Detailed list of publications is available at Google Scholar
Published Works
Vuruputoor, V., Starovoitov, A., Cai, Y., Liu, Y., Rahmatpour, N., Hedderson, T.A., Wilding, N., Wegrzyn, J.L., Goffinet, B. Submitted. Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana. BioRxiv. https://doi.org/10.1101/2023.10.30.564737
Kirbis, A., Rahmatpour, N., Dong, S., Yu, J., van Gessel, N., Waller, M., Reski, R., Lang, D., Rensing, S.A., Temsch,E.M., Wegrzyn, J.L., Goffinet, B., Liu, Y., Szövényi. P. Submitted. Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space. BioRxiv. https://doi.org/10.1101/2022.05.17.492078
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). G3: Genes, Genomes, Genetics. https://doi.org/10.1093/g3journal/jkad189
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., Wegrzyn, J.L. Submitted. Urban living can rescue Darwin’s finches from the lethal effects of invasive vampire flies. BioRxiv. https://doi.org/10.1101/2023.03.06.531275
Corcoran, D., Urban, M.C., Wegrzyn, J. and Merow, C. Submitted. Virus evolution affected early COVID-19 spread. medRxiv. https://doi.org/10.1101/2020.09.29.20202416
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. Evolutionary Applications. https://doi.org/10.1101/2022.08.02.502577
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
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
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
Buckley, L.B., Carrington, E, Dillon, M.E., García-Robledo, C, Roberts, S.B., Wegrzyn, J.L., 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., 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
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): 315–334. https://doi.org/10.1093/treephys/tpac115
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
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
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
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
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. Oxford University Press, G3. 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
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
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
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
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
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. Nat Ecol Evol. 4: 250-260. https://doi.org/10.1038/s41559-019-1054-4
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. 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
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
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
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
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
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
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.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
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
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. 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. 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
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 Science. 7: 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 Phytologist. 205: 627–641. https://doi.org/10.1111/nph.13074
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 Phytologist. 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. 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