Publications

Publications from the Landry Lab

Profile on Google Scholar

Preprints

Dandage R, Després PC, Yachie N & CR Landry, beditor: A computational workflow for designing libraries of guide RNAs for CRISPR base editing. bioRxiv doi:https://doi.org/10.1101/426973

Nielly-Thibault L & CR Landry, Differences between the de novo proteome and its non-functional precursor can result from neutral constraints on its birth process, not necessarily from natural selection alone. bioRxiv doi:https://doi.org/10.1101/289330 (2018)

Durand E, Gagnon-Arsenault I, Hatin I, Nielly-Thibault L, Namy O & CR Landry, The high turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations. bioRxiv doi:https://doi.org/10.1101/329730 (2018)

Published work

2018

N’guyen GQ, Martin N, Jain M, Lagace L, Landry CR & M Filteau, A systems biology approach to explore the impact of maple tree dormancy release on sap variation and maple syrup quality. Scientific Reports, 8:14658 (2018)

Despres PC, Dube AK, Nielly-Thibault L, Yachie N & CR Landry, Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast. G3 

Dionne U, Chartier FJM, de los Santos YL, Lavoie N, Bernard DN,  Banerjee SL, Otis F, Jacquet K, Tremblay MG, Jain M, Bourassa S, Gish GD, Gagné JP, Poirier GG, Laprise P, Voyer N, Landry CR, Doucet N & Bisson N, Direct phosphorylation of SRC Homology 3 domains by tyrosine kinase receptors disassembles ligand-induced signalling networks. Molecular Cell 70:1-13 (2018)

Wolters JF, Charron G, Gaspary A, Landry CR, Fiumera AC & Fiumera HI, Mitochondrial recombination reveals mito-mito epistasis in yeast. Genetics 209:307-319 (2018)

Chrétien AE, Gagnon-Arsenault I, Dubé AK, Barbeau X, Després PC, Lamothe C, Dion-Côté AM, Lagüe P & CR Landry, Extended linkers improve the detection of protein-protein interactions (PPIs) by dihydrofolate reductase protein-fragment complementation assay (DHFR PCA) in living cells. Molecular & Cellular Proteomics 17:373-383 (2018)

2017

Hénault M*, Eberlein C*, Charron G, Durand E, Nielly-Thibault L, Martin H & Landry CR, Yeast population genomics goes wild: the case of Saccharomyces paradoxus. In: Polz M, Rajora OP (eds) Population genomics: microorganisms. Springer (2017)

Samandi S, Roy AV, Delcourt V, Lucier JF, Gagnon J, Beaudoin MC, Vanderperre B, Breton MA, Motard J, Jacques JF, Brunelle M, Gagnon-Arsenault I, Fournier I, Ouangraoua A, Hunting DJ, Cohen AA, Landry CR, Scott MS & Roucou X, Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins. eLife 6:e27860 (2017)

Landry CR & Diss G, Molecular dependency impacts on the compensating ability of paralogs: a response to Veitia. Trends in Genetics 33:657-658 (2017)

Leducq JB*, Henault M*, Charron G, Nielly-Thibault L, Terrat Y, Fiumera HL, Shapiro BJ & Landry CR, Mitochondrial recombination and introgression during speciation by hybridization. Molecular Biology and Evolution 34:1947-1959 (2017)

Eberlein C, Nielly-Thibault L, Maaroufi H, Dubé AK, Leducq JB, Charron G & Landry CR, The rapid evolution of an ohnolog contributes to the ecological specialization of incipient yeast species. Molecular Biology and Evolution 34:2173-2186 (2017)

Charron G & Landry CR, No evidence for extrinsic post-zygotic isolation in a wild Saccharomyces yeast system. Biology Letters 13:20170197 (2017)

Marsit S, Leducq JB, Durand E, Marchant A, Filteau M & Landry CR, Evolutionary biology through the lens of budding yeast comparative genomics. Nature Reviews Genetics 18:581-598 (2017)

Peris D, Moriarty RV, Alexander WG, Baker EC, Sylvester K, Sardi M, Langdon QK, Libkind D, Wang QM, Bai FY, Leducq JB, Charron G, Landry CR, Sampaio JP, Gonçalves P, Hyma KE, Fay JC, Sato TK & Hittinger CT, Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnology for Biofuels 10:78 (2017)

Diss G, Gagnon-Arsenault I, Dion-Coté AM, Vignaud H, Ascencio DI, Berger CM & Landry CR, Gene duplication can impart fragility, not robustness, in the yeast protein interaction network. Science 355:630-634 (2017)

Hébert FO, Grambauer S, Barber I, Landry CR & Aubin-Horth N, Major host transitions are modulated through transcriptome-wide reprogramming events in Schistocephalus solidus, a threespine stickleback parasite. Molecular Ecology 26:1118–1130 (2017)

Xia W, Nielly-Thibault L, Charron G, Landry CR, Kasimer D, Anderson JB & Kohn LM, Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland. Molecular Ecology 26:995–1007 (2017)

Hénault M & CR Landry. When nuclear-encoded proteins and mitochondrial RNAs do not get along, species split apart. EMBO Reports 18:8–10 (2017)

 

2016

 

Caron D, Byrne DP, Thebault P, Soulet D, Landry CR, Eyers PA & Elowe S, Mitotic phosphotyrosine network analysis reveals that tyrosine phosphorylation regulates Polo-like kinase 1 (PLK1). Science Signaling 9:rs14 (2016)

Filteau M, Charron G & Landry CR, Identification of the fitness determinants of budding yeast on a natural substrate. The ISME Journal 11:959–971 (2016)

Bleuven C & Landry CR, Molecular and cellular bases of adaptation to a changing environment in microorganisms. Proceedings of the Royal Society B 283:20161458 (2016)

Peris D, Langdon QK, Moriarty RV, Sylvester K, Bontrager M, Charron G, Leducq JB, Landry CR, Libkind D & Hittinger CT, Complex ancestries of lager-brewing hybrids were shaped by standing variation in the wild yeast Saccharomyces eubayanus. PLoS Genetics 12:e1006155 (2016)

Hébert FO, Grambauer S, Barber I, Landry CR & Aubin-Horth N, Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite. GigaScience 5:24 (2016)

Leducq JB*, Nielly-Thibault L*, Charron G*, Eberlein C, Verta JP, Samani P, Sylvester K, Hittinger CT, Bell G & Landry CR, Speciation driven by hybridization and chromosomal plasticity in a wild yeast. Nature Microbiology 1:15003 (2016)

Landry CR, Analysis of biological systems. Invited book review for The Quarterly Review of Biology (2016)

Verta JP, Landry CR & Mackay J, Dissection of expression-quantitative trait locus and allele specificity using a haploid/diploid plant system – insights into compensatory evolution of transcriptional regulation within populations. New Phytologist 211:159–171 (2016)

Barbosa R, Almeida P, Safar SVB, Santos RO, Morais PB, Nielly-Thibault L, Leducq JB, Landry CR, Gonçalves P, Rosa CA & Sampaio JP, Evidence of natural hybridization in Brazilian wild lineages of Saccharomyces cerevisiae. Genome Biology and Evolution 18:317–329 (2016)

Filteau M, Hamel V & Landry CR,  La levure à vin – Modèle d’étude des gènes et des maladies humaines dans un contexte personnalisé. Médecine/Sciences 32:332–334 (2016)

Michnick SW, Landry CR, Levy ED, Diss G, Ear PH, Kowarzyk J, Malleshaiah MK, Messier V & Tchekanda E, Protein-fragment complementation assays for large-scale analysis, functional dissection, and spatiotemporal dynamic studies of protein-protein interactions in living cells. Cold Spring Harbor Protocol (2016)

Michnick SW, Levy ED, Landry CR, Kowarzyk J & Messier V, The dihydrofolate reductase protein-fragment complementation assay: a survival-selection assay for large-scale analysis of protein-protein interactions. Cold Spring Harbor Protocol (2016)

Diss G & Landry CR, Combining the dihydrofolate reductase protein-fragment complementation assay with gene deletions to establish genotype-to-phenotype maps of protein complexes and interaction networks. Cold Spring Harbor Protocol (2016)

 

2015

 

Filteau M, Hamel V, Pouliot MC, Gagnon-Arsenault I, Dubé AK & Landry CR, Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds. Molecular Systems Biology 11:832 (2015)

Filteau M, Vignaud H, Rochette S, Diss G, Chrétien AE, Berger CM & Landry CR, Multi-scale perturbations of protein interactomes reveal their mechanisms of regulation, robustness and insights into genotype-phenotype maps. Briefings in Functional Genomics 15:130–137 (2015)

Eberlein C, Leducq JB & Landry CR, The genomics of wild yeast populations sheds lights on the domestication of man’s best (micro) friend. Molecular Ecology 24:5309-5311 (2015)

Nigg M, Laroche J, Landry CR & Bernier L, RNAseq analysis highlights specific transcriptome signatures of yeast and mycelial growth phases in the Dutch elm disease fungus Ophiostoma novo-ulmi. G3: Genes|Genomes|Genetics 5:2487-2495 (2015)

Torres-Quiroz F, Filteau M & Landry CR, Feedback regulation between autophagy and PKA. Autophagy 11:1181-1183 (2015)

Freel KC, Charron G, Leducq JB, Landry CR & Schacherer J, Lachancea quebecensis sp. nov., a yeast species consistently isolated from the tree bark in the Canadian province of Quebec. International Journal of Systematic and Evolutionary Microbiology 65:3392-3399 (2015)

Filteau M, Diss G, Torres-Quiroz F, Dubé AK, Schraffl A, Bachmann VA, Gagnon-Arsenault I, Chrétien AE, Steunou AL, Dionne U, Côté J, Bisson N, Stefan E & Landry CR, Systematic identification of signal integration by protein kinase A. PNAS 112:4501-4506 (2015)

Hebert FO, Phelps L, Samonte I, Panchal M, Grambauer S, Barber I, Kalbe M, Landry CR & Aubin-Horth N, Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes. Parasites & Vectors 8:225 (2015)

Landry CR, Zhong X, Nielly-Thibault L & Roucou X, Found in translation: functions and evolution of a recently discovered alternative proteome. Current Opinion in Structural Biology 32:74–80 (2015)

Boutchueng-Djidjou M, Collard-Simard G, Fortier S, Hébert SS, Kelly I, Landry CR & Faure RL, The last enzyme of the de novo purine synthesis pathway 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) plays a central role in insulin signalling and the Golgi/endosomes protein network. Molecular and Cellular Proteomics 14:1079-1092 (2015)

Stockwell SR, Landry CR & Rifkin SA, The yeast galactose network as a quantitative model for cellular memory. Molecular BioSystems 11:28-37 (2015)

Samani P, Low-Decarie E, McKelvey K, Bell T, Burt A, Koufopanou V, Landry CR & Bell G, Metabolic variation in natural populations of wild yeast. Ecology and Evolution 5:722-732 (2015)

Rochette S*, Diss G*, Filteau M, Leducq JB, Dubé AK & Landry CR, Genome-wide protein-protein interaction screening by Protein-fragment Complementation Assay (PCA) in living cells. Journal of Visualized Experiments 97:e52255 (2015)

 

2014

 

Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR & Moses AM, Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. PLoS Computational Biology 12:e1003977 (2014)

Charron G*, Leducq JB* & Landry CR, Chromosomal variation segregates within incipient species and correlates with reproductive isolation. Molecular Ecology 23:4362-4372 (2014)

Landry CR, Freschi L, Zarin T & Moses AM, Turnover of protein phosphorylation evolving under stabilizing selection. Frontiers in Genetics 5:245 (2014)

Goldman A, Roy J, Bodenmiller B, Wanka S, Landry CR, Aebersold R & Cyert MS, The calcineurin signaling network evolves via conserved kinase-phosphatase modules that transcend substrate identity.  Molecular Cell 55:422-435 (2014)

Leducq JB*, Charron G*, Samani P, Dubé AK, Sylvester K, James B, Almeida P, Sampaio JP, Hittinger CT, Bell G & Landry CR, Local climatic adaptation in a widespread microorganism. Proceedings of the Royal Society B 281:20132472 (2014)

Freschi L, Osseni M & Landry CR, Functional divergence and evolutionary turnover in mammalian phosphoproteomes. PLoS Genetics 10:e1004062 (2014)

Landry CR & Aubin-Horth N, Recent advances in ecological genomics: from phenotypic plasticity to convergent and adaptive evolution and speciation. In: Landry C, Aubin-Horth N (eds) Ecological Genomics. Advances in Experimental Medicine and Biology, 781. Springer, Dordrecht (2014)

Rochette S, Gagnon-Arsenault I, Diss G & Landry CR, Modulation of the yeast protein interactome in response to DNA damage. Journal of Proteomics 100:25-36 (2014)

Diss G, Ascencio D, DeLuna A & Landry CR, Molecular mechanisms of paralogous compensation and the robustness of cellular networks. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 322:488-499 (2014)

Charron G, Leducq JB, Bertin C, Dubé AK & Landry CR, Exploring the northern limit of the distribution of Saccharomyces cerevisiae and Saccharomyces paradoxus in North America. FEMS Yeast Research 14:281-288 (2014)

 

2013

 

Landry CR*, Levy ED*, Abd Rabbo D, Tarassov K & Michnick SW, Extracting insight from noisy cellular networks. Cell 155:983–989 (2013)

Diss G, Dubé AK, Boutin J, Gagnon-Arsenault I & Landry CR, A systematic approach for the genetic dissection of protein complexes in living cells. Cell Reports 3:2155–2167 (2013)
See also Nature Methods 10:821 (2013)

Diss G, Filteau M, Freschi L, Leducq JB, Rochette S, Torres-Quiroz F & Landry CR, Integrative avenues for exploring the dynamics and evolution of protein interaction networks. Current Opinion in Biotechnology 24:775-783 (2013)

Verta JP, Landry CR & Mackay JJ, Are long-lived trees poised for evolutionary change? Single locus effects in the evolution of gene expression networks in spruce. Molecular Ecology 22:23692379 (2013)

Gagnon-Arsenault I, Marois Blanchet FC, Rochette S, Diss G, Dubé AK & Landry CR, Transcriptional divergence plays a role in the rewiring of protein interaction networks after gene duplication. Journal of Proteomics 81:112-125 (2013)

Freschi L, Torres-Quiroz F, Dubé AK & Landry CR, qPCA: a scalable assay to measure the perturbation of protein-protein interactions in living cells. Molecular BioSystems 9:36-43 (2013)

 

2012

 

Leducq JB, Charron G, Diss G, Gagnon-Arsenault I, Dubé AK & Landry CR, Evidence for the robustness of protein complexes to inter-species hybridization. PLoS Genetics 8:e1003161 (2012)

Goyette G*, Boulais J*, Carruthers NJ, Landry CR, Jutras I, Duclos S, Dermine JF, Michnick SW, LaBoissière S, Lajoie G, Barreiro L, Thibault P & Desjardins M, Proteomic characterization of phagosomal membrane microdomains during phagolysosome biogenesis and evolution. Molecular & Cellular Proteomics 11:1365-1377 (2012)

Pavey SA, Bernatchez L, Aubin-Horth N & Landry CR, What is needed for next-generation ecological and evolutionary genomics? Trends in Ecology and Evolution 27:673-678 (2012)

Landry CR & Rifkin SA, The genotype-phenotype maps of systems biology and quantitative genetics: distinct and complementary. In: Soyer O (eds) Evolutionary Systems Biology. Advances in Experimental Medicine and Biology, 751. Springer, New York (2012)

Diss G, Freschi L & Landry CR, Where do phosphosites come from and where do they go after gene duplication? International Journal of Evolutionary Biology 2012:843167 (2012)

Levy ED, Michnick SW & Landry CR, Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information. Philosophical Transactions of The Royal Society B Biological Sciences 367:2594-606 (2012)

Lee S, Thebault P, Freschi L, Beaufils S, Blundell TL, Landry CR, Bolanos-Garcia VM & Elowe S, Characterization of spindle checkpoint kinase Mps1 reveals a domain with functional and structural similarities to tetratricopeptide repeat motifs of the Bub1 and BubR1 checkpoint kinases. The Journal of Biological Chemistry 287:5988-6001 (2012)

 

2011

 

Landry CR, A cellular roadmap for the plant kingdom. Science 333:532-533 (2011)

Freschi L, Courcelles M, Thibault P, Michnick SW & Landry CR, Phosphorylation network rewiring by gene duplication. Molecular Systems Biology 7:504 (2011)

Michnick SW, Ear PH, Landry C, Malleshaiah MK & Messier V, Protein-fragment complementation assays for large-scale analysis, functional dissection and dynamic studies of protein-protein interactions in living cells. In: Luttrell L, Ferguson S (eds) Signal transduction protocols. Methods in Molecular Biology 756. Humana Press, Totowa NJ (2011)

 

2010

 

Landry CR & Rifkin SA, Chromatin regulators shape the genotype-phenotype map. Molecular Systems Biology 6:434 (2010)

Boulais J, Trost M, Landry CR, Dieckmann R, Levy ED, Soldati T, Michnick SW, Thibault P & Desjardins M, Molecular characterization of the evolution of phagosomes. Molecular Systems Biology 6:423 (2010)

Landry CR & Aubin-Horth N, Gene network architecture as a canvas for the interpretation of ecological genomics investigations. Molecular Ecology 19:5084-5085 (2010)

Moses AM & Landry CR, Moving from transcriptional to phospho-evolution: generalizing regulatory evolution? Trends in Genetics 26:462-467 (2010)

Di Poi C, Diss G & Freschi L, Biodiversity matters in a changing world. Biology Letters 7:4-6 (2010) **Student initiative**

Levy ED*, Landry CR* & Michnick SW, Signaling through cooperation. Science 328:983-984 (2010)

Michnick SW, Ear PH, Landry CR, Malleshaiah MK & Messier V, A toolkit of protein-fragment complementation assays for studying and dissecting large-scale and dynamic protein-protein interactions in living cells. In: Weissman J, Guthrie C, Fink G (eds.) Guide to yeast genetics: functional genomics, proteomics and other systems analysis. Methods in Enzymology 470. Elsevier Press, New York USA (2010)

Fontanillas P, Landry CR, Wittkopp PJ, Russ C, Gruber JD, Nusbaum C & Hartl DL, Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Molecular Ecology 19:212–227 (2010)

 

2009

 

Landry CR*, Levy ED* & Michnick SW, Weak functional constraints on phosphoproteomes. Trends in Genetics 25:193-197 (2009)

Levy ED*, Landry CR* & Michnick SW, How perfect can protein interactomes be? Science Signalling 2:pe11 (2009)

Landry CR, Systems biology spins off a new model for the study of canalization. Trends in Ecology and Evolution 24:63-66 (2009)

 

2008

 

Cheung V, Chua G, Batada NN, Landry CR, Michnick SW, Hughes TR & Winston F, Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PloS Biology 6:e277 (2008)

Tarassov K*, Messier V*, Landry CR*, Radinovic S*, Serna Molina MM, Shames I, Malitskaya Y, Vogel J, Bussey H & Michnick SW, An in vivo map of the yeast protein interactome. Science 320:1465-1479 (2008)

Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL & Thomas WK, A Genome-wide view of the spectrum of spontaneous mutations in yeast. Proceedings of the National Academy of Sciences of the United States of America 105:9272-9277 (2008)

Brown KM, Landry CR, Hartl DL & Cavalieri D, Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Molecular Ecology 17:2985-2997 (2008)

 

2007

 

Stefan E, Aquin S, Berger N, Landry CR, Nyfeler B, Bouvier M & Michnick SW, Quantification of dynamic protein complexes using Renilla luciferase-fragment complementation applied to protein kinase A activities in vivo. Proceedings of the National Academy of Sciences of the United States of America 104:16916-16921 (2007)

Landry CR*, Lemos B*, Rifkin SA, Dickinson WJ & Hartl DL, Genetic properties influencing the evolvability of gene expression. Science 317:118-121 (2007)

Landry CR, Castillo-Davis CI, Ogura A, Liu JS & Hartl DL, Systems-level analysis and evolution of the Drosophila phototransduction cascade. Proceedings of the National Academy of Sciences of the United States of America 104:3283-3288 (2007)

Landry CR & Aubin-Horth N, Ecological annotation of genes and genomes through ecological genomics. Molecular Ecology 16:4419-4421 (2007)

Landry CR, Hartl DL & Ranz JM, Genome clashes in hybrids: insights from gene expression. Heredity 99:483-493 (2007)

Lemos B, Landry CR, Fontanillas P, Renn SP, Kulathinal R, Brown KM & Hartl DL, Evolution of Genomic Expression. In Pagel M, Pomiankowski A (eds) Evolutionary genomics and proteomics. Sinauer Associates, Sunderland, MA (2007)

Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL, Cavalieri D, Jander G & Queitsch C, Indel array: an affordable alternative for genotyping. Plant Journal 51:727-737 (2007)

 

2006

 

Landry CR, Townsend JP, Hartl DL & Cavalieri D, Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 15:575-591 (2006)

Landry CR, Oh J, Hartl DL & Cavalieri D, Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene 366:343-351 (2006)

 

2005

 

Landry CR, Wittkopp PJ, Taubes CH, Ranz JM, Clark AG & Hartl DL, Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171:1813-1822 (2005)

Giuntini E, Mengoni A, De Filippo C, Cavalieri D, Aubin-Horth N, Landry CR, Becker A & Bazzicalupo M, Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics 6: 158 (2005)

Aubin-Horth N, Landry CR, Letcher BH & Hofmann HA, Alternative life-histories shape brain gene expression profiles in males of the same population. Proceedings of the Royal Society B 272:1655-1662 (2005)

 

2003

 

Landry C, Geyer LB, Arakaki Y, Uehara T & Palumbi SR, Recent speciation in the Indo-West Pacific: rapid evolution of gamete recognition and sperm morphology in cryptic species of sea urchin. Proceedings of the Royal Society B 270:1839-1847 (2003)

Bernatchez L & Landry C, MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? Journal of Evolutionary Biology 16:363-377 (2003)

 

2001

 

Landry C & Bernatchez L, Comparative analysis of population structure across environments and geographic scales at major histocompatibility complex and microsatellite Atlantic salmon (Salmo salar). Molecular Ecology 10:2525-2540 (2001)

Landry C, Garant D, Duchesne P & Bernatchez L, “Good genes as heterozygosity”: the major histocompatibility complex and mate choice in Atlantic salmon (Salmo salar). Proceedings of the Royal Society B 268:1279-1285 (2001)