Publications


Recent publications (last two years). See full list of publications (2008-2020) here.

2020

Alock et al. [14 authors incl. Beiko, R.G.] 2020. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48: D517-D525.

Benner, I., Irwin, A.J and Finkel, Z.V. 2020. Capacity of the common Arctic picoeukaryote Micromonas to adapt to a warming ocean. Limnology and Oceanography Letters 5(2):221-227.

Bretherton, L., Hillhouse, J., Kamalanathan, M., Finkel, Z.V., Irwin, A.J. and Quigg, A. 2020. Trait-dependent variability of the response of marine phytoplankton to oil and dispersant exposure. Marine Pollut. Bull. 153: 110906.

Burki, F., Roger, A.J., Brown, M.W. and Simpson, A.G.B. 2020. The new tree of eukaryotes. Trends Ecol. Evol. 35: 43-55.

Colp, M. and Archibald, J.M. 2020. The language of symbiosis: insights from protist biology. In: Cellular dialogs in the holobiont, Bosch, T.. and Hadfield, M. (eds.), CRC Press, in press.

Connors, J., Dunn, K.A., Allott, J., Bandsma, R., Rashid, M., Otley, A.R., Bielawski, J.P. and Van Limbergen, J. 2020. The relationship between fecal bile acids and microbiome community structure in pediatric Crohn’s disease. ISME J. 14: 702-713.

Cui, T.T., Dawson, T.J., McLatchie, S., Dunn, K.A., Bielawski, J.P., Walsh, D.A. 2020. Modelling free- living and particle-associated bacterial assemblages across the deep and hypoxic Lower St. Lawrence Estuary. MSphere, in press.

de Vries, J., de Vries, S., Curtis, B.A., Zhou, H., Penny, S., Feussner, K., Pinto, D.M., Steinert, M., Cohen, A., von Schwartzenberg, K. and Archibald, J.M. 2020. Heat stress response in the closest algal relatives of land plants reveals conserved stress signalling circuits. Plant J., in press.

Doolittle, W.F. 2020. Evolution’s next major transition. Curr Biol., in press.

Doolittle, W.F. 2020. Why I am not a creationist: the devil in the details. Physics in Canada 76: 1, in press.

Doolittle, W.F. 2020. Evolution: Two domains of life or three? Curr. Biol. 30: R177-R179.

Douglas, G.M., Bielawski, J.P., Langille, M.G.I. 2020. Re-evaluating the relationship between missing heritability and the microbiome. Microbiome, in press.

Finkel, Z.V., Liang, Y., Nanjappa, D., Bretherton, L., Brown, C.M., Quigg, A. and Irwin, A.J. 2020. A ribosomal sequence-based oil sensitivity index for phytoplankton groups. Marine Pollut. Bull. 151: 110798.

Finkel, Z.V. and Irwin, A.J. 2020. Phytoplankton. In Gargaud et al. (Eds), Encyclopedia of Astrobiology, Springer. 10.1007/978-3-642-27833-4_5416-1.

Gallot-Lavallée, L. and Archibald, J.M. 2020. Spotlight: Phagocytosis in a shape-shifting bacterium. Trends Microbiol., in press.

Gradone, J.C., Oliver, M.J., Davies, A.R., Irwin, A., Moffat, C. 2020. Sea surface kinetic energy as a proxy for phytoplankton light limitation in the summer pelagic Southern Ocean.  J. Geophys. Res: Oceans, in press.

Gray, M.W., Burger, G., Derelle, R., Klimes, V., Leger, M.M., Sarrasin, M., Vlcek, C., Roger, A.J., Elias, M. and Lang, B.F. 2020. The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome. BMC Biol. 18: 22.

Gray, M.W. and Gopalan, V. 2020. Piece by piece: Building a ribozyme. J. Biol. Chem. 295: 2313-2323.

Ho, L.S.T., Dinh, V., Matsen IV, F.A., Suchard, M.A. 2020. On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model. Journal Math. Biol. 80(4): 1119–1138.

Jabre, L. and Bertrand, E.M. 2020. Interactive effects of iron and temperature on the growth of Fragilariopsis cylindrus. Limnology and Oceanography Letters, LOL2-19-0069, in press.

Johnston, B.P. and McCormick, C. 2020. Herpes viruses and the unfolded protein response. Viruses 12(1), 17.

Jones, C.M.A., Connors, J., Dunn, K.A., Bielawski, J.P., Comeau, A.M., Langille, M.G.I. and *Van Limbergen, J. 2020. Bacterial taxa and functions are predictive of sustained remission following exclusive enteral nutrition in pediatric Crohn’s Disease. Inflamm. Bowel Dis., Jan. 21; pii: izaa001.

Karimi, K., Farid A.H., Sargolzaei M., Myles S., Miar Y. 2020. Linkage disequilibrium, effective population size and genomic inbreeding rates in American mink using denotyping-by-sequencing data. Frontiers in Genetics 11:223.

Layton, K.K.S., Dempson, B., Snelgrove, P.V.R., Duffy, S.J., Messmer, A.M., Paterson, I.G., Jeffery, N.W., Kess, T., Horne, J.B., Salisbury, S.J., Ruzzante, D.E., Bentzen, P., Côté, D., Nugent, C.M., Ferguson, M.M., Leong, J.S., Koop, B.F., Bradbury, I.R. 2020. Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish. Evol. Applications, online https://doi.org/10.1111/eva.12922.

Linquist, S., Doolittle, W.F. and Palazzo, A.F. 2020. Getting clear about the F-word in genomics. PloS Genetics, online doi.org/10.1371/journal.pgen.1008702.

Mutshinda, C.M., Irwin, A.J., Sillanpää, M.J. 2020. A Bayesian framework for robust quantitative trait locus mapping and outlier detection.  Int. J. Biostat., in press.

Najle, S.R. et al. (incl. Slamovits, C.H.) 2020. Genome-wide transcriptional analysis of Tetrahymena thermophile response to exogenous cholesterol. J. Eukaryot. Microbiol. 67: 209-222.

Nejman, D. et al. [56 authors incl. Langille, M.G.I.] 2020. The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science, in press.

Novick, A. and Doolittle, W.F. 2020. Horizontal persistence and the complexity hypothesis. Biol. Philos. 35: 2.

Omar, T., Ziltenera, P., Chamberlaina, E., Cheng, Z. and Johnston, B. 2020. Role of γδT cells in Pseudomonas aeruginosa lung infection. Infection and Immunity 88(6): e00171-20.

Omta, A.W., Talmy, D., Inomura, K., Irwin, A.J., Finkel, Z.V., Sher, D., Liefer, J.D., Follows, M.J. 2020. Quantifying nutrient throughput and DOM production by algae in continuous culture. J. Theor. Biol. 494:110214. 10.1016/j.jtbi.2020.110214.

Palau, M., Piqué, N., Comeau, A.M., Douglas, G.M., Ramírez-Lázaro, M.J., Lario, S., Calvet, X., Langille, M.G.I. and Miñana-Galbis, D. 2020. Detection of Helicobacter pylori microevolution and multiple infection from gastric biopsies by housekeeping gene amplicon sequencing. Pathogens 9(2), pii: E97.

Pang, Z., Raudonis R., McCormick C., and Cheng Z. 2020. Early growth response 1 deficiency protects host against Pseudomonas aeruginosa lung infection. Infection and Immunity 88(1):e00678-719.

Peabody, M.A., Lau, W.Y.V., Hoad, G.R., Jia, B., Maguire, F., Gray, K.L., Beiko, R.G., Brinkman, F.S.L. 2020. PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data. Bioinformatics 36: 3043-3048.

Pringle, E.S., Robinson, C.A., Crapoulet, N., Monjo, A.L.-A., Bouzanis, K., Leidal, A.M., Lewis, S.M., Gaston, D., Uniacke, J., McCormick, C. 2020. E KSHV lytic mRNA is efficiently translated in the absence of eIF4F. bioRxiv 356162; online: https://doi.org/10.1101/356162.

Pringle, E.S., Wertman, J., Melong, N., Coombs, A.J., Young, A.L., O’Leary, D., Veinotte, C., Robinson, C.-A., Ha, M.N., Dellaire, G., Druley, T.E., McCormick, C., Berman, J.N. 2020. The zebrafish xenograft platform – a novel tool for modeling KSHV-associated diseases. Viruses 12(1): 12.

Rahim, M.M., Parsons, B., Price, E.L., Slaine, P.D., Chilvers, B.L., Seaton, G.S., Wight, A., Medina-Luna, D., Dey, S., Grandy, S.L., Anderson, L.E., Zamorano Cuervo, N., Grandvaux, N., Gaglia, M.M., Kelvin, A.A., Khaperskyy, D.A., McCormick, C., Makrigiannis, A.P. 2020. Defective influenza A virus RNA products mediate MAVS-dependent upregulation of human leukocyte antigen class I proteins. Journal of Virology Apr 2020, JVI.00165-20; doi: 10.1128/JVI.00165-20.

Rotteveel, L. and Sterling, S.M. 2020. Five aluminum seasonality regimes identified in chronically acidified rivers of Nova Scotia. Environ. Sci. Technol. 54: 807-817.

Ruzzante, D.E., Simons, A.P., McCracken, G.R., Habit, E., Walde, S.J. 2020. Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites. PROCB, in press.

Sibbald, S.J. & Archibald, J.M. 2020. Genomic insights into plastid evolution. Genome Biol. Evol. Accepted pending revision. (Invited review article).

Susko, E. and Roger, A.J. 2020. On the use of information criteria for model selection in phylogenetics. Mol. Biol. Evol. 37: 549-562.

Tanifuji, G., Kamikawa, R., Moore, C.E., Mills, T., Onodera, N.T., Kashiyama, Y., Archibald, J.M., Inagaki, Y. and Hashimoto, T. 2020. Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis. Genome Biol. Evol. 12: 3926-3937.

Valenzuela-Aguayo, F., McCracken, G.R., Manosalva, A., Habit E., Ruzzante, D.E. 2020. Anthropogenic habitat fragmentation effects on connectivity, diversity and persistence of the endemic Percilia irwini, in the Biobío system in Chile. Evolutionary Applications 13: 794-807.

Wu, L., Zeng, T., Deligios, M., Milanesi, L., Langille, M.G.I., Zinellu, A., Rubino, S., Carru, C., Kelvin, D. 2020. Age-related variation of bacterial and fungal communities in different body habitats across the young, elderly and centenarians in Sardinia. mSphere 5:e00558-19.

Zhao, J., Azad, M.B., Bertrand, E.M. et al. 2020. Canadian Science Meets Parliament: Building relationships between scientists and policymakers. Science and Public Policy, https://doi.org/10.1093/scipol/scz062.

2019

Archibald, J.M. 2019. Genomics reveals alga-associated cyanobacteria hiding in plain sight. Proc. Natl. Acad. Sci. USA 116: 15757-15759.

Asman, A.K.M., Curtis, B.A. and Archibald, J.M. 2019. Nucleomorph small RNAs in cryptophyte and chlorarachniophyte algae. Genome Biol. Evol. 11: 1117-1134.

Bolyen, E. et al. [100 authors, incl. Langille, M.G.I., Douglas, G.M.] 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37: 852-857.

Chen, W., Kenney, T., Bielawski, J.P. and Gu, H. 2019. Testing adequacy for DNA substitution models. BMC Bioinformatics 20: 349.

Colp, M.J. and Archibald, J.M. 2019. Evolution: New protist predators under the sun. Curr. Biol. 29: R936-R938.

DesRoches, C.T., Inkpen, S.A. and Green, T.L. 2019 The eroding artificial/natural distinction? Some consequences for ecology and economics. In M. Nagatsu and A. Ruzzene (Eds.), Contemporary Philosophy and Social Science: An Interdisciplinary Dialogue, Bloomsbury Publishing, London, UK.

de Vries, S., de Vries, J., Archibald, J.M. and Slamovits, C.S. 2019. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle- specific gene expression. bioRxiv; online May 31, doi: https://doi.org/10.1101/656496.

Doolittle, W.F. 2019. Making evolutionary sense of Gaia. Trends Ecol. Evol. 34: 889-894.

Doolittle, W.F. 2019. Speciation without species: a final word. Philos. Theory Practice Biol. 11: 14.

Douglas, G.M. and Langille, M.G.I. 2019. Current and promising approaches to identify horizontal gene transfer events in metagenomes. Genome Biol. Evol. 11: 2750-2766.

Dunn, K.A., Kenny, T., Gu., H. and Bielawski, J.P. 2019. Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates. BMC Evol. Biol. 19: 22.

Frail-Gauthier, J.L., Mudie, P.J., Simpson, A.G.B. & Scott, D.B. 2019. Mesocosm and microcosm experiments on the feeding of temperate salt marsh foraminifera. J. Foraminiferal Res. 49: 259-274.

Galindo, L.J., Torruella, G., Moreira, D., Eglit, Y., Simpson, A.G.B., Völcker, E., Clauß, S. and López- García, P. 2019. Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi. Philos. Trans. R Soc. Lond. B Biol. Sci. 374: 20190094.

Grisdale, C.J., Smith, D.R. and Archibald, J.M. 2019. Relative mutation rates in nucleomorph-bearing algae. Genome Biol. Evol. 11: 1045-1053.

Haas, S., Desai, D.K., LaRoche, J., Pawlowicz, R. and Wallace, D.W.R. 2019. Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater. Environ Microbiol. 21(10): 3927-3952.

Hess, S., Eme, L., Roger, A.J. and Simpson, A.G.B. 2019. A natural toroidal microswimmer with a rotary eukaryotic flagellum. Nat. Microbiol. 4: 1620-1626.

Houfani, A.A., Větrovský, T., Navarrete, O.U., Štursová, M., Tláskal, V., Beiko, R.G., Boucherba, N., Baldrian, P., Benallaoua, S. and Jorquera, M.A. 2019. Cellulase-hemicellulase activities and bacterial community composition of different soils from Algerian ecosystems. Microb Ecol. 77: 713-725.

Jones, C.T., Susko, E. and Bielawski, J.P. 2019. Looking for Darwin in genomic sequences: Validity and success depends on the relationship between model and data. Methods Mol. Biol. 1910: 399- 426.

Jones, C.T., Youssef, N., Susko, E. and Bielawski, J.P. 2019. A phenotype-genotype codon model for detecting adaptive evolution. Syst. Biol., Nov. 15; pii: syz075.

Karnkowska, A., Treitli, S.C., Brzoň, O., Novák, L., Vacek, V., Soukal, P., Barlow, L.D., Herman, E.K., Pipaliya, S., Pánek, T., Žihala, D., Petrželková, R., Butenko, A., Eme, L., Stairs, C.W., Roger, A.J., Eliáš, M., Dacks, J.B. and Hampl, V. 2019. The oxymonad genome displays canonical eukaryotic complexity in the absence of a mitochondrion. Mol. Biol. Evol. 36: 2292-2312.

Kim, J.I., Shin, H., Škaloud, P., Jung, J., Yoon, H.S., Archibald, J.M. & Shin, W. 2019. Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation. BMC Evol. Biol. 19: 20.

Lax, G., Lee, W.J., Eglit, Y. and Simpson, A.G.B. 2019. Ploeotids represent much of the phylogenetic diversity of euglenids. Protist 170: 233-257.

Leger, M.M., Kolisko, M., Stairs, C.W. and Simpson, A.G.B. 2019. Mitochondrion-related organelles in free-living protists, pp. 287-308 in J. Tachezy (Ed.), Hydrogenosomes and mitosomes: mitochondria of anaerobic eukaryotes, 2nd edition. Springer Cham.

Levine, A., Wine, E., Assa, A., Sigall Boneh, R., Shaoul, R., Kori, M., Cohen, S., Peleg, S., Shamali, H., On, A., Millman, P., Abramas, L., Ziv-Baran,T., Grant, S., Abitbol, G., Dunn, K.A., Bielawski, J.P. and Van Limbergen, J. 2019. Crohn’s Disease Exclusion Diet Plus Partial Enteral Nutrition Induces Sustained Remission in a Randomized Controlled Trial. Gastroenterology 157: 440-450

Louropoulou, E., Gledhill, M., Browning, T.J., Desai, D.K., Barraqueta, J.M., Tonnard, M., Sarthou, G., Planquette, H., Bowie, A.R., Schmitz, R.A., LaRoche, J. and Achterberg, E.P. 2019. Regulation of the phytoplankton Heme b iron pool during the North Atlantic spring bloom. Front Microbiol. 10: 1566.

Maguire, F., Rehman, M.A., Carrillo, C., Diarra, M.S. and Beiko, R.G. 2019. Identification of primary antimicrobial resistance drivers in agricultural nontyphoidal Salmonella enterica serovars by using machine learning. mSystems 4(4); pii: e00211-219.

McCain, J.S.P and Bertrand, E.M. 2019. Prediction and consequences of cofragmentation in metaproteomics. J. Proteome Res. 18: 3555-3566.

Michl, S.C., Beyer, M., Ratten, J.M., Hasler, M., LaRoche, J. and Schulz, C. 2019. A diet-change modulates the previously established bacterial gut community injuveile brown trout (Salmo trutta). Sci Rep. 9(1): 2339.

Mingrone, J., Susko, E. and Bielawski, J. 2019. ModL: exploring and restoring regularity when testing for positive selection. Bioinformatics 35: 2545-2554.

More, K., Simpson, A.G.B. and Hess, S. 2019. Two new marine species of Placopus (Vampyrellida, Rhizaria) that perforate the theca of Tetraselmis (Chlorodendrales, Viridiplantae). J. Eukaryot. Microbiol. 66: 560-573.

Muñoz-Gómez, S.A., Durnin, K., Eme, L., Paight, C., Lane, C.E., Saffo, M.B. and Slamovits, C.H. 2019. Nephromyces represents a diverse and novel lineage of the apicomplexa that has retained apicoplasts. Genome Biol Evol. 11(10): 2727-2740.

Muñoz-Gómez, S.A., Hess, S., Burger, G., Lang, B.F., Susko, E., Slamovits, C.H. and Roger, A.J. 2019. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife Feb. 21; 8. pii: e42535.

Nadukkalam Ravindran, P., Bentzen, P., Bradbury, I.R. and Beiko, R.G. 2019. RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data. Mol. Ecol. Resour. 19: 272-282.

Najle, S.R., Hernández, J., Ocaña-Pallarès, E., García Siburu, N., Nusblat, A.D., Nudel, C.B., Slamovits, C.H. and Uttaro, A.D. 2019. Genome-wide transcriptional analysis of Tetrahymena thermophile response to exogenous cholesterol. J. Eukaryot. Microbiol., Nov 9, doi:10.1111/jeu.12774.

Nearing, J.T., Connors, J., Whitehouse, S., Van Limbergen, J., Macdonald, T., Kulkarni, K. and Langille, M.G.I. 2019. Infectious complications are associated with alterations in the gut microbiome in pediatric patients with acute lymphoblastic leukemia. Front Cell. Infect. Microbiol. 9: 28.

Novick, A. and Doolittle, W.F. 2019. How microbes “jeopardize” the modern synthesis. PLoS Genet. 15: e1008166.

O’Malley, M.A., Leger, M.M., Wideman, J.G. and Ruiz-Trillo, I. 2019. Concepts of the last eukaryotic common ancestor. Nature Ecol. Evol. 3: 338-344.

Paight, C., Slamovits, C.H. Saffo, M.B. and Lane, C.E. 2019. Nephromyces encodes a urate metabolism pathway and predicted peroxisomes, demonstrating that these are not ancient losses of Apicomplexans. Genome Biol. Evol. 11: 41-53.

Saito, M.A., Bertrand, E.M. Duffy, M.E., Gaylord, D.A., Held, N.A., Hervey, W.J. 4th, Hettich, R.L., Jagtap, P.D., Janech, M.G., Kinkade, D.B., Leary, D.H., McIlvin, M.R., Moore, E.K., Morris, R.M., Neely, B.A., Nunn, B.L., Saunders, J.K., Shepherd, A.I., Symmonds, N.I. and Walsh, D.A. 2019. Progress and challenges in ocean metaproteomics and proposed best practices for data sharing. J. Proteome Res. 18: 1461-1476.

Sibbald, S.J., Hopkins, J.F., Filloramo, G.V. and Archibald, J.M. 2019. Ubiquitin fusion proteins in complex algae: implications for the spread of eukaryotic photosynthesis. BMC Genomics 20: 38.

Simpson, A.G.B. and Cepicka, I. 2019. Amitochondriate protists (Diplomonads, Parabasalids and Oxymonads). In Encyclopedia of Microbiology, 4th Edition, Elsevier.

Singh et al. [21 co-authors, incl. Langille, M.G.I.] 2019. Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway. Nat. Commun. 10: 89.

Tikhonenkov, D.V., Jhin, S.H., Eglit, Y., Miller, K., Plotnikov, A., Simpson, A.G.B. and Park, J.S. 2019. Ecological and evolutionary patterns in the enigmatic protest genus Percolomonas (Heterolobosea; Discoba) from diverse habitats. PLoS One 14(8): e0216188.

Wang, H.-C., Susko, E. and Roger, A.J. 2019. The relative importance of modeling site pattern heterogeneity versus partition-wise heterotachy in phylogenomic inference. Syst. Biol. 68: 1003- 1019.

Wideman, J.G., Novick, A., Munoz-Gomez, S. and Doolittle, W.F. 2019. Neutral evolution of cellular phenotypes. Curr. Op. Gen. Dev. 58-59: 87-94.

Wideman, J.G., Inkpen, S.A., Doolittle, W.F. and Richards, T.A. 2019. Philos. Trans. R Soc. Lond. B Biol. Sci. 374: 20190100.

Wideman, J.G., Lax, G., Leonard, G., Milner, D.S., Rodríguez-Martínez, R., Simpson, A.G.B. and Redfield, R.J. 2019. Relative mutation rates in nucleomorph-bearing algae. Genome Biol. Evol. 11: 1045-1053.

Willis, C., Desai, D. and LaRoche, J. 2019. Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the northern north Atlantic. FEMS Microbiol. Lett. 366:; pii: fnz152.

Wu, M., McCain, J.S.P., Rowland, E., Middag, R., Sandgren, M., Allen, A.E. and Bertrand, E.M. 2019. Manganese and iron deficiency in southern ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators. Nat. Commun. 10: 3582.

Youssef, N., Budd, A. and Bielawski, J.P. 2019. Introduction to Genome Biology and Diversity. In Evolutionary Genomics: Statistical and Computational Methods, Maria Anisimova (ed.), 2nd edition, pp. 3-32, Humana press.

Yurgel, S.N., Nearing J.T., Douglas G.M. and Langille M.G.I. 2019. Metagenomic functional shifts to plant induced environmental changes. Front Microbiol. 10: 1682.

Zorz, J., Willis, C., Comeau, A.M., Langille, M.G.I. Johnson, C.L., Li, W.K.W. and LaRoche, J. 2019. Drivers of regional bacterial community structure and diversity in the northwest Atlantic Ocean. Front Microbiol. 10: 281.

 

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