Publications – compgenomics

Detailed list of publications is available at Google Scholar

Published Works

Castellano, K.R., Neitzey, M.L., Starovoitov, A., Barrett, G.A., Reid, N.M., Vuruputoor, V.S., Webster, C.N., Storer, J.M., Pauloski, N.R., Ameral, N.J., McEvoy, S.L., McManus, M.C., Puritz, J.B., Wegrzyn, J.L., and O’Neill, R.J. (2025). Genome assembly of a living fossil, the Atlantic horseshoe crab Limulus polyphemus, reveals lineage-specific whole-genome duplications, transposable element-based centromeres, and a ZW sex chromosome system. Molecular Biology and Evolution, 42(2): msaf021. https://doi.org/10.1093/molbev/msaf021

Kirbis, A., Rahmatpour, N., Dong, S., Yu, J., Waser, L., Huang, H., van Gessel, N., Waller, M., Reski, R., Lang, D., Rensing, S.A., Temsch, E.M., Wegrzyn, J.L., Goffinet, B., Liu, Y., and Szövényi, P. (2025). Comparative analysis using a chromosome-scale genome assembly for Funaria hygrometrica suggests greater collinearity in mosses than in seed plants. Communications Biology, 8(1): 330. https://doi.org/10.1038/s42003-025-07749-x

Patel, N., Vuruputoor, V.S., Rahmatpour, N., Liu, Y., Szövényi, P., Goffinet, B., and Wegrzyn, J.L. (2025). Immediate premeiotic transcriptomic effects following nonchemically induced whole genome duplication in the moss Funaria hygrometrica. New Phytologist, 247(1). https://doi.org/10.1111/nph.70208

Lötter, A., Bruna, T., Duong, T.A., Barry, K., Lipzen, A., Daum, C., Yoshinaga, Y., Grimwood, J., Jenkins, J.W., Talag, J., Borevitz, J., Lovell, J.T., Schmutz, J., Wegrzyn, J.L., and Myburg, A.A. (2025). A haplotype-resolved reference genome for Eucalyptus grandis. G3: Genes, Genomes, Genetics, 15(7): jkaf112. https://doi.org/10.1093/g3journal/jkaf112

Nenasheva, N., Pitzschel, C., Webster, C.N., Hart, A.J., Wegrzyn, J.L., Bengtsson, M.M., and Hoff, K.J. (2025). Annotation of protein-coding genes in 49 diatom genomes from the Bacillariophyta clade. Scientific Data, 12(1): 985. https://doi.org/10.1038/s41597-025-05306-z

Vuruputoor, V.S., Starovoitov, A., Cai, Y., Liu, Y., Rahmatpour, N., Hedderson, T.A., Wilding, N., Wegrzyn, J.L., and Goffinet, B. (2024). Crossroads of assembling a moss genome: Navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana. G3: Genes, Genomes, Genetics, 14(7): jkae104. https://doi.org/10.1093/g3journal/jkae104

Bryant, M.J., Coello, A.M., Glendening, A.M., Hilliman, S.A., Jara, C.F., Pring, S.S., Rodríguez Rivera, A., Santiago Membreño, J., Nigro, L., Pauloski, N., Graham, M.R., King, T., Jockusch, E.L., O’Neill, R.J., Wegrzyn, J.L., Santibáñez-López, C.E., and Webster, C.N. (2024). Unveiling the genetic blueprint of a desert scorpion: A chromosome-level genome of Hadrurus arizonensis provides the first reference for Parvorder Iurida. Genome Biology and Evolution, 16(5): evae097. https://doi.org/10.1093/gbe/evae097

Neale, D.B., Zimin, A.V., Meltzer, A., Bhattarai, A., Amee, M., Figueroa Corona, L., Allen, B.J., Puiu, D., Wright, J., De La Torre, A.R., McGuire, P.E., Timp, W., Salzberg, S.L., and Wegrzyn, J.L. (2024). A genome sequence for the threatened whitebark pine. G3: Genes, Genomes, Genetics, 14(5): jkae061. https://doi.org/10.1093/g3journal/jkae061

McEvoy, S.L., Grady, P.G.S., Pauloski, N., O’Neill, R.J., and Wegrzyn, J.L. (2024). Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology. Evolutionary Applications, 17: e13669. https://doi.org/10.1111/eva.13669

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. (2024). Conserving a threatened North American walnut: A chromosome-scale reference genome for butternut (Juglans cinerea). G3: Genes, Genomes, Genetics, 14(1): jkad189. https://doi.org/10.1093/g3journal/jkad189

Bush, J., Webster, C., Wegrzyn, J., Simon, C., Wilcox, E., Khan, R., Weisz, D., Dudchenko, O., Lieberman Aiden, E., and Frandsen, P. (2024). Chromosome-level genome assembly and annotation of a periodical cicada species: Magicicada septendecula. Genome Biology and Evolution, 16(1): evae001. https://doi.org/10.1093/gbe/evae001

Knutie, S.A., Webster, C.N., Vaziri, G.J., Albert, L., Harvey, J.A., LaRue, M., Verrett, T.B., Soldo, A., Koop, J.A.H., Chaves, J.A., and Wegrzyn, J.L. (2024). Urban living can rescue Darwin’s finches from the lethal effects of invasive vampire flies. Global Change Biology, 30(1): e17145. https://doi.org/10.1111/gcb.17145

Kaya, Z., Taşkıran, B., Uluğ, A., Güvendiren, A.D., Wegrzyn, J.L., and Neale, D.B. (2023). Association genetics of wood traits in European black poplar (Populus nigra L.). Tree Genetics & Genomes, 19(4): 38. https://doi.org/10.1007/s11295-023-01612-y

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. (2023). Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes. Applications in Plant Sciences, 11(4): e11533. https://doi.org/10.1002/aps3.11533

Buckley, L.B., Carrington, E., Dillon, M.E., García-Robledo, C., Roberts, S.B., Wegrzyn, J.L., and Urban, M.C. (2023). Characterizing biological responses to climate variability and extremes to improve biodiversity projections. PLOS Climate, 2(6): e0000226. https://doi.org/10.1371/journal.pclm.0000226

Visser, E.A., Kampmann, T.P., Wegrzyn, J.L., and Naidoo, S. (2023). Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms. Plant, Cell & Environment, 46(5): 1705-1725. https://doi.org/10.1111/pce.14522

Velasco, V.M., Ferreira, A., Zaman, S., Noordermeer, D., Ensminger, I., and 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: Genes, Genomes, Genetics, 13(2): jkac304. https://doi.org/10.1093/g3journal/jkac304

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., and 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): 315–334. https://doi.org/10.1093/treephys/tpac115

Lötter, L., Duong, T.A., Candotti, J., Mizrachi, E., Wegrzyn, J.L., Myburg, A.A. (2023). Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids. GigaScience, 12: giad064. https://doi.org/10.1093/gigascience/giad064

Figueroa-Corona, L., Moreno-Letelier, A., Ortega-Del Vecchyo, D., Peláez, P., Gernandt, D. S., Eguiarte, L. E., Wegrzyn, J., & Piñero, D. (2022). Changes in demography and geographic distribution in the weeping pinyon pine (Pinus pinceana) during the Pleistocene. Ecology and Evolution, 12, e9369. https://doi.org/10.1002/ece3.9369

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): 1-10. https://doi.org/10.1038/s41598-022-11689-5

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, 8: 1-13. https://doi.org/10.1038/s41477-022-01129-7

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): 1-16. https://doi.org/10.1186/s12870-022-03518-8

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, 109(6): 1591-1613. https://doi.org/10.1111/tpj.15657

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. https://doi.org/10.1002/ece3.8611

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. G3: Genes|Genomes|Genetics, 12(2): jkab421. https://doi.org/10.1093/g3journal/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. https://doi.org/10.1111/1755-0998.13484

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, 72(4): 110-112. https://doi.org/10.1073/pnas.2115639118

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): e2115640118. https://doi.org/10.1073/pnas.2115640118

Neale, D.B., Zimin, A.V., Zaman, S., Scott, A.D., Shrestha, B., Workman, R.E., Puiu, D., Allen, B.J., Moore, Z.J., Sekhwal, M.K., De La Torre, A.R., McGuire, P.E., Burns, E., Timp, W., Wegrzyn, J.L., and Salzberg, S.L. (2022). Assembled and Annotated 26.5 Gbp Coast Redwood Genome: A Resource for Estimating Evolutionary Adaptive Potential and Investigating Hexaploid Origin. G3: Genes|Genomes|Genetics, 12(1): jkab380. https://doi.org/10.1093/g3journal/jkab380

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. https://doi.org/10.1093/bib/bbab238

Urban, M.C., Merow, C., Wegrzyn, J.L., Maitner, B.S. and Corcoran, D. (2021). How to Publish at Pandemic Speed. BioScience, 71(10): 1001-1003. https://doi.org/10.1093/biosci/biab084

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): 1220. https://doi.org/10.3390/f12091220

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. https://doi.org/10.1007/s00468-021-02125-8

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, 9(6): e11439. https://doi.org/10.1002/aps3.11439

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. https://doi.org/10.3389/fgene.2021.661440

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): 3907-3919. https://doi.org/10.1534/g3.120.401612

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. https://doi.org/10.1016/j.ympev.2020.106965

Trouern‐Trend, A.J.G, Falk, T.T, Zaman, S.G, Caballero, M.U, 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. The Plant Journal, 102(2): 410-423. https://doi.org/10.1111/tpj.14630

Hart, A. J.G, Ginzburg, S.U, Xu, M. (Sam)U, Fisher, C. R.G, Rahmatpour, N.G, Mitton, J. B., Paul, R.P, and Wegrzyn, J. L. (2020). EnTAP: Bringing faster and smarter functional annotation to non‐model eukaryotic transcriptomes. Molecular Ecology Resources, 20: 591-604. https://doi.org/10.1111/1755-0998.13106

Fisher, C.R.G, Wegrzyn, J.L. and Jockusch, E.L. (2019). Co-option of wing-patterning genes underlies the evolution of the treehopper helmet. Nature Ecology & Evolution, 4: 250-260. https://doi.org/10.1038/s41559-019-1054-4

Spoor, S., Wytko, C., Soto, B., Chen, M., Almsaeed, A., Condon, B., Herndon, N., Hough, H., Jung, S., Staton, M., Wegrzyn, J., Main, D., Feltus, F. A., & Ficklin, S. P. (2020). Tripal and Galaxy: Supporting reproducible scientific workflows for community biological databases. Database, baaa032. https://doi.org/10.1093/database/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. Evolutionary Applications, 13: 228– 241. https://doi.org/10.1111/eva.12860

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. https://doi.org/10.3390/microorganisms7090315

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. Frontiers in Plant Science, 10:813. https://doi.org/10.3389/fpls.2019.00813

Caballero, M.U and Wegrzyn, J.L. (2019). gFACs: Filtering, analysis, and conversion to unify genome annotations across alignment and gene prediction frameworks. Genomics, Proteomics, and Bioinformatics, 17(3): 305-310. https://doi.org/10.1016/j.gpb.2019.04.002

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

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, baz100. https://doi.org/10.1093/database/baz100

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, baz077. https://doi.org/10.1093/database/baz077

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

Wang, L., Jiang, Z., Huang, D., Wegrzyn, J.L., et al. (2018). JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process. BMC Genomics, 19, 183. https://doi.org/10.1186/s12864-018-4507-2

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. https://doi.org/10.1093/g3journal/jkab421

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.L., Williams, J., Woodhouse, M., Yu, J., and Main, D. (2018). AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database, 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. (2017). Finding loci associated with 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

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

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

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

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

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

Wegrzyn, J., Staton, M., Grau, E., Cronn, R., & Nelson, C. D. (2017). Community standards for genomic resources, genetic conservation, and data integration. In R. A. Sniezko, G. Man, V. Hipkins, K. Woeste, D. Gwaze, J. T. Kliejunas, & B. A. McTeague (Eds.), Gene conservation of tree species—banking on the future (pp. 28-29). U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. https://research.fs.usda.gov/treesearch/55236

Grau, E. S., Demurjian, S. A., Vasquez-Gross, H. A., Gessler, D. G., Neale, D. B., & Wegrzyn, J. L. (2017). TreeGenes and CartograTree: Enabling visualization and analysis in forest tree genomics. In R. A. Sniezko, G. Man, V. Hipkins, K. Woeste, D. Gwaze, J. T. Kliejunas, & B. A. McTeague (Eds.), Gene conservation of tree species—banking on the future (p. 117). U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. https://research.fs.usda.gov/treesearch/55100

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. bax052. https://doi.org/10.1093/database/bax052

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

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

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

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. The Plant Journal. 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

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 Science. 7: 484. https://doi.org/10.3389/fpls.2016.00484

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 Phytologist. 205: 627–641. https://doi.org/10.1111/nph.13074

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, 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). Genetics. 185(3): 969-982. https://doi.org/10.1534/genetics.110.115543

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

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

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

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

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

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

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

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

Gessler, D. D. G., Bulka, B., Sirin, E., Vasquez-Gross, H., Yu, J., & Wegrzyn, J. L. (2013). iPlant SSWAP (Simple Semantic Web Architecture and Protocol) enables semantic pipelines for biodiversity. Semantics for Biodiversity (S4BioDiv 2013), 101.

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 Phytologist. 197: 162–176. https://doi.org/10.1111/nph.12003

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

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., 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

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., 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

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

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

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

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

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

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

Jermstad, K. D., Eckert, A. J., Kinloch, B. B. Jr., Davis, D. A., Burton, D. C., Mix, A. D., Wegrzyn, J. L., & Neale, D. B. (2011). A sugar pine consensus map: Comparative mapping between the Pinus subgenus Pinus and the subgenus Strobus. In Keane, R. E., Tomback, D. F., Murray, M. P., & Smith, C. M. (Eds.), The future of high-elevation, five-needle white pines in Western North America: Proceedings of the High Five Symposium (28-30 June 2010; Missoula, MT) (pp. 140-144). Proceedings RMRS-P-63. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. https://research.fs.usda.gov/treesearch/38210.

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

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

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

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

Wegrzyn, J. L., Bark, S. J., Funkelstein, L., Mosier, C., Yap, A., Kazemi-Esfarjani, P., La Spada, A. R., Sigurdson, C., O’Connor, D. T., & Hook, V. (2010). Proteomics of dense core secretory vesicles reveal distinct protein categories for secretion of neuroeffectors for cell–cell communication. Journal of Proteome Research, 9(10), 5067–5080. https://doi.org/10.1021/pr1003104.

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

Scalfi, M.; Troggio, M.; Wegrzyn, J.L.; Vendramin, G.G.; La Porta, N.; Neale, D.B. (2010). Genetic structure and adaptive genes of natural Alpine populations of Norway spruce: a high- throughput genotyping approach. INTERNATIONAL FORESTRY REVIEW, 12 (5): 107. handle: http://hdl.handle.net/10449/19394

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., 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

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

Begley, T.P., Hook, V., Hwang, S.-R., Wegrzyn, J. and Bark, S. (2008). Neuropeptides: Chemical Activity Profiling and Proteomic Approaches. In Wiley Encyclopedia of Chemical Biology, T.P. Begley (Ed.). https://doi.org/10.1002/9780470048672.wecb381

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

Gessler, D. D. G., Bulka, B., Sirin, E., Kang, Y., Klinov, P., Vasquez-Gross, H., Yu, J., & Wegrzyn, J. L. (2012). iPlant Semantic Web Platform uses SSWAP (Simple Semantic Web Architecture and Protocol) to enable semantic pipelines across distributed web and high-performance computing resources. The platform facilitates semantic pipelines using transaction-time reasoning and ontologies for service discovery and integration across distributed and high-performance computing resources. https://km.aifb.kit.edu/sites/swc/2012/submissions/swc2012_submission_18.pdf.

Wheeler, N., Wegrzyn, J. , Harry, D., & Merk, H. L. Conifer Translational Genomics Network Online Module 6: Genetic Markers.

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