A list of microbe-related research published by members of the 蓝莓视频 Centre for Microbial Research since 2017. This collection is organized by member using the newest APA citation guidelines.
William Anderson
Bai, Y., Moo-Young, M., & Anderson, W. A. (2019). A mechanistic model for gas鈥撀聯liquid mass transfer prediction in a rocking disposable bioreactor. Biotechnology and Bioengineering, 116(8), 1986鈥1998.
Bai, Y., Moo-Young, M., & Anderson, W. A. (2019). Characterization of power input and its impact on mass transfer in a rocking disposable bioreactor. Chemical Engineering Science, 209, 115183.
Cholewinski, A., Dadzie, E., Sherlock, C., Anderson, W. A., Charles, T. C., Habib, K., Young, S. B., & Zhao, B. (2022). A critical review of microplastic degradation and material flow analysis towards a circular economy. Environmental Pollution (Barking, Essex: 1987), 315, 120334.
Derraik, J. G. B., Anderson, W. A., Connelly, E. A., & Anderson, Y. C. (2020). Rapid Review of SARS-CoV-1 and SARS-CoV-2 Viability, Susceptibility to Treatment, and the Disinfection and Reuse of PPE, Particularly Filtering Facepiece Respirators. International Journal of Environmental Research and Public Health, 17(17), Article 17.
Harfoot, R., Yung, D. B. Y., Anderson, W. A., Wild, C. E. K., Coetzee, N., Hern谩ndez, L. C., Lawley, B., Pletzer, D., Derraik, J. G. B., Anderson, Y. C., & Qui帽ones-Mateu, M. E. (2022). Ultraviolet-C Irradiation, Heat, and Storage as Potential Methods of Inactivating SARS-CoV-2 and Bacterial Pathogens on Filtering Facepiece Respirators. Pathogens, 11(1), Article 1.
Kaur, A., Anderson, W. A., Tanvir, S., & Kansal, S. K. (2019). Solar light active silver/iron oxide/zinc oxide heterostructure for photodegradation of ciprofloxacin, transformation products and antibacterial activity. Journal of Colloid and Interface Science, 557, 236鈥253.
Liu, M., Bauman, L., Nogueira, C. L., Aucoin, M. G., Anderson, W. A., & Zhao, B. (2022). Antimicrobial polymeric composites for high-touch surfaces in healthcare applications. Current Opinion in Biomedical Engineering, 22, 100395.
Muralidharan, S. K., Bauman, L., Anderson, W. A., & Zhao, B. (2020). Recyclable antimicrobial sulphonated poly (ether ether ketone) 鈥撀聯 copper films: Flat vs micro-pillared surfaces. Materials Today Communications, 25, 101485.
Schmidt, T., & Anderson, W. A. (2017). Biotrickling Filtration of Air Contaminated with 1-Butanol. Environments, 4(3), 57.
Tanvir, F., Yaqub, A., Tanvir, S., & Anderson, W. A. (2017a). Colorimetric enumeration of bacterial contamination in water based on 尾-galactosidase gold nanoshell activity. Enzyme and Microbial Technology, 99, 49鈥撀聯56.
Tanvir, F., Yaqub, A., Tanvir, S., & Anderson, W. A. (2017b). Poly-L-arginine Coated Silver Nanoprisms and Their Anti-Bacterial Properties. Nanomaterials, 7(10), Article 10.
Marc Aucoin
Blondeel, E. J. M., & Aucoin, M. G. (2018). Supplementing glycosylation: A review of applying nucleotide-sugar precursors to growth medium to affect therapeutic recombinant protein glycoform distributions. Biotechnology Advances, 36(5), 1505鈥1523.
Boegel, S. J., Gabriel, M., Sasges, M., Petri, B., D鈥橝gostino, M. R., Zhang, A., Ang, J. C., Miller, M. S., Meunier, S. M., & Aucoin, M. G. (2021). Robust Evaluation of Ultraviolet-C Sensitivity for SARS-CoV-2 and Surrogate Coronaviruses. Microbiology Spectrum, 9(2), e00537-21.
Bruder, M. R., & Aucoin, M. G. (2022). Utility of Alternative Promoters for Foreign Gene Expression Using the Baculovirus Expression Vector System. Viruses, 14(12), Article 12.
Bruder, M. R., & Aucoin, M. G. (2023). Evaluation of Virus-Free Manufacture of Recombinant Proteins Using CRISPR-Mediated Gene Disruption in Baculovirus-Infected Insect Cells. Vaccines, 11(2), 225.
Bruder, M. R., Walji, S.-D., & Aucoin, M. G. (2021). Comparison of CRISPR鈥揅as9 Tools for Transcriptional Repression and Gene Disruption in the BEVS. Viruses, 13(10), Article 10.
Dare, E. V., Gabriel, M., Begum, A., Sasges, M., & Aucoin, M. G. (2017). The effect of hydrogen peroxide produced during ultraviolet disinfection of CHO cell culture media. Process Biochemistry, 61, 147-聙鈥155.
Delumeau, L.-V., Asgarimoghaddam, H., Alkie, T., Jones, A. J. B., Lum, S., Mistry, K., Aucoin, M. G., DeWitte-Orr, S., & Musselman, K. P. (2021). Effectiveness of antiviral metal and metal oxide thin-film coatings against human coronavirus 229E. APL Materials, 9(11), 111114.
Gabriel, M. A., Dare, E. V., Meunier, S. M., Campbell, J. L., Sasges, M. R., & Aucoin, M. G. (2019). Ultraviolet irradiation of trypsin, lysozyme and 尾-galactosidase: How does UVC affect these enzymes when used as a secondary barrier against adventitious agents? Vaccine, 37(43), 6518鈥撀聯6525.
Ganobis, C. M., Al-Abdul-Wahid, M. S., Renwick, S., Yen, S., Carriero, C., Aucoin, M. G., & Allen-Vercoe, E. (2020). 1D 1H NMR as a Tool for Fecal Metabolomics. Current Protocols in Chemical Biology, 12(3), e83.
Havaei, S. M., Aucoin, M. G., & Jahanian-Najafabadi, A. (2021). Pseudomonas Exotoxin-Based Immunotoxins: Over Three Decades of Efforts on Targeting Cancer Cells With the Toxin. Frontiers in Oncology, 11, 781800.
Lall, D., Miscevic, D., Bruder, M., Westbrook, A., Aucoin, M., Moo-Young, M., & Perry Chou, C. (2021). Strain engineering and bioprocessing strategies for biobased production of porphobilinogen in Escherichia coli. Bioresources and Bioprocessing, 8(1), 1鈥16.
Liu, M., Bauman, L., Nogueira, C. L., Aucoin, M. G., Anderson, W. A., & Zhao, B. (2022). Antimicrobial polymeric composites for high-touch surfaces in healthcare applications. Current Opinion in Biomedical Engineering, 22, 100395.
Logan, M., Manalil, J., Notte, C., Kearse, C., George, S., Zeiser, A., Farrell, P., & Aucoin, M. G. (2019). A flow cytometric granularity assay for the quantification of infectious virus. Vaccine, 37(47), 7090-聙聯7099.
Logan, M., Rinas, K., McConkey, B., & Aucoin, M. G. (2022). Vero cells gain renal tubule markers in low-calcium and magnesium chemically defined media. Scientific Reports, 12(1), Article 1.
Lourenco Nogueira, C., Boegel, S. J., Shukla, M., Ngo, W., Jones, L., & Aucoin, M. G. (2022). Antiviral Activity of Contemporary Contact Lens Care Solutions against Two Human Seasonal Coronavirus Strains. Pathogens, 11(4), Article 4.
Marcali, M., Aucoin, M. G., & Ren, C. (2021). Hemagglutination Assay to Quantify Influenza A Virus Like Particles in Droplets. MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 985鈥撀聯986.
Marcali, M., Chen, X., Aucoin, M. G., & Ren, C. L. (2022). Droplet formation of biological non-Newtonian fluid in T-junction generators. II. Model for final droplet volume prediction. Physical Review E, 105(2), 025106.
Meunier, S. M., Sasges, M. R., & Aucoin, M. G. (2017). Evaluating ultraviolet sensitivity of adventitious agents in biopharmaceutical manufacturing. Journal of Industrial Microbiology and Biotechnology, 44(6), 893鈥撀聯909.
Moussa, H. I., Chan, W. Y., Logan, M., Aucoin, M. G., & Tsui, T. Y. (2020). Limitation in Controlling the Morphology of Mammalian Vero Cells Induced by Cell Division on Asymmetric Tungsten-Silicon Oxide Nanocomposite. Materials, 13(2), Article 2.
Moussa, H. I., Logan, M., Chan, W. Y., Wong, K., Rao, Z., Aucoin, M. G., & Tsui, T. Y. (2018). Pattern-dependent mammalian cell (Vero) morphology on tantalum/silicon oxide 3D nanocomposites. Materials, 11(8).
Moussa, H. I., Logan, M., Siow, G. C., Phann, D. L., Rao, Z., Aucoin, M. G., & Tsui, T. Y. (2017). Manipulating mammalian cell morphologies using chemical-mechanical polished integrated circuit chips. Science and Technology of Advanced Materials, 18(1), 839鈥撀聯856.
Moussa, H. I., Logan, M., Wong, K., Rao, Z., Aucoin, M. G., & Tsui, T. Y. (2018). Nanoscale-textured tantalum surfaces for mammalian cell alignment. Micromachines, 9(9).
Nogueira, C. L., Boegel, S. J., Shukla, M., Ngo, W., Jones, L., & Aucoin, M. G. (2022). The impact of a rub and rinse regimen on removal of human coronaviruses from contemporary contact lens materials. Contact Lens and Anterior Eye, 45(6), 101719.
Quattrociocchi, M., Boegel, S. J., & Aucoin, M. G. (2021). Enhanced characterization of yeast hydrolysate combining acid digestion and 1D-1H NMR targeted profiling. The Canadian Journal of Chemical Engineering, 99(S1), S7鈥揝17.
Shafiee, F., Aucoin, M. G., & Jahanian-Najafabadi, A. (2019). Targeted Diphtheria Toxin-Based Therapy: A Review Article. Frontiers in Microbiology, 10.
Srirangan, K., Akawi, L. K., Chou, C. P., Aucoin, M. G., Stacey, L. E., & Newton, C. (2017). Use of a case on metabolically engineered Escherichia coli to develop a framework for the design and analysis of bioprocesses. International Journal of Engineering Education, 33(2), 751鈥760.
Tsui, T. Y., Logan, M., Moussa, H. I., & Aucoin, M. G. (2018). What鈥檚 happening on the other side? Revealing nano-meter scale features of mammalian cells on engineered textured tantalum surfaces. Materials, 12(1).
Varga, J. F. A., Brunner, S. R., Cheng, G., Min, D., Aucoin, M. G., Doxey, A. C., & Dixon, B. (2022). Identification and characterization of a novel peptide from rainbow trout (Oncorhynchus mykiss) with antimicrobial activity against Streptococcus iniae. Developmental & Comparative Immunology, 137, 104518.
Walji, S.-D., & Aucoin, M. G. (2020). A critical evaluation of current protocols for self-sterilizing surfaces designed to reduce viral nosocomial infections. American Journal of Infection Control, 48(10), 1255鈥1260.
Walji, S.-D., Bruder, M. R., & Aucoin, M. G. (2021). Virus matrix interference on assessment of virucidal activity of high-touch surfaces designed to prevent hospital-acquired infections. Antimicrobial Resistance & Infection Control, 10(1), 133.
Wulff, D., Chan, A., Liu, Q., Gu, F. X., & Aucoin, M. G. (2020). Characterizing internal cavity modulation of corn starch microcapsules. Heliyon, 6(10).
Yip, A., Smith-Roberge, J., Khorasani, S. H., Aucoin, M. G., & Ingalls, B. P. (2022). Calibrating spatiotemporal models of microbial communities to microscopy data: A review. PLOS Computational Biology, 18(10), e1010533.
Trevor Charles
Ali, S., Jenkins, B., Cheng, J., Lobb, B., Wei, X., Egan, S., Charles, T. C., McConkey, B. J., Austin, J., & Doxey, A. C. (2020). Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. Molecular Microbiology, 114(6), 979鈥990.
Brumwell, S. L., MacLeod, M. R., Huang, T., Cochrane, R. R., Meaney, R. S., Zamani, M., Matysiakiewicz, O., Dan, K. N., Janakirama, P., Edgell, D. R., Charles, T. C., Finan, T. M., & Karas, B. J. (2019). Designer Sinorhizobium meliloti strains and multi-functional vectors enable direct inter-kingdom DNA transfer. PloS One, 14(6), e0206781.
Cheng, J., Lam, K. N., Engel, K., Hall, M., Neufeld, J. D., & Charles, T. C. (2017). Metagenomic cosmid libraries suitable for functional screening in proteobacteria. In Functional Metagenomics: Tools and Applications (pp. 1鈥11).
Cheng, J., Romantsov, T., Engel, K., Doxey, A. C., Rose, D. R., Neufeld, J. D., & Charles, T. C. (2017). Functional metagenomics reveals novel 尾-galactosidases not predictable from gene sequences. PloS One, 12(3), e0172545.
Cholewinski, A., Dadzie, E., Sherlock, C., Anderson, W. A., Charles, T. C., Habib, K., Young, S. B., & Zhao, B. (2022). A critical review of microplastic degradation and material flow analysis towards a circular economy. Environmental Pollution (Barking, Essex: 1987), 315, 120334.
D鈥橝lessio, M., Nordeste, R., Doxey, A. C., & Charles, T. C. (2017). Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti. MSystems, 2(5), e00035-17.
Donovan, M., Lynch, M. D. J., Mackey, C. S., Platt, G. N., Washburn, B. K., Vera, D. L., Trickey, D. J., Charles, T. C., Wang, Z., & Jones, K. M. (2020). Metagenome-Assembled Genome Sequences of Five Strains from the Microtus ochrogaster (Prairie Vole) Fecal Microbiome. Microbiology Resource Announcements, 9(2), e01310-19.
Eckhard, U., Bandukwala, H., Mansfield, M. J., Marino, G., Cheng, J., Wallace, I., Holyoak, T., Charles, T. C., Austin, J., Overall, C. M., & Doxey, A. C. (2017). Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella. Nature Communications, 8(1), 521.
Fuentes, A., Herrera, H., Charles, T. C., & Arriagada, C. (2020). Fungal and Bacterial Microbiome Associated with the Rhizosphere of Native Plants from the Atacama Desert. Microorganisms, 8(2), 209.
Gupta, P. K., Gharedaghloo, B., Lynch, M., Cheng, J., Strack, M., Charles, T. C., & Price, J. S. (2020). Dynamics of microbial populations and diversity in NAPL contaminated peat soil under varying water table conditions. Environmental Research, 191, 110167.
Heil, J. R., Lynch, M. D. J., Cheng, J., Matysiakiewicz, O., D鈥橝lessio, M., & Charles, T. C. (2017). The Completed PacBio Single-Molecule Real-Time Sequence of Methylosinus trichosporium Strain OB3b Reveals the Presence of a Third Large Plasmid. Genome Announcements, 5(49), e01349-17.
Lam, K. N., Martens, E. C., & Charles, T. C. (2018). Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome. MSystems, 3(3), e00195-17.
LeBlanc, N., & Charles, T. C. (2022). Bacterial genome reductions: Tools, applications, and challenges. Frontiers in Genome Editing, 4, 957289.
Lobb, B., Hodgson, R., Lynch, M. D. J., Mansfield, M. J., Cheng, J., Charles, T. C., Neufeld, J. D., Craig, P. M., & Doxey, A. C. (2020). Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens. MSystems, 5(2), e00145-20.
Martinez, A. R., Heil, J. R., & Charles, T. C. (2019). An engineered GFP fluorescent bacterial biosensor for detecting and quantifying silver and copper ions. Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine, 32(2), 265鈥272.
Nett, R. S., Nguyen, H., Nagel, R., Marcassa, A., Charles, T. C., Friedberg, I., & Peters, R. J. (2020). Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon. MSphere, 5(3), e00292-20.
Ryan, M. J., Schloter, M., Berg, G., Kostic, T., Kinkel, L. L., Eversole, K., Macklin, J. A., Schelkle, B., Kazou, M., Sarand, I., Singh, B. K., Fischer, D., Maguin, E., Ferrocino, I., Lima, N., McClure, R. S., Charles, T. C., de Souza, R. S. C., Kiran, G. S., 鈥 Sessitsch, A. (2021). Development of Microbiome Biobanks鈥擟hallenges and Opportunities. Trends in Microbiology, 29(2), 89鈥92.
Smyth, S. J., & Charles, T. C. (2021). Impacts on International Research Collaborations from DSI/ABS Uncertainty. Trends in Biotechnology, 39(5), 430鈥433.
Soto, J., Ortiz, J., Herrera, H., Fuentes, A., Almonacid, L., Charles, T. C., & Arriagada, C. (2019). Enhanced Arsenic Tolerance in Triticum aestivum Inoculated with Arsenic-Resistant and Plant Growth Promoter Microorganisms from a Heavy Metal-Polluted Soil. Microorganisms, 7(9), 348.
Thakor, A., Cheng, J., & Charles, T. C. (2023). Isolation of Genes Encoding Carbon Metabolism Pathways from Complex Microbial Communities. Methods in Molecular Biology (Clifton, N.J.), 2555, 115鈥123.
Thomas-Barry, G., St Martin, C. C. G., Lynch, M. D. J., Ramsubhag, A., Rouse-Miller, J., & Charles, T. C. (2021). Driving factors influencing the rhizobacteriome community structure of plants adapted to multiple climatic stressors in edaphic savannas. The Science of the Total Environment, 769, 145214.
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., V谩zquez-Baeza, Y., Gonz谩lez, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., 鈥 Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth鈥檚 multiscale microbial diversity. Nature, 551(7681), 457鈥463.
Tran, T. T., & Charles, T. C. (2020). Lactic acid containing polymers produced in engineered Sinorhizobium meliloti and Pseudomonas putida. PloS One, 15(3), e0218302.
Varaljay, V. A., Charles, T. C., & Daniel, R. (2022). Editorial: Functional Metagenomics for Enzyme Discovery. Frontiers in Microbiology, 13, 956106.
Zhang, X., Liang, S., Wu, Q., Charles, T. C., He, R., Wu, J., Zhao, Y., Zhao, Z., & Wang, H. (2022). Mode of action of nanochitin whisker against Fusarium pseudograminearum. International Journal of Biological Macromolecules, 217, 356鈥366.
Alexis Dolphin
Hodgins, H. P., Chen, P., Lobb, B., Tremblay, B. J., Mansfield, M. J., Lee, V. C., Lee, P.-G., Coffin, J., Wei, X., Duggan, A. T., Dolphin, A. E., Renaud, G., Dong, M., & Doxey, A. C. (2022). Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains (p. 2022.06.30.498301). bioRxiv.
Andrew Doxey
Adegboye, M. F., Lobb, B., Babalola, O. O., Doxey, A. C., & Ma, K. (2018). Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil. Genome Announcements, 6(26), e00632-18.
Ali, S., Jenkins, B., Cheng, J., Lobb, B., Wei, X., Egan, S., Charles, T. C., McConkey, B. J., Austin, J., & Doxey, A. C. (2020). Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. Molecular Microbiology, 114(6), 979鈥990.
Banerjee, A., Doxey, A. C., Mossman, K., & Irving, A. T. (2021). Unraveling the Zoonotic Origin and Transmission of SARS-CoV-2. Trends in Ecology & Evolution, 36(3), 180鈥184.
Banerjee, A., Doxey, A. C., Tremblay, B. J.-M., Mansfield, M. J., Subudhi, S., Hirota, J. A., Miller, M. S., McArthur, A. G., Mubareka, S., & Mossman, K. (2020). Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus. The Journal of General Virology, 101(12), 1251鈥1260.
Banerjee, A., El-Sayes, N., Budylowski, P., Jacob, R. A., Richard, D., Maan, H., Aguiar, J. A., Demian, W. L., Baid, K., D鈥橝gostino, M. R., Ang, J. C., Murdza, T., Tremblay, B. J.-M., Afkhami, S., Karimzadeh, M., Irving, A. T., Yip, L., Ostrowski, M., Hirota, J. A., 鈥 Mossman, K. (2021). Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses. IScience, 24(5), 102477.
Bano, L., Kiel, M., Sales, G., Doxey, A. C., Mansfield, M. J., Wami, H. T., Schiavone, M., Rossetto, O., Pirazzini, M., Dobrindt, U., & Montecucco, C. (2020). Genome Sequence of the Fish Brain Bacterium Clostridium tarantellae. Microbiology Resource Announcements, 9(16).
Cheng, J., Romantsov, T., Engel, K., Doxey, A. C., Rose, D. R., Neufeld, J. D., & Charles, T. C. (2017). Functional metagenomics reveals novel 尾-galactosidases not predictable from gene sequences. PloS One, 12(3), e0172545.
D鈥橝lessio, M., Nordeste, R., Doxey, A. C., & Charles, T. C. (2017). Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti. MSystems, 2(5), e00035-17.
Doxey, A. C., Mansfield, M. J., & Lobb, B. (2019). Exploring the Evolution of Virulence Factors through Bioinformatic Data Mining. MSystems, 4(3).
Doxey, A. C., Mansfield, M. J., & Montecucco, C. (2018). Discovery of novel bacterial toxins by genomics and computational biology. Toxicon鈥: Official Journal of the International Society on Toxinology, 147, 2鈥12.
Eckhard, U., Bandukwala, H., Mansfield, M. J., Marino, G., Cheng, J., Wallace, I., Holyoak, T., Charles, T. C., Austin, J., Overall, C. M., & Doxey, A. C. (2017). Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella. Nature Communications, 8(1), 521.
Eckhard, U., Bl枚chl, C., Jenkins, B. G. L., Mansfield, M. J., Huber, C. G., Doxey, A. C., & Brandstetter, H. (2020). Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis. Scientific Reports, 10(1), 19052.
Ghasemi, M., Jenkins, B., Doxey, A. C., & Sivaloganathan, S. (2020). A study of nitric oxide dynamics in a growing biofilm using a density dependent reaction-diffusion model. Journal of Theoretical Biology, 485, 110053.
Hodgins, H. P., Chen, P., Lobb, B., Tremblay, B. J., Mansfield, M. J., Lee, V. C., Lee, P.-G., Coffin, J., Wei, X., Duggan, A. T., Dolphin, A. E., Renaud, G., Dong, M., & Doxey, A. C. (2022). Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains (p. 2022.06.30.498301). bioRxiv.
Kumaresan, D., Stephenson, J., Doxey, A. C., Bandukwala, H., Brooks, E., Hillebrand-Voiculescu, A., Whiteley, A. S., & Murrell, J. C. (2018). Aerobic proteobacterial methylotrophs in Movile Cave: Genomic and metagenomic analyses. Microbiome, 6(1), 1.
Lobb, B., Adegoke, A. A., Ma, K., Doxey, A. C., & Aiyegoro, O. A. (2018). Metagenomic Sequencing of Wastewater from a South African Research Farm. Microbiology Resource Announcements, 7(16).
Lobb, B., Hodgson, R., Lynch, M. D. J., Mansfield, M. J., Cheng, J., Charles, T. C., Neufeld, J. D., Craig, P. M., & Doxey, A. C. (2020). Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens. MSystems, 5(2), e00145-20.
Lobb, B., Tremblay, B. J.-M., Moreno-Hagelsieb, G., & Doxey, A. C. (2020). An assessment of genome annotation coverage across the bacterial tree of life. Microbial Genomics, 6(3).
Lobb, B., Tremblay, B. J.-M., Moreno-Hagelsieb, G., & Doxey, A. C. (2021). PathFams: Statistical detection of pathogen-associated protein domains. BMC Genomics, 22(1), 663.
Lu, X., Heal, K. R., Ingalls, A. E., Doxey, A. C., & Neufeld, J. D. (2020). Metagenomic and chemical characterization of soil cobalamin production. The ISME Journal, 14(1), 53鈥66.
Mansfield, M. J., & Doxey, A. C. (2018). Genomic insights into the evolution and ecology of botulinum neurotoxins. Pathogens and Disease, 76(4).
Mansfield, M. J., Sugiman-Marangos, S. N., Melnyk, R. A., & Doxey, A. C. (2018). Identification of a diphtheria toxin-like gene family beyond the Corynebacterium genus. FEBS Letters, 592(16), 2693鈥2705.
Mansfield, M. J., Tremblay, B. J.-M., Zeng, J., Wei, X., Hodgins, H., Worley, J., Bry, L., Dong, M., & Doxey, A. C. (2020). Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PLoS Pathogens, 16(12), e1009181.
Mansfield, M. J., Wentz, T. G., Zhang, S., Lee, E. J., Dong, M., Sharma, S. K., & Doxey, A. C. (2019). Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins. Scientific Reports, 9(1), 1634.
Mendler, K., Chen, H., Parks, D. H., Lobb, B., Hug, L. A., & Doxey, A. C. (2019). AnnoTree: Visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Research, 47(9), 4442鈥4448.
Min, D., Doxey, A. C., & Neufeld, J. D. (2021). AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology. GigaScience, 10(2).
Orrell, K. E., Mansfield, M. J., Doxey, A. C., & Melnyk, R. A. (2020). The C. difficile toxin B membrane translocation machinery is an evolutionarily conserved protein delivery apparatus. Nature Communications, 11(1), 432.
Ross, A. A., Doxey, A. C., & Neufeld, J. D. (2017). The Skin Microbiome of Cohabiting Couples. MSystems, 2(4).
Spasov, E., Tsuji, J. M., Hug, L. A., Doxey, A. C., Sauder, L. A., Parker, W. J., & Neufeld, J. D. (2020). High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. The ISME Journal, 14(7), Article 7.
Sugiman-Marangos, S. N., Gill, S. K., Mansfield, M. J., Orrell, K. E., Doxey, A. C., & Melnyk, R. A. (2022). Structures of distant diphtheria toxin homologs reveal functional determinants of an evolutionarily conserved toxin scaffold. Communications Biology, 5(1), 375.
Tian, S., Xiong, X., Zeng, J., Wang, S., Tremblay, B. J.-M., Chen, P., Chen, B., Liu, M., Chen, P., Sheng, K., Zeve, D., Qi, W., Breault, D. T., Rodr铆guez, C., Gerhard, R., Jin, R., Doxey, A. C., & Dong, M. (2022). Identification of TFPI as a receptor reveals recombination-driven receptor switching in Clostridioides difficile toxin B variants. Nature Communications, 13(1), 6786.
Tremblay, B. J.-M., Lobb, B., & Doxey, A. C. (2021). PhyloCorrelate: Inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling. Bioinformatics (Oxford, England), btaa1105.
Varga, J. F. A., Brunner, S. R., Cheng, G., Min, D., Aucoin, M. G., Doxey, A. C., & Dixon, B. (2022). Identification and characterization of a novel peptide from rainbow trout (Oncorhynchus mykiss) with antimicrobial activity against Streptococcus iniae. Developmental & Comparative Immunology, 137, 104518.
Wentz, T. G., Tremblay, B. J. M., Bradshaw, M., Doxey, A. C., Sharma, S. K., Sauer, J.-D., & Pellett, S. (2021). Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster. Frontiers in Microbiology, 12, 787726.
Zhang, S., Lebreton, F., Mansfield, M. J., Miyashita, S.-I., Zhang, J., Schwartzman, J. A., Tao, L., Masuyer, G., Mart铆nez-Carranza, M., Stenmark, P., Gilmore, M. S., Doxey, A. C., & Dong, M. (2018). Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium. Cell Host & Microbe, 23(2), 169-176.e6.
Bernard Duncker
Zhao, K., Larasati, Duncker, B. P., & Li, D. (2019). Continuous Cell Characterization and Separation by Microfluidic Alternating Current Dielectrophoresis. Analytical Chemistry, 91(9), 6304鈥6314.
John Honek
Honek, J. F. (2019). Commentary on 鈥淐urrent Challenges in the Development of Vaccines and Drugs Against Emerging Vector-borne Diseases鈥 by Professor Kwang-sun Kim, Pusan National University, Republic of Korea. Current Medicinal Chemistry, 26(17), 3201鈥3204.
Suttisansanee, U., & F. Honek, J. (2017). Hydroxamate Inhibitor Profiling of Both Zn2+- and Ni2+-Activated Glyoxalase I Metalloenzymes Having Diverse Quaternary Structures. Letters in Drug Design & Discovery, 14(7), 843鈥852.
Suttisansanee, U., & Honek, J. F. (2019). Preliminary Characterization of a Ni2+-Activated and Mycothiol-Dependent Glyoxalase I Enzyme from Streptomyces coelicolor. Inorganics, 7(8), Article 8.
Urquhart, T., Howie, B., Zhang, L., Leung, K. T., & Honek, J. F. (2021). Bioconjugation of Bacteriophage Pf1 and Extension to Pf1-Based Bionanomaterials. Current Nanoscience, 17(1), 139鈥150.
Laura Hug
Co, R., & Hug, L. A. (2020). A Need for Improved Cellulase Identification from Metagenomic Sequence Data. Applied and Environmental Microbiology, 87(1), e01928-20.
Co, R., & Hug, L. A. (2021). Prediction, enrichment and isolation identify a responsive, competitive community of cellulolytic microorganisms from a municipal landfill. FEMS Microbiology Ecology, 97(5), fiab065.
Collins-Fairclough, A. M., Co, R., Ellis, M. C., & Hug, L. A. (2018). Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River. MSphere, 3(5), e00346-18.
Daniel S. Gr茅goire, Nikhil A. George, & Laura A. Hug. (2023). Microbial methane cycling in a landfill on a decadal time scale [Preprint]. Microbiology.
Douglas, A. J., Hug, L. A., & Katzenback, B. A. (2021). Composition of the North American Wood Frog (Rana sylvatica) Bacterial Skin Microbiome and Seasonal Variation in Community Structure. Microbial Ecology, 81(1), 78鈥92.
Goff, K. L., & Hug, L. A. (2022). Environmental Potential for Microbial 1,4-Dioxane Degradation Is Sparse despite Mobile Elements Playing a Role in Trait Distribution. Applied and Environmental Microbiology, 88(7), e02091-21.
Hilts, A. S., Hunjan, M. S., & Hug, L. A. (2021). Adapting Macroecology to Microbiology: Using Occupancy Modeling To Assess Functional Profiles across Metagenomes. MSystems, 6(6), e00790-21.
Hinz, A., Xing, L., Doukhanine, E., Hug, L. A., Kassen, R., Ormeci, B., Kibbee, R. J., Wong, A., MacFadden, D., & Nott, C. (2022). SARS-CoV-2 detection from the built environment and wastewater and its use for hospital surveillance. FACETS, 7, 82鈥97.
Hug, L. A. (2018). Sizing Up the Uncultured Microbial Majority. MSystems, 3(5), e00185-18.
Hug, L. A., & Co, R. (2018). It Takes a Village: Microbial Communities Thrive through Interactions and Metabolic Handoffs. MSystems, 3(2), e00152-17.
Jensen, G., Krogstad, K., Rezanezhad, F., & Hug, L. A. (2022). Microbial Community Compositional Stability in Agricultural Soils During Freeze-Thaw and Fertilizer Stress. Frontiers in Environmental Science, 10, 908568.
Johnson, L. A., & Hug, L. A. (2019). Distribution of reactive oxygen species defense mechanisms across domain bacteria. Free Radical Biology and Medicine, 140, 93鈥102.
Johnson, L. A., & Hug, L. A. (2022). Cloacimonadota metabolisms include adaptations in engineered environments that are reflected in the evolutionary history of the phylum. Environmental Microbiology Reports, 14(4), 520鈥529.
Krogstad, K., Gharasoo, M., Jensen, G., Hug, L. A., Rudolph, D., Van Cappellen, P., & Rezanezhad, F. (2022). Nitrogen Leaching From Agricultural Soils Under Imposed Freeze-Thaw Cycles: A Column Study With and Without Fertilizer Amendment. Frontiers in Environmental Science, 10.
M茅heust, R., Castelle, C. J., Matheus Carnevali, P. B., Farag, I. F., He, C., Chen, L.-X., Amano, Y., Hug, L. A., & Banfield, J. F. (2020). Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog. The ISME Journal, 14(12), Article 12.
Mendler, K., Chen, H., Parks, D. H., Lobb, B., Hug, L. A., & Doxey, A. C. (2019). AnnoTree: Visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Research, 47(9), 4442鈥4448.
Murray, A. E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., K盲mpfer, P., Konstantinidis, K. T., Lane, C. E., Papke, R. T., Parks, D. H., Rossello-Mora, R., Stott, M. B., Sutcliffe, I. C., Thrash, J. C., Venter, S. N., Whitman, W. B., Acinas, S. G., Amann, R. I., Anantharaman, K., 鈥 Reysenbach, A.-L. (2020). Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5(8), Article 8.
Sauk, A. H., & Hug, L. A. (2022). Substrate-restricted methanogenesis and limited volatile organic compound degradation in highly diverse and heterogeneous municipal landfill microbial communities. ISME Communications, 2(1), Article 1.
Spasov, E., Tsuji, J. M., Hug, L. A., Doxey, A. C., Sauder, L. A., Parker, W. J., & Neufeld, J. D. (2020). High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. The ISME Journal, 14(7), Article 7.
Viljakainen, V. R., & Hug, L. A. (2021a). The phylogenetic and global distribution of bacterial polyhydroxyalkanoate bioplastic-degrading genes. Environmental Microbiology, 23(3), 1717鈥1731.
Viljakainen, V. R., & Hug, L. A. (2021b). New approaches for the characterization of plastic-associated microbial communities and the discovery of plastic-degrading microorganisms and enzymes. Computational and Structural Biotechnology Journal, 19, 6191鈥6200.
Brian Ingalls
Ahmadzadegan, A., Hamadeh, A., Sukumaran, M. K., & Ingalls, B. (2018). Bioaugmentation Approaches for Suppression of Antibiotic Resistance: Model-Based Design. In R. Tempo, S. Yurkovich, & P. Misra (Eds.), Emerging Applications of Control and Systems Theory: A Festschrift in Honor of Mathukumalli Vidyasagar (pp. 193鈥204). Springer International Publishing.
Braniff, N., & Ingalls, B. (2018). New opportunities for optimal design of dynamic experiments in systems and synthetic biology. Current Opinion in Systems Biology, 9, 42鈥48.
Braniff, N., Pearce, T., Lu, Z., Astwood, M., Forrest, W. S. R., Receno, C., & Ingalls, B. (2022). NLoed: A Python package for nonlinear optimal experimental design in systems biology (p. 2021.06.03.446189). bioRxiv.
Braniff, N., Richards, A., & Ingalls, B. (2019). Optimal Experimental Design for a Bistable Gene Regulatory Network. IFAC-PapersOnLine, 52(26), 255鈥261.
Braniff, N., Scott, M., & Ingalls, B. (2019). Component Characterization in a Growth-Dependent Physiological Context: Optimal Experimental Design. Processes, 7(1), Article 1.
Chavez Rodriguez, L., Gonz谩lez-Nicol谩s, A., Ingalls, B., Streck, T., Nowak, W., Xiao, S., & Pagel, H. (2022). Optimal design of experiments to improve the characterisation of atrazine degradation pathways in soil. European Journal of Soil Science, 73(1), e13211.
Chavez Rodriguez, L., Ingalls, B., Schwarz, E., Streck, T., Uksa, M., & Pagel, H. (2020). Gene-Centric Model Approaches for Accurate Prediction of Pesticide Biodegradation in Soils. Environmental Science & Technology, 54(21), 13638鈥13650.
Diep, P., Boucinha, A., Kell, B., Yeung, B. A., Chen, X., Tsyplenkov, D., Serra, D., Escobar, A., Gnanapragasam, A., Emond, C. A., Sajtovich, V. A., Mahadevan, R., Kilkenny, D. M., Gini-Newman, G., Kaern, M., & Ingalls, B. (2021). Advancing undergraduate synthetic biology education: Insights from a Canadian iGEM student perspective. Canadian Journal of Microbiology, 67(10), 749鈥770.
Gidvani, R. D., Sudmant, P., Li, G., DaSilva, L. F., McConkey, B. J., Duncker, B. P., & Ingalls, B. P. (2012). A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations. BMC Systems Biology, 6.
Ingalls, B. P., Duncker, B. P., Kim, D. R., & McConkey, B. J. (2007). Systems level modeling of the cell cycle using budding yeast. Cancer Informatics, 3, 367鈥380.
Kim, D. R., Gidvani, R. D., Ingalls, B. P., Duncker, B. P., & McConkey, B. J. (2011). Differential chromatin proteomics of the MMS-induced DNA damage response in yeast. Proteome Science, 9.
Malwade, A., Nguyen, A., Sadat-Mousavi, P., & Ingalls, B. P. (2017). Predictive Modeling of a Batch Filter Mating Process. Frontiers in Microbiology, 8.
Treloar, N. J., Braniff, N., Ingalls, B., & Barnes, C. P. (2022). Deep Reinforcement Learning for Optimal Experimental Design in Biology (p. 2022.05.09.491138). bioRxiv.
Venkiteswaran, J. J., Schiff, S. L., & Ingalls, B. P. (2019). Quantifying the fate of wastewater nitrogen discharged to a Canadian river. FACETS, 4(1), 315鈥335.
Yip, A., Smith-Roberge, J., Khorasani, S. H., Aucoin, M. G., & Ingalls, B. P. (2022). Calibrating spatiotemporal models of microbial communities to microscopy data: A review. PLOS Computational Biology, 18(10), e1010533.
Yilan Liu
Chen, J., Liu, Y., Diep, P., Jo, A., Nesb酶, C., Edwards, E., Papangelakis, V., & Mahadevana, R. (2020). Complete Genome Sequence of Acidithiobacillus ferridurans JAGS, Isolated from Acidic Mine Drainage. Microbiology Resource Announcements, 9(13).
Chen, J., Liu, Y., Diep, P., & Mahadevan, R. (2021). Genomic analysis of a newly isolated acidithiobacillus ferridurans jags strain reveals its adaptation to acid mine drainage. Minerals, 11(1), 1鈥14.
Chen, J., Liu, Y., Diep, P., & Mahadevan, R. (2022a). Genetic engineering of extremely acidophilic Acidithiobacillus species for biomining: Progress and perspectives. Journal of Hazardous Materials, 438.
Chen, J., Liu, Y., Diep, P., & Mahadevan, R. (2022b). Harnessing synthetic biology for sustainable biomining with Fe/S-oxidizing microbes. Frontiers in Bioengineering and Biotechnology, 10.
Chen, R., Liu, Y., Zhong, W., Hao, X., Mu, T., Yang, M., & Xing, J. (2022). Ribosome-binding Sequences (RBS) Engineering of Key Genes in Escherichia coli for High Production of Fatty Alcohols. Biotechnology and Bioprocess Engineering, 27(4), 615鈥623.
Kramer, L., Hankore, E. D., Liu, Y., Liu, K., Jimenez, E., Guo, J., & Niu, W. (2018). Characterization of carboxylic acid reductases for biocatalytic synthesis of industrial chemicals. ChemBioChem, 19(13), 1452鈥1460.
Liu, Y., Benitez, M. G., Chen, J., Harrison, E., Khusnutdinova, A. N., & Mahadevan, R. (2021). Opportunities and Challenges for Microbial Synthesis of Fatty Acid-Derived Chemicals (FACs). Frontiers in Bioengineering and Biotechnology, 9.
Liu, Y., Chen, J., Crisante, D., Jaramillo Lopez, J. M., & Mahadevan, R. (2020). Dynamic Cell Programming with Quorum Sensing-Controlled CRISPRi Circuit. ACS Synthetic Biology, 9(6), 1284鈥1291.
Liu, Y., Chen, J., Khusnutdinova, A. N., Correia, K., Diep, P., Batyrova, K. A., Nemr, K., Flick, R., Stogios, P., Yakunin, A. F., & Mahadevan, R. (2020). A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution. Biotechnology for Biofuels, 13(1).
Liu, Y., Chen, J., Raj, K., Baerg, L., Nathan, N., Philpott, D. J., & Mahadevan, R. (2023). A Universal Strategy to Promote Secretion of G+/G- Bacterial Extracellular Vesicles and Its Application in Host Innate Immune Responses. ACS Synthetic Biology, 12(1), 319鈥328.
Liu, Y., Chen, J., & Thygesen, A. (2018). Efficient One-Step Fusion PCR Based on Dual-Asymmetric Primers and Two-Step Annealing. Molecular Biotechnology, 60(2), 92鈥99.
Liu, Y., He, X., Lim, W., Mueller, J., Lawrie, J., Kramer, L., Guo, J., & Niu, W. (2018). Deciphering molecular details in the assembly of alpha-type carboxysome. Scientific Reports, 8(1).
Liu, Y., Khusnutdinova, A., Chen, J., Crisante, D., Batyrova, K., Raj, K., Feigis, M., Shirzadi, E., Wang, X., Dorakhan, R., Wang, X., Stogios, P. J., Yakunin, A. F., Sargent, E. H., & Mahadevan, R. (2022). Systems engineering of Escherichia coli for n-butane production. Metabolic Engineering, 74, 98鈥107.
Kesen Ma
Adegboye, M. F., Lobb, B., Babalola, O. O., Doxey, A. C., & Ma, K. (2018). Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil. Genome Announcements, 6(26), e00632-18.
Alharbi, F., Knura, T., Siebers, B., & Ma, K. (2022). Thermostable and O2-Insensitive Pyruvate Decarboxylases from Thermoacidophilic Archaea Catalyzing the Production of Acetaldehyde. Biology, 11(8), 1247.
Asokumar, N., Kim, S. D., & Ma, K. (2018). Alcohol Dehydrogenases Catalyzing the Production of Ethanol at High Temperatures. Innovative Energy & Research, 07(04).
Dawood, A., & Ma, K. (2020). Applications of Microbial 尾-Mannanases. Frontiers in Bioengineering and Biotechnology, 8.
E. Ibrahim, N., & Ma, K. (2017). Industrial Applications of Thermostable Enzymes from Extremophilic Microorganisms. Current Biochemical Engineering, 4(2), 75鈥98.
Hao, J., Wang, P., Kang, Y., He, H., Luo, H., Kim, S., Niu, L., Jiang, H., & Ma, K. (2019). Degradation of Perfluorooctane Sulfonamide by Acinetobacter Sp. M and Its Extracellular Enzymes. Chemistry 鈥 An Asian Journal, 14(16), 2780鈥2784.
Kim, S. D., Zhu, X., Jin, Y., Nguyen, T. N., Johnston, K., Li, A., Zhang, X., Zhao, J., & Ma*, K. (2019). Differential Solvent Production by Clostridium beijerinckii NRRL-B593 Grown on Carbohydrates and Peptides. Advances in Biochemistry and Biotechnology.
Lobb, B., Adegoke, A. A., Ma, K., Doxey, A. C., & Aiyegoro, O. A. (2018). Metagenomic Sequencing of Wastewater from a South African Research Farm. Microbiology Resource Announcements, 7(16).
Ma, K. (2018). Beneficial Characteristics and Evaluation Criteria of Probiotics. Int J Food Biosci Vol: 1, Issu: 1 (19-26).
Rahman, Md. S., Xu, C. (Charles), Ma, K., Guo, H., & Qin, W. (2017). Utilization of by-product glycerol from bio-diesel plants as feedstock for 2,3-butanediol accumulation and biosynthesis genes response of Klebsiella variicola SW3. Renewable Energy, 114, 1272鈥1280.
Rahman, Md. S., Xu, C. (Charles), Ma, K., Nanda, M., & Qin, W. (2017). High Production of 2,3-butanediol by a Mutant Strain of the Newly Isolated Klebsiella pneumoniae SRP2 with Increased Tolerance Towards Glycerol. International Journal of Biological Sciences, 13(3), 308鈥318.
Sun, Y., Wang, H., Ma, K., & Shao, W. (2018). Construction and characterization of the GFAT gene as a novel selection marker in Aspergillus nidulans. Applied Microbiology and Biotechnology, 102(18), 7951鈥7962.
Tse, C., Ibrahim, N. E., & Ma, K. (2017). Characterization of an Alcohol Dehydrogenase of the Hyperthermophilic Archaeon Hyperthermus Butylicus. Journal of Applied Microbiology and Biochemistry, 2(1).
Wang, Q., Sha, C., Wang, H., Ma, K., Wiegle, J., Abomohra, A. E.-F., & Shao, W. (2021). A novel bifunctional aldehyde/alcohol dehydrogenase catalyzing reduction of acetyl-CoA to ethanol at temperatures up to 95聽掳C. Scientific Reports, 11, 1050.
Wang, Y., Liu, H., Peng, Y., Tong, L., Feng, L., & Ma, K. (2018a). New pathways for the biodegradation of diethyl phthalate by Sphingobium yanoikuyae SHJ. Process Biochemistry, 71, 152鈥158.
Wang, Y., Liu, H., Peng, Y., Tong, L., Feng, L., & Ma, K. (2018b). Characterization of the diethyl phthalate-degrading bacterium Sphingobium yanoikuyae SHJ. Data in Brief, 20, 1758鈥1763.
Zhang, L., Xu, D., Huang, Y., Zhu, X., Rui, M., Wan, T., Zheng, X., Shen, Y., Chen, X., Ma, K., & Gong, Y. (2017). Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease. Scientific Reports, 7(1), Article 1.
Shannon Majowicz
Bitzegeio, J., Majowicz, S., Matysiak-Klose, D., Sagebiel, D., & Werber, D. (2019). Estimating age-specific vaccine effectiveness using data from a large measles outbreak in Berlin, Germany, 2014/15: Evidence for waning immunity. Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 24(17), 1800529.
C么t茅, D., Durant, S., MacEachen, E., Majowicz, S., Meyer, S., Huynh, A.-T., Laberge, M., & Dub茅, J. (2021). A rapid scoping review of COVID-19 and vulnerable workers: Intersecting occupational and public health issues. American Journal of Industrial Medicine, 64(7), 551鈥566.
Desta, B. N., Gobena, T., Macuamule, C., Fayemi, O. E., Ayolabi, C. I., Mmbaga, B. T., Thomas, K. M., Dodd, W., Pires, S. M., Majowicz, S. E., & Hald, T. (2022). Practicalities of implementing burden of disease research in Africa: Lessons from a population survey component of our multi-partner FOCAL research project. Emerging Themes in Epidemiology, 19(1), 4.
Devleesschauwer, B., Pires, S. M., Young, I., Gill, A., Majowicz, S. E., & study team. (2019). Associating sporadic, foodborne illness caused by Shiga toxin-producing Escherichia coli with specific foods: A systematic review and meta-analysis of case-control studies. Epidemiology and Infection, 147, e235.
Diplock, K. J., Dubin, J. A., Leatherdale, S. T., Hammond, D., Jones-Bitton, A., & Majowicz, S. E. (2018). Observation of High School Students鈥 Food Handling Behaviors: Do They Improve following a Food Safety Education Intervention? Journal of Food Protection, 81(6), 917鈥925.
Diplock, K. J., Leatherdale, S. T., & Majowicz, S. E. (2017). Diarrhea ain鈥檛 dope: Canada needs to consider the food safety implications of edible cannabis. Canadian Journal of Public Health = Revue Canadienne De Sante Publique, 108(4), e455.
Gohari, M. R., Taylor, M., MacKinnon, M. C., Panagiotoglou, D., Galanis, E., Kaplan, G. G., Cook, R. J., Patrick, D. M., Ethelberg, S., & Majowicz, S. E. (2022). Patterns of enteric infections in a population-wide cohort study of sequelae, British Columbia, Canada. Epidemiology and Infection, 151, e7.
Graells, T., Lambraki, I. A., Cousins, M., L茅ger, A., Lillepold, K., Henriksson, P. J. G., Troell, M., Carson, C. A., Parmley, E. J., Majowicz, S. E., Wernli, D., & J酶rgensen, P. S. (2022). Studying Factors Affecting Success of Antimicrobial Resistance Interventions through the Lens of Experience: A Thematic Analysis. Antibiotics (Basel, Switzerland), 11(5), 639.
Hopwood, P., MacEachen, E., Majowicz, S. E., Meyer, S. B., & Amoako, J. (2022). 鈥淲e need to talk to each other鈥: Crossing traditional boundaries between public health and occupational health to address COVID-19. Frontiers in Public Health, 10, 1046628.
John, P., Varga, C., Cooke, M., & Majowicz, S. E. (2022). Incidence, Demographic, and Seasonal Risk Factors of Infections Caused by Five Major Enteric Pathogens, Ontario, Canada, 2010-2017. Foodborne Pathogens and Disease, 19(4), 248鈥258.
Lambraki, I. A., Chadag, M. V., Cousins, M., Graells, T., L茅ger, A., Henriksson, P. J. G., Troell, M. F., Harbarth, S., Wernli, D., J酶rgensen, P. S., Carson, C. A., Parmley, E. J., & Majowicz, S. E. (2023). Factors impacting antimicrobial resistance in the South East Asian food system and potential places to intervene: A participatory, one health study. Frontiers in Microbiology, 13, 992507.
Lambraki, I. A., Cousins, M., Graells, T., L茅ger, A., Abdelrahman, S., Desbois, A. P., Gallagher, R., Staaf Larsson, B., Mattson, B., Henriksson, P., Troell, M., S酶gaard J酶rgensen, P., Wernli, D., Carson, C. A., Parmley, E. J., & Majowicz, S. E. (2022). Governing Antimicrobial Resistance (AMR) in a Changing Climate: A Participatory Scenario Planning Approach Applied to Sweden in 2050. Frontiers in Public Health, 10, 831097.
Lambraki, I. A., Cousins, M., Graells, T., L茅ger, A., Henriksson, P., Harbarth, S., Troell, M., Wernli, D., S酶gaard J酶rgensen, P., Desbois, A. P., Carson, C. A., Parmley, E. J., & Majowicz, S. E. (2022). Factors influencing antimicrobial resistance in the European food system and potential leverage points for intervention: A participatory, One Health study. PloS One, 17(2), e0263914.
Lambraki, I. A., Majowicz, S. E., Parmley, E. J., Wernli, D., L茅ger, A., Graells, T., Cousins, M., Harbarth, S., Carson, C., Henriksson, P., Troell, M., & J酶rgensen, P. S. (2021). Building Social-Ecological System Resilience to Tackle Antimicrobial Resistance Across the One Health Spectrum: Protocol for a Mixed Methods Study. JMIR Research Protocols, 10(6), e24378.
L茅ger, A., Lambraki, I., Graells, T., Cousins, M., Henriksson, P. J. G., Harbarth, S., Carson, C. A., Majowicz, S. E., Troell, M., Parmley, E. J., J酶rgensen, P. S., & Wernli, D. (2021a). Characterizing social-ecological context and success factors of antimicrobial resistance interventions across the One Health spectrum: Analysis of 42 interventions targeting E. coli. BMC Infectious Diseases, 21(1), 873.
L茅ger, A., Lambraki, I., Graells, T., Cousins, M., Henriksson, P. J. G., Harbarth, S., Carson, C., Majowicz, S., Troell, M., Parmley, E. J., J酶rgensen, P. S., & Wernli, D. (2021b). AMR-Intervene: A social-ecological framework to capture the diversity of actions to tackle antimicrobial resistance from a One Health perspective. The Journal of Antimicrobial Chemotherapy, 76(1), 1鈥21.
Major, M., Majowicz, S. E., Oremus, M., Jimenez, L. J., Angulo, F. J., & Horton, S. (2022). Systematic literature review of SARS-CoV-2 seroprevalence surveys in Canada through April 2021. IJID Regions, 4, 157鈥164.
Majowicz, S. E. (2020). Using Market Availability Data to Support Foodborne Disease Outbreak Investigations. American Journal of Public Health, 110(3), 278鈥280.
Majowicz, S. E., Hammond, D., Dubin, J. A., Diplock, K. J., Jones-Bitton, A., Rebellato, S., & Leatherdale, S. T. (2017). A longitudinal evaluation of food safety knowledge and attitudes among Ontario high school students following a food handler training program. Food Control, 76, 108鈥116.
Majowicz, S. E., Parmley, E. J., Carson, C., & Pintar, K. (2018). Identifying non-traditional stakeholders with whom to engage, when mitigating antimicrobial resistance in foodborne pathogens (Canada). BMC Research Notes, 11(1), 170.
Pires, S. M., Desta, B. N., Mughini-Gras, L., Mmbaga, B. T., Fayemi, O. E., Salvador, E. M., Gobena, T., Majowicz, S. E., Hald, T., Hoejskov, P. S., Minato, Y., & Devleesschauwer, B. (2021). Burden of foodborne diseases: Think global, act local. Current Opinion in Food Science, 39, 152鈥159.
Pires, S. M., Majowicz, S., Gill, A., & Devleesschauwer, B. (2019). Global and regional source attribution of Shiga toxin-producing Escherichia coli infections using analysis of outbreak surveillance data. Epidemiology and Infection, 147, e236.
Speed, K. A., Meyer, S. B., Hanning, R. M., & Majowicz, S. E. (2017). 鈥淗ighly processed, highly packaged, very unhealthy. But they are low risk鈥: Exploring intersections between community food security and food safety. Health Promotion and Chronic Disease Prevention in Canada, 37(10), 323鈥332.
Varga, C., John, P., Cooke, M., & Majowicz, S. E. (2020). Spatial and space-time clustering and demographic characteristics of human nontyphoidal Salmonella infections with major serotypes in Toronto, Canada. PloS One, 15(7), e0235291.
Varga, C., John, P., Cooke, M., & Majowicz, S. E. (2021). Area-Level Clustering of Shiga Toxin-Producing Escherichia coli Infections and Their Socioeconomic and Demographic Factors in Ontario, Canada: An Ecological Study. Foodborne Pathogens and Disease, 18(7), 438鈥447.
Wernli, D., J酶rgensen, P. S., Parmley, E. J., Troell, M., Majowicz, S., Harbarth, S., L茅ger, A., Lambraki, I., Graells, T., Henriksson, P. J. G., Carson, C., Cousins, M., Skoog St氓hlgren, G., Mohan, C. V., Simpson, A. J. H., Wieland, B., Pedersen, K., Schneider, A., Chandy, S. J., 鈥 Pittet, D. (2020). Evidence for action: A One Health learning platform on interventions to tackle antimicrobial resistance. The Lancet. Infectious Diseases, 20(12), e307鈥揺311.
Brendan McConkey
Ali, S., Jenkins, B., Cheng, J., Lobb, B., Wei, X., Egan, S., Charles, T. C., McConkey, B. J., Austin, J., & Doxey, A. C. (2020). Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. Molecular Microbiology, 114(6), 979鈥990.
Gromala, M., Neufeld, J. D., & McConkey, B. J. (2021). Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds. Applied and Environmental Microbiology, 87(7), e02914-20.
Logan, M., Rinas, K., McConkey, B., & Aucoin, M. G. (2022). Vero cells gain renal tubule markers in low-calcium and magnesium chemically defined media. Scientific Reports, 12(1), Article 1.
Jenine McCutcheon
Lutz, S., McCutcheon, J., McQuaid, J. B., & Benning, L. G. (2018). The diversity of ice algal communities on the Greenland Ice Sheet as revealed by oligotyping. Microbial Genomics, 4(3).
McCutcheon, J., Lutz, S., Williamson, C., Cook, J. M., Tedstone, A. J., Vanderstraeten, A., Wilson, S. A., Stockdale, A., Bonneville, S., Anesio, A. M., Yallop, M. L., McQuaid, J. B., Tranter, M., & Benning, L. G. (2021). Mineral phosphorus drives glacier algal blooms on the Greenland Ice Sheet. Nature Communications, 12(1).
McCutcheon, J., Nothdurft, L. D., Webb, G. E., Shuster, J., Nothdurft, L., Paterson, D., & Southam, G. (2017). Building biogenic beachrock: Visualizing microbially-mediated carbonate cement precipitation using XFM and a strontium tracer. Chemical Geology, 465, 21鈥34.
McCutcheon, J., Power, I. M., Shuster, J., Harrison, A. L., Dipple, G. M., & Southam, G. (2019). Carbon Sequestration in Biogenic Magnesite and Other Magnesium Carbonate Minerals. Environmental Science and Technology, 53(6), 3225鈥3237.
McCutcheon, J., & Southam, G. (2018). Advanced biofilm staining techniques for TEM and SEM in geomicrobiology: Implications for visualizing EPS architecture, mineral nucleation, and microfossil generation. Chemical Geology, 498, 115鈥127.
McCutcheon, J., Turvey, C. C., Wilson, S. A., Hamilton, J. L., & Southam, G. (2017). Experimental deployment of microbial mineral carbonation at an asbestos mine: Potential applications to carbon storage and tailings stabilization. Minerals, 7(10).
Nicholes, M. J., Williamson, C. J., Tranter, M., Holland, A., Poniecka, E., Yallop, M. L., Anesio, A., Poniecka, E., Benning, L., McQuaid, J., Lutz, S., McCutcheon, J., Hodson, A., Hanna, E., Irvine-Fynn, T., Cook, J., Bamber, J., Tedstone, A., Box, J., 鈥 The Black & Bloom Group. (2019). Bacterial dynamics in supraglacial habitats of the Greenland ice sheet. Frontiers in Microbiology, 10(JUL).
Williamson, C. J., Cook, J., Tedstone, A., Yallop, M., McCutcheon, J., Poniecka, E., Campbell, D., Irvine-Fynn, T., McQuaid, J., Tranter, M., Perkins, R., & Anesio, A. (2020). Algal photophysiology drives darkening and melt of the Greenland Ice Sheet. Proceedings of the National Academy of Sciences of the United States of America, 117(11), 5694鈥5705.
Tizazu McKennon
Ogunsona, E. O., Muthuraj, R., Ojogbo, E., Valerio, O., & Mekonnen, T. H. (2020). Engineered nanomaterials for antimicrobial applications: A review. Applied Materials Today, 18, 100473.
Ojogbo, E., Ward, V., & Mekonnen, T. H. (2020). Functionalized starch microparticles for contact-active antimicrobial polymer surfaces. Carbohydrate Polymers, 229, 115422.
Christine Moresoli
Khouri, J., Penlidis, A., & Moresoli, C. (2020). Heterogeneous method of chitosan film preparation: Effect of multifunctional acid on film properties. Journal of Applied Polymer Science, 137(18), 48648.
Le Gou茅, E., Gardrat, C., Romain, M., Rollini, M., Moresoli, C., & Coma, V. (2022). Effect of oleic acid on the release of tetrahydrocurcumin in chitosan-based films. Food Hydrocolloids, 124, 107202.
Ranamukhaarachchi, S. A., Peiris, R. H., & Moresoli, C. (2017). Fluorescence spectroscopy and principal component analysis of soy protein hydrolysate fractions and the potential to assess their antioxidant capacity characteristics. Food Chemistry, 217, 469鈥475.
Kirsten M眉ller
Cameron, E. S., Schmidt, P. J., Tremblay, B. J.-M., Emelko, M. B., & M眉ller, K. M. (2021). Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities. Scientific Reports, 11(1), Article 1.
M眉ller, K. M., Chhun, A., Guildford, S. J., Yakobowski, S. J., & Jonlija, M. (2017). Molecular and ecological characterization of toxic cyanobacteria from the Bay of Quinte (Lake Ontario) and Maumee Bay (Lake Erie). Journal of Great Lakes Research, 43(6), 1067鈥1083.
Nema, M., Hanson, M. L., & M眉ller, K. M. (2019). Phylogeny of the egg-loving green alga Oophila amblystomatis (Chlamydomonadales) and its response to the herbicides atrazine and 2,4-D. Symbiosis, 77(1), 23鈥39.
Ross, A. A., M眉ller, K. M., Weese, J. S., & Neufeld, J. D. (2018). Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia. Proceedings of the National Academy of Sciences, 115(25).
Schmidt, P. J., Cameron, E. S., M眉ller, K. M., & Emelko, M. B. (2022). Ensuring That Fundamentals of Quantitative Microbiology Are Reflected in Microbial Diversity Analyses Based on Next-Generation Sequencing. Frontiers in Microbiology, 13, 728146.
Josh Neufeld
Al-Ajeel, S., Spasov, E., Sauder, L. A., McKnight, M. M., & Neufeld, J. D. (2022). Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems. Water Research X, 15.
Bai, X., McKnight, M. M., Neufeld, J. D., & J Parker, W. (2023). Simultaneous nitrification, denitrification, and phosphorus removal from municipal wastewater at low temperature. Bioresource Technology, 368, 128261.
Bai, X., McKnight, M. M., Neufeld, J. D., & Parker, W. J. (2022). Nitrogen removal pathways during simultaneous nitrification, denitrification, and phosphorus removal under low temperature and dissolved oxygen conditions. Bioresource Technology, 354, 127177.
Beaver, R. C., Engel, K., Binns, W. J., & Neufeld, J. D. (2022). Microbiology of barrier component analogues of a deep geological repository. Canadian Journal of Microbiology, 68(2), 73鈥90.
Bik, H. M., Alexiev, A., Aulakh, S. K., Bharadwaj, L., Flanagan, J., Haggerty, J. M., Hird, S. M., Jospin, G., Lang, J. M., Sauder, L. A., Neufeld, J. D., Shaver, A., Sethi, A., Eisen, J. A., & Coil, D. A. (2019). Microbial community succession and nutrient cycling responses following perturbations of experimental saltwater aquaria. MSphere, 4(1).
Cavaco, M. A., St.聽Louis, V. L., Engel, K., St.聽Pierre, K. A., Schiff, S. L., Stibal, M., & Neufeld, J. D. (2019). Freshwater microbial community diversity in a rapidly changing High Arctic watershed. FEMS Microbiology Ecology, 95(11), fiz161.
Cheng, J., Lam, K. N., Engel, K., Hall, M., Neufeld, J. D., & Charles, T. C. (2017). Metagenomic cosmid libraries suitable for functional screening in proteobacteria. In Functional Metagenomics: Tools and Applications (pp. 1鈥11).
Cheng, J., Romantsov, T., Engel, K., Doxey, A. C., Rose, D. R., Neufeld, J. D., & Charles, T. C. (2017). Functional metagenomics reveals novel 尾-galactosidases not predictable from gene sequences. PloS One, 12(3), e0172545.
Coyotzi, S., Doxey, A. C., Clark, I. D., Lapen, D. R., Van Cappellen, P., & Neufeld, J. D. (2017). Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity. Environmental Microbiology, 19(3), 1189鈥1208.
De Palma, G., Lynch, M. D. J., Lu, J., Dang, V. T., Deng, Y., Jury, J., Umeh, G., Miranda, P. M., Pastor, M. P., Sidani, S., Pinto-Sanchez, M. I., Philip, V., McLean, P. G., Hagelsieb, M.-G., Surette, M. G., Bergonzelli, G. E., Verdu, E. F., Britz-McKibbin, P., Neufeld, J. D., 鈥 Bercik, P. (2017). Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice. Science Translational Medicine, 9(379).
Duguma, D., Hall, M. W., Smartt, C. T., Debboun, M., & Neufeld, J. D. (2019). Microbiota variations in Culex nigripalpus disease vector mosquito of west nile virus and saint louis encephalitis from different geographic origins. PeerJ, 2019(1).
Duguma, D., Hall, M. W., Smartt, C. T., & Neufeld, J. D. (2017a). Effects of organic amendments on microbiota associated with the Culex nigripalpus mosquito vector of the Saint Louis encephalitis and West Nile viruses. MSphere, 2(1).
Duguma, D., Hall, M. W., Smartt, C. T., & Neufeld, J. D. (2017b). Temporal Variations of Microbiota Associated with the Immature Stages of Two Florida Culex Mosquito Vectors. Microbial Ecology, 74(4), 979鈥989.
Element, G., Engel, K., Neufeld, J. D., Casselman, J. M., van Coeverden de Groot, P., Greer, C. W., & Walker, V. K. (2020). Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus). Environmental Microbiology, 22(8), 3112鈥3125.
Element, G., Engel, K., Neufeld, J. D., Casselman, J. M., Van Coeverden De Groot, P. J., & Walker, V. K. (2021). Distinct intestinal microbial communities of two sympatric anadromous arctic salmonids and the effects of migration and feeding. Arctic Science, 7(3), 634鈥654.
Garcia, S. L., Mehrshad, M., Buck, M., Tsuji, J. M., Neufeld, J. D., McMahon, K. D., Bertilsson, S., Greening, C., & Peura, S. (2021). Freshwater chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations. MSystems, 6(3).
Gromala, M., Neufeld, J. D., & McConkey, B. J. (2021). Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds. Applied and Environmental Microbiology, 87(7), e02914-20.
Gwak, J.-H., Jung, M.-Y., Hong, H., Kim, J.-G., Quan, Z.-X., Reinfelder, J. R., Spasov, E., Neufeld, J. D., Wagner, M., & Rhee, S.-K. (2020). Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants. ISME Journal, 14(2), 335鈥346.
Hall, M. W., Singh, N., Ng, K. F., Lam, D. K., Goldberg, M. B., Tenenbaum, H. C., Neufeld, J. D., Beiko, R. G., & Senadheera, D. B. (2017). Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity. Npj Biofilms and Microbiomes, 3(1).
Hamilton, E. F., Element, G., van Coeverden de Groot, P., Engel, K., Neufeld, J. D., Shah, V., & Walker, V. K. (2019). Anadromous arctic char microbiomes: Bioprospecting in the high arctic. Frontiers in Bioengineering and Biotechnology, 7(FEB).
Hern谩ndez, M., Neufeld, J. D., & Dumont, M. G. (2017). Enhancing functional metagenomics of complex microbial communities using stable isotopes. In Functional Metagenomics: Tools and Applications (pp. 139鈥150).
Kvas, S., Rahn, J., Engel, K., Neufeld, J. D., Villeneuve, P. J., Trevors, J. T., Lee, H., Scroggins, R. P., & Beaudette, L. A. (2017). Development of a microbial test suite and data integration method for assessing microbial health of contaminated soil. Journal of Microbiological Methods, 143, 66鈥77.
Liu, K., Schiff, S. L., Wu, L., Molot, L. A., Venkiteswaran, J. J., Paterson, M. J., Elgood, R. J., Tsuji, J. M., & Neufeld, J. D. (2022). Large Fractionation in Iron Isotopes Implicates Metabolic Pathways for Iron Cycling in Boreal Shield Lakes. Environmental Science and Technology, 56(20), 14840鈥14851.
Lobb, B., Hodgson, R., Lynch, M. D. J., Mansfield, M. J., Cheng, J., Charles, T. C., Neufeld, J. D., Craig, P. M., & Doxey, A. C. (2020). Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens. MSystems, 5(2), e00145-20.
Lu, X., Heal, K. R., Ingalls, A. E., Doxey, A. C., & Neufeld, J. D. (2020). Metagenomic and chemical characterization of soil cobalamin production. The ISME Journal, 14(1), 53鈥66.
Lu, X., Nicol, G. W., & Neufeld, J. D. (2018). Differential responses of soil ammonia-oxidizing archaea and bacteria to temperature and depth under two different land uses. Soil Biology and Biochemistry, 120, 272鈥282.
Lu, X., Seuradge, B. J., & Neufeld, J. D. (2017). Biogeography of soil Thaumarchaeota in relation to soil depth and land usage. FEMS Microbiology Ecology, 93(2).
Lu, X., Taylor, A. E., Myrold, D. D., & Neufeld, J. D. (2020). Expanding perspectives of soil nitrification to include ammonia-oxidizing archaea and comammox bacteria. Soil Science Society of America Journal, 84(2), 287鈥302.
Min, D., Doxey, A. C., & Neufeld, J. D. (2021). AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology. GigaScience, 10(2).
Neufeld, J. D. (2023). Microbes 鈥楻鈥 us. Environmental Microbiology, 25(1), 177鈥178.
Pronk, G. J., Mellage, A., Milojevic, T., Smeaton, C. M., Engel, K., Neufeld, J. D., Rezanezhad, F., & Van Cappellen, P. (2020). Carbon turnover and microbial activity in an artificial soil under imposed cyclic drainage and imbibition. Vadose Zone Journal, 19(1).
Ross, A. A., Doxey, A. C., & Neufeld, J. D. (2017). The Skin Microbiome of Cohabiting Couples. MSystems, 2(4).
Ross, A. A., M眉ller, K. M., Weese, J. S., & Neufeld, J. D. (2018). Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia. Proceedings of the National Academy of Sciences, 115(25).
Ross, A. A., Rodrigues Hoffmann, A., & Neufeld, J. D. (2019). The skin microbiome of vertebrates. Microbiome, 7(1).
Sauder, L. A., Albertsen, M., Engel, K., Schwarz, J., Nielsen, P. H., Wagner, M., & Neufeld, J. D. (2017). Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. ISME Journal, 11(5), 1142鈥1157.
Sauder, L. A., Albertsen, M., Engel, K., Schwarz, J., Nielsen, P. H., Wagner, M., & Neufeld, J. D. (2020). Correction: Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system (The ISME Journal, (2017), 11, 5, (1142-1157), 10.1038/ismej.2016.192). ISME Journal, 14(9), 2366.
Sauder, L. A., Engel, K., Lo, C.-C., Chain, P., & Neufeld, J. D. (2018). Candidatus Nitrosotenuis aquarius," an ammonia-oxidizing archaeon from a freshwater aquarium biofilter. Applied and Environmental Microbiology, 84(19).
Schiff, S. L., Tsuji, J. M., Wu, L., Venkiteswaran, J. J., Molot, L. A., Elgood, R. J., Paterson, M. J., & Neufeld, J. D. (2017). Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry. Scientific Reports, 7(1), Article 1.
Seuradge, B. J., Oelbermann, M., & Neufeld, J. D. (2017). Depth-dependent influence of different land-use systems on bacterial biogeography. FEMS Microbiology Ecology, 93(2).
Spasov, E., Tsuji, J. M., Hug, L. A., Doxey, A. C., Sauder, L. A., Parker, W. J., & Neufeld, J. D. (2020). High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. The ISME Journal, 14(7), Article 7.
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., V谩zquez-Baeza, Y., Gonz谩lez, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., 鈥 Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth鈥檚 multiscale microbial diversity. Nature, 551(7681), 457鈥463.
Tsuji, J. M., Tran, N., Schiff, S. L., Venkiteswaran, J. J., Molot, L. A., Tank, M., Hanada, S., & Neufeld, J. D. (2020). Anoxygenic photosynthesis and iron鈥搒ulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes. The ISME Journal, 14(11), Article 11.
Tsuji, J., Shaw, N., Nagashima, S., Venkiteswaran, J., Schiff, S., Hanada, S., Tank, M., & Neufeld, J. (2020). Type I photosynthetic reaction center in an anoxygenic phototrophic member of the Chloroflexota [Preprint]. Microbiology.
Umbach, A. K., Stegelmeier, A. A., & Neufeld, J. D. (2021). Archaea are rare and uncommon members of the mammalian skin microbiome. MSystems, 6(4).
Vachon, M. A., Engel, K., Beaver, R. C., Slater, G. F., Binns, W. J., & Neufeld, J. D. (2021). Fifteen shades of clay: Distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction. Scientific Reports, 11(1).
Jozef Nissimov
Johns, C. T., Grubb, A. R., Nissimov, J. I., Natale, F., Knapp, V., Mui, A., Fredricks, H. F., Van Mooy, B. A. S., & Bidle, K. D. (2019). The mutual interplay between calcification and coccolithovirus infection. Environmental Microbiology, 21(6), 1896鈥1915.
Knowles, B., Bonachela, J. A., Behrenfeld, M. J., Bondoc, K. G., Cael, B. B., Carlson, C. A., Cieslik, N., Diaz, B., Fuchs, H. L., Graff, J. R., Grasis, J. A., Halsey, K. H., Haramaty, L., Johns, C. T., Natale, F., Nissimov, J. I., Schieler, B., Thamatrakoln, K., Frede Thingstad, T., 鈥 Bidle, K. D. (2020). Temperate infection in a virus鈥揾ost system previously known for virulent dynamics. Nature Communications, 11(1).
Laber, C. P., Hunter, J. E., Carvalho, F., Collins, J. R., Hunter, E. J., Schieler, B. M., Boss, E., More, K., Frada, M., Thamatrakoln, K., Brown, C. M., Haramaty, L., Ossolinski, J., Fredricks, H., Nissimov, J. I., Vandzura, R., Sheyn, U., Lehahn, Y., Chant, R. J., 鈥 Bidle, K. D. (2018). Coccolithovirus facilitation of carbon export in the North Atlantic. Nature Microbiology, 3(5), 537鈥547.
Nissimov, J. I., & Bidle, K. D. (2017). Stress, death, and the biological glue of sinking matter. Journal of Phycology, 53(2), 241鈥244.
Nissimov, J. I., Campbell, C. N., Probert, I., & Wilson, W. H. (2022). Aquatic virus culture collection: An absent (but necessary) safety net for environmental microbiologists. Applied Phycology, 3(1), 211鈥225.
Nissimov, J. I., Pagarete, A., Ma, F., Cody, S., Dunigan, D. D., Kimmance, S. A., & Allen, M. J. (2017). Coccolithoviruses: A review of cross鈥恔ingdom genomic thievery and metabolic thuggery. Viruses, 9(3).
Nissimov, J. I., Talmy, D., Haramaty, L., Fredricks, H. F., Zelzion, E., Knowles, B., Eren, A. M., Vandzura, R., Laber, C. P., Schieler, B. M., Johns, C. T., More, K. D., Coolen, M. J. L., Follows, M. J., Bhattacharya, D., Van Mooy, B. A. S., & Bidle, K. D. (2019). Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology. Environmental Microbiology, 21(6), 2182鈥2197.
Nissimov, J. I., Vandzura, R., Johns, C. T., Natale, F., Haramaty, L., & Bidle, K. D. (2018). Dynamics of transparent exopolymer particle production and aggregation during viral infection of the coccolithophore, Emiliania huxleyi. Environmental Microbiology, 20(8), 2880鈥2897.
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., V谩zquez-Baeza, Y., Gonz谩lez, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., 鈥 Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth鈥檚 multiscale microbial diversity. Nature, 551(7681), 457鈥463.
Maren Oelbermann
Badewa, E. A., Yeung, C. C., Rezanezhad, F., Whalen, J. K., & Oelbermann, M. (2022). Spring Freeze鈥揟haw Stimulates Greenhouse Gas Emissions From Agricultural Soil. Frontiers in Environmental Science, 10.
Baskerville, M., Bazrgar, A., Reddy, N., Ofosu, E., Thevathasan, N., Gordon, A. M., & Oelbermann, M. (2021). Greenhouse gas emissions from riparian zones are related to vegetation type and environmental factors. Journal of Environmental Quality, 50(4), 847鈥857.
Baskerville, M., Reddy, N., Ofosu, E., Thevathasan, N. V., & Oelbermann, M. (2021). Vegetation Type Does not Affect Nitrous Oxide Emissions from Riparian Zones in Agricultural Landscapes. Environmental Management, 67(2), 371鈥383.
Bichel, A., Oelbermann, M., & Echarte, L. (2017). Impact of residue addition on soil nitrogen dynamics in intercrop and sole crop agroecosystems. Geoderma, 304, 12鈥18.
Buchanan, S. W., Baskerville, M., Oelbermann, M., Gordon, A. M., Thevathasan, N. V., & Isaac, M. E. (2020). Plant diversity and agroecosystem function in riparian agroforests: Providing ecosystem services and land-use transition. Sustainability (Switzerland), 12(2).
De Carlo, N. D., Oelbermann, M., & Gordon, A. M. (2019a). Carbon dioxide emissions: Spatiotemporal variation in a young and mature riparian forest. Ecological Engineering, 138, 353鈥361.
De Carlo, N. D., Oelbermann, M., & Gordon, A. M. (2019b). Spatial and temporal variation in soil nitrous oxide emissions from a rehabilitated and undisturbed riparian forest. Journal of Environmental Quality, 48(3), 624鈥633.
Jiang, R. W., Mechler, M. A. A., & Oelbermann, M. (2020). Softwood biochar and greenhouse gas emissions: A field study over three growing seasons on a temperate agricultural soil. Canadian Journal of Soil Science, 102(1), 197鈥211.
L茅vesque, V., Oelbermann, M., & Ziadi, N. (2020). Biochar in temperate soils: Opportunities and challenges. Canadian Journal of Soil Science, 102(1), 1鈥26.
Lutes, K., Oelbermann, M., Thevathasan, N. V., & Gordon, A. M. (2019). Assessing the impact of fertilizer application on net soil-derived emission budgets from a temperate willow (Salix miyabeana) short rotation coppice system. Biomass and Bioenergy, 120, 135鈥143.
Mafa-Attoye, T. G., Baskerville, M. A., Ofosu, E., Oelbermann, M., Thevathasan, N. V., & Dunfield, K. E. (2020). Riparian land-use systems impact soil microbial communities and nitrous oxide emissions in an agro-ecosystem. Science of the Total Environment, 724.
McTavish, M. J., Cray, H. A., Murphy, S. D., Bauer, J. T., Havrilla, C. A., Oelbermann, M., & Sayer, E. J. (2020). Sustainable management of grassland soils. In Soils and Landscape Restoration (pp. 95鈥124).
Mechler, M. A. A., Jiang, R. W., Silverthorn, T. K., & Oelbermann, M. (2018). Impact of biochar on soil characteristics and temporal greenhouse gas emissions: A field study from southern Canada. Biomass and Bioenergy, 118, 154鈥162.
Obregon, D., Mafa-Attoye, T. G., Baskerville, M., Mitter, E. K., de Souza, L. F., Oelbermann, M., Thevathasan, N. V., Tsai, S. M., & Dunfield, K. E. (2023). Functionality of methane cycling microbiome during methane flux hot moments from riparian buffer systems. Science of the Total Environment, 870.
Oelbermann, M., Echarte, L., Marroquin, L., Morgan, S., Regehr, A., Vachon, K. E., & Wilton, M. (2017). Estimating soil carbon dynamics in intercrop and sole crop agroecosystems using the Century model. Journal of Plant Nutrition and Soil Science, 180(2), 241鈥251.
Oelbermann, M., Morgan, S., & Echarte, L. (2022). Elevated carbon dioxide and temperature effects on soil properties from sole crops and intercrops. Soil Use and Management, 38(1), 435鈥447.
Seuradge, B. J., Oelbermann, M., & Neufeld, J. D. (2017). Depth-dependent influence of different land-use systems on bacterial biogeography. FEMS Microbiology Ecology, 93(2).
Ziadi, N., Oelbermann, M., Price, G., & Whalen, J. (2020). Biochar amendments for sustainable soil management. Canadian Journal of Soil Science, 102(1), vii鈥搗iii.
Wayne Parker
Bai, X., McKnight, M. M., Neufeld, J. D., & J Parker, W. (2023). Simultaneous nitrification, denitrification, and phosphorus removal from municipal wastewater at low temperature. Bioresource Technology, 368, 128261.
Bai, X., McKnight, M. M., Neufeld, J. D., & Parker, W. J. (2022). Nitrogen removal pathways during simultaneous nitrification, denitrification, and phosphorus removal under low temperature and dissolved oxygen conditions. Bioresource Technology, 354, 127177.
Spasov, E., Tsuji, J. M., Hug, L. A., Doxey, A. C., Sauder, L. A., Parker, W. J., & Neufeld, J. D. (2020). High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. The ISME Journal, 14(7), Article 7.
Sherry Schiff
Cavaco, M. A., St.聽Louis, V. L., Engel, K., St.聽Pierre, K. A., Schiff, S. L., Stibal, M., & Neufeld, J. D. (2019). Freshwater microbial community diversity in a rapidly changing High Arctic watershed. FEMS Microbiology Ecology, 95(11), fiz161.
Cejudo, E., Schiff, S., & Taylor, W. (2020). Epilithic algae from an urban river preferentially use ammonium over nitrate. International Aquatic Research, 12, 30鈥39.
Schiff, S. L., Tsuji, J. M., Wu, L., Venkiteswaran, J. J., Molot, L. A., Elgood, R. J., Paterson, M. J., & Neufeld, J. D. (2017). Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry. Scientific Reports, 7(1), Article 1.
St. Pierre, K. A., St. Louis, V. L., Schiff, S. L., Lehnherr, I., Dainard, P. G., Gardner, A. S., Aukes, P. J. K., & Sharp, M. J. (2019). Proglacial freshwaters are significant and previously unrecognized sinks of atmospheric CO 2. Proceedings of the National Academy of Sciences, 116(36), 17690鈥17695.
Tsuji, J. M., Tran, N., Schiff, S. L., Venkiteswaran, J. J., Molot, L. A., Tank, M., Hanada, S., & Neufeld, J. D. (2020). Anoxygenic photosynthesis and iron鈥搒ulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes. The ISME Journal, 14(11), Article 11.
Tsuji, J., Shaw, N., Nagashima, S., Venkiteswaran, J., Schiff, S., Hanada, S., Tank, M., & Neufeld, J. (2020). Type I photosynthetic reaction center in an anoxygenic phototrophic member of the Chloroflexota [Preprint]. Microbiology.
Venkiteswaran, J. J., Schiff, S. L., & Ingalls, B. P. (2019). Quantifying the fate of wastewater nitrogen discharged to a Canadian river. FACETS, 4(1), 315鈥335.
Matthew Scott
Braniff, N., Scott, M., & Ingalls, B. (2019). Component Characterization in a Growth-Dependent Physiological Context: Optimal Experimental Design. Processes, 7(1), Article 1.
Greulich, P., Dole啪al, J., Scott, M., Evans, M. R., & Allen, R. J. (2017). Predicting the dynamics of bacterial growth inhibition by ribosome-targeting antibiotics. Physical Biology, 14(6), 065005.
Jaramillo鈥怰iveri, S., Broughton, J., McVey, A., Pilizota, T., Scott, M., & El Karoui, M. (2022). Growth鈥恉ependent heterogeneity in the DNA damage response in Escherichia coli. Molecular Systems Biology, 18(5).
Jun, S., Si, F., Pugatch, R., & Scott, M. (2018). Fundamental principles in bacterial physiology鈥攈istory, recent progress, and the future with focus on cell size control: A review. Reports on Progress in Physics, 81(5), 056601.
Scott, M. (2021). Metabolic models predict evolutionary dynamics. Nature Ecology & Evolution, 5(5), 560鈥561.
Scott, M., & Hwa, T. (2022). Shaping bacterial gene expression by physiological and proteome allocation constraints. Nature Reviews Microbiology.
Maria Strack
Bieniada, A., & Strack, M. (2021). Steady and ebullitive methane fluxes from active, restored and unrestored horticultural peatlands. Ecological Engineering, 169, 106324.
Bienida, A., Dat茅, V., Andersen, R., Nwaishi, F., Price, J., Mahmood, Md. S., & Strack, M. (2020). Methane emissions from fens in Alberta鈥檚 boreal region: Reference data for functional evaluation of restoration outcomes. Wetlands Ecology and Management, 28(4), 559鈥575.
Brown, C. M., Strack, M., & Price, J. S. (2017). The effects of water management on the CO2 uptake of Sphagnum moss in a reclaimed peatland. Mires and Peat, 20, 1鈥15.
Brummell, M., Lazcano, C., & Strack, M. (2017). The effects of Eriophorum vaginatum on N2O fluxes at a restored, extracted peatland. Ecological Engineering, 106, 287鈥295.
Clark, L. M., Strachan, I. B., Strack, M., Roulet, N. T., Knorr, K.-H., & Teickner, H. (2022). Years of extraction determines CO2 and CH4 emissions from an actively extracted peatland in eastern Québec, Canada. Biogeosciences Discussions, 1鈥38.
Coulas, M., Parsons, C., Saraswati, S., & Strack, M. (2021). Organic matter decomposition at a constructed fen in the Athabasca Oil Sands region: Effect of substrate type and environmental conditions. Science of The Total Environment, 776, 145708.
Davidson, S. J., Smith, M., Prystupa, E., Murray, K., Nwaishi, F. C., Petrone, R. M., & Strack, M. (2021). High sulfate concentrations maintain low methane emissions at a constructed fen over the first seven years of ecosystem development. The Science of the Total Environment, 789, 148014.
Davidson, S. J., Strack, M., Bourbonniere, R. A., & Waddington, J. M. (2019). Controls on soil carbon dioxide and methane fluxes from a peat swamp vary by hydrogeomorphic setting. Ecohydrology, 12(8).
Davidson, S. J., Van Beest, C., Petrone, R., & Strack, M. (2019). Wildfire overrides hydrological controls on boreal peatland methane emissions. Biogeosciences, 16(13), 2651鈥2660.
Engering, A., Davidson, S. J., Xu, B., Bird, M., Rochefort, L., & Strack, M. (2022). Restoration of a boreal peatland impacted by an in-situ oil sands well-pad 2: Greenhouse gas exchange dynamics. Restoration Ecology, 30(3), e13508.
Gupta, P. K., Gharedaghloo, B., Lynch, M., Cheng, J., Strack, M., Charles, T. C., & Price, J. S. (2020). Dynamics of microbial populations and diversity in NAPL contaminated peat soil under varying water table conditions. Environmental Research, 191, 110167.
Lazcano, C., Deol, A. S., Brummell, M. E., & Strack, M. (2020). Interactive effects of vegetation and water table depth on belowground C and N mobilization and greenhouse gas emissions in a restored peatland. Plant and Soil, 448(1), 299鈥313.
Lazcano, C., Robinson, C., Hassanpour, G., & Strack, M. (2018). Short-term effects of fen peatland restoration through the moss layer transfer technique on the soil CO2 and CH4 efflux. Ecological Engineering, 125, 149鈥158.
Lemmer, M., Rochefort, L., & Strack, M. (2020). Greenhouse Gas Emissions Dynamics in Restored Fens After In-Situ Oil Sands Well Pad Disturbances of Canadian Boreal Peatlands. Frontiers in Earth Science, 8.
MacDonald, E., Brummell, M. E., Bieniada, A., Elliot, J., Engering, A., Gauthier, T.-L., Saraswati, S., Touchette, S., Tourmel-Courchesne, L., & Strack, M. (2018). Using the Tea Bag Index to characterize decomposition rates in restored peatlands.
Munir, T., Khadka, B., Xu, B., & Strack, M. (2017). Partitioning Forest鈥怓loor Respiration into Source Based Emissions in a Boreal Forested Bog: Responses to Experimental Drought. Forests, 8(3), 75.
Munir, T. M., Khadka, B., Xu, B., & Strack, M. (2017). Mineral nitrogen and phosphorus pools affected by water table lowering and warming in a boreal forested peatland. Ecohydrology, 10(8), e1893.
Nugent, K. A., Strachan, I. B., Strack, M., Roulet, N. T., Str枚m, L., & Chanton, J. P. (2021). Cutover Peat Limits Methane Production Causing Low Emission at a Restored Peatland. Journal of Geophysical Research: Biogeosciences, 126(12), e2020JG005909.
Rankin, T., Strachan, I. B., & Strack, M. (2018). Carbon dioxide and methane exchange at a post-extraction, unrestored peatland. Ecological Engineering, 122, 241鈥251.
Saraswati, S., Parsons, C. T., & Strack, M. (2019). Access roads impact enzyme activities in boreal forested peatlands. Science of The Total Environment, 651, 1405鈥1415.
Saraswati, S., & Strack, M. (2019). Road Crossings Increase Methane Emissions From Adjacent Peatland. Journal of Geophysical Research: Biogeosciences, 124(11), 3588鈥3599.
Schmidt, M., Davidson, S. J., & Strack, M. (2022). CO2 uptake decreased and CH4 emissions increased in first two years of peatland seismic line restoration. Wetlands Ecology and Management, 30(2), 313鈥329.
Strack, M., Softa, D., Bird, M., & Xu, B. (2018). Impact of winter roads on boreal peatland carbon exchange. Global Change Biology, 24(1), e201鈥揺212.
Valerie Ward
Banerjee, A., & Ward, V. (2022). Production of recombinant and therapeutic proteins in microalgae. Current Opinion in Biotechnology, 78, 102784.
Chatzivasileiou, A. O., Ward, V., Edgar, S. M., & Stephanopoulos, G. (2019). Two-step pathway for isoprenoid synthesis. Proceedings of the National Academy of Sciences, 116(2), 506鈥511.
Kabernick, D. C., Gostick, J. T., & Ward, V. C. A. (2022). Kinetic characterization and modeling of sequentially entrapped enzymes in 3D鈥恜rinted PMMA microfluidic reactors for the synthesis of amorphadiene via the isopentenol utilization pathway. Biotechnology and Bioengineering, 119(5), 1239鈥1251.
Luo, Z., Liu, N., Lazar, Z., Chatzivasileiou, A., Ward, V., Chen, J., Zhou, J., & Stephanopoulos, G. (2020). Enhancing isoprenoid synthesis in Yarrowia lipolytica by expressing the isopentenol utilization pathway and modulating intracellular hydrophobicity. Metabolic Engineering, 61, 344鈥351.
Malekghasemi, S., Kariminia, H.-R., Plechkova, N. K., & Ward, V. C. A. (2021). Direct transesterification of wet microalgae to biodiesel using phosphonium carboxylate ionic liquid catalysts. Biomass and Bioenergy, 150, 106126.
Ojogbo, E., Ward, V., & Mekonnen, T. H. (2020). Functionalized starch microparticles for contact-active antimicrobial polymer surfaces. Carbohydrate Polymers, 229, 115422.
Palage, A. M., & Ward, V. C. (2022). Strategies for production of hydrophobic compounds. Current Opinion in Biotechnology, 75, 102681.
Ward, V. C. A., Chatzivasileiou, A. O., & Stephanopoulos, G. (2018). Metabolic engineering of Escherichia coli for the production of isoprenoids. FEMS Microbiology Letters, 365(10).
Ward, V. C. A., Chatzivasileiou, A. O., & Stephanopoulos, G. (2019). Cell free biosynthesis of isoprenoids from isopentenol. Biotechnology and Bioengineering, 116(12), 3269鈥3281.
Ward, V. C. A., Munch, G., Cicek, N., & Rehmann, L. (2017). Direct Conversion of the Oleaginous Yeast Rhodosporidium diobovatum to Biodiesel Using the Ionic Liquid [C2mim][EtSO4]. ACS Sustainable Chemistry & Engineering, 5(6), 5562鈥5570.
Ward, V. C. A., & Rehmann, L. (2019). Fast media optimization for mixotrophic cultivation of Chlorella vulgaris. Scientific Reports, 9(1), 19262.
Zhang, Y., Ward, V., Dennis, D., Plechkova, N. V., Armenta, R., & Rehmann, L. (2018). Efficient Extraction of a Docosahexaenoic Acid (DHA)-Rich Lipid Fraction from Thraustochytrium sp. Using Ionic Liquids. Materials, 11(10), Article 10.