Islam-Faridi N, Yu J, Huff M, Mandal M, Lasky JR, Noorai RE, Lasky JR, Saski C, Ficklin S, Drautz-Moses DI, Fitzsimmons S, Fan S, Conrad A, Schuster SC, Abbott AG, Westbrook J, Holliday JA, Nelson CD, Georgi L, Hebard FV (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 (In Press).

Islam-Holmes HR, Haywood M, Hutchison R, Zhang Q, Edsall C, Hall TL, Baisch D, Holliday JA, Vlaisavljevich E (2020) Focused Ultrasound Extraction (FUSE) for the Rapid Extraction of DNA from Tissue Matrices. Methods in Ecology and Evolution
(In press).

Islam-Isabel N, Holliday JA, Aitken SN (2020) Forest genomics: Advancing climate adaptation, forest health,
productivity, and conservation. Evolutionary Applications 13(1): 3-10.

Guerra, F.P., Suren, H., Holliday, JA. et al. (2019) Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa. BMC Genomics 20, 875

Westbrook JW, Zhang Q, Mandal MK, Jenkins EV, Barth LE, Jenkins JW, Grimwood J, Schmutz J, Holliday JA (2019) Optimizing genomic selection for blight resistance in American chestnut backcross populations: A trade‐off with American chestnut ancestry implies resistance is polygenic. Evolutionary Applications 13(1).

Zhang M, Suren H, Holliday JA (2019) Phenotypic and genomic local adaptation across latitude and altitude in Populus trichocarpa. Genome Biology and Evolution 11(8): 2256-72.

Westbrook JW, Holliday JA, Newhouse A, Powell WA (2019) A plan to diversify transgenic blight-tolerant American chestnut population. Plants Planet People DOI: 10.1002/ppp3.10061

Acosta JJ, Fahrenkrog AM, Neves LG, Resende MFR, Dervinis C, Davis JM, Holliday JA, Kirst M (2019) Exome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the Conifers Pinus taeda and Pinus elliottii. Genome Biology and Evolution 11(2): 508-520.

Holliday JA, Hallerman EM, Haak D. (2018) Genotyping and sequencing technologies in population genetics and genomics. In Population Genomics Concepts, Strategies, and Approaches. Rajora O, ed. Springer.

Holliday JA, Aitken SN, Cook JEK, Fady B, Gonzalez-Martinez SC, Heuertz M, Jaramillo-Correa JP, Lexer C, Staton M, Whetten RW, Plomion C (2017) Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. Molecular Ecology 26(3): 706-17.

Yeaman S, Hodgins KA, Lotterhos KE, Suren H, Nadeau S, Degner JC, Nurkowski KA, Smets P, Wang T, Gray LK, Liepe KJ, Hamann A, Holliday JA, Whitlock MC, Rieseberg LH, Aitken SN (2016) Convergent local adaptation to climate in distantly related conifers. Science 353(6306): 1431-33.

Suren H, Hodgins KA, Yeaman S, Nurkowski KA, Smets P, Rieseberg LH, Aitken SN, Holliday JA (2016) Exome capture from the spruce and pine giga-genomes. Molecular Ecology Resources 16(5): 1136-46.

Zhang M, Zhou L, Bawa R, Suren H, Holliday JA (2016) Recombination rate variation, hitchhiking, and demographic history shape deleterious load in poplar. Molecular Biology and Evolution 33(11): 2899-2910.

Holliday JA, Zhou L, Bawa R, Zhang M, Oubida RW (2016) Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients in Populus trichocarpa. New Phytologist 209(3): 1240-51.

Bawa R, Holliday JA. (2016) Genomics of speciation in angiosperm trees. In Genomics of Angiosperm Trees. Cronk Q and Groover A, eds. Springer.

Oubida RW, Gantulga D, Zhang M, Bawa R, Holliday JA (2015) Partitioning of multivariate phenotypes using regression trees reveals complex patterns of adaptation to climate across the range of black cottonwood (Populus trichocarpa). Frontiers in Plant Science 6:181.

Zhou L, Bawa R, Holliday JA (2014) Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa). Molecular Ecology 23(10): 2486-99.

Yeaman S, Hodgins KA, Suren H, Nurkowski KA, Rieseberg LH, Holliday, JA, Aitken SN (2014) Conservation and divergence of gene expression plasticity following ~140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (natural hybrid populations of Picea glauca and Picea engelmannii). New Phytologist. 203(2): 578-91.

Constanza Manrique-Carpintero N, Tokuhisa JG, Ginzberg I, Holliday JA, Veilleux RE (2013). Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species. G3: Genes, Genomes, Genetics. 3(9): 1467-79

Collakova E, Klumas C, Suren H, Myers E, Heath LS, Holliday JA, Grene R (2013) Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce. BMC Plant Biology. 13:72.

Zhou L, Holliday JA (2012) Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture. BMC Genomics 13:703.

Grene R, Klumas C, Suren H, Yang K, Collakova E, Myers E, Heath LS, Holliday JA (2012) Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). Frontiers in Plant Science. 3:241.

Reid KE, Holliday JA, Yuen, M, Aitken SN, Bohlmann J (2012) Sequencing of Sitka spruce (Picea sitchensis) cDNA libraries constructed from autumn buds and foliage reveals autumn-specific spruce transcripts. Tree Genetics & Genomes. 9(3): 683-91.

Holliday JA, Wang TL, Aitken SN (2012) Predicting adaptive phenotypes from multilocus genotypes in Sitka spruce (Picea sitchensis) using Random Forest. G3: Genes, Genomes, Genetics. 2(9): 1085-1093.

Holliday JA, Suren H, Aitken SN (2012) Divergent selection and heterogeneous migration rates across the range of Sitka spruce (Picea sitchensis). Proceedings of the Royal Society B: Biological Sciences. 279 (1734): 1675-83.

Dauwe R, Holliday JA, Aitken SN, Mansfield S. Metabolic dynamics during autumn cold acclimation within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis) (2012) New Phytologist. 194(1): 192-205.

Holliday JA, Ritland K, Aitken SN (2010) Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis). New Phytologist 188(2): 501-514.

Holliday JA, Yuen M, Ritland K, Aitken SN (2010) Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests. Molecular Ecology 19(18): 3857-64.

Holliday JA. (2009) Genomics of cold hardiness in forest trees. In Plant Cold Hardiness: From the Laboratory to the Field. Tanino, K. and Gusta L., eds. CABI. Oxfordshire.

Holliday JA, Ralph SG, White R, Bohlmann J, Aitken SN. (2008) Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis). New Phytologist 178(1): 103-22.

Aitken SN, Yeaman S, Holliday JA, Wang T, Curtis-McLane S. (2008) Adaptation, migration or extirpation: Climate change outcomes for tree populations. Evolutionary Applications 1(1): 95-111.





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