Wong C., D’Odorico P., Bhathena Y., Arain A., Ensminger I. (2019). Carotenoid based vegetation indices for accurate monitoring of the phenology of photosynthesis at the leaf-scale in deciduous and evergreen trees. Remote Sensing of Environment, 233: 111407 (10.1016/j.rse.2019.111407).

Van Ghelder, C., Parent G.J., Rigault P., Prunier J., Giguère I., Caron S., Stival Sena J., Deslauriers A., Bousquet J., Esmenjaud D., Mackay J. (2019). The large repertoire of conifer NLR conifer resistance genes includes drought responsive and highly diversified RNLs. Scientific Reports, 9: 11614 (10.1038/s41598-019-47950-7).

Coursolle, C., Otis-Prud’homme, G., Lamothe, M., Isabel. 2019. Measuring Rapid A–Ci Curves in Boreal Conifers: Black Spruce and Balsam Fir. Frontiers in Plant Science, 10: 1276 (10.3389/fpls.2019.01276).

Hassegawa M., Savard M., Lenz P.R.N., Duchateau E., Gelinas N., Bousquet J., Achim A. 2019. White spruce wood quality for lumber products: priority traits and their enhancement through tree improvement. Forestry, An International Journal of Forest Research, 2019;00: 1–22 (10.1093/forestry/cpz050).

Lochhead K., Ghafghazi S., LeMay V., Bull G.Q. 2019. Examining the vulnerability of localized reforestation strategies to climate change at a macroscale. Journal of Environmental Management, 252: 109625 (10.1016/j.jenvman.2019.109625).

Jackman S.D., Mozgacheva T., Chen S., O’Huiginn B., Bailey L., Birol I., Jones S.J.M. 2019. ORCA: A Comprehensive Bioinformatics Container Environment for Education and Research. Bioinformatics (10.1093/bioinformatics/btz278).

Celedon, J., and Bohlmann, J. 2019. Oleoresin defenses in conifers: chemical diversity, terpene synthases, and limitations of oleoresin defense under climate change. New Phytologist (10.1111/nph.15984).

Jackman, S.D., Coombe, L., Warren, R.L., Kirk, H., Trinh, E., McLeod, T., Pleasance, S., Pandoh, P., Zhao, Y., Coope, R.J., Bousquet, J., and Bohlmann, J. 2019. Largest complete mitochondrial genome of a gymnosperm, Sitka spruce (Picea sitchensis), indicates complex physical structure. bioRxiv (10.1101/601104).

Lenz, P., Nadeau, S., Mottet, M.-J., Perron, M., Isabel, I., Beaulieu, J., and Bousquet, J. 2019. Multi-trait genomic selection for weevil resistance, growth and wood quality traits in Norway spruce. Evolutionary Applications (10.1111/eva.12823).

Lin, D., Coombe, L., Jackman, S., Gagalova, K., Warren, R., Hammond, S., McDonald, H., Kirk, H., Pandoh, P., Zhao, Y., Moore, R., Mungall, A., Ritland, C., Doerksen, T., Jaquish, B., Bousquet, J., Jones, S., Bohlmann, J., and Birol, I. 2019. Complete chloroplast genome sequence of an Engelmann spruce (Picea engelmannii) genotype from western Canada. Microbiology Resource Announcements, 8(24): e00382-19 (10.1128/MRA.00382-19).

Lin, D., Coombe, L., Jackman, S., Gagalova, K., Warren, R., Hammond, S., Kirk, H., Pandoh, P., Zhao. Y., Moore, R., Mungall, A., Ritland, C., Doerksen, T., Jaquish, B., Isabel, N., Bousquet, J., Jones, S., Bohlmann, J., and Birol, I. 2019. Complete chloroplast genome sequence of a white spruce (Picea glauca) genotype from eastern Canada. Microbiology Resource Announcements, 8(23): e00381-19 (10.1128/MRA.00381-19).

Parent, G., Méndez-Espinoza, C., Giguère, I., Mageroy, M., Charest, M., Bauce, E., Bohlmann, J., and Mackay, J. 2019. Hydroxyacetophenone defenses in white spruce against spruce budworm. Evolutionary Applications (accepted).

Warren, R.L., Coombe, L., Mohamadi, H., Zhang, J., Jaquish, B., Isabel, N., Jones, S.J.M., Bousquet, J., Bohlmann, J., and Birol, I. 2019. ntEdit: scalable genome sequence polishing. Bioinformatics, 35(21): 4430-4432 (10.1093/bioinformatics/btz400).

Whitehill, J.G.A., and Bohlmann, J. 2019. A molecular and genomic reference system for conifer defense against insects. Plant, Cell, & Environment (10.1111/pce.13571).

Whitehill, J.G.A., Yuen, M.M.S., Henderson, H., Madilao, L., Kshatriya, K., Bryan, J., Jaquish, B., and Bohlmann, J. 2019. Functions of stone cells and oleoresin terpenes in the conifer defense syndrome. New Phytologist, 221: 1503-1517 (10.1111/nph.15477).


Azaiez, A., Pavy, N., Gérardi, S., Laroche, J., Boyle, B., Gagnon, F., Mottet, M.-J., Beaulieu, J. and Bousquet, J. 2018. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics, 19: 942 (13p.) (10.1186/s12864-018-5247-z).

Celedon, J.M. and Bohlmann, J. 2018. An extended model of heartwood secondary metabolism informed by functional genomics. Tree Physiology, 38: 311-319 (10.1093/treephys/tpx070).

Coombe, L., Zhang, J., Vandervalk, B.P., Chu, J., Jackman, S.D., Birol, I., and Warren, R.L. 2018. ARKS: chromosome-scale scaffolding of human genome drafts with linked reads. BMC Bioinformatics, 19: 234 (10p.) (10.1186/s12859-018-2243-x).

Housset, J.M., Nadeau, S., Isabel, N., Depardieu, C., Duchesne, I., Lenz, P., and Girardin, M.P. 2018. Tree rings provide a new class of phenotypes for genetic associations that foster insights into adaptation of conifers to climate change. New Phytologist, 2: 630-645 (10.1111/nph.14968).

Jackman, S.D., Coombe, L., Chu, J., Warren, R.L., Vandervalk, B.P., Yeo, S., Xue, Z., Mohamadi, H., Bohlmann, J., Jones, S.J.M., and Birol, I. 2018. Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinformatics, 19: 393 (10.1186/s12859-018-2425-6).

Khan, H., Mohamadi, H., Vandervalk, B.P., Warren, R.L., Chu, J., and Birol, I. 2018. ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. Bioinformatics, 34: 1697-1704 (10.1093/bioinformatics/btx839).

Lamara, M.,Parent, G.J.,Giguère, I., Beaulieu, J., Bousquet, J., and MacKay, J. 2018. Association genetics of acetophenone defence against spruce budworm in mature white spruce. BMC Plant Biology, 18: 231 (15p.) (10.1186/s12870-018-1434-y).

Lochhead, K., LeMay, V., Bull, G., Schwab, O., and Halperin, J. 2018. Multivariate estimation for accurate and logically-consistent forest attributes maps at macroscales. Canadian Journal of Forest Research, 48: 345–359 (10.1139/cjfr-2017-0221).

Méndez-Espinoza, C., Parent, G.J., Lenz, P., Rainville, A., Tremblay, L., Adams, G., McCartney, A., Bauce, E., and MacKay, J. 2018. Genetic control and evolutionary potential of a constitutive resistance mechanism against the spruce budworm (Choristoneura fumiferana) in white spruce (Picea glauca). Heredity, 121: 142–154 (10.1038/s41437-018-0061-6).

Parent, G.J., Giguère, I., Mageroy, M., Bohlmann, J., and MacKay, J.J. 2018. Evolution of the biosynthesis of two hydroxyacetophenones in plants. Plant, Cell & Environment, 41: 620-629 (10.1111/pce.13134).

Stival Senna, J., Giguère, I., Rigault, P., Bousquet, J. and Mackay, J.J. 2018. Expansion of the dehydrin gene family in conifers is associated with considerable structural diversity and drought-responsive expression. Tree Physiology, 38: 442-456 (10.1093/treephys/tpx125).

Tsai, C.J., Harding, S., and Cooke, J. 2018. Branching out: a new era of investigating physiological processes in forest trees using genomic tools. Tree Physiology, 38: 303–310 (10.1093/treephys/tpy026).

Yeo, S., Coombe, L., Warren, R.L., Chu, J., and Birol, I. 2018. ARCS: scaffolding genome drafts with linked reads. Bioinformatics, 34: 725-731 (10.1093/bioinformatics/btx675).


Celedon, J.M., Yuen, M.M.S., Chiang, A., Henderson, H., Reid, K.E. and Bohlmann, J. 2017. Cell-type and tissue specific transcriptomes of the white spruce (Picea glauca) bark unmask fine-scale spatial patterns of constitutive and induced conifer defense. The Plant Journal, 92: 710-726 (10.1111/tpj.13673).

Ghafghazi, S., Lochhead, K., Mathey, A., Forsell, N., Leduc, S., Mabee, W. and Bull, G.Q. 2017. Estimating mill residue surplus in Canada: A spatial forest fibre cascade modelling approach. Forest Products Journal, 67: 205-218 (10.13073/FPJ-D-16-00031).

Godbout, J., Tremblay, L.,  Levasseur, C., Lavigne, P., Rainville, A., MacKay, J., Bousquet, J. and Isabel, N. 2017. Development of a traceability system based on a SNP array for large-scale production of high-value white spruce (Picea glauca). Frontiers in Plant Science, 8: 1264 (13p.) (10.3389/fpls.2017.01264).

Kucuk, E., Chu, J., Vandervalk, B.P., Hammon, A., Warren, R.L. and Birol, I. 2017. Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinformatics, 33: 1782-1788 (10.1093/bioinformatics/btx405).

Lenz, P., Beaulieu, J., Clement, S., Mansfield, S., Desponts, M. and Bousquet, J. 2017. Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana). BMC Genomics, 18: 335 (17p.) (10.1186/s12864-017-3715-5).

Mageroy, M.H., Jancsik, S., Yuen, M.M.S., Fischer, M., Withers, S.G., Paetz, C., Schneider, B. and Bohlmann, J. 2017. A conifer UDP-sugar dependent glycosyltransferase contributes to acetophenone metabolism and defense against insects. Plant Physiology, 175: 641-651 (10.1104/pp.17.00611).

Mageroy, M.H, Lachance, D., Jancsik, S., Parent, G., Séguin, A., MacKay, J. and Bohlmann, J. 2017. In vivo function of Pgßglu-1 in the release of acetophenones in white spruce. PeerJ, 5: e3535 (11p.) (10.7717/peerj.3535).

Pavy, N., Lamothe, M., Pelgas, B., Gagnon, F., Birol, I., Bohlmann, J., Mackay, J., Isabel, N. and Bousquet, J. 2017. A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. The Plant Journal, 90: 189-203 (10.1111/tpj.13478).

Prunier, J., Caron, S., Lamothe, M., Blais, S., Bousquet, J., Isabel, N. and  Mackay, J. 2017. Gene copy number variations and adaptive evolution: the genomic architecture of gene CNVs revealed by genetic mapping and their adaptive role in a non domesticated species, white spruce. Molecular Ecology, 26: 5989-6001 (10.1111/mec.14337).

Rossi, S. and Isabel, N. 2017. The timing of bud break in warming conditions: variation among seven sympatric conifers. International Journal of Biometeorology, 61: 1983-1991 (doi.10.1007/s00484-017-1391-4).


Coombe, L., Warren, R.L., Yang, C., Vandervalk, B.P., Mayo, M., Moore, R.A., Pleasance, S., Coope, R.J., Bohlmann, J., Holt, R.A., Jones, S.J.M. and Birol, I. 2016. Assembly of the complete Sitka spruce chloroplast genome using 10X Genomics’ GemCode sequencing data. PLoS ONE, 11: 1-13 (10.1371/journal.pone.0163059).

Geisler, K., Jensen, N.B., Yuen, M.M.S., Madilao, L. and Bohlmann, J. 2016. Modularity of conifer diterpene resin acid biosynthesis: P450 enzymes of different CYP720B clades use alternative substrates and converge on the same products. Plant Physiology, 171: 152-164 (10.1104/pp.16.00180).

Jackman, S.D., Warren, R.L., Gibb, E.A., Vandervalk, B.P., Mohamadi, H., Chu, J., Raymond, A., Pleasance, S., Coope, R., Wildung, M.R., Ritland, C.E., Bousquet, J., Jones, S.J., Bohlmann, J. and Birol, I. 2016. Organellar genomes of white spruce (Picea glauca): Assembly and annotation. Genome Biology and Evolution, 8: 29-41 (10.1093/gbe/evv244).

Lamara, M., Raherison, E., Lenz, P., Beaulieu, J., Bousquet, J. and Mackay, J. 2016. Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce. New Phytologist, 210: 240-255 (10.1111/nph.13762).

Lochhead, K., Ghafghazi, S., Havlik, P., Forsell, N., Obersteiner, M., Bull, G. and Mabee, W. 2016. Price trends and volatility scenarios for designing forest sector transformation. Energy Economics, 57: 184-191 (ENEECO-D-13-00353R1).

Park, Y.-S., Beaulieu, J. and Bousquet, J. 2016. Multi-varietal forestry integrating genomic selection and somatic embryogenesis. In Park, Y.-S., Bonga, J. & Moon, H.-K. (eds). Vegetative Propagation of Forest Trees. National Institute of Forest Science, Seoul, South Korea. Pp. 302-322.

Pavy, N., Gagnon, F., Deschênes, A., Boyle, B., Beaulieu, J. and Bousquet, J. 2016. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from boreal black spruce (Picea mariana). Molecular Ecology Resources, 16: 588-598 (0.1111/1755-0998.12468).

Whitehill, J.G.A., Henderson, H., Schuetz, M., Skyba, O., Yuen, M.M.S., King, J., Samuels, A.L., Mansfield, S.D. and Bohlmann, J. 2016. Histology and cell wall biochemistry of stone cells in the physical defense of conifers against insects. Plant, Cell & Environment, 39: 1646-1661 (10.1111/pce.12654).

Whitehill, J.G.A., Henderson, H., Strong, W., Jaquish, B. and Bohlmann, J. 2016. Functions of Sitka spruce stone cells as a physical defense against white pine weevil. Plant, Cell & Environment, 39: 2545-2556 (10.1111/pce.12810).