University of Connecticut University of UC Title Fallback Connecticut

Publications

Detailed list of publications is available at Google Scholar

Sablok, G., Chen, T.-W., Lee, C.-C., Yang, C., Gan, R.-C., Wegrzyn, J., Porta, N. L., Nayak, K. C., Huang, P.-J., Varotto, C., & Tang, P. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications. DNA Research. doi: 10.1093/dnares/dsw044

Lind, B. M., Friedline, C. J., Wegrzyn, J., Maloney, P. E., Vogler, D. R., Neale, D. B., & Eckert, A. J. 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. doi: 10.1111/mec.14106

Carrasco, A., Wegrzyn, J. L., Durán, R. et al. (2017). Expression profiling in Pinus radiata infected with Fusarium circinatum. Tree Genetics & Genomes, 13: 46.

Frelin, O., Dervinis, C., Wegrzyn, J. L. et al. (2017). Drought stress in Pinus taeda L. induces coordinated transcript accumulation of genes involved in the homogentisate pathway. Tree Genetics & Genomes, 13, 27.

Wei, L.,  Katin-Grazzini, L., Gu, X., Wang, X., El-Tanbouly, R., Yer, H., Thammina, C., Inguagiato, J., Guillard, K., McAvoy, R. J., Wegrzyn, J., 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.

Cronn, R., Dolan, P. C., Jogdeo, S., Wegrzyn, J. L., Neale, D. B., St. Clair, J. B., & Denver, D. R. (2017). Transcription through the eye of a needle: Daily and annual cycles of gene expression variation in douglas-fir needles. bioRxiv, 117374.

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. GigaScience6(1), 1-4.

Velotta, J. P., Wegrzyn, J. L., Ginzburg, S., Kang, L., Czesny, S., O'Neill, R. J., McCormick, S. D., Michalak, P. and Schultz, E. T. (2017), Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife. Mol Ecol, 26, 831–848.

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.

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. 94,3093-3099.

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), 1-10.

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), 1-12.

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.

Lind, B. M., Friedline, C. J., Wegrzyn, J. L., Maloney, P. E., Vogler, D. R., Neale, D. B., & Eckert, A. J. (2016). When local means local: Polygenic signatures of local adaptation within whitebark pine (Pinus albicaulis Engelm.) across the Lake Tahoe Basin, USA. bioRxiv, 056317.

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.

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), 1-10.

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), 1-12.

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.

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.

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, 77(3), 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.

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: Genetic associations within a landscape context. 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.