Publications

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Recent publications (last two years).

See full list of publications (2008-2022) here.

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2022

Banerjee et al. [incl. F. Maguire] (2022) Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, beta, delta, and omicron variants. Med NY (Cell Press, Apr. 2022). doi: 10.1016/j.medj.2022.04.002.

Bertrand, E.M., Bannon, C., Rapp, I. (2022) Community Interaction Co-Limitation: Nutrient Limitation in a Marine Microbial Community Context. Frontiers in Microbiology, in press.

Bjorndahl P, Bielawski JP, Liu L, Zhou W, Gu H. (2022) Novel Application of Survival Models for Predicting Microbial Community Transitions with Variable Selection for Environmental DNA. Appl. Environ Microbiol. 88(6): e0214621.

Blaxter, M. et al. [incl. Archibald, J. M.]. 2022. Why sequence all eukaryotes? Proc. Natl. Acad. Sci. USA 119(4): e2115636118.

Chen X, Wei W, Xiao X, Wallace D, Hu C, Zhang L, Batt J, Liu J, Gonsior M, Zhang Y, LaRoche J, Hill P, Xu D, Wang J, Jiao N, Zhang R. (2022) Heterogeneous viral contribution to dissolved organic matter processing in a long-term macrocosm experiment. Environ Int. 158: 106950.

Doolittle, W.F. (2022) All about levels: Transposable elements as selfish DNAs and drivers of evolution. Biology and Philosophy, in press.

Duerschlag J, Mohr W, Ferdelman TG, LaRoche J, Desai D, Croot PL, Voß D, Zielinski O, Lavik G, Littmann S, Martínez-Pérez C, Tschitschko B, Bartlau N, Osterholz H, Dittmar T, Kuypers MMM. (2022) Niche partitioning by photosynthetic plankton as a driver of CO2-fixation across the oligotrophic South Pacific Subtropical Ocean. ISME J. 16(2):465-476.

Duguay BA, Herod A, Pringle ES, Monro SMA, Hetu M, Cameron CG, McFarland SA, McCormick C. (2022) Photodynamic inactivation of human coronaviruses. Viruses 14(1): 110.

Ebenezer, V., Y Hu, O Carnicer, AJ Irwin, MJ Follows, ZV Finkel (2022) Elemental and macromolecular composition of the marine Chloropicophyceae, a major group of oceanic photosynthetic picoeukaryotes. Limnology & Oceanography 67: 540-551.

Griffiths et al. (incl. F. Maguire) (2022) Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. GigaScience 11:giac003.

Herod, A., Emond-Rheault, J-G, Tamber, S., Goodridge, L., Levesque, R.C., Rohde, J. (2022) Genomic and phenotypic analysis of SspH1 identifies a new Salmonella effector, SspH3. Mol. Microbiol. 117(4): 770-789.

Ho, L.S.T., Susko, E. (2022) Ancestral state reconstruction with large numbers of sequences and edge-length estimation. J. Mathematical Biol. 84:21.

Ho, L.S.T., Dinh, V. (2022) Searching for Minimal Optimal Neural Networks. Statistics and Probability Letters 183: 109353.

Joy-Warren, H.L., A.C. Alderkamp, G.L. van Dijken, L.J. Jabre, E.M. Bertrand, E.N. Baldonado, M.W. Glickman, K.M. Lewis, R. Middag, K. Seyitmuhammedov, K.E. Lowry, W. van de Poll, K.R. Arrigo (2022) Springtime phytoplankton responses to light and iron availability along the western Antarctic Peninsula. Limnology and Oceanography, Feb. 2022.

Karakach, T.K., F Taverna, J Barra (2022) Error Modelled Gene Expression Analysis (EMOGEA) provides a superior overview of time course RNA-Seq Measurements and low count gene expression. BioRxiv; doi: https://doi.org/10.1101/2022.02.18.481000

Kember M., Grandy S., Raudonis R., Cheng Z. (2022) Non-canonical host intracellular niche links to new antimicrobial resistance mechanism. Pathogens 11(2):220.

Kennedy et al. [incl. D. Gaston] (2022) NAD+ depletion enhances rovirus-induced oncolysis in multiple myeloma. Molecular Therapy Oncolytics 24: 695-706.

Kim JI, Maguire F, Tsang KK, Gouliouris T, Peacock SJ, McAllister TA, McArthur AG, Beiko RG. (2022) Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective. Clin Microbiol Rev., May 25: e0017921.

LaRoche, J. and Robicheau, B.M. (2022) The Pelagic Light-Dependent Microbiome. In: Stal, L.J., Cretoiu, M.S. (Eds), The Marine Microbiome. The Microbiomes of Humans, Animals, Plants, and the Environment, Vol 3, Springer, Cham. https://doi.org/10.1007/978-3-030-90383-1_9. Book chapter.

Lawniczak et al. [incl. Archibald, J. M.] 2022. Standards recommendations for the Earth BioGenome Project. Proc. Natl. Acad. Sci. USA 119, 4: e2115636118.

Lee, BD; Gitter, A; Greene, CS; Raschka, S; Maguire, F; Titus, AJ; Kessler, MD; Lee, AJ,; Chevrette, MG,; Stewart, PA; Britto-Borges, T; Cofer, EM; Yu, K-H; Carmona, JJ; Fertig, EJ; Kalinin, AA; Signal, B; Lengerich, BJ; Triche, TJ; Boca, SM (2022) Ten Quick Tips for Deep Learning in Biology. PLoS Comput. Biol. 18(3): e1009803.

Lewin et al. [incl. Archibald, J. M.] 2022. The Earth BioGenome Project 2020: starting the clock. Proc. Natl. Acad. Sci. USA. 119, 4: e2115636118.

Li, ZK, Y Zhang, W Li, AJ Irwin, ZV Finkel (2022) Conservation and architecture of housekeeping genes in the model marine diatom Thalassiosira pseudonana. New Phytologist 234: 1363-76.

Luo Y., Zhang W., Cheng Y., Lu Q., Guo Y., Wen G., Shao H., Cheng Z., Luo Q., and Zhang T. (2022) Droplet digital PCR-based detection and quantification of GyrA Thr-86-Ile mutation based fluoroquinolone-resistant Campylobacter jejuni. Microbiology Spectrum 10(2): e02769-21.

McCain, J.S.P. and E.M. Bertrand (2022) Phytoplankton antioxidant systems and their contributions to cellular elemental stoichiometry. Limnology and Oceanography Letters 7(2): 96-111.

McCain, J.S.P., A.E. Allen, E.M. Bertrand (2022) Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom. ISME Journal 16, 569–579.

Moran, M., E. B. Kujawinski, W. F. Schroer, S. A. Amin, N.R. Bates, E.M. Bertrand, R. Braakman, C. T. Brown, M. W Covert, S. C Doney, S. T Dyhrman, A. S Edison, A.M. Eren, N. M. Levine, L. Li, A. C. Ross, M. A. Saito, A. E. Santoro, D. Segrè, A. Shade, M. B Sullivan, A. Vardi. (2022) Microbial metabolites in the marine carbon cycle. Nature Microbiology 7, 508-523.

Muñoz-Gómez S.A., Susko E., Williamson K., Eme L., Slamovits C.H., Moreira D., López-García P. and Roger A.J. (2022) Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria. Nat. Ecol. Evol. 6: 253-262.

Mutshinda, CM, A Mishra, ZV Finkel, CE Widdicombe, AJ Irwin (2022) Bayesian two-part modeling of phytoplankton biomass and occurrence. Hydrobiologia 849: 1247-1300.

Nearing JT, Douglas GM, Hayes M, MacDonald J, Desai D, McCormick N, Jones JMA, Wright R, Dhanani A, Comeau AM, Langille MGI (2022). Microbiome differential abundance methods produce different results across 38 datasets. Nature Communications 13:342.s.

Nguyen, C.V., Ho, L.S.T., Xu, H., Dinh, V., Nguyen, B. (2022) Bayesian Pool-based Active Learning with Abstention Feedbacks. Neurocomputing 471: 242-250. 

Pérez S, Manosalva A, Colin N, González J, Habit E, Ruzzante DE, Górski K. (2022) Juvenile salmon influence on the diet of native Puye Galaxias maculatus in lakes and estuaries of Patagonian fjords. Biological Invasions 24: 81–92.

Pesaranghader A, Matwin S, Sokolova M, Grenier JC, Beiko RG, Hussin J. (2022) deepSimDEF: deep neural embeddings of gene products and Gene Ontology terms for functional analysis of genes. Bioinformatics 38: 3051-3061.

Robicheau, B., J. Tolman, E.M. Bertrand, J. LaRoche (2022) Highly resolved interannual phytoplankton community dynamics of the coastal Northwest Atlantic. ISME Commun. 2, 38.

Rossi, M., Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher (2022) MONI: A Pangenomic Index for Finding Maximal Exact Matches. J. Comput. Biol. 29(2): 169-187.

Rossi, M., Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher (2022) Finding Maximal Exact Matches Using the r-Index. J. Comput. Biol. 29(2): 188-194.

Salisbury SJ, McCracken GR, Perry R, Keefe D, Layton KKS, Kess T, Nugent CM, Bradbury IR, Koop BF, Ferguson MM, Ruzzante DE (2022). The genomic consistency of the loss of Anadromy in an Arctic Fish (Salvelinus alpinus). The American Naturalist 199(5): 617-635.

Salisbury SJ, Ruzzante DE. (2022) Genetic causes and consequences of sympatric morph divergence in Salmonidae: a search for mechanisms. Annual Reviews in Animal Biosciences, 10: 81-106.https://doi.org/10.1146/annurev-animal-051021-080709

Sanderson et al. [including F. Maguire, R.G. Beiko] (2022) Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents. BioRxiv; doi: https://doi.org/10.1101/2022.04.11.487771

Smith P, Beaumont L, Bernacchi CJ, Byrne M, Cheung W, Conant RT, Cotrufo F, Feng X, Janssens I, Jones H, Kirschbaum MUF, Kobayashi K, LaRoche J, Luo Y, McKechnie A, Penuelas J, Piao S, Robinson S, Sage RF, Sugget DJ, Thackeray SJ, Way D, Long SP. (2022) Essential outcomes for COP26. Global Change Biol. 28(1):1-3.

Sterling, S.M., Clair, T.A., Rotteveel, L., O’Driscoll, N., Houle, D., Halfyard, E., Keys, K. (2022) Kejimkujik calibrated catchments: A benchmark dataset for long-term impacts of terrestrial and freshwater acidification. Hydrological Processes 36(2): e14477.

Tashyreva, D., Simpson, A.G.B., Prokopchuk, G., Škodová-Sveráková, I, Butenko, A., Hammond, M., George, E.E., Flegontova, O., Záhonová, K., Faktorová, D., Yabuki, A., Horák, A., Keeling, P.J., Lukeš, J. (2022) Diplonemids – A review on “new” flagellates on the oceanic block. Protist 173: 125868.

Tymoshuk KM, Delgado ML, McCracken GR, Alonso M, Górski K, Habit E, Ruzzante DE. (2022) Drainage reversal with no lineage expansion, a case of competitive exclusion? The genetics of Galaxias maculatus in two connected trans-Andean systems. Biol. J. Linnean Soc. 136(2): 213-225.

Valenzuela-Aguayo F, McCracken GR, Manosalva A, Habit EA, Ruzzante DE. 2022. Connectivity, diversity, and hybridization between two endemic fish species (genus Percilia) in a complex temperate landscape. Conservation Genetics 23: 23-33.

Valenzuela-Valderas, K.N., Moreno-Hagelsieb, G.M., Rohde, J.R., Garduno, R.A. (2022). The Functional Differences between the GroEL Chaperonin of Escherichia coli and the HtpB Chaperonin of Legionella pneumophila Can Be Mapped to Specific Amino Acid Residues. Biomolecules 12(1): 59.

van Lersel, L., Janssen, R., Jones, M., Murakami, Y., Zeh, N. (2022) A practical fixed-parameter algorithm for constructing tree-child networks from multiple binary trees. Algorithmica 84: 917-960.

Vasquez-Rifo A., Cook J., McEwan D.L., Shikara D., Ausubel F.M., Di Cara F., Cheng Z. (2022) ABCDs of the relative contributions of Pseudomonas aeruginosa quorum sensing systems to virulence in diverse non-vertebrate hosts. mBio 13(2): e0041722.

Verburgt, C., KA Dunn, JP Bielawski, AR Otley, MB Heyman, W Sunseri, D Shouval, A Levine, T de Meij, JS Hyams, LA Denson, S Kugathasan, MA Benninga, WJ de Jonge, JE Van Limbergen* (2022) P711 stool microbiome communities predict remission in pediatric Crohn’s disease patients even after start of treatment. Journal of Crohn’s and Colitis 16(1): i608-i608.

Wijesundara N.M., Lee S.F., Davidson R., Cheng Z., and Rupasinghe V.H.P. (2022) Carvacrol suppresses inflammatory biomarkers production by lipoteichoic acid and peptidoglycan-stimulated human tonsil epithelial cells. Molecules 14(3):503.

Youssef N., Susko E., Roger A.J. and Bielawski J.P. (2022) Evolution of amino acid propensities under stability-mediated epistasis. Mol. Biol. Evol. 39(3): msac030.

Zhang, X., Hu, Y., Eme, L., Maruyama, S., Eveleigh, R. J. M., Curtis, B. A., Sibbald, S. J., Hopkins, J. F., Filloramo, G. V., van Wijk, K., & Archibald, J. M. 2022. TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. STAR Protocols 3: 101175.

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2021

Baldwin SJ, Slaine PD, Keltie E, Palit S, McKinnell SL, Longpre BE, Ko KR, Green J, Markle G, Kim JS, McCormick C., Frampton JP. (2021) Non-Woven Textiles Formed from Contact-Drawn Poly(Ethylene Oxide) Nanofibers Provide Tunable Filtration and Virucidal Properties via Entrapment of Silver Nanoparticles. ACS Applied Polymer Materials 3(8): 4245-55. 

Bastide, P., Ho, L.S.T. , Baele, G., Lemey, P., Suchard, M.A. 2021. Efficient Bayesian inference of general Gaussian models on large phylogenetic trees. Annals Applied Stat., 15(2): 971-997.

Behnke, J., Cohen, A.M., LaRoche, J. 2021. N-linked glycosylation enzymes in the diatom Thalassiosira oceanica exhibit a diel cycle in transcript abundance and favor for NXT-type sites. Sci. Rep. 11(1): 3227.

Bernardino, M. and R.G. Beiko (2021) Genome-scale prediction of bacterial promoters. 2021 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pp. 01-08, doi: 10.1109/CIBCB49929.2021.9562938. 

Bhatia, M.P., S Waterman, DO Burgess, PL Williams, RM Bundy, T Mellett, M Roberts, Bertrand, EM (2021) Glaciers and Nutrients in the Canadian Arctic Archipelago Marine System. Global Biogeochem. Cycles 35(8): e2021GB006976. 

Blais, C. & Archibald, J.M. 2021. The past, present and future of the Tree of Life. Curr Biol. R314-R321.

Bôto, M.L., Magalhães, C., Perdigão, R., Alexandrino, D.A.M., Fernandes, J.P., Bernabeu, A.M., Ramos, S., Carvalho, M.F., Semedo, M., LaRoche, J. , Almeida, C.M.R., Mucha A.P. 2021. Harnessing the potential of native microbial communities for bioremediation of oil spills in the Iberian Peninsula NW Coast. Front. Microbiol. 12: 633659.

Brunet, T.D.P., Doolittle, W.F., Bielawski, J.P. 2021. The role of purifying selection in the origin and maintenance of complex function. Studies Hist. Phil. Biol. Biomed. Sci. C., 87:125-135.

Carnicer, O., Irwin, A.J. , Finkel, Z.V. 2021. Traits influence dinoflagellate C:N:P. Eur. J. Phycology, 10.1080/09670262.2021.1914860.

Cook, J., Douglas, G.M., Zhang, J., Glick, B.R., Langille, M.G.I., Liu, K.H., Cheng, Z. 2021. Transcriptomic profiling of Brassica napus responses to Pseudomonas aeruginosa. Innate Immun. 27(2): 143-157.

Cram JA, Gray MW, McFarland K, Hollins A. (2021) Microbiota of Crassostrea virginica larvae during a hatchery crash and under normal production: Amplicon sequence data. Data Brief 40:107755. 

Daboor, S.M., Rohde, J.R., Cheng, Z. 2021. Disruption of the extracellular polymeric network of Pseudomonas aeruginosa biofilms by alginate lyase enhances pathogen eradication by antibiotics. J. Cyst. Fibros. 20(2):264-270.

Daboor, S., Raudonis R., and Cheng Z. (2021) Characterizations of the viability and gene expression of dispersal cells from Pseudomonas aeruginosa biofilms released by alginate lyase and tobramycin. PLoS One 16(10): e0258950. 

Davies T, Watts S, McClure K, Migicovsky Z, Myles S (2021) Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii). PLoS ONE 17(3): e0250751. 

DeClercq V, Nearing JT, Langille MGI (2021) Investigation of the impact of commonly used medications on the oral microbiome of individuals living without major chronic conditions. PLoS One, 16(12): e0261032. 

Dinh, V., Ho, L.S.T. (2021). Convergence of maximum likelihood supertree reconstruction. AIMS Mathematics 6(8): 8870-8883 

Doolittle, W.F. and Neto, C.A. (2021) A chemostat model for evolution by persistence, clade selection and its explanatory autonomy. Philosophy of Science, in press. 

Doolittle, W.F. 2021. All about levels: Transposable elements as selfish DNAs and drivers of evolution. Biology and Philosophy, in press.

Douglas, G.M., Langille, M.G.I. 2021. A primer and discussion on DNA-based microbiome data and related bioinformatic analyses. Peer Community in Genomics, doi.org/10.31219/osf.io/3dybg.

Dunn, K.A., Connors, J., Bielawski, J.P., Nearing, J.T., Langille, M.G.I., Van Limbergen, J., Fernandez, C.V., MacDonald, T., Kulkarni, K. 2021. Investigating the gut microbial community and genes in children with differing levels of change in serum asparaginase activity during pegaspargase treatment for acute lymphoblastic leukemia. Leuk. Lymphoma 62(4): 927-936.

Dunn, K.A, Forbrigger Z, Connors J, Rahman M, Cohen A, Van Limbergen J.*, Langille MGI, Stadnyk AW, Bielawski JP, Penny S, MacDonald T, Kulkarni K (2021) Gut bacterial gene changes following pegaspargase treatment in pediatric patients with acute lymphoblastic leukemia. Leukemia & Lymphoma, 62(13):3244-3255. 

Einfeldt, A.L., Kess, T., Wringe, B., Bradbury, I.R., Fisher, J., den Heyer, C., Ruzzante, D.E., Bentzen, P. 2021. Chromosome level reference of Atlantic halibut Hippoglossus hippoglossus provides insight into the evolution of sexual determination systems. Mol. Ecol. Res. 21: 1686-1696.

Ettahi, K., Lhee, D., Sung, J.Y., Simpson, A.G.B. , Park, J.S., Yoon, H.S. 2021. Evolutionary history of mitochondrial genomes in Discoba, including the extreme Halophile Pleurostomum flabellatum (Heterolobosea). Genome Biol. Evol. 13(2): evaa241.

Filloramo, G.V., Blanche, E., Curtis, B.A., Archibald, J.M. 2021. Re-examination of two diatom reference genomes using long-read sequencing. BMC Genomics, 22(1): 379.

Fürst-Jansen, J. M. R., de Vries, S. von Schwartzenberg, K. Archibald, J. M. & de Vries, J. (2021) Submergence of the filamentous Zygnematophyceae Mougeotia induces differential gene expression patterns associated with photosynthesis. Protoplasma, Dec. 22 doi: 10.1007/s00709-021-01730-1. 

González-Morales, N., Océane Marescal, Szilárd Szikora, Miklos Erdelyi, Péter Bíró, Tuana Mesquita, József Mihály, Frieder Schöck (2021) Oxoglutarate dehydrogenase coordinates myofibril growth by maintaining amino acid homeostasis. bioRxiv; doi: https://doi.org/10.1101/2021.12.13.472149. 

Haas, S., Robicheau, B.M., Subhadeep Rakshit, Tolman, J., Algar, C.K., LaRoche, J., Wallace, D.W.R. 2021. Physical mixing in coastal waters controls and decouples nitrification via biomass dilution. PNAS 118(18): e2004877118.

Hart, K.A., Kennedy, G.W., Sterling, S.M. (2021) Distribution, Drivers, and Threats of aluminum in groundwater in Nova Scotia, Canada. Water 13: 1578. 

Herman EK, Greninger A, van der Giezen M, Ginger ML, Ramirez-Macias I, Miller HC, Morgan MJ, Tsaousis AD, Velle K, Vargová R, Záhonová K, Najle SR, MacIntyre G, Muller N, Wittwer M, Zysset-Burri DC, Eliáš M, Slamovits CH, Weirauch MT, Fritz-Laylin L, Marciano-Cabral F, Puzon GJ, Walsh T, Chiu C, Dacks JB. (2021) Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri. BMC Biol. 19(1):142. 

Heiss, A.A., Warring, S.D., Lukacs, K., Favate, J., Yang, A., Gyaltshen, Y., Filardi, C., Simpson, A.G.B., Kim, E. 2021. Description of Imasa heleensis, gen. nov., sp. nov. (Imasidae, fam. nov.), a deep-branching marine Malawimonad and possible key taxon in understanding early eukaryotic evolution. J. Eukaryot. Microbiol. 68(2): e12837.

Horvath, R., Hawe, N., Lam, C., Mestnikov, K., Eji-Lasisi, M., Rohde, J., Sadowski, I. (2021) TORC1 signaling modulates Cdk8-dependent GAL gene expression in Saccharomyces cerevisiae. Genetics 219(4): iyab168. 

Horvathova, L., Žarsky, V., Panek, T., Derelle, R., Pyrih, J., Motyčkova, A., Klapšťova, V., Klimeš, V., Petrů, M., Vaitova, Z., Čepička, I., Harant, K., Gray, M.W., Guilvout, I., Francetic, O., Lang, B.F., Vlček, C., Tsaousis, A.D., Eliaš, M., and Doležal, P. 2021. Ancestral mitochondrial protein secretion machinery. Nature Commun., doi: https://doi.org/10.1101/790865.

Huang, Y., Ragush, C.M., Johnston, L.H., Hall, M.W., Beiko, R.G., Jamieson, R.C., Truelstrup, H.L. (2021) Changes in Bacterial Communities During Treatment of Municipal Wastewater in Arctic Wastewater Stabilization Ponds. Frontiers in Water 3: 710853. 

Inkpen, S.A., Doolittle, W.F. 2021. Adaptive regeneration across scales: Replicators and interactors from limbs to forests. Philosophy, Theory and Practice in Biology, 13: 1.

Jabre, L., A. E. Allen, J. S. P. McCain, J. P. McCrow, N. Tenenbaum, J. L. Spackeen, R. E. Sipler, B. R. Green, D. A. Bronk, D. A. Hutchins, E. M. Bertrand (2021) Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean. PNAS 118 (30): e2107238118. 

Jiao, N. et al. [34 authors incl. J. LaRoche) 2021. Correcting a major error in assessing organic carbon pollution in natural waters. Sci. Adv. 7, eabc7318.

Karimi, K., Farid, A.H., Myles, S., Miar, Y. 2021. Detection of selection signatures for response to Aleutian mink disease virus infection in American mink. Sci. Rep. 11(1): 2944.

Kenney, T. , Gu, H. , Huang, T. 2021. Poisson PCA: Poisson Measurement Error corrected PCA, with application to microbiome data. Biometrics, http://doi.org/10.1111/biom.13384.

Kess, T., Dempson JB, Lehnert SJ, Layton K, Einfeldt A, Bentzen P, Salisbury SJ, Messmer A, Duffy S, Ruzzante DE, Nugent CM, Ferguson MM, Leong JS, Koop BF, Bradbury IR. (2021) Genomic basis of extreme deep-water adaptation in sympatric Arctic charr (Salvelinus alpinus) morphs. Molecular Ecology, 30(18): 4415-4432. 

Kess, T., Einfeldt, A.L., Wringe, B., Lehnert, S.J., Layton, K.K.S., McBride, M., Robert, D., Fisher, J., Le Bris, A., den Heyer, C., Shackell, N., Ruzzante, D.E. , Bentzen, P., Bradbury, I.R. 2021. A putative structural variant and environmental variation associated with genomic divergence across the Northwest Atlantic in Atlantic Halibut. ICES J. Marine Sci., doi.org/10.1093/icesjms/fsab061.

Lax, G., Kolisko, M., Eglit, Y., Lee, W.J., Yubuki, N., Karnkowska, A., Leander, B.S., Burger, G., Keeling ,P.J., Simpson, A.G.B. 2021. Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Mol. Phylogenet. Evol. 159: 107088.

Lawniczak, M.K. et al. [50+ authors incl. Archibald, J.M.] 2021. Standards recommendations for the Earth BioGenome Project. Cell Genomics, in press.

Layton KKS, Snelgrove PVR, Dempson JB, Kess T, Lehnert SJ, Bentzen P, Duffy SJ, Messmer AM, Stanley RRE, DiBacco C, Salisbury SJ, Ruzzante DE, Nugent CM, Ferguson MM, Leong JS, Koop B, Bradbury IR. 2021. Genomic evidence of past and future climate-linked loss in a migratory Arctic fish. Nature Climate Change 11: 158-165.

Lewin, H.A. et al. [120+ authors incl. Archibald, J.M.] 2021. The Earth BioGenome Project 2020: starting the clock. Cell Genomics, in press.

Li, Z-K., Li, W., Zhang, Y., Hu, Y., Sheward, R., Irwin, A.J., Finkel, Z.V. 2021. Dynamic photophysiological stress response of a model diatom to ten environmental stresses. J Phycol. 57: 484-495.

Liang, Y., L. Bretherton, C.M. Brown, U. Passow, A.S. Quigg, A.J. Irwin, Z.V. Finkel 2021. Transcriptome-wide responses of aggregates of the diatom Odontella aurita to oil. Mar. Ecol. Prog. Ser., 671: 67-79.

Liu, L., Gu, H., Van Limbergen, J., Kenney, T. 2021. SuRF: A new method for sparse variable selection, with application in microbiome data analysis. Stat. Med. 40(4): 897-919.

MacNeil L, Missan S, Luo J, Trappenberg T, LaRoche J. (2021) Plankton classification with high-throughput submersible holographic microscopy and transfer learning. BMC Ecol Evol. 21(1): 1-11. 

Maculins et al. [22 authors incl. Rohde, J.] (2021) Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response. Elife 10: e62320. 

McCain, J.S.P., Tagliabue, A., Susko, E., Achterberg, E.P., Allen, E., Bertrand, E.M. (2021). Cellular costs underpin micronutrient limitation in phytoplankton. Science Advances 7: eabg6501. 

McCormick, N, Earle M, Ha C, Hakes L, Evans A, Anderson L, Stoddart AK, Langille MGI, Gagnon GA. (2021) Biological and physico-chemical mechanisms accelerating the acclimation of Mn-removing biofilters. Water Res. 207:117793. 

McGinty, N., A Barton, DG Johns, ZV Finkel, AJ Irwin (2021) Niche conservation in copepods between ocean basins. Ecography 44: 1653-1664. 

McGinty, N., Barton, A.D., Record, N.R., Finkel, Z.V. , Johns, D.G., Stock, C.A., Irwin, A.J. 2021. Anthropogenic climate change impacts on copepod trait biogeography. Glob. Chang Biol. 27(7): 1431-1442.

McKenna et al. [incl. Archibald, J.M.] 2021. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life. Wellcome Open Res. 6:254. 

Migicovsky, Z., Gardner, K.M., Richards, C., Thomas, Chao C., Schwaninger, H.R., Fazio, G., Zhong, G.Y., Myles, S. 2021. Genomic consequences of apple improvement. Hortic. Res. 8(1): 9.

Migicovsky, Z, Yeats TH, Watts S, Song J, Forney CF, Burgher-MacLellan K, Somers DJ, Vrebalov J, van Velzen R, Giovannoni JG, Rose JKC, Myles, S. (2021) Apple ripening is controlled by a NAC transcription factor. Frontiers in Genetics 12:671300. 

Migicovsky, Z, Cousins P, Jordan LM, Myles S., Striegler RK, Verdegaal P, Chitwood DH (2021) Grapevine rootstocks affect growth-related scion phenotypes. Plant Direct 5:e00324. 

Mirzayi C, et al. [incl. Langille, MGI] (2021) Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine 27:1885-1892. 

More, K. Simpson, A.G.B. & Hess, S. (2021) Description of the marine predator Sericomyxa perlucida gen. et sp. nov., a cultivated representative of the deepest branching lineage of vampyrellid amoebae (Vampyrellida, Rhizaria). Journal of Eukaryotic Microbiol. 68: e12864. 

Nanjappa, D., Y Liang, L Bretherton, C Brown, A Quigg, AJ Irwin, ZV Finkel (2021) Contrasting transcriptomic responses of a microbial eukaryotic community to oil and dispersant. Environmental Pollution 288: 117774. 

Nearing, J.T., Langille, M.G.I. 2021. Identifying biases and their potential solutions in human microbiome studies. Microbiome, 9: 113.

Novick, A., Doolittle, W.F. 2021. ’Species’ without species. Studies in History and Philosophy of Science, in press.

Petrou, E.L., Fuentes-Pardo, A.P., Rogers, L.A., Orobko, M., Tarpey, C., Jiménez-Hidalgo, I., Moss, M.L., Yang, D., Pitcher, T.J., Sandell, T., Lowry, D., Ruzzante, D.E., Hauser, L. 2021. Functional genetic diversity in an exploited marine species and its relevance to fisheries management. Proc. Biol. Sci. 288(1945): 20202398.

Pipaliya, S., Santos, R., Salas-Leiva, D., Balmer, E.A., Wirdnam, C.D., Roger, A.J., Hehl, A.B., Faso, C., Dacks, J.B. 2021. Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata. BMC Biol., doi: https://doi.org/10.1101/2021.02.11.43067 3

Price, G.W., Langille, M.G.I., Yurgel, S.N. 2021. Microbial co-occurrence network analysis of soils receiving short- and long-term applications of alkaline treated biosolids. Sci. Total Environ. 751: 141687.

Prystupa, S., McCracken, G.R., Perry, R., Ruzzante, D.E. 2021. Population Abundance and Structure in Yukon Arctic Grayling Using Genomics and Close-Kin Mark-Recapture. Ecol. Evol. 11: 4763-4773.

Rakib, M.R.H., Zeh, N., Milios, E. (2021) Efficient clustering of short text streams using online-offline clustering. Proceedings of the 21st ACM Symposium on Document Engineering, Article 5: 1-10. 

Roger A.J., Susko E., Leger, M.M. 2021. Evolution: Reconstructing the timeline of Eukaryogenesis. Curr. Biol. 31(4): R193-R196.

Rotteveel, L. and Sterling, S.M. 2021. The Surface Water Chemistry (SWatCh) database: A standardized global database of water chemistry to facilitate large-sample hydrological research. Earth Syst. Sci. Data Discuss [preprint in review] https://doi.org/10.5194/essd-2021-43

Rowarth, N.M., Curtis, B.A., Einfeldt, A.L., Archibald, J.M., Lacroix, C.R., Gunawardena, A.H.L.A.N. 2021. RNA-Seq analysis reveals potential regulators involved in program cell death and remodeling of lace plant leaves (Aponogeton madagascariensis). BMC Plant Biol., 21: 375.

Rybarski, A.E., Nitsche, F., Park, J.S., Filz, P., Schmidt, P., Kondo, R., Simpson, A.G.B., Arndt, H. (2021) Revision of the phylogeny of Placididea (Stramenopiles): Molecular and morphological diversity of novel placidid protists from extreme aquatic environments. European J. Protistology 81: 125809. 8 

Saeidi, M., Milios, E. and Zeh, N. (2021) Graph convolutional networks for categorizing online harassment on Twitter. 20th IEEE International Conference on Machine Learning and Applications (ICMLA), pp. 946-951. 

Saeidi, M., Milios, E., Zeh, N. (2021) Graph representation learning in Document Wikification. In: Barney Smith, E.H., Pal, U. (Eds), Document Analysis and Recognition – ICDAR 2021 Workshops. Lecture Notes in Computer Science, Vol. 12917, Springer, Cham. 

Saeidi, M., Milios, E., Zeh, N. (2021) Contextualized knowledge base sense embeddings in Word Sense Disambiguation. In: Barney Smith, E.H., Pal, U. (eds), Document Analysis and Recognition – ICDAR 2021 Workshops. Lecture Notes in Computer Science, Vol. 12917, Springer, Cham. 

Salas-Leiva, D.E., Tromer, E.C., Curtis, B.A., Jerlstrom-Hultqvist, J., Kolisko, M., Yi, Z., Salas-Leiva, J.S., Gallot-Lavallée, L., Kops, J.J.P.L., Archibald, J.M., Simpson, A.G.B., & Roger, A.J. 2021. Genomic analysis finds no evidence of canonical eukaryotic DNA processing systems in a free-living protist. Nat. Comm. 12:6003.

Sibbald, S.J., Lawton, M., Archibald, J.M. 2021. Mitochondrial genome evolution in pelagophyte algae. Genome Biol. Evol. 13(3): evab018.

Slaine, P.D., Kleer, M., Duguay, B.A., Pringle, E.S., Kadijk, E., Ying, S., Balgi, A., Roberge, M., McCormick, C., Khaperskyy, D.A. 2021. Thiopurines activate an antiviral unfolded protein response that blocks influenza A virus glycoprotein accumulation. J. Virol. Mar 24: JVI.00453-21.

Stairs C.W., Táborski P., Kolisko M., Pánek T., Eme L., Hradilová M., Vlček C., Jerlström-Hultqvist J., Roger A.J. and Čepička I. (2021) Anaeramoebae are a deeply divergent lineage of eukaryotes that clarify the transition from anaerobic mitochondria to hydrogenosomes. Curr. Biol. 31: 5605-5612. 

Sultan M, Nearing JT, Brown JM, Hyynh TT, Cruickshank BM, Lamoureaux E, Vidovic D, Dahn ML, Fernando W, Coyle KM, Giacomantonio CA, Langille MGI, Marcato P 2021. An in vivo genome-wide shRNA screen identifies BCL6 as a targetable paclitaxel resistance mediator in breast cancer. Mol. Oncology, 15(8): 2046-2064.

Susko, E., Steel, M., Roger, A.J. 2021. Conditions under which distribution of edge length ratios on phylogenetic trees can be used to order evolutionary events. J. Theor. Biol. 526: 110788.

Susko E. and Roger A.J. 2021. Long branch attraction biases in phylogenetics. Syst. Biol. 70(4): 838-843.

Tice AK, Žihala D, Pánek T, Jones RE, Salomaki E, Nenarokov S, Burki F, Eliáš M, Eme L, Roger A.J., Rokas A, Shen X, Strassert JFH, Kolísko M, Brown MW. (2021) PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PLoS Biol. 19(8): e3001365. 

Tsang, K.K., Maguire, F., Zubyk, H.L., Chou, S., Edalatmand, A., Wright, G.D., Beiko, R.G., McArthur, A.G. 2021. Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance. Microb. Genom. Jan; 7(1): 000500.

Valach, M., Gonzalez Alcazar, J.A., Sarrasin, M., Lang, B.F., Gray, M.W., Burger, G. 2021. An unexpectedly complex mitoribosome in Andalucia godoyi, a protist with the most bacteria-like mitochondrial genome. Mol. Biol. Evol. 38(3): 788-804.

van Lersel, L., Janssen, R., Jones, M., Murakami, Y., Zeh, N. (2021) A unifying characterization of tree-based networks and orchard networks using cherry covers. Advances in Applied Math 129: 102222. 

Verburgt, C., KA Dunn, J Bielawski, A Otley, M Heyman, W Sunseri, D Shouval, A Levine, T de Meij, J Hyams, L Denson, S Kugathasan, M Benninga, W de Jonge, J Van Limbergen* (2021) OP32 Stool microbiome communities predict remission in treatment-naïve Pediatric Crohn’s Disease patients. Journal of Crohn’s and Colitis 15 (Supplement 1): S030. 

Watts S, McElroy M, Migicovsky Z, Maassen H, van Velzen R, Myles S (2021) Cannabis labelling is associated with genetic variation in terpene synthase genes. Nature Plants 7:1330–1334. 

Watts S, Migicovsky Z, McClure K, Yu C, Amyotte B, Baker T, Bowlby D, Burgher-MacLellan K, Butler L, Donald RG, Fan L, Fillmore S, Flewelling J, Gardner K, Hodges M, Hughes T, Jagadeesan V, Lewis N, MacDonell E, MacVicar L, McElroy M, Money D, O’Hara M, Ong Q, Vinqvist-Tymchuk M, Rupasinghe HPV, DeLong JM, Forney CF, Song J, Myles S (2021) Quantifying apple diversity: a 9 phenomic characterization of Canada’s Apple Biodiversity Collection. Plants, People, Planet 3(6): 747-760. 

Wijesundara, N.M., Lee, S.F., Cheng, Z., Davidson, R., Rupasinghe, H.P.V. 2021. Carvacrol exhibits rapid bactericidal activity against Streptococcus pyogenes through cell membrane damage. Sci. Rep. 11(1): 1487.

Williams, P.L., D Burgess, SN Waterman, M Roberts, EM Bertrand, M Bhatia (2021) Nutrient and Carbon Export from a Tidewater Glacier to the Coastal Ocean in the Canadian Arctic Archipelago. Journal of Geophysical Research Biogeosci. 126(9): e2021JG006289. 

Wright, V., Archibald, J.M., Beinart, R., Dawson, M.N., Hentschel, U., Keeling, P.J., Lopez, J.V., Martín-Durán, J.M., Petersen, J.M., Sigwart, J.D., Simakov, O., Sutherland, K.R., Sweet, M., Talbot, N., Thompson, A.W., Bender, S., Harrison, P.W., Rajan, J., Cochrane, G., Berriman, M., Lawniczak, M. & Blaxter, M. 2021. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life. Wellcome Open Res. 6:254

Wright, R.J., Bosch, R., Langille, M.G.I., Gibson, M.I., Christie-Oleza, J.A. 2021. A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere. Microbiome, 10.21203/rs.3.rs-104576/v1

Wright, R.J., Langille, M.G.I., Walker, T.R. 2021. Food or just a free ride? A meta-analysis reveals the global diversity of the plastisphere. ISME J., 15: 789-806.

Wringe, B., Bradbury, I.R., Fisher, J., den Heyer, C., Ruzzante, D.E., Bentzen, P. 2021. Chromosome level reference of Atlantic halibut Hippoglossus hippoglossus provides insight into the evolution of sexual determination systems. Mol. Ecol. Res., online https://doi.org/10.1111/1755-0998.13369

Youssef, N., Susko, E., Roger, A.J. and Bielawski, J.P. (2021) Shifts in amino acid preferences as proteins evolve: a synthesis of experimental and theoretical work. Protein Science 30:2009-2028. 

Zeng Q, Yang Z, Wang F, Li D, Liu Y, Wang D, Zhao X, Li Y, Wang Y, Feng X, Chen J, Li Y, Zheng Y, Kenney T, Gu H, Feng S, Li S, He Y, Xu X, Dai W. (2021) Association between metabolic status and gut microbiome in obese populations. Microb. Genom. 7(8):000639. 

Zhang, J., Cook, J., Nearing, J.T., Zhang, J., Raudonis, R., Glick, B.R., Langille, M.G.I., Cheng, Z. 2021. Harnessing the plant microbiome to promote the growth of agricultural crops. Microbiol. Res. 245: 126690.

Zhang, T., Li C., Zhang Z., Wang C., Roger A.J. and Gao F. 2021. Characterization and comparative analyses of mitochondrial genomes in single-celled eukaryotes to shed light on the diversity and evolution of linear molecular architecture. Int. J. Mol. Sci. 22:2546.

Zhang, Y., Li, Z., Schulz, K.G., Hu, Y., Irwin, A.J., Finkel, Z.V. 2021. Growth- dependent changes in elemental stoichiometry and macromolecular allocation in the coccolithophore Emiliania huxleyi under different environmental conditions. Limnol. Oceanogr., 66(8): 2999-3009.

Žárský V., Klimeš V., Pačes J., Vlček C., Hradilová M., Beneš V., Nývltová E., Hrdý I., Pyrih J., Mach J., Barlow L., Stairs C.W., Eme L., Hall N., Eliáš M., Dacks J.B., Roger, A.J. and Tachezy J. 2021. The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba. Mol. Biol. Evol. 38(6): 2240-2259.