Publications

Published manuscripts (*undergraduate, **graduate, ***postdoctoral researcher)

Pre-Prints

McLaughlin, C. M., Hinshaw, C., Sandoval-Arango, S., Zavala-Paez, M.**, and J.A. Hamilton (In Revision) Redlisting genetics: towards incorporation of genomic data in conservation assessments. Preprint Available.

Di Santo, L.**, Mead, A.***, Wright, J. and J.A. Hamilton (In Revision) Genomic signature of reproductive isolation between the last two remnant populations of Torrey pine (Pinus torreyana ​Parry) Preprint Available

Rana, S.K.***, Lindstrom, J.**, Lehrer, M.A.***, Ahlering, M., and J.A. Hamilton (In Review) Forecasting hotspots of grassland suitability under climate change for restoration. Preprint Available.

2024

Melton, A.E.***, Faske, T. M., Sniezko, R.A. Thibault, T., Williams, W., Parchman, T., and J.A. Hamilton (Accepted - Molecular Ecology) Genomics-driven monitoring of Fraxinus latifolia (Oregon ash) for conservation and EAB-resistance breeding. Preprint Available.* Special Issue on Conservation Genomics - Making a Difference *

Bolte, C.E.***, Phannareth, T., Zavala-Paez, M.**, Sutara, B.*, Can, F., Fitzpatrick, M., Holliday, J., Keller, S., and J.A. Hamilton (2024) Genomic insights into hybrid zone formation: the role of climate, landscape, and demography in the emergence of a novel hybrid lineage between Populus trichocarpa and P. balsamifera. Molecular Ecology. 33: e17430.

​Zavala-Paez, M**, Holliday, J., and J.A. Hamilton (2024) Leveraging whole genome sequencing to estimate telomere length in plants. Molecular Ecology Resources. 2: e13899.

Sullivan, L. L., Portlas, Z.M.*, Jaeger, K., Hoffner, M.*, and J.A. Hamilton (2024) Climate and habitat type interact to influence contemporary dispersal potential in Prairie Smoke (Geum triflorum). Ecology and Evolution. 14: e11231.

2023

Lindstrom, J.**, Ahlering, M, and J.A. Hamilton (2023) Seed sourcing for climate-resilient grasslands: the role of seed source diversity during early restoration establishment. Ecology and Evolution. 13: e10756 

Lehrer, M.A.*** and J.A. Hamilton (2023) Preserving range-wide genetic diversity of Fraxinus nigra. Tree Seed Working Group News Bulletin, Canadian Forest Genetics Association 74: 17-21.

​Kulbaba, M., Yoko, Z.**, and J.A. Hamilton (2023) Chasing the fitness optimum: temporal variation in the genetic and environmental expression of life-history traits for a perennial plant. Annals of Botany
* Featured Perspective by Meredith Zettlemoyer
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​Keagy, J., Drummond, C., Gilbert, K., Grozinger, C., Hamilton, J., Hines, H., Lasky, J., Logan, C., Sawers, R., and T. Wagner (2023) Landscape transcriptomics as a tool for addressing global change effects across diverse species. Molecular Ecology Resources 

2022

Volk, K.**, Braasch, J.***, Ahlering, M., and J.A. Hamilton (2022) Environmental contributions to the evolution of trait differences in Geum triflorum​: implications for restoration. American Journal of Botany *Special Issue on 'Approaches to the study of quantitative fitness-related traits' 

​Di Santo, L.N.**, Hoban, S.M., Parchman, T.L., Wright, J.W., and J.A. Hamilton (2022) Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana) with implications for rare species conservation. Molecular Ecology 31: 4622-4639.

Benomar, L., Elferjani, R., Hamilton, J.A., O'Neill, G. A., Echchakoui, S., Bergeron, Y., and L. Mebarek (2022) Bibliometric analysis of the structure and evolution of research on assisted migration. Current Forestry Reports

VanWallendael, A., Lowry, D.B., and J.A. Hamilton (2022) One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems. Current Opinion in Plant Biology. 66: 102152
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​Galla, S., Brown, L., Couch-Lewis, Y., Cubrinovska, I., Eason, D., Gooley, R., Hamilton, J.A., Heath, J., Hauser, S., Latch, E., Matocq, M., Richardson, A., Wold, J., Hogg, C., Santure, A., and T. Steeves (2022) The relevance of pedigrees in the conservation genomics era. Molecular Ecology 31: 41-54.

2021

Di Santo, L.N.**, Polgar, M.*, Nies, S.*, Hodgkiss, P., Canning, C.A., Wright, J.W. and J.A. Hamilton (2021) Seed morphology and emergence variability in a conservation collection of Pinus torreyana. AOB Plants. 13 (5): plab058.

Braasch, J.E.***, Di Santo, L.N.**, Tarble, Z.*, Prasifka, J.R., and J.A. Hamilton (2021) Testing for evolutionary change in restoration: a genomic comparison between ex situ, native and commercial seed sources of Helianthus maximiliani. ​Evolutionary Applications. 14: 2206-2220.

Di Santo, L, N.** and J. A. Hamilton (2021) Environmental and geographic data optimize ex situ collections and the preservation of adaptive evolutionary potential. Conservation Biology 35: 733-744.

Huff, M., Wu, D., Seaman, J., Zhebentyayeva, Kelly, L., Islam-Faridi, Nelson, C., Cooper, E., Best, T., Steiner, K., Koch, J., Romero-Severson, J., Carlson, J., Bugga, R., and Staton M. 2021. A high quality reference genome for Fraxinus pennsylvanica for ash species restoration and research. Molecular Ecology Resources. 

Lazic D, Hipp AL, Carlson JE, Gailing O. 2021. Use of genomic resources to assess adaptive divergence and introgression in oaks. Forests 12:690, 18 pages.

2020

Stanton BJ, Haiby K, Gantz G, Shuren R, Hall R, Johnson LJ, Weathers TC, Wu D, Islam-Faridi N; Best T, Stanish A, Staton M, Carlson JE. 2020. Inter-Specific Hybridization of Alnus rubra and Alnus rhombifolia: Preliminary Report of a New Taxon and DNA Marker Resources for Bioenergy Feedstock Production. Tree Genetics & Genomes, 16:70, 13 pages.

Wang W, Carlson CH, Smart LB, Carlson JE. 2020. Transcriptome analysis of contrasting resistance to herbivory by Empoasca fabae in two shrub willow species and their hybrid progeny. PLOS ONE, 15(7): e0236586.

Staton M, Addo-Quaye C, Cannon N, Yu J, Zhebentyayeva T,.....,Carlson JE. 2020. A reference genome assembly and adaptive trait analysis of Castanea mollissima 'Vanuxem', a source of resistance to chestnut blight in restoration breeding. Tree Genetics and Genomes, 16:57, 23 pages.

Tchatchoua TD, Poethig RS, Doody E, Weathers TC, Swartz K, Mathieson I, Zembower N, Zhebentyayeva T, Carlson JE. 2020. Genetic diversity of Faidherbia albida populations in the Sudano Sahelian region of Cameroon, using SSR (Simple Sequence Repeat) markers. African Journal of Biotechnology, 19(7): 415-425.

Soltani N, Best T, Grace D, Nelms C, Shumaker K, Romero-Severson J, Moses D, Schuster S, Staton M, Carlson J, Gwinn K. 2020. Transcriptome profiles of Quercus rubra responding to increased O3 stress. BMC Genomics, 21(1): 1-18.

Guo L, Guo S, Xu J, He L, Carlson JE, Hou X. 2020. Phylogenetic analysis based on chloroplast genome uncover evolutionary relationship of all the nine species and six cultivars of tree peony. Industrial Crops and Products, 153: p.112567, (https://doi.org/10.1016/j.indcrop.2020.112567), 10 pages.

Bourguiba H, Scotti I, Sauvage C, Zhebentyayeva T, Ledbetter C, Krška B, Remay A, D'Onofrio C, Iketani H, Christen D, Krichen L. 2020. Genetic Structure of a Worldwide Germplasm Collection of Prunus armeniaca L. Reveals Three Major Diffusion Routes for Varieties Coming From the Species' Center of Origin. Frontiers in Plant Science, 11: 638.

Yu J, Conrad AO, Decroocq V, Zhebentyayeva T, Williams DE, Bennett D, Roch G, Audergon JM, Dardick C, Liu Z, Abbott AG, 2020. Distinctive gene expression patterns define endodormancy to ecodormancy transition in apricot and peach. Frontiers in Plant Science, 11: 180.

Merkle SA, Vieitez FJ, Corredoira E, Carlson JE. 2020. 10.1 Castanea spp. Chestnut. In R. Litz, F. Alfaro, & J. Hormaza (Eds.), Biotechnology of Fruit and Nut Crops (2nd ed.). CAB International, published January 2020, pages 206 – 237. CABI cat # 9781780648279.

2019

Conrad AO, Yu J, Staton ME, Audergon JM, Roch G, Decroocq V, Knagge K, Chen H, Zhebentyayeva T, Liu Z, Dardick C. 2019. Association of the phenylpropanoid pathway with dormancy and adaptive trait variation in apricot (Prunus armeniaca). Tree Physiology, 39(7): 1136-1148.

Bell TH, Kaminsky LM, Gugino BK, Carlson JE, Malik RJ, Hockett KL, Trexler RV. 2109. Factoring Ecological, Societal, and Economic Considerations into Inoculant Development. Trends in Biotechnology, 37(2): 140-151.

Kim HS, Park W, Lim HG, Eom S, Lee JH, Carlson JE, Ahn SJ. 2019. NaCl-induced CsRCI2E and CsRCI2F interact with aquaporin CsPIP2;1 to reduce water transport in Camelina sativa L. Biochemical and biophysical research communications, 513(1):213-8.

Bell T, Hockett KL, Alcalá-Briseño RI, Barbercheck M, Beattie GA, Brun MA, Carlson JE, Chung T, Collins A, Emmett B, Esker P, Garrett KA, Glenna L, Gugino B, del mar Jimenez-Gasco M, Kinkel L, Kovac J, Kowalski KP, Kuldau G, Leveau JHJ, Michalska-Smith MJ, Myrick J, Peter K, Shade A, Stopnisek N, Tan X, Welty AT, Wickings K, Yergeau E. 2019. Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities. Phytobiomes Journal 3:3-21.

Wu D, Koch J, Coggeshall M, Carlson J. 2019. The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species, Plant Molecular Biology, 99 (3):251-264.

2018

Tuskan GA, Groover AT, Schmutz J, DiFazio SP, Myburg A, Grattapaglia D, Smart LB, Yin T, Aury JM, Kremer A, Leroy T, Le Provost G, Plomion C, Carlson JE, Randall, J, Westbrook J, Grimwood J, Muchero W, Jacobson D, Michener JK. 2018. Hardwood tree genomics: Unlocking woody plant biology. Frontiers in Plant Science, 9, p.1799, 9 pages.

Weathers TC, Kazyak DC, Stauffer JR, Jr., Kulp MA, Moore SE, King TL, Carlson JE. 2018. Neutral Genetic and Phenotypic Variation Within and Among Isolated Headwater Brook Trout Populations, Transactions of the American Fisheries Society, 148(1) 58-72, 15 pages.

Scully E., Geib SM, Mason CJ, Carlson JE, Tien M, Chen H-Y, Harding S, Tsai C-J, Hoover K. 2018. Host-plant induced changes in microbial community structure and midgut gene expression in an invasive polyphage (Anoplophora glabripennis)" Scientific Reports, 8(1), p.9620, 16 pages.

2017

Harmon M, Lane T, Staton M, Coggeshall MV, Best T, Chen CC, Liang H, Zembower N, Drautz-Moses DI, Hwee YZ, Schuster SC, Schlarbaum SE, Carlson JE, Gailing O. 2017. Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.). BMC Research Notes, 10(1), p.369, 7 pages.

Ćalić I, Koch J, Carey D, Addo-Quaye C, Carlson JE, Neale DB, 2017. Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.). BMC Genomics, 18(1), p.547, 14 pages.

Wu Y, Zhang R, Staton M, Schlarbaum S, Coggeshall M, Romero-Severson J, Carlson J, Liang H, Xu Y, Drautz-Moses D, Schuster S, Gailing O. 2017. Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing. Annals of Forest Research, 60(2): 343-350.

Konar A, Choudury O, Bullis R, Fiedler L, Kruser J, Stephens M, Gailing O, Schlarbaum S, Coggeshall MV, Staton ME, Carlson JE, Emrich S, Romero-Severson J. 2017. High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra. BMC Genomics, 18(1):417, 12 pages.

Gailing O, Staton ME, Lane T, Schlarbaum SE, Nipper R, Owusu SA, Carlson JE. 2017. Construction of a Framework Genetic Linkage Map in Gleditsia triacanthos L. Plant Molecular Biology Reporter, Volume 35(2): 177-187.

2016

Lane T, Best T, Zembower N, Davitt J, Henry N, Xu Y, Koch J, Liang H, McGraw J, Schuster S, Shim D, Coggeshall M, Carlson JE, Staton ME. 2016. The green ash transcriptome and identification of genes responding to abiotic and biotic stresses. BMC Genomics 17:702, 16 pages.

Herr JR, Scully ED, Geib SM, Hoover K, Carlson JE, Geiser DM. 2016. Genome sequence of Fusarium isolate MYA-4552 from the midgut of Anoplophora glabripennis, an invasive, wood-boring beetle. Genome Announcements 4(4):e00544-16, 2 pages.

Carroll RA, Jones C, Best T, Shumaker K, Carlson J. 2016. Gene expression in hardwood trees species exposed to ozone. Journal of Undergraduate Research and Scholarly Excellence, Volume VII: 32-35.

Odom T, Williams KN, Best T, Zembower N, Shumaker K, Carlson J. 2016. An analysis of gene expression induced by elevated atmospheric ozone in hardwood trees native to Eastern North America. Journal of Undergraduate Research and Scholarly Excellence, Volume VII: 36-40.

Owusu S, Schlarbaum S, Carlson J, Gailing O. 2016. Pollen gene flow and molecular identification of full-sib families in small and isolated population fragments of Gleditsia triacanthos L. Botany, 94: 523-532.

2015

Staton ME, Best TO, Khodwekar SD, Owusu SA, Xu T, Yu Y, Jennings TN, Knaus BJ, Cronn RC, Arumuganathan AK, Coggeshall MV, Gailing O, Liang H, Romero-Severson J, Schlarbaum SE, Carlson JE. 2015. Preliminary genomic characterization of ten hardwood tree species from multiplexed low coverage whole genome sequencing. PLoS ONE 10(12): e0145031.

Staton M, Zhebentyayeva T, Olukolu B, Fang GC, Nelson D, Carlson JE, Abbott AG. 2015. Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics. 16:744, 14 pages.

Pang T, Guo L, Shim D, Cannon N, Tang S, Chen J, Carlson JE, Xia X, Yin W. 2015. Characterization of the transcriptome of the xerophyte Ammopiptanthus mongolicus under drought stress by 454 pyrosequencing. PLoS ONE 10(8): e0136495, 25 pages.

Chen C-C, Xu Y, Xu T, Staton M, Stott G, Bukles O, Schlarbaum SE, Carlson JE, Liang H. 2015. Diversity level of genomic microsatellites in redbay (Persea borbonia L.) generated by Illumina sequencing. Journal of Plant Science and Molecular Breeding. 4:2, 5 pages.

Khodwekar S, Staton M, Coggeshall MV, Carlson JE, Gailing O. 2015. Nuclear microsatellite markers for population genetic studies in sugar maple (Acer saccharum Marsh.). Ann. For. Res. 58(2): 1-12.

Zhang X, Carlson A, Tian Z, Staton M, Schlarbaum SE, Carlson JE, Liang H. 2015. Genetic characterization of Liriodendron seed orchards with EST-SSR markers. Journal of Plant Science and Molecular Breeding. 4:1, 9 pages.

Diningrat DS, Widiyanto SM, Pancoro A, Shim D, Panchangam B, Zembower N, Carlson, J.E., 2015. Identification of Terminal Flowering1 (TFL1) Genes Associated with the Teak (Tectona grandis) Floral Development Regulation Using RNA-seq. Research Journal of Botany, 10(1): 1-13.

Diningrat DS, Widiyanto SM, Pancoro A, Shim D, Panchangam B, Zembower N, Carlson, J.E., 2015. Transcriptome of Teak (Tectona grandis, Lf) in Vegetative to Generative Stages Development. Journal of Plant Sciences, 10(1): 1-14.

Chen CC, Bates R, Carlson J. 2015. Effect of environmental and cultural conditions in medium pH and plant growth performance of Douglas-fir (Pseudotsuga menziesii) shoot culture, F1000Research, 3:298, 14 pages.

2014 and earlier

Diningrat DS, Widiyanto SM, Pancoro1 A, Iriawati, Shim D, Panchangam B, Zembower N, Carlson JE. 2014. Transcriptomes of Teak (Tectona grandis, L.f) in Vegetative to Generative Transition Stage Development. International Journal of Innovation and Applied Studies, 9(3): 1416-1427.

Scully E, Geib SM, Carlson JE, Tien M, Hoover K. 2014. Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles. BMC Genomics, 15:1096, 21 pages.

Meinhardt LW, Thomazella DPT, Teixeira PJPL, Costa GGL, Carazzolle MF, Schuster SC, Carlson JE, Guiltinan MJ, Mieczkowski P, Farmer A, Ramaraj T, Crozier J, Davis RE, Shao J, Melnick RL, Pereira GAG, Bailey BA. 2014. Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: Mechanisms of the biotrophic and necrotrophic phases. BMC Genomics, 15(1): 164, 25 pp.

Sha T, Liang H, Yan D, Zhao Y, Han X, Carlson JE, Xia X, Yin W. 2013. Populus euphratica: the transcriptomic response to drought stress. Plant Molecular Biology 83(6): 539-557.

Owusu SA, Staton M, Jennings TN, Schlarbaum S, Coggeshall MV, Romero-Severson J, Carlson JE, Gailing O. 2013. Development of Genomic Microsatellites in Gleditsia triacanthos (Fabaceae) Using Illumina Sequencing. Applications in Plant Sciences, 1(12): 1300050, 4 pp.

Fang GC, Blackmon BP, Staton ME, Nelson CD, Kubisiak TL, Olukolu BA, Henry D, Zhebentyayeva Y, Saski CA, Cheng CH, Monsanto M, Ficklin S, Atkins M, Georgi LL, Barakat A, Wheeler N, Carlson JE, Sederoff R, Abbott AG. 2013. A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map. Tree Genetics & Genomes, 9(2): 525-537.

Petit RJ, Carlson J, Curtu AL, Loustau ML, Plomion C, González-Rodríguez A, Sork V, Ducousso A. 2013. Fagaceae trees as models to integrate ecology, evolution and genomics. New Phytologist, 197: 369 - 371.

Hsu C-Y, Adams JP, No K, Liang H, Meilan R, Pechanova O, Barakat A, Carlson JE, Page GP, Yuceer C. 2012. Overexpression of Constans Homologs CO1 and CO2 Fails to Alter Normal Reproductive Onset and Fall Bud Set in Woody Perennial Poplar. PLoS ONE 7(9): e45448, 14 pages.

Costa GGL, Cabrera OG, Tiburcio RA, Medrano FM, Carazzolle MF, Thomazella DPT, Schuster SC, Carlson JE, Guiltinan MJ, Bailey BA, Mieckowski P, Pereira CAG, Meinhardt LW. 2012. The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao. Fungal Biology, 116 (5): 551-562.

Kremer K, Abbott AG, Carlson JE, Manos PS, Plomion C, Sisco P, Staton ME, Ueno S, Vendramin GG. 2012. Genomics of Fagaceae (Review). Tree Genetics & Genomes, 8(3): 583-610.

Frost CJ, Dean JM, Smyers EC, Mescher MC, Carlson JE, De Moraes CM, Tooker JF. 2012. A petiole-galling insect herbivore decelerates leaf lamina litter decomposition rates. Functional Ecology 26: 628-636.

Barakat A, Staton M, Cheng C-H, Park J, Buang N, Yassin M, Ficklin S, Yeh C-C, Hebard F, Baier K, Powell W, Schuster S, Wheeler N, Abbott A, Carlson J, Sederoff R. 2012. Chestnut resistance to the blight disease: insights from transcriptome analysis. BMC Plant Biology, 12:38, 14 pages.

Barakat A, Yassin NBM, Park J, Choi A, Herr J, Carlson JE. 2011. Comparative and phylogenomic analyses of cinnamoyl-CoA reductase and cinnamoyl-CoA-reductase-like gene family in land plants. Plant Science 181: 249-257.

Hsu C-Y, Adams JP, Kim H, No K, Ma C, Strauss SH, Drnevich J, Vandervelde L, Ellis JD, Rice BM, Wickett N, Gunter LE, Tuskan GA, Brunner AM, Page GP, Barakat A, Carlson JE, dePamphilis CW, Luthe DS, Yuceer C. 2011. FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar, PNAS 108(26): 10756-10761.

Bagniewska-Zadworna A, Zenkteler M, Zenkteler E, Wojciechowicz MK, Barakat A, Carlson JE. 2011. A successful application of the embryo rescue technique as a model for studying crosses between Salix viminalis and Populus species. Australian Journal of Botany 59: 382-392.

Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Rounsley S, Kudrna D, Paterson AH, Pires JC, Soltis DE, Chamala S, Barbazuk B, Soltis PS, Albert VA, Ma H, Mandoli D, Banks J, Carlson J, Tomkins J, dePamphilis C, Wing RA, Leebens-Mack J. 2011. A Physical Map for the Amborella Genome Sheds Light on the Evolution of Angiosperm Genome Structure. Genome Biology, 12:R48, 14 pages.

Barakat A, Choi A, Yassin NBM, Sun Z, Carlson JE. 2011. Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus. Gene 479 (1-2): 37-46.

Liang H, Barakat A, Schlarbaum SE, Carlson JE. 2011. Organization of the chromosome region harboring a FLORICAULA/LEAFY gene in Liriodendron. Tree Genetics & Genomes 7(2): 373-384.

Barakat A, Bagniewska-Zadworna A, Frost CJ, Carlson JE. 2010. Phylogeny and expression profiling of CAD and CAD-like genes in hybrid Populus (P. deltoides x P. nigra): evidence from herbivore damage for subfunctionalization and functional divergence. BMC Plant Biology 10:100, 11 pages.

Liang H, Barakat A, Schlarbaum SE, Mandoli DF, Carlson J. 2010. Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots and eudicots. GENOME 53: 533 - 544.

Wall PK, LeebensMack J, Chanderbali A, Barakat A, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster S, Soltis DE, Soltis PS, Altman N, dePamphilis CW. 2009. Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics, 10:347. 19 pages.

Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell W, Wheeler N, Sederoff R, Carlson JE. 2009. Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biology, 9:51, 11 pages.

Barakat A, Bagniewska-Zadworna A, Plakkat U, Choi A, DiLoreto DS, Carlson JE. 2009. The cinnamyl alcohol dehydro-genase gene family in Populus: phylogeny, organization, and expression. BMC Plant Biology, 9:26. 15 pages.

Morse AM, Peterson DG, M. Islam-Faridi, Smith KE, Garcia SA, Kubisiak TL, Amerson HV, Carlson JE, Nelson CD, Davis JM, 2009. Evolution of Genome Size and Complexity in Pinus. PLoS ONE 4(2): e4332. 11 pages.

Swanson J-D, Carlson JE, Guiltinan MJ. 2008. Flower development and floral gene expression in Theobroma cacao. International Journal of Plant Sciences, 169(9):1187-1199.

Frost CJ, Mescher MC, Dervinis C, Davis JM, Carlson JE, De Moraes CM. 2008. Priming defense genes and metabolites in hybrid poplar by the green leaf volatile cis-3-hexenyl acetate. New Phytologist, 180(3): 722-734.

Liang H, Frost CJ, Wei X, Brown NR, Carlson JE, Tien M. 2008. A novel approach toward lignin modification to facilitate cellulosic ethanol production: introducing a tyrosine-rich cell wall peptide gene in poplar. Clean 36(8): 662-668.

Liang H, Carlson JE, Leebens-Mack JH, Wall PK, Mueller LA, BuzgoM, Landherr LL, Hu Y, DiLoreto DS, Ilut DC, Field D, Tanksley SD, Ma H, dePamphilis CW. 2008. An EST Database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genetics & Genomes 4(3): 419-433.

Soltis DE, Albert VA, Leebens-Mack J, Palmer J, Wing R, dePamphilis C, Ma H, Carlson JE, Altman N, Kim S, Wall PK, Zuccolo A, Soltis P. 2008. The Amborella Genome: An Evolutionary Reference for Plant Biology. Genome Biology 9:402, 6 pages.

Barakat A, Wall PK, DiLoreto S, dePamphilis CW, Carlson JE. 2007. Conservation and divergence of microRNAs in Populus. BMC Genomics 8:481, 16 pages.

Barakat A, Wall K, Leebens-Mack J, Wang YJ, Carlson JE, dePamphilis CW. 2007. Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. The Plant Journal 51(6):991-1003.

Liang H, Fang EG, Tomkins JP, Luo M, Kudrna D, Arumuganathan K, Zhao S, Schlarbaum SE, Banks JA, dePamphilis CW, Mandoli DF, Wing RA, Carlson JE. 2007. Development of a BAC library resource for yellow poplar (Liriodendron tulipifera) and the identification of genomic regions associated with flower development and lignin biosynthesis. Tree Genetics & Genomes 3(3): 215 - 225.

Tuskan GA, et al. 2006. The Genome of Western Black Cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313: 1596-1604.

Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis D, Doyle JJ, Soltis P, Carlson JE, Arumuganathan K, Barakat A, Albert V, Ma H, dePamphilis CW. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Research 16: 738 - 749.

St. Clair S, Carlson JE, Lynch J. 2005. Evidence for Oxidative Stress in Sugar Maple Stands Growing on Acidic, Nutrient Imbalanced Forest Soils. Oecologia 145: 258 - 269.

Traore A, Xing Z, Bonser A, Carlson JE. 2005. Optimization of a Protocol for Sterilization and In Vitro Establishment of Vegetative Buds from Mature Douglas-Fir Trees. Hortscience 40: 1464 - 1468.

Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo M-J, Frohlich MW, Perl-Treves R, Schlarbaum S, Bliss B, Tanksley S, Oppenheimer DG, Soltis PS, Ma H, dePamphilis CW, Leebens-Mack JH. 2005. Floral Gene Resources from Basal Angiosperms for Comparative Genomics Research. BMC Plant Biology 5:5, 15 pp.