiu, D., Workman, R., Britton, M., Zaman, S., Caballero, M., Read, A., Bogdanove, A., Burns, E., Wegrzyn J.L., Timp, W., Salzberg, S. and Neale, D., 2020. A Reference Genome Sequence for Giant Sequoia. G3: Genes|Genomes|Genetics, 10(11), pp.3907-3919.

Li, J., West, J. B., Hart, A., Wegrzyn, J. L., Smith, M. A., Domec, J., Loopstra, C. A., Casola, C. (2021) Extensive variation in drought-induced gene expression changes between loblolly pine genotypes. Frontiers in Genetics, 12:659.

Rahmatpour, N., Perera, N. V., Singh, V., Wegrzyn, J.L. L., & Goffinet, B. (2021). High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae. Molecular Phylogenetics and Evolution, 154, 106965.

Trouern‐Trend, A.J., Falk, T., Zaman, S., Caballero, M., Neale, D.B., Langley, C.H., Dandekar, A.M., Stevens, K.A. and Wegrzyn J.L. (2020), Comparative genomics of six Juglans species reveals disease‐associated gene family contractions. Plant J.

Hart, A. J., Ginzburg, S., Xu, M. (Sam), Fisher, C. R., Rahmatpour, N., Mitton, J. B., Paul, R., and Wegrzyn J.L., EnTAP: Bringing faster and smarter functional annotation to non‐model eukaryotic transcriptomes. Mol Ecol Resour. 2019; 00: 1– 14.

Fisher, C.R., Wegrzyn J.L., & Jockusch, E.L. Co-option of wing-patterning genes underlies the evolution of the treehopper helmet. Nat Ecol Evol (2019).

Corcoran, D., Urban, M.C., Wegrzyn J., and Merow, C., 2020. Virus evolution affected early COVID-19 spread. medRxiv.

Shawna Spoor, Connor Wytko, Brian Soto, Ming Chen, Abdullah Almsaeed, Bradford Condon, Nic Herndon, Heidi Hough, Sook Jung, Meg Staton, Jill Wegrzyn, Dorrie Main, F Alex Feltus, Stephen P Ficklin, Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases, Database, Volume 2020, 2020, baaa032,

Wegrzyn J.L., Falk, T., Grau, E, Buehler, S., Ramnath, R., Herndon, N. Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. Evol Appl. 2019; 13: 228– 241.

Caballero, M., & Wegrzyn J.L., (2019). gFACs: Filtering, analysis, and conversion to unify genome annotations across alignment and gene prediction frameworks. Genomics, Proteomics, & Bioinformatics.

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:

Visser, E. A., Wegrzyn, J. L., Steenkamp, E. T., Myburg, A. A., and Naidoo, S. (2019). Dual RNA-Seq analysis of the pine-Fusarium circinatum interaction in resistant (Pinus tecunumanii) and susceptible (Pinus patula) hosts. Microorganisms. 7 (9): 315.

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.

Buble, K., Jung, S., Humann, J. L., Yu, J., Cheng, C. H., Lee, T., Ficklin, S. P., Hough, H., Condon, B., Staton, M. E., Wegrzyn, J. L., and Main, D. (2019). Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps. Database. 2019.

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.

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.

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

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.

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.

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.L., 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.

Ence, D., Smith, K. M., Kirst, M., Yandell, M., Wegrzyn J.L., Nelson, C. D., & Davis, J. (2018, October). Forward genetic analysis defines candidate genes for fusiform rust resistance in loblolly pine and avirulence in Cronartium quercuum f. sp fusiforme. Phytopathology, 108 (10), 171-172.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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