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

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

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(1): e0280827.

de Bernardo, G., Gagie, T., Ladra, S., Navarro, G., Seco, D. (2023) Faster compressed quadtrees.  J.  Computer and System 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 JB (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.

Hall, M.H., Wellappuli, N.C., Huang, R.C., Wu, K., Lam, D.K., Glogauer, M., Beiko, R.G., Senadheera, D.B. Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution. ISME Comm. 3: article 23.

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.

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.

Li, Z., Zhang, Y., Li, W., Irwin, A.J., Finkel, Z.V. (2023) Common environmental stress responses in a model marine diatom. New Phytol., online July 24^th.

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(2): 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. and Dellaire, G. (2023) PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates.  Nucleic Acids Res. 51: 3185-3204.

McCormick, NE, Earle M, Stoddart AK, Langille MGI, Gagnon GA (2023) Understanding the impact of different source water types on the biofilm characteristics and microbial communities of manganese removing biofilters. Environ. Sci.: Water Res. Technol. 9: 48-61.

McGinty, N., AJ Irwin, ZV Finkel, S Dutkiewicz (2023) Using ecological partitions to assess zooplankton biogeography and seasonality. Frontiers 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. Current Biol. 33: 1099-1111.

Mutshinda, CM, A Mishra, ZV Finkel, AJ Irwin (2023) Density regulation amplifies environmentally induced population fluctuations. Peer 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 and 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.

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.

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. Environ. Microbiol., on line June 28^th.

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., online June 8: e12988.

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

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, RM, 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.

Thilakarathna, WPDW, Langille, MGI, Rupasinghe, HPV (2023) Hepatotoxicity of polymeric proanthocyanidins is caused by translocation of bacterial lipopolysaccharides through impaired gut epithelium. Toxicology Letters379: 35-47.

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 flexnerihighlights differences in GBP repertoire and in GBP1 motif requirements. Pathog Dis. 81: ftad005.

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., and 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. Journal of 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. Mathematical 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: article 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.

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.

Alanko, J.N., Slizovskiy, I.B., Lokshtanov, D., Gagie, T., Noyes, NR, Boucher, C. (2022) Syotti: scalable bait design for DNA enrichment.  Bioinformatics 38 (Suppl. 1):  i177-i184.

Amirian, MM, AJ Irwin, ZV Finkel (2022). Extending the Monod Model of Microbial Growth with Memory. Front. Mar. Sci., Vol. 9: doi.10.3389/fmars.2022.963734

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 3: 422-432.

Bannon, C., Rapp, I. & Bertrand, E.M. (2022) Community Interaction Co-Limitation: Nutrient Limitation in a Marine Microbial Community Context.  Frontiers in Microbiol. 13: 846890.

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. 8(6): e0214621.

Blaxter, M. et al. [incl. Archibald, J. M.] (2022) Why sequence all eukaryotes? Proc. Natl. Acad. Sci. USA119(4): e2115636118.

Brown, N.K., Gagie, T., Rossi, M. (2022) RLBWT Tricks.  SEA 2022, Vol. 233, 16:1-16:16.

Carnicer, O., AJ Irwin, ZV Finkel (2022) Traits influence dinoflagellate C:N:P. Eur. J. Phycology 57: 154-165.

Chan, K. et al. (incl. F. Maguire) (2022) Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors. Heliyon, e12744.

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.

Clarke S, McCracken GR; Humphries S; Ruzzante DE; Grant J; Fraser D. (2022) Demographic resilience of brook trout populations subjected to experimental size-selective harvesting. Evol. Applications 15: 1792-1805.

Cook J., Hui J., Zhang J., Kember M., Berrue F., Zhang J., and Cheng Z. (2022) Production of quorum sensing-related metabolites and phytoalexins during Pseudomonas aeruginosa–Brassica napus interaction.Microbiology 168(8): 001212.

Cramer et al. (incl. L. Ho) (2022) Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States. PNAS 119 (15): e2113561119.

Cramer et al. (incl. L. Ho) (2022) The United States COVID-19 Forecast Hub dataset. Scientific Data 9: 462.

DeCoste, RC; Walsh, NM; Gaston, D; Ly, TY; Pasternak, S; Cutler, S; Nightingale, M; Carter, MD (2022) RB1-deficient squamous cell carcinoma: the proposed source of combined Merkel cell carcinoma. Modern Pathology 35: 1829-1836.

Doolittle, W.F. (2022) All about levels: Transposable elements as selfish DNAs and drivers of evolution.  Biol. Philos 37: 24-44.

Douglas, GM, Hayes MG, Langille MGI, Borenstein E (2022). Integrating phylogenetic and functional data in microbiome studies. Bioinformatics 38: 5055-63.

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.

Dunn, KA, MacDonald T, Rodrigues GJ, Forbrigger Z, Bielawski JP, Langille MGI, Van Limbergen J.* Kulkarni K (2022) Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense. Frontiers Cellular Infect. Microbiol. 12: 924707.

Durante, CA, Loizaga R, McCracken G, Crespo EA, Ruzzante DE (2022) Commerson’s dolphin population structure: Evidence for female philopatry and male dispersal. Scientific Rep.12: 22219.

Ebeneezer, T.E., & 27 others (incl. A. Simpson) (2022) Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world. Open Biology 11: bio059561.

Ferragina, P., Manzini, G., Gagie, T., Köppl, D., Navarro, G., Striani, M., Tosoni, F. (2022) Improving Matrix-vector Multiplication via Lossless Grammar-Compressed Matrices.  Proc. VLDB Endow. 15(10): 2175-2187.

Francisco, A.P., Gagie, T., Köppl, D., Ladra, S., Navarro, G. (2022) Graph compression for adjacency-matrix multiplication.  SN Comput. Sci. 3(3): 193.

Fürst-Jansen, J.M.R., de Vries, S., Lorenz, M., von Schwartzenberg, K., Archibald, J.M. and de Vries, J. (2022) Submergence of the filamentous Zygnematophyceae mougeotia induces differential gene expression patterns associated with core metabolism and photosynthesis. Protoplasma 259: 1157-1174.

Gagie, T. (2022) Simple worst-case optimal adaptive prefix-free coding.  ESA 2022: 57:1-57:5.

Gagie, T. (2022) On representing the degree sequences of sublogarithmic-degree wheeler graphs. SPIRE2022: 250-256.

Gagie, T., Saeidi, M., Sapucaia, A. (2022) Ruler wrapping. Int. J. Comput. Geometry & Applic. 1-10.

Gagie, T., Kashgouli, S., Langmead, B. (2022) KATKA: A KRAKEN-Like Tool with k Given at Query Time.  SPIRE 2022: 191-197.

Gaston, D., Crawford, Z, Weeks, A, Carter, M, Croul, S. (2022) Diagnosis of adult glioma: A comparison of a custom NGS AmpliSeq panel to WHO 2016 glioma classification practice guidelines.  Canadian J. Pathol.14(2): 36-48.

Gerbracht J.V., Harding T., Simpson A.G.B., Roger A.J., Hess S. (2022) Comparative transcriptomics reveals the molecular toolkit used by an algivorous protist for cell wall perforation. Curr. Biol. 32:3374-3384.

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 et al. (35 authors incl. D. Gaston) (2023) The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information. Microbial Genom. 9(1): mgen000908.

Grandy S., Raudonis R., Cheng Z. (2022) The identification of Pseudomonas aeruginosa persisters using flow cytometry. Microbiol. 168: 001252.

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.

Gulavi, E., Mwendwa, F., Atandi, DO, Okiro PO, Hall M., Beiko RG, Adam RD (2022) Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study. BMC Microbiol. 22: 270.

Hassler, G., Max Tolkoff, William Allen, Lam Si Tung Ho, Philippe Lemey, Marc  Suchard (2022) Inferring phenotypic trait evolution on large trees with many incomplete measurements. J.  Amer. Statistical Assoc. 117 (538): 678–692.

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.

Herod, A., Ryu, J., Rohde, J. (2022) Lamda red recombineering in Shigella flexneri.  J. Methods Mol. Biol.2523: 9-21.

Hess S., Williams S.K., Busch A., Irisarri I., Delwiche C.F., de Vries S., Darienko T., Roger A.J., Archibald J.M., Buschmann H., von Schwartzenberg K. and de Vries J. (2022) A phylogenomically informed five-order system for the closest relatives of land plants. Curr. Biol. 32:4473-4482.

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 Letters183: 109353.

Ho, L.S.T., Dinh, V. (2022). When can we reconstruct the ancestral state? A unified theory. TheoreticalPopulation Biol. 148: 22–27.

Hu, YY, AJ Irwin, ZV Finkel (2022) Improving quantification of particulate phosphorus. Limnology and Oceanography: Methods 20: 729-740.

Inkpen, S.A. and Doolittle, W.F. (2022) Can Microbial Communities Regenerate? The University of Chicago Press. [Book]

Jones, C., Susko, E., and Bielawski, J.P. (2022) Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis. BMC Ecol. Evol. 22:140.

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 67(4): 800-815.

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; 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, J.I., 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. 35: e00179-21.

Kim, J.I., Tanifuji, G., Minseok, J., Shin, W. & Archibald, J.M. (2022) Gene loss, pseudogenization and genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics. BMC Biol. 20: 227.

Kim, J.I., Jo, B.Y., Park, M.G., Yoo, Y.D., Shin, W. & Archibald, J.M. 2022. Evolutionary dynamics and lateral gene transfer in raphidophycean plastid genomes. Front. Plant Sci. 13: 896138.

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. 

Lawniczak et al. [incl. Archibald, J. M.] 2022. Standards recommendations for the Earth BioGenome Project. Proc. Natl. Acad. Sci. USA 119(4): e2115639118.

Lean, C.H., Doolittle, W.F. and Bielawski, J.B. (2022). Community-level evolutionary processes: Linking community genetics with replicator-interactor theory. Proc. Natl. Acad. Sci. USA 119: e2202538119. 

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): e2115635118.

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.

Liu, C., Kenney, T., Beiko, R.G. and Gu, H. (2022) The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes based on Phylogenetic Profiles. Syst. Biol., Jul 29: syac052.

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. Microbiol. Spectrum 10(2): e02769-21.

MacDonald, E., Dunn, K.A., Bielawski, J.P., VanLimbergen, J., Kulkarni, K. and MacDonald, T., 2022. The Bacterial Chaperone High-Temperature Protein G (HtpG) Decreases in Abundance with Induction Therapy in Children with Acute Lymphoblastic Leukemia. Blood 140 (Suppl. 1), 11852-11853.

MacDonald, J., Dunn, K.A., Bielawski, J.P., Langille, M.G., Kulkarni, K. and MacDonald, T., 2022. Impact of Antibiotic Use for Febrile Neutropenia on Gut Microbiome Phyla in Children with Leukemia and Lymphoma. Blood 140 (Suppl. 1), 11868-11869.

MacNeil L, Desai DK, Costa M, LaRoche J. (2022) Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf.  Sci. Rep. 12: 13078.

Massey, M.D.B., Arif, S., Embuldeniya, S., Nanglu, K. and Bielawski, J., 2022. Ten simple rules for succeeding as an underrepresented STEM undergraduate. PLOS Computational Biol. 18(6), e1010101.

Matthey-Doret, C., Colp., M.J., Escoll, P., Thierry, A., Moreau, P., Curtis, B.A., Sahr, T., Sarrasin, M., Gray, M.W., Lang B.F., Archibald, J.M., Buchrieser, C. and Koszul, R. (2022) Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization. Genome Res. 32: 1698-1710.

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.

McCallum, MK; Patriquin, G; Davis, I; MacDonald, T; Gaston, D; LeBlanc, J; Shabi, Y; Johnston, BL (2022) Factors contributing to a coronavirus disease 2019 (COVID-19) outbreak on a mixed medical-surgical unit in a Canadian acute-care hospital. Antimicrob.Stewardship & Healthcare Epidemiol. 2(1): e151.

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 Microbiol. 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.

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.

Nguyen, C.N., Ho, L.S.T., Dinh, V., Hassner, T., Nguyen, C.V. (2022) Generalization Bounds for Deep Transfer Learning Using Majority Predictor Accuracy. The International Symposium on Information Theory and Its Applications (ISITA).

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.

Pickering, B. et al. (incl. F. Maguire) (2022) Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Nature Microbiol. 7: 2011–2024.

Pringle ES, Duguay BA, Bui-Marinos MP, Mulloy RP, Landreth SL, Desireddy KS, Dolliver SM, Ying S, Caddell T, Tooley TH, Slaine PD, Bearne SL, Falzarano D, Corcoran JA, Khaperskyy DA, McCormick C. (2022) Thiopurines inhibit coronavirus Spike protein processing and incorporation into progeny virions. PLOS Pathogens 18(9): e1010832.

Raes EJ, Tolman J, Desai D, Ratten JM, Zorz J, Robicheau BM, Haider D, LaRoche J. (2022) Seasonal bacterial niche structures and chemolilthoautotrophic ecotypes in a North Atlantic fjord.  Sci. Rep. 12: 15335.

Raphenya et al. (incl. F. Maguire) (2022) Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing. Scientific Data 9: 341.

Rasmussen, S; Stueck, A; Colwell, B; Gaston, D; Carter, M (2022) Gastrointestinal stromal tumors caused by novel germline variants in SDHB and KIT: a report of two cases and literature review. Clinical J. Gastroenterol.15: 869-875.

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.

Rotteveel, L., Heubach, F. & Sterling, S.M. (2022) The Surface Water Chemistry (SWatCh) database: A standardized global database of water chemistry to facilitate large-sample hydrological research. Earth Syst. Sci. Data 14(10): 4667-4680.

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. Ann. Rev. Animal Biosci. 10: 81-106.

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.  Microb. Genom. 8: mgen000880.

Schock, F. and Gonzalez-Morales, N. (2022) The insect perspective on Z-disc structure and biology.  J. Cell Sci. 135: jcs260179

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. Hydrol. Processes 36(2): e14477.