Publications

W

Recent publications (last two years).

See full list of publications (2008-2024) here.

W

2024

Cayer, L.G.J., Surendran, A., Karakach, T., Aukema, H.M., Ravandi, A. (2024) Valvular Prostaglandins are elevated in severe human aortic valve stenosis. Arteriosclerosis, Thrombosis, and Vascular Biol., advance online 10.1161/ATVBAHA.123.320001.

Collienne, L., Whidden, C., Gavryushkin, A. (2024) Ranked subtree prune and regraft. Bull. Math Biol. 86: 24.

Davoudi, P., Do, D.N., Colombo, S., Rathgeber, B., Sargolzaei, M., Plastow, G., Wang, Z., Hu, G., Valipour, S., Miar, Y.(2024) Genome-wide association studies for economically important traits in mink using copy number variation. Scientific Rep. 14: 24.

Eglit, Y., Shiratori, T., Jerlström-Hultqvist, J., Williamson, K., Roger, A.J., Ishida, K.I., Simpson, A.G.B. (2024) Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora. Curr. Biol. 34: 451–459.

Haider, D., Hall, M.W., LaRoche, J., Beiko, R.G. (2024) Mock microbial community meta-analysis using different trimming of amplicon read lengths. Environ. Microbiol. 26: e16566.

Markowski, E. & Susko, E. (2024) Performance of topology tests under extreme selection bias. Mol. Biol. Evol. 41: msad280.

Northrup, V., Perez, L. J., Edgett, B. A., Karakach, T., Simpson, J.A., Brunt, K.R. (2024) Intron retention is a mechanism of erythropoietin regulation in brain cell models. Gene 898: 148099.

Parsons, B.D., Medina-Luna, D., Scur, M., Pinelli, M., Gamage, G.S., Chilvers, R.A., Hamon, Y., Ahmed, I.H.I., Savary, S., Makrigiannis, A.P., Braverman, N.E., Rodriguez-Alcazar, J.F., Latz, E., Karakach, T.K., Di Cara, F. (2024) Peroxisome deficiency underlies failures in hepatic immune cell development and antigen presentation in a severe Zellweger disease model. Cell Reports 43: 113744.

Rithidech, K.N., Peanlikhit, T., Honikel, L., Li, J., Liu, J., Karakach, T., Zimmerman, T., Welsh, J. (2024) Consumption of apigenin prevents radiation-induced gut dysbiosis in male C57BL/6J mice exposed to silicon ions. Radiation Res., advance online 10.1667/ RADE-23-00110.1.

Vahedi, S.M., Salek Ardestani, S., Banabazi, M.H., Clark, K.F. (2024) Strong selection signatures for Aleutian disease tolerance acting on novel candidate genes linked to immune and cellular responses in American mink (Neogale vison). Sci. Rep. 14: 1035. 

Weston, E.J., Eglit, Y., Simpson, A.G. (2024) Kaonashia insperata gen. et sp. nov., a eukaryotrophic flagellate, represents a novel major lineage of heterotrophic stramenopiles. J. Eukaryot. Microbiol. 71: e13003.

Zhang, W., Kenney, T., Ho, L.S.T. (2024) Evolutionary shift detection with ensemble variable selection. BMC Ecol. Evol. 24: 11.

W

2023

Ahmed, O.Y., Rossi, M., Gagie, T., Boucher, C., Langmead, B. (2023) SPUMONI 2: improved classification using a pangenome index of minimizer digests. Genome Biol. 24: 122.

Alcock, B.P. et al. [incl. Maguire, F. & Beiko, RG] (2023) CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 51: D690-D699.

Baños, H., Susko, E., Roger, A.J. (2023) Is over-parameterization a problem for Profile Mixture Models? Syst. Biol.:syad063.

Behnke, J., Cai, Y., Gu, H., LaRoche, J. (2023) Short-term response to iron resupply in an iron-limited open ocean diatom reveals rapid decay of iron-responsive transcripts. PLoS ONE 18: e0280827.

Biswas, D., De Silva, A., Mercer, A., Sarkar, S., Kienesberger, P., Langille, M., Vasantha Rupasinghe, H.P., Pulinilkunnil, T. (2023) Supplementation of cyanidin-3-0-B-glucoside-rich haskap berry extract atatenuates hepatic lipid dysregulation in diet-induced obese mice. J. Funct. Foods 108: 105635.

Bojko, J., Behringer, D.C., Bateman, K.S., Stentiford, G.D., Clark, K.F. (2023) Pseudohepatospora borealis n. gen. n. sp. (Microsporidia: Enterocytozoonida): A microsporidian pathogen of the Jonah crab (Cancer borealis).  J. Invertebr. Pathol. 197: 107886.

Bougon, J., Kadijk, E., Gallot-Lavallee, L., Curtis, B., Landers, M., Archibald, J.M., Khaperskyy, D.A. (2023) Influenza A virus NS1 effector domain is required for PA-X mediated host shutoff. bioRxiv [preprint] 2023.10.02.560421.

Boutagayout, A., Belmalha, S., Nassiri, L., El Alami, N., Jiang, Y., Lahlali, R., Bouiamrine, E.H. (2023) Weed competion, land equivalent ratio and yield potential of faba bean (Vicia faba L.)-cereals (Triticum aestivum L. and/or Avena sativa L.) intercropping under low-input conditions in Mednes region, Morocco. Vegetos (Springer): 1-14.

Cai, Y., Gu, H., Kenney, T. (2023) Rank selection for non-negative matrix factorization. Statistics in Med. 42: 676–5693.

Carnicer, O., Hu, Y.Y., Ebenezer, V., Irwin, A.J., Finkel, Z.V. (2023) Genomic architecture constrains macromolecular allocation in dinoflagellates. Protist 174: 125992.

Collier, J.L. et al. [incl. Archibald, J.M.] (2023) The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses. Curr. Biol. 33: 5199-5207.

Collier, J.L. et al. [incl. Archibald, J.M.] (2023) Herpes-like viral elements and universal subtelomeric ribosomal RNA genes in a chromosome-scale thraustochytrid genome assembly. bioRxiv [preprint] 2023.06.15.545109.

Cozzi, D., Rossi, M., Rubinacci, S., Gagie, T., Köppl, D., Boucher, C., Bonizzoni, P. (2023) μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. Bioinformatics 39: btad552.

de Bernardo, G., Gagie, T., Ladra, S., Navarro, G., Seco, D. (2023) Faster compressed quadtrees.  J. Computer Syst. Sci. 131: 86-104.

Delgado, ML, Manosalva A., Urbina, MA, Dalziel, AC, Habit, E., Link, O., Ruzzante, DE (2023) Does the loss of diadromy imply the loss of salinity tolerance? A gene expression study with replicate non-diadromous populations of Galaxias maculatus. Mol. Ecol. 32: 2219–2233.

Douglas, GM, Kim S., Langille MGI, Shapiro BJ (2023) Efficient computation of contributional diversity metrics from microbiome data with FuncDiv.  Bioinformatics 39: btac809.

Ebenezer, V., Y Hu, O Carnicer, AJ Irwin, MJ Follows, ZV Finkel (2023) Elemental and macromolecular composition of the marine Chloropicophyceae, a major group of oceanic photosynthetic picoeukaryotes. Limnology & Oceanography 67: 540-551.

Feng, X., et al. [incl. Archibald, J.M.] (2023) Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. bioRxiv [preprint]: 2023 Feb 1: 2023.01.31. 526407. doi:10.1101/2023.01.31.526407

Gallot-Lavallée, L, Jerlström-Hultqvist, J, Zegarra-Vidarte, P, Salas-Leiva, DE, Stairs, CW, Čepička, I, Roger, AJ, Archibald, JM. (2023) Massive intein content in Anaeramoeba reveals aspects of intein mobility in eukaryotes. Proc. Natl. Acad. Sci. USA 120: e2306381120.

Getz, L.J., Brown, J.M., Sobot, L., Chow, A., Mahendrarajah, J., Thomas, N.A. (2023) Attenuation of a DNA cruciform by a conserved regulator directs T3SS1 mediated virulence in Vibrio parahaemolyticus. Nucleic Acids Res. 51: 6156–6171.

Gigeroff, A.S., Eglit, Y., Simpson, A.G.B. (2023) Characterisation and cultivation of new lineages of Colponemids, a critical assemblage for inferring alveolate evolution. Protist. 174: 125949.

Gill, I.S. et al. [incl. Gaston, D.] (2023) The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information. Microbial Genomics 9: mgen000908.

González Morales, N., Marescal, O., Szikora, S., Katzemich, A., Correia-Mesquita, T., Bíró, P., Erdelyi, M., Mihály, J., & Schöck, F. (2023). The oxoglutarate dehydrogenase complex is involved in myofibril growth and Z-disc assembly in Drosophila. J. Cell Sci. 136:  jcs260717.

Grandy, S., Scur, M., Dolan, K., Nickerson, R., Cheng, Z. (2023) Using model systems to unravel host-Pseudomonas aeruginosa interactions. Env. Microbiol. 25: 1765–1784.

Hall, M.H., Wellappuli, N.C., Huang, R.C., Wu, K., Lam, D.K., Glogauer, M., Beiko, R.G., Senadheera, D.B. (2023) Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution. ISME Comm. 3: 51.

Hall, S., Méthé, D., Stewart-Clark, S., Clark, F. (2023) Size and site specific transcriptomic responses of blue mussel (Mytilus edulis) to acute hypoxia. Marine Genomics 71: 101060.

Hansen, L.G., Larsen, L.E., Rasmussen, T.B., Miar, Y., Lassuniére, R., Jørgensen, C.S., Ryt-Hansen, P. (2023) Investigation of the SARS-CoV-2 post-vaccination antibody response in Canadian farmed mink. Vaccine 41: 7387–7394.

Hayes, M.G., Langille, M.G.I., Gu, H. (2023) Cross-study analyses of microbial abundance using generalized common factor methods. BMC Bioinformatics 24: 380.

Hehenberger, E., Guo, J., Wilken, S., Hoadley, K., Sudek, L., Poirier, C., Dannebaum, R., Susko, E., Worden, A.Z. (2023) Phosphate limitation responses in marine green algae are linked to reprogramming of the tRNA epitranscriptome and codon usage bias. Mol. Biol. Evol. 40: msad251.

Hendricks, A., Mackie, CM, Luy, E., Sonnichsen, C., Smith, J., Grundke, I., Tavasoli, M., Furlong, A., Beiko, RG, LaRoche, J., Sieben V. (2023) Compact and automated eDNA sampler for in situ monitoring of marine environments. Sci. Rep. 13: 5210.

Higuera, A., Salas-Leiva, D.E., Curtis, B.A., Patiño, L.H., Zhao, D., Jerlström-Hultqvist, J, Dlutek, M., Muñoz, M., Roger, A.J., Ramírez, J.D. (2023) Draft genomes of Blastocystis subtypes from human samples of Colombia. Parasites & Vectors 16: 52.

Hu, G., Do, D.N., Manafiazar, G., Kelvin, A.A., Sargolzaei, M., Plastow, G., Wang, Z., Miar, Y. (2023) Population genomics of American mink using genotype data. Frontiers Genet. 14: 1221683.

Jerlström-Hultqvist, J., Gallot-Lavallée, L., Salas-Leiva, D.E., Curtis, B.A., Záhonová, K., Čepička, I., Stairs, C.W., Pipaliya, S., Dacks, J.B., Archibald, J.M., Roger, A.J. (2023) A unique symbiosome in an anaerobic single-celled eukaryote. bioRxiv [preprint] 2023.03.03.530753

Jiang, Y. et al. (2023) The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat. Plant J. 114: 209–224.

Jones, C., Meynell, L., Neto, C., Susko, E. and Bielawski, J.P. (2023) The role of the ecological scaffold in the origin and maintenance of whole-group trait altruism in microbial populations. BMC Ecol. Evol. 23:11.

Kmochová, T. et al. [incl. Gaston, D.] (2023) Autosomal dominant ApoA4 mutations present as tubulointerstitial kidney disease with medullary amyloidosis. Kidney Int. S0085-2538(23)00859-1. Advance online.

Koepper, S., Kelley, S., Thakur, K.K. and Clark, K.F. (2023) Interspecies and spatial differences in the shell microbiome of Atlantic rock crab Cancer irrotatus and European green crab Carcinus maenas from Atlantic Canada. Front. Mar. Sci. 10: 1152544.

Koepper, S., Fraser, K.F., McClure, J.T., Revie, C.W., Stryhn, H., Thakur, K.K. (2023) Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada.  Front. Microbiol. 14: 1245818.

Lampe, R.H., Coale, T.H., Forsch, K.O., Jabre, L.J., Kekuewa, S., Bertrand, E.M., Horák, A., Oborník, M., Rabines, A.J., Rowland, E., Zheng, H., Andersson, A.J., Barbeau, K.A., Allen, A.E. (2023) Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton. Nature Comm. 14: 7215.

Li, Z., Zhang, Y., Li, W., Irwin, A.J., Finkel, Z.V. (2023) Common environmental stress responses in a model marine diatom. New Phytol. 240: 272-284.

Liu, C., Kenny, T., Beiko, R.G., Gu, H. (2023) The community coevolution model with application to the study of evolutionary relationships between genes based on phylogenetic profiles. Syst. Biol. 72: 559-574.

Lloyd, AW, Percival, D, Langille, MGI, Yurgel, SN* (2023) Changes to soil microbiome resulting from synergetic effects of fungistatic compounds Pyrimethanil and Fluopyram in lowbush blueberry agriculture, with nine fungicide products tested. Microorganisms 11: 410.

MacDonald, T., Dunn, KA, MacDonald, J., Langille, MGI, Van Limbergen, JE*, Bielawski, JP, Kulkarni, K. (2023) The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients. Front. Cell. Infect. Microbiol. 13: 1102501.

Magpali, L. and Bielawski, J.P. (2023) Why are whales big? Genes behind ocean giants.  Trends Genet. 39: 436-438.

Mathavarajah, S., Vergunst, K.L., Habib, E.B., Williams, S.K., He, R., Maliougina, M., Park, M., Salsman, J., Roy, S., Braasch, I., Roger, A.J., Langelaan, D.N., Dellaire, G. (2023) PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates. Nucleic Acids Res. 51: 3185-3204.

McCormick, N., Earle, M., Kent, A., Ha, C., Hakes, L., Anderson, L., Stoddart, A.K., Langille, M.G.I., Gagnon, G.A. (2023) Betaproteobacteria are a key component of surface water biofilters that maintain sustained manganese removal in response to fluctuations in influent water temperature. Water Res. 244: 120515.

McCracken, G.R., Gaston, D., Pettipas, J., Loder, A., Majer, A., Grudeski, E., Labbé, G., Joy, B.K., Patriquin, G., LeBlanc, J.J. (2023) Neglected SARS-CoV-2 variants and potential concerns for molecular diagnostics: a framework for nucleic acid amplification test target site quality assurance. Microbiol. Spectrum 11: e0076123.

McGinty, N., AJ Irwin, ZV Finkel, S Dutkiewicz (2023) Using ecological partitions to assess zooplankton biogeography and seasonalityFrontiers 10: 989770.

Muñoz-Gómez, SA, Cadena LR, Gardiner AT, Leger MM, Sheikh S, Connell LB, Bilý T, Kopejtka K, Beatty JT, Koblížek M, Roger AJ, Slamovits CH, Lukeš J, Hashimi H. (2023) Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60. Curr. Biol. 33: 1396.

Mutshinda, CM, A Mishra, ZV Finkel, AJ Irwin (2023) Density regulation amplifies environmentally induced population fluctuationsPeer Journal 11: e14701.

Nearing, JT, DeClercq V, Langille MGI (2023) Investigating the oral microbiome in retrospective and prospective cases of prostate, colon, and breast cancer. NPJ Biofilms Microbiomes 9:23.

Neto, C.A. and Doolittle, W.F. (2023) A chemostat model for evolution by persistence, clade selection and its explanatory autonomy. Philos Sci. 90: 21-38.

Nguyen, L., Taeruma, S.J., Jasso-Selles, D.E., Slamovits, C.H., Silberman, J.D., Gile, G.H. (2023) True molecular phylogenetic position of the cockroach gut commensal Lophomonas blattarum (Lophomonadida, Parabasalia). J. Eukaryot. Microbiol. 70: e12988.

Paerl, R.W., Curtis, N.P., Bittner, M.J., Cohn, M.R., Gifford, S.M., Bannon, C.C., Rowland, E., Bertrand, E.M. (2023) Use and detection of a vitamin B1 degradation product yields new views of the marine B1 cycle and plankton metabolite exchange. mBio 14: e0006123.

Papale, F. and Doolittle, W.F. (2023) Towards a more general theory of evolution by natural selection: a manifesto.  Philosophy, Theory and Practice in Biology, in press.

Rius, M., Rest, J.S., Filloramo, G., Vanclova, A., Archibald, J.M., Collier, J.L. (2023) Horizontal gene transfer and fusion spread carotenogenesis among diverse heterotrophic protists. Genome Biol. Evol. 15(3): evad029.

Rolin, J., Horricks, R.A., Stephen, J., Watson, K., Clark, K.F., Lewis-McCrea, L.M., Reid, G.K. (2023) Changes in bacterial communities in chilled American lobster (Homarus americanus) tissues following mortality.  LWT 185: 115136.

Saha, E., Ho, L.S.T., Tran, G. (2023) SPADE4: Sparsity and Delay embedding based forecasting of epidemics.  Bulletin of Math. Biol. 85: 71.d

Salisbury, S.J., Perry R, Keefe D, McCracken GR, Layton KKS, Kess T, Bradbury IR, Ruzzante DE (2023) Geography, environment, and colonization history interact with morph type to shape genomic variation in an Arctic fish. Mol. Ecol. 32: 3025-3043.

Sheward, R.M., JD Liefer, AJ Irwin, ZV Finkel (2023) Elemental stoichiometry of the key calcifying marine phytoplankton Emiliania huxleyi under ocean climate change: a meta-analysis. Global Change Biol. 29: 4259-4278.

Soto, M.A., Desai, D., Bannon, C., LaRoche, J., Bertrand, E.M. (2023) Cobalamin producers and prokaryotic consumers in the Northwest Atlantic. Environ. Microbiol. 25: 1300-1313.

Suzuki-Tellier, S., Kiørboe, T., Simpson, A.G.B. (2023) The function of the feeding groove of ‘typical excavate’ flagellates. J. Eukaryot. Microbiol., Dec. 18: e13016.

Thapa, P.C., Do, D.N., Manafiazar, G., Miar, Y. (2023) Coat color inheritance in American mink. BMC Genomics 24: 234.

Thilakarathna, WPDW, Langille, MGI, Rupasinghe, HPV (2023) Hepatotoxicity of polymeric proanthocyanidins is caused by translocation of bacterial lipopolysaccharides through impaired gut epithelium. Toxicology Lett. 379: 35-47.

Valach, M., Benz, C., Aguilar, L.C., Gahura, O., Faktorová, D., Zíková, A., Oeffinger, M., Burger, G., Gray, M.W., Lukeš, J. (2023) Miniature RNAs are embedded in an exceptionally protein-rich mitoribosome via an elaborate assembly pathway. Nucleic Acids Res. 51: 6443–6460.

Valach, M. et al. [incl. Gray, M.W.] (2023) Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes. BMC Biol. 21: 99.

Valeva, S.V., Degabriel M, Michal F, Gay G, Rohde JR, Randow F, Lagrange B, Henry T. (2023) Comparative study of GBP recruitment on two cytosol-dwelling pathogens, Francisella novicida and Shigella flexneri highlights differences in GBP repertoire and in GBP1 motif requirements. Pathog Dis. 81: ftad005.

Valenzuela-Valderas, K.N., Farrashzadeh, E., Chang, Y.Y., Shi, Y., Raudonis, R., Leung, B.M., Rohde, J.R., Enninga, J., Cheng, Z. (2023) RACK1 promotes Shigella flexneri actin-mediated invasion, motility, and cell-to-cell spreading. iScience 26: 108216.

Verburgt, C.M., Dunn, KA, Otley, A, Heyman, MB, Verstraete, S, Sunseri, W, Sylvester, F, De Meij, T, Comeau, AM, Langille, MGI, de Jonge, WJ, Benninga, MA, Van Limbergen, JE* (2023) Personalised Azithromycin + Metronidazole (PAZAZ), in combination with standard induction therapy, to achieve a faecal microbiome community structure and metagenome changes associated with sustained remission in paediatric Crohn’s Disease (CD): protocol of a pilot study. BMJ Open 13: e064944.

Verburgt, C.M., Dunn, K.A., Ghiboub, M., Lewis, J.D., Wine, E., Sigall Boneh, R., Gerasimidis, K., Shamir, R., Penny, S., Pinto, D.M., Cohen, A., Bjorndahl, P., Svolos, V., Bielawski, J.P., Benninga, M.A., de Jonge, W.J., Van Limbergen, J.E.* (2023) Successful dietary therapy in Paediatric Crohn’s disease is associated with shifts in bacterial dysbiosis and inflammatory metabotype towards healthy controls. J. Crohn’s and Colitis 7: 61-72.

Vu, N.L., Nguyen, T.P., Nguyen, B.T., Dinh, V., Ho, L.S.T. (2023) When can we reconstruct the ancestral state? Beyond Brownian motion. J. Math. Biol. 86: 88.

Wilcox, M.A., Jeffery, N.W., DiBacco, C., Bradbury, I.R., Lowen, B., Wang, Z., Beiko, R.G., Stanley, R.R.E. (2023) Integrating seascape resistances and gene flow to produce area-based metrics of functional connectivity for marine conservation planning. Landscape Ecol. 38: 2189-2205.

Wright, RJ, Comeau, AM, Langille, MGI (2023) From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools. Microb. Genomics 9: mgen000949.

Wright, RJ, Pewarchuk ME, Marshall EA, Murray B, Rosin MP, Laronde DM, Zhang L, Lam WL, Langille MGI, Rock LD (2023) Exploring the microbiome of oral epithelial dysplasia as a predictor of malignant progression. BMC Oral Health 23: 206.

Xu, L., Kong, D., Wang, L., Gu, H., Kenney, T., Xu, X. (2023) Proportional stochastic generalized Lotka–Volterra model with an application to learning microbial community structures. Applied Mathematics and Computation 448: 127932.

Zadjelovic, V., Wright, R.J., Borsetto, C., Quartey, J., Cairns, T.N., Langille, M.G.I., Wellington, E. M.H., Christie-Oleza, J.A. (2023) Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere. Microbiome 11: 225.

Zhang, W., Liang, G., Cheng, Z., Guo, Y., Jiang, B., Liu, T., Liao, W., Lu, Q., Wen, G., Zhang, T., Luo, Q. (2023) Flos populi (Male Inflorescence of Populus tomentosa Carrière) Aqueous extract suppresses Salmonella pulloruminfection by affecting T3SS-1. Pathogens 12: 790.

Zhang, X., Hu, Y., Cheng, Z., Archibald, J.M. (2023) HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes. STAR Protocols 4: 102014.