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 (doi.org/10.1093/treephys/tpy026).

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 (doi.org/10.1111/nph.14968).

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

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 (doi.org/10.1093/bioinformatics/btx839).

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 (doi.org/10.1111/pce.13134).

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

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 (doi.10.1093/treephys/tpx125).


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 (17p.) (doi.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 (doi.org/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.) (doi.org/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 (doi.org/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.) (doi.org/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 (doi.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.) (doi.org/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 (doi.org/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 (doi.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(9): e0163059 (13p.) (doi.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 (doi.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 (doi.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 (doi.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 (doi.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 (doi.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 (doi.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 (doi.10.1111/pce.12810).