Publications

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Recent publications (last two years).

See full list of publications (2008-2021) here.

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2021

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.

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.

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.

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.

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.

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.

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.

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.

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.

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., 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.

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.

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.

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.

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.

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.

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.

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.

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.

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. Cell Genomics. In Press.

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

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.

W

2020

Alcock et al. [24 authors incl. Beiko, R.G.] 2020. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48: D517-D525.

Amirian, M.M., Towers, I.N., Jovanoski, Z., Irwin, A.J. 2020. Memory and mutualism in species sustainability: A time-fractional Lotka-Volterra model with harvesting. Heliyon 6(9): e04816.

Archibald, J.M. 2020. Cryptomonads. Curr. Biol. 30(19): R1114-R1116

Attwood, KM, Robichaud A, Westhaver LP, Castle EL, Brandman DM, Balgi AD, Roberge M, Colp P, Croul S, Kim I, McCormick C , Corcoran JA, Weeks A. 2020. Raloxifene prevents stress granule dissolution, impairs translational control and promotes cell death during hypoxia in glioblastoma cells. Cell Death Dis.11: 989.

Behnke, J. & LaRoche, J. 2020. Iron uptake proteins in algae and the role of Iron Starvation-Induced Proteins (ISIPs). Eur. J. Phycol. 55(3), 339-360.

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, Chapter 2. Boca Ratoni.

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.

Crouse, A., Schramm, C., Emond-Rheault, J.G., Herod, A., Kerhoas, M., Rohde, J., Gruenheid, S., Kukavica-Ibrulj, I., Boyle, B., Greenwood, C.M.T., Goodridge, L.D., Garduno, R., Levesque, R.C., Malo, D., Daigle, F. 2020. Combining whole-genome sequencing and multimodel phenotyping to identify genetic predictors of Salmonella virulence. mSphere 5(3): e00293-20.

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, 5(3): e00364-20.

Delgado, M.L., Ruzzante, D.E. 2020. Investigating diadromy in fishes and its loss in an -omics era. iScience 23(12):101837.

Delgado, M.L., Manosalva, A., Urbina, M.A., Habit, E., Link, O., Ruzzante, D.E. 2020. Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments. Mol. Ecol. 29(24): 4857-4870.

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., 103: 1025-1048.

de Vries, J., de Vries, S., Archibald, J.M., Slamovits, C.H. 2020. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiol. Ecol. 96(11): fiaa184.

Dinh, V. and Ho, L.S.T. 2020. Consistent feature selection for analytic deep neural networks. Neural Information Processing Systems (NeurIPS 2020), arXiv:2010.08097v1.

Doolittle, W.F. 2020. Could this pandemic usher in evolution’s next major transition?. Curr Biol., 30: R841-R870.

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

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

Doolittle, W.F. 2020. Is the Earth an organism? Aeon, Dec 3.

Douglas, G.M., Bielawski, J.P., Langille, M.G.I. 2020. Re-evaluating the relationship between missing heritability and the microbiome. Microbiome, 8: 87.

Douglas, G.M., Maffei, V.J., Zaneveld, J.R., Yurgel, S.N., Brown, J.R., Taylor, C.M., Huttenhower, C., Langille, M.G.I 2020. PICRUSt2 for prediction of metagenome functions. Nat. Biotechnol. 38(6): 685-688.

Faktorová, D., et al. [incl. Slamovits, C.H.] 2020. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat. Methods 17(5): 481-494.

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. doi: 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., 28(6): 428-430.

Gallot-Lavallée, L. and Archibald, J.M. 2020. Evolutionary biology: Viral rhodopsins illuminate algal evolution. Curr. Biol. 30(24): R1469-R1471.

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, 125(3): e2019JCO15646.

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.

Hassler, G., Tolkoff, M.R., Allen, W.L., Ho, L.S.T., Lemey, P., Suchard, M.A. 2020. Inferring phenotypic trait evolution on large trees with many incomplete measurements. J. Amer. Stat. Assoc., doi: 10.1080/01621459.2020.1799812.

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.

Ho, L.S.T., Schaeffer, H., Tran, G., Ward, R. 2020. Recovery guarantees for polynomial coefficients from weakly dependent data with outliers. J. Approx. Theory 259: 105472.

Ho, L.S.T., Nguyen, B.T., Dinh, V., Nguyen, D. 2020. Posterior concentration and fast convergence rates for generalized Bayesian learning. Information Sci. 538: 372-383.

Jabre, L. and Bertrand, E.M. 2020. Interactive effects of iron and temperature on the growth of Fragilariopsis cylindrus. Limnology and Oceanography Letters, 5: 363-370.

Jabre, L., Allen, A.E., McCain, J.S.P., McCrow, J.P., Tenenbaum, N., Spackeen, J.E., Sipler, R.E., Green, B.R., Bronk, D.A., Hutchins, D.A., Bertrand, E.M. 2020 Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean. PNAS, doi: 10.1073/pnas.2107238118.

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., 26(7):1026-1037.

Jones, C.T., Youssef, N., Susko, E., Bielawski, J.P. 2020. A phenotype-genotype codon model for detecting adaptive evolution. Syst Biol. 69(4): 722-738.

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.

Kenney, T., Gao, J., Gu, H. 2020. Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes. BMC Bioinformatics 21(1): 450.

Kenney, T., Gu, H. Huang, T. 2020. Poisson PCA: Poisson measurement error corrected PCA, with application to microbiome data. Biometrics; Oct 2. doi: 10.1111/biom.13384.

Kim, J.I., Jeong, M., Archibald, J.M., Shin, W. 2020. Comparative plastid genomics of non-photosynthetic Chrysophytes: Genome reduction and compaction. Front Plant Sci.11: 572703.

Kolisko, M., Flegontova, O., Karnkowska, A., Lax, G., Maritz, J.M., Pánek, T., Táborský, P., Carlton, J.M., Čepička, I., Horák, A., Lukeš, J., Simpson, A.G.B., Tai, V. 2020. EukRef-excavates: seven curated SSU ribosomal RNA gene databases. Database (Oxford), Nov 20: baaa080.

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, 135(5): 1055-1068.

Lax, G., Simpson, A.G.B. 2020. The molecular diversity of phagotrophic Euglenids examined using single-cell methods. Protist 171(5): 125757.

Li, Z., Li, W., Zhang, Y., Hu, Y., Sheward, R., Irwin, A.J. , Finkel, Z.V. 2020. Dynamic photophysiological stress response of a model diatom to ten environmental stresses. J. Phycol. 57(2): 484-495.

Li, Z.K., Dai, G.Z., Zhang, Y., Xu, K., Li, Z.K.,Bretherton, L., Finkel, Z.V., Irwin, A.J., Juneau, P., Qiu, B.S. 2020. Photosynthetic adaptation to light availability shapes the ecological success of bloom-forming cyanobacterium Pseudanabaena to iron limitation. J. Phycol. 56(6): 1457-1467.

Linquist, S., Doolittle, W.F. and Palazzo, A.F. 2020. Getting clear about the F-word in genomics. PLoS Genetics 16(4): e1008702.

Maguire, F., Jia, B., Gray, K.L., Lau, W.Y.V., Beiko, R.G., Brinkman, F.S.L. 2020. Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands. Microb. Genom. 6(10): mgen000436.

Matzov, D., Taoka, M., Nobe, Y., Yamauchi, Y., Halfon, Y., Asis, N., Zimermann, E., Rozenberg, H., Bashan, A., Bhushan, S., Isobe, T., Gray, M.W., Yonath, A., Shalev-Benami, M. 2020. Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis. Nucleic Acids Res. 48(20): 11750-11761.

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., DOI: 10.1515/ijb-2019-0038.

Mutshinda, C.M., Finkel, Z.V., Widdicombe, C.E., Irwin, A.J. 2020. A trait-based clustering for phytoplankton biomass modeling and prediction. Diversity 12: 295.

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