Publications

2024

Depardieu, C., Lenz P., Marion, J., Nadeau S., Bégin C., Marchand W., Girardin M.P., Gessler A., Treydte K., Bousquet J., Savard M.M. & Isabel N. 2024. Contrasting physiological strategies explain heterogeneous responses to severe drought conditions within local populations of a widespread conifer. Science of the Total Environment. Sous presse.

Hung, T.-H., Wu, E.T.Y., Zeltins, P., Jansons, A., Ullah, A., Erbilgin, N., Bohlmann, J., Bousquet, J., Birol, I., Clegg, S. & Mackay, JJ. 2024. Long-insert sequence capture detects high copy numbers in the defence beta-glucosidase gene βglu-1 with large variations in Picea glauca but not Picea abies. BMC Genomics, 25: 118 (16p.).

Lo, T., Coombe L., Gagalova, K., Marr, A., Warren, R.L., Kirk, H., Pandoh, P., Zhao, Y., Moore, R.A., Mungall, A.J., Ritland, C., Pavy, N., Jones, S.M.J., Bohlmann, J., Bousquet, J., Birol, I. & Thomson, A. 2024. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.  G3 – Genes Genomes Genetics, 14: jkad247 (16p.) (10.1093/g3journal/jkad247)

Tumas, H., Ilska, J.J., Gérardi, S., Laroche, J., A’Hara, S., Boyle, B., Janes, M., McLean, P., Lopez, G., Lee, S.J., Cottrell, J., Gorjanc, G., Bousquet, J., Woolliams, J.A. & MacKay, J.J. 2024. High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers. G3 – Genes Genomes Genetics. Sous presse.

2023

Nadeau, S., Beaulieu J., Gezan, S.A., Perron, M., Bousquet, J. & Lenz, P.R.N. 2023. Increasing genomic prediction accuracy for unphenotyped full-sib families by modeling additive and dominance effects
with large datasets in white spruce. Frontiers in Plant Science, 14: 1137834 (24p.) (10.3389/fpls.2023.1137834).

Soro, A., Lenz, P., Roussel, J.-R., Larochelle, F., Bousquet, J. & Achim, A. 2023. The phenotypic and genetic effects of drought-induced stress on apical growth, ring width, wood density and biomass in white spruce seedlings. New Forests, 54: 789-811 (10.1007/s11056-022-09939-5). 

Soro, A., Lenz, P., Roussel, J.-R., Pothier, D., Bousquet, J. & Achim, A. 2023. The phenotypic and genetic effects of drought-induced stress on wood specific conductivity and anatomical properties in white spruce seedlings, and relationships with growth and wood density. Frontiers in Plant Science, 14: 1297314 (17p.) (10.3389/fpls.2023.1297314).

2022

Afshinfard, A., Jackman, S.D., Wong, J., Coombe, L., Chu, J., Nikolic, V., Dilek, G., Malkoç, Y., Warren, R.L. & Birol, I. 2022. Physlr: Next-Generation Physical Maps. DNA, 2: 116-130 (10.3390/dna2020009).

Beaulieu, J., Lenz, P. & Bousquet, J. 2022. Metadata analysis indicates biased estimation of genetic parameters and gains using pedigree information instead of genomic-based approaches in tree breeding. Scientific Reports, 12: 3933 (10p.) (10.1038/s41598-022-06681-y).

Benomar, L., Bousquet, J., Perron, M., Beaulieu, J. & Lamara, M. 2022. Tree maladaptation under mid-latitude early spring warming and late cold spells: implications for assisted migration. Frontiers in Plant Science, 13: 920852 (12p.) (10.3389/fpls.202).

Gagalova, K.K., Warren, R.L., Coombe, L., Wong, J., Nip, K.M., Yuen, M.M.S., Whitehill, J.G.A., Celedon, J.M., Ritland, C., Taylor, G.A., Cheng, D., Plettner, P., Hammond, S.A., Mohamadi, H., Zhao, Y., Moore, R.A., Mungall, A.J., Boyle, B., Laroche, J., Cottrell, J., Mackay, J.J., Lamothe, M., Gérardi, S., Isabel, N., Pavy, N., Jones, S.J.M., Bohlmann, J., Bousquet, J. & Birol, I. 2022. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. The Plant Journal, 111: 1469-1485 (10.111/tpj.15889).

Gagalova, K.K., Whitehill, J.G.A., Culibrk, L., Lin, D., Lévesque-Tremblay, V., Keeling, C.I., Coombe, L., Yuen, M.M.S., Birol, I., Bohlmann, J. , Jones, S.J.M. 2022. The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont. G3 Genes Genomes Genetics, 12:jkac038 (10.1093/g3journal/jkac038 ).

Harikumar, A., D’Odorico, P., & Ensminger, I. 2022. Combining spectral, spatial-contextual, and structural information in multispectral UAV data for spruce crown delineation. Remote Sensing, 14: 244-263 (10.3390/rs14092044).

Laverdière, J.P., Lenz, P., Nadeau, S., Depardieu, C., Isabel, N., Perron, M., Beaulieu, J. & Bousquet, J. 2022. Breeding for adaptation to climate change: genomic selection for drought response in a white spruce multi-site polycross test. Evolutionary Applications, 15: 383-402
(10.1111/eva.13348).

Rashidi-Jouybari, I., Lenz, P., Beaulieu, J., Nadeau, S., Bousquet, J. & Achim, A. 2022. Muli-trait selection for improved solid wood physical and flexural properties in white spruce (Picea glauca). Forestry, 95: 492-503 (h10.1093/forestry/cpac006).

Soro, A., Lenz, P., Hassegawa, M., Roussel, J.-R., Bousquet, J. & Achim, A. 2022. Genetic influence on components of wood density in white spruce. Forestry, 75: 153-165 (10.1093/forestry/cpab044).

Wong, C.Y.S., Mercado, L.M., Arain, M.A. & Ensminger, I. 2022. Remotely sensed carotenoid dynamics improve modelling photosynthetic phenology in conifer and deciduous forests. Agriculture and Forest Meteorology, 321: 108977 (10.1016/j.agrformet.2022.108977 ).

2021

Bousquet, J., Gérardi, S., de Lafontaine, G., Jaramillo-Correa, J.P., Pavy, N., Prunier, J., Lenz, P. & Beaulieu, J. 2021. Spruce population genomics. In Population Genomics: Forest Trees. Ed. O.P. Rajora. Springer, 64p.  (link.springer.com/chapter/10.1007/13836_2021_96#citeas).

Coombe, L., Li, J.X., Lo, T., Wong, J., Nikolic, V., Warren, R.L. & Birol, I. 2021. LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinformatics, 22: 534 (10.1186/s12859-021-04451-7).

Depardieu, C., Gérardi, S., Nadeau, S., Parent, G., Mackay, J., Lenz, P., Bousquet, J. & Isabel, N. 2021. Connecting tree-ring phenotypes, association genomics, and transcriptomics to decipher the genomic architecture of drought tolerance in a widespread conifer. Molecular Ecology, 30: 3898-3917 (10.1111/mec.15846). Cet article a été désigné pour la page de couverture du numéro du mois d’août 2021 du journal et à fait l’objet d’un article de perspective publié au pages 3893-3895 de ce même numéro.

Depardieu, C., M. Girardin, S. Nadeau, S. Gérardi, P. Lenz, M. Lamothe, J. Bousquet & N. Isabel. 2021. L’amélioration de la résilience des forêts face aux épisodes climatiques extrêmes: savoir lire entre les cernes. Climatoscope 3 (Octobre): 64-69 (https://climatoscope.ca/wp-content/uploads/2021/10/Le_Climatoscope_Num3_2021_Depardieu.pdf)

D’Odorico,, P., Schönbeck, L., Vitali, V., Meusburger, K., Schaub, M., Ginzler, C., Zweifel, R., Marjorie, V., Velasco, E., Gisler, J., Gessier, A. & Ensminger, I. 2021. Drone‐based physiological index reveals long‐term acclimation and drought stress responses in trees. Plant, Cell & Environment, 44: 3552-3570 (10.1111/pce.14177).

Galeano, E., Bousquet, J. & Thomas, B.R. 2021. SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program. Scientific Reports, 11: 4990 (14p.) (10.1038/s41598-021-84566-2).

Girardin, M.P., Isabel, N., Guo, X.J., Lamothe, M., Duchesne, I. & Lenz, P. 2021. Annual aboveground carbon uptake enhancements from assisted gene flow in boreal black spruce forests are not long-lasting. Nature Communications, 12: 1169 (15p.) (10.1038/s41467-021-21222-3).

Harikumar, A., Suyi, W. & Ensminger, I. 2021. A band grouping based approach for phenotype-class mapping of tree genotypes using spectro-temporal information in hyperspectral time-series UAV data. IEEE International Geoscience and Remote Sensing Symposium IGARSS, (10.1109/IGARSS47720.2021.9555063).

Laoué, J., Depardieu, C., Gérardi, S., Lamothe, M., Bomal, C., Azaiez, A., Gros-Louis, M.C., Laroche, J., Boyle, B., Hammerbacher, A., Isabel N. & Bousquet, J. 2021. Combining QTL mapping and transcriptomics to decipher the genetic architecture of phenolic compounds metabolism in the conifer white spruce. Frontiers in Plant Science, 112: 793 (20p.) (10.3389/fpls.2021.675108).

Royer-Tardif, S., Boisvert-Marsh, L., Godbout, J., Isabel, N. & Aubin. I. 2021. Finding common ground: Toward comparable indicators of adaptive capacity of tree species to a changing climate. 2021. Ecology and evolution, 11: 13081-13100 (10.1002/ece3.8024).

Thiffault, N., Raymond, P., Lussier, J.-M., Aubin, I., Roy-Tardif, S., D’Amato, A., Doyon, F., Lafleur, B., Perron, M., Bousquet, J., Isabel, N., Carles, S., Lupien, P. & Malenfant, A. 2021. Sylviculture d’adaptation aux changements climatiques: des concepts à la réalité. The Forestry Chronicle, 97: 28-42 (10.5558/tfc2021-005).

Thiffault, N., Raymond, P., Lussier, J.-M., Aubin, I., Roy-Tardif, S., D’Amato, A., Doyon, F., Lafleur, B., Perron, M., Bousquet, J., Isabel, N., Carles, S., Lupien, P. & Malenfant, A. 2021. Sylviculture d’adaptation aux changements climatiques : des concepts à la réalité. The Forestry Chronicle, 97: 28-42 (10.5558/tfc2021-005 ).

Whitehill, J.G.A., Yuen, M.M.S. & Bohlmann, J. 2021. Constitutive and insect-induced transcriptomes of weevil-resistant and susceptible sitka spruce. Plant-Environment Interactions, 2:137-147
(10.1002/pei3.10053).

2020

Ahmed, S., Lemay, V., Yanchuk, A., Robinson, A., Marshall, P. & Bull, G. 2020. Meta-modelling to quantify yields of white spruce and hybrid spruce provenances in the canadian boreal forest. Evolutionary Applications, 13: 62-75 (10.3390/f11060609).

Beaulieu, J., Nadeau, S., Ding, C., Celedon, J.M., Azaiez, A., Ritland, C., Laverdière, J.-P., Deslauriers, M., Adams, G., Fullarton, M., Bohlmann, J., Lenz, P. & Bousquet, J. 2020. Genomic selection for resistance to spruce budworm in white spruce and relationships with growth and wood quality traits. Evolutionary Applications, 13: 2704-2722 (10.1111/eva.13076).

Bernard, A. & Gélinas, N. 2020. Assessment of a public participation tool by experts: a case study of Québec, Canada. Natural Resources, 11: 283-307 (10.4236/nr.2020.117017).

Bernard, A., Gélinas, N. & Bélanger, L. 2020. Bilan de la gestion intégrée des ressources et du territoire au Québec. Forestry Chronicle, 96: 90-99 (10.5558/tfc2020-014).

Birol, I. & De La Torre, A.R. 2020. Sequencing and assembling the nuclear and organelle genomes of North American spruces. In The Spruce Genome. Eds. I. Porth & A.R. De La Torre. Springer Nature, 8p. (10.1007/978-3-030-21001-4_1).

Celedon, J., Whitehill, J., Madilo, L. & Bohlmann, J. 2020. Gymnosperm glandular trichomes: expanded dimensions of the conifer terpenoid defense system. Scientific Reports, 10: 12464 (9p.) (10.1038/s41598-020-69373-5).

Chamberland, V., Robichaud, F., Perron, M., Gélinas, N., Bousquet, J. & Beaulieu, J. 2020. Conventional versus genomic selection for white spruce improvement: a cost-benefit analysis for plantations on Québec public lands. Tree Genetics and Genomes, 16: 17 (16p.)  (10.1007/s11295-019-1409-7).

Coombe, L., Nokolic, V., Chu, J., Birol, I. & Warren R.L. 2020. ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs. Bioinformatics, 26: 3885-3887 (10.1093/bioinformatics/btaa253).

Depardieu, C., Girardin, M.P., Nadeau, S., Lenz, P., Bousquet, J. & Isabel, N. 2020. Adaptive genetic variation to drought in a widely distributed conifer suggests a potential for increasing forest resilience in a drying climate. New Phytologist, 227: 427-439 (10.111/nph.16551).

D’Odorico, P., Besik, A., Wong, C.Y.S., Isabel, N. & Ensminger, I. 2020. High-throughput drone based remote sensing reliably tracks phenology in thousands of conifer seedlings. New Phytologist, 226: 1667-1681 (10.1111/nph.16488).

Hafezqorani, S., Yang, C., Lo, T., Nip, K.M., Warren, R.L. & Birol, I. 2020. Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data. GigaScience, 9(6): 1-7 (10.1093/gigascience/giaa061).

Hassegawa, M., Savard, M., Lenz, P.R.N., Duchateau, E., Gélinas, N., Bousquet, J. & Achim, A. 2020. White spruce wood quality for lumber products: priority traits and their enhancement through tree improvement. Forestry, 93: 16-37 (10.1093/forestry/cpz050).

Isabel, N., Holliday, J.A. & Aitken, S.N. 2020. Forest genomics: advancing climate adaptation, forest health, productivity, and conservation. Presentation of the Evolutionary Applications special issue of January 2020. Evolutionary Applications, 13: 3-10 (10.1111/eva.12902).

Jackman, S.D., Coombe, L., Warren, R.L., Kirk, H., Trinh, E., MacLeod, T., Pleasance, S., Pandoh, P., Zhao, Y., Coope, R.J., Bousquet, J., Bohlmann, J., Jones, S.J.M., Birol, I. 2020. Complete mitochondrial genome of a gymnosperm, Sitka spuce (Picea sitchensis), indicates a complex physical structure. Genome Biology and Evolution, 12: 1174-1179 (10.1093/gbe/evaa108).

Lenz, P.R.N., Nadeau, S., Azaiez, A., Gérardi, S., Deslauriers, M., Perron, M., Isabel, N., Beaulieu, J. & Bousquet, J. 2020. Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce. Heredity, 124: 562-578 (10.1038/s41437-019-0290-3).

Lenz, P.R.N., Nadeau, S., Mottet, M.-J., Perron, M., Isabel, I., Beaulieu, J. & Bousquet, J. 2020. Multi-trait genomic selection for weevil resistance, growth and wood quality traits in Norway spruce. Evolutionary Applications, 13: 76-94 (10.1111/eva.12823).

Lo, T., Coombe, L., Lin, D., Warren, R., Kirk, H., Pandoh, P., Zhao, Y., Moore, R., Mungall, A., Ritland, C., Bousquet, J., Jones, S., Bohlmann, J., Thomson, A. & Birol, I. 2020. Complete chloroplast genome sequence of a black spruce (Picea mariana) from Eastern Canada. Microbiology Resource Announcements, 8(23): e00381-19 (4p.) (10.1128/MRA.00877-20).

Marchand, W., Girardin, M.P., Hartmann, H., Depardieu, C., Isabel, N., Gauthier, S., Boucher, E. & Bergeron, Y. 2020. Strong overestimation of water-use efficiency responses to rising CO2 in tree-ring studies. Global Change Biology, 26: 4538-4558 (10.1111/gcb.15166).

Nip, K.M., Chiu, R., Yang, C., Chu, J., Mohamadi, H., Warren, R. & Birol, I.  2020. RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes. Genome Research, 30(8): 1191-1200 (10.1101/gr.260174.119).

Parent, G., Méndez-Espinoza, C., Giguère, I., Mageroy, M., Charest, M., Bauce, E., Bohlmann, J. & Mackay, J. 2020. Hydroxyacetophenone defenses in white spruce against spruce budworm. Evolutionary Applications, 13: 62-75 (10.1111/eva.12885).

Wong, C.Y.S, D’Odorico, P., Arain, M.A. & Ensminger, I. 2020. Tracking the phenology of photosynthesis using carotenoid-sensitive and near-infrared reflectance vegetation indices in a temperate evergreen and mixed deciduous forest. New Phytologist, 226: 1682-1695 (10.1111/eva.13076).

2019

Celedon, J. & Bohlmann, J. 2019. Oleoresin defenses in conifers: chemical diversity, terpene synthases, and limitations of oleoresin defense under climate change. New Phytologist, 224: 1444-1463 (10.1111/nph.15984).

Coursolle, C., Otis-Prud’homme, G., Lamothe, M. & Isabel, N. 2019. Measuring rapid A–Ci curves in boreal conifers: black spruce and balsam fir. Frontiers in Plant Science, 10: 1276 (9p.) (10.3389/fpls.2019.01276).

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, 35(21): 4448-4450 (10.1093/bioinformatics/btz278).

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. & Birol, I. 2019. Complete chloroplast genome sequence of an Engelmann spruce (Picea engelmannii) genotype from western Canada. Microbiology Resource Announcements, 8(24): e00382-19 (3p.) (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. & Birol, I. 2019. Complete chloroplast genome sequence of a white spruce (Picea glauca) genotype from eastern Canada. Microbiology Resource Announcements, 8(23): e00381-19 (4p.) (10.1128/MRA.00381-19).

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 (14p.)(10.1016/j.jenvman.2019.109625).

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 (13p.) (10.1038/s41598-019-47950-7).

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

Whitehill, J.G.A. & Bohlmann, J. 2019. A molecular and genomic reference system for conifer defense against insects. Plant, Cell, & Environment, 42: 2844-2859 (10.1111/pce.13571).

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

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 (14p.) (10.1016/j.rse.2019.111407).

2018

Azaiez, A., Pavy, N., Gérardi, S., Laroche, J., Boyle, B., Gagnon, F., Mottet, M.-J., Beaulieu, J. & 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. & 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. & 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. & 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 216: 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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).

Warren, R.L. 2018. Visualizing genome synteny with xmatchview. Journal of Open Source Software, 3: 497-500 (10.21105/joss.00497).

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

2017

Celedon, J.M., Yuen, M.M.S., Chiang, A., Henderson, H., Reid, K.E. & 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. & 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. & 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. & 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. & 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. & 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. & 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).

Mohamadi, H., Khan, H. & Birol, I. 2017. ntCard: a streaming algorithm for cardinality estimation in genomics data. Bioinformatics, 33: 1324-1330 (10.1093/bioinformatics/btw832).

Pavy, N., Lamothe, M., Pelgas, B., Gagnon, F., Birol, I., Bohlmann, J., Mackay, J., Isabel, N. & 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. & 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. & 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).

Yang, C., Chu, J., Warren, R.L. & Birol, I. 2017. NanoSim: nanopore sequence read simulator based on statistical characterization. GigaScience, 6: 1-6 (10.1093/gigascience/gix010).

Yeo, S., Coombe, L., Warren, R.L., Chu, J. & Birol, I. 2017. ARCS: scaffolding genome drafts with linked reads. Bioinformatics, 43: 725 (10.1093/bioinformatics/btx675).

2016

Aubin, I., Munson, A.D., Cardou, G., Burton, P.J., Isabel, N., Pedlar, J.H., Paquette, A., Taylor, A.R., Delagrange, S., Kebli, H., Messier, C., Shipley, B., Valladares, F., Kattge, J., Boisvert-Marsh, L. & McKenney, D. 2016. Traits to stay, traits to move: a review of functional traits to assess sensitivity and adaptive capacity of temperate and boreal trees to climate change. Environmental Reviews, 24: 164-186 (10.1139/er-2015-0072).

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. & Birol, I. 2016. Assembly of the complete Sitka spruce chloroplast genome using 10X Genomics’ GemCode sequencing data. PLoS ONE 11(9): e0163059 (13p.) (10.1371/journal.pone.0163059).

Geisler, K., Jensen, N.B., Yuen, M.M.S., Madilao, L. & 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. & 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. & 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. & 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. & 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. & 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. & 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. & 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).