Publications by the Charlebois Lab


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12.

Fitness effects of a demography-dispersal trade-off in expanding Saccharomyces cerevisiae mats. *Rebekah Hall, *Akila Bandara, Daniel A. Charlebois. Physical Biology, 21: 026001 (2024). *Equal contribution.

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11.

Machine learning to identify clinically relevant Candida yeast species. Shamanth A. Shankarnarayan, Daniel A. Charlebois. Medical Mycology, 62: myad134, (2024).

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10.

Quantitative systems-based prediction of antimicrobial resistance. Daniel A. Charlebois. npj Systems Biology and Applications, 9: 40 (2023).

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9.

Identification and elimination of antifungal tolerance in Candida auris. *Samira Rasouli Koohi, *Shamanth A. Shankarnarayan, Clare Maristela Galon, Daniel A. Charlebois. Biomedicines, 11: 898 (2023). *Equal contribution.

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8.

Non-genetic resistance facilitates survival while hindering the evolution of drug resistance due to intraspecific competition. Joshua Guthrie, Daniel A. Charlebois. Physical Biology, 19: 066001 (2022).

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7.

Machine learning for antimicrobial resistance research and drug development. Shamanth A. Shankarnarayan, Joshua Guthrie, Daniel A. Charlebois. The Global Antimicrobial Resistance Epidemic – Innovative Approaches and Cutting-Edge Solutions, Guillermo Téllez (Ed.), ISBN: 978-1-80356-042-7 (2022).

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6.

Lattice-based Monte Carlo simulation of the effects of nutrient concentration and magnetic field exposure on yeast colony growth and morphology. Rebekah Hall, Daniel A. Charlebois. In Silico Biology, 14: 53-69 (2021).

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5.

Synthetic gene circuits for antimicrobial resistance and cancer research. *Kevin S. Farquhar, *Michael Tyler Guinn, Gábor Balázsi, Daniel A. Charlebois. Synthetic Genomics – From Natural to Synthetic Genomes, Michael Fernandez-Nino and Luis H. Reyes (Eds.), ISBN: 978-1-83969-639-8 (2021). *Equal contribution.

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4.

Does transcriptional heterogeneity promote genetic drug resistance? Kevin S. Farquhar, Samira Rasouli Koohi, Daniel A. Charlebois. BioEssays, 43: 2100043 (2021).

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3.

Advancing antimicrobial resistance research through quantitative modeling and synthetic biology. Kevin S. Farquhar, Harold Flohr, Daniel A. Charlebois. Frontiers in Bioengineering and Biotechnology, 8: 583415 (2020).

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2.

Book review on “A world beyond physics: The emergence and evolution of life” by Stuart A. Kauffman. Rebekah Hall, Daniel A. Charlebois. The Quarterly Review of Biology, 95: 133-134 (2020).

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1.

Engineered gene networks enable non-genetic drug resistance and enhanced cellular robustness. Brendan Camellato, Ian J. Roney, Afnan Aziz, Daniel A. Charlebois, Mads Kaern. Engineering Biology, doi: 10.1049/enb.2019.0009 (2019).

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Previous Publications by Dr. Charlebois


22.

Role of network-mediated stochasticity in mammalian drug resistance. Kevin Farquhar, Daniel A. Charlebois, Mariola Szenk, Joseph Cohen, Dmitry Nevozhay, Gabor Balazsi, Nature Communications, doi: 10.1038/s41467-019-10330-w (2019).

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21.

Modeling cell population dynamics. Daniel A. Charlebois, Gabor Balazsi. In Silico Biology, 13: 21-39 (2019)

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20.

Multiscale effects of heating and cooling on genes and gene networks. Daniel A. Charlebois, Kevin Hauser, Sylvia Marshall, Gabor Balazsi, Proceeding of the National Academy of Sciences of the United States of America, doi: 10.1073/pnas.1810858115 (2018).

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19.

Negative regulation gene circuits with efflux pump control. *Daniel A. Charlebois, *Junchen Diao, Dmitry Nevozhay, Gabor Balazsi. Methods in Molecular Biology, 1772: 25-43 (2018). *Equal contribution.

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18.

Frequency-dependent selection: A diversifying force in microbial populations. Daniel A. Charlebois, Gabor Balazsi. Molecular Systems Biology, 12: 880 (2016).

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17.

Backward evolution from gene network dynamics. Merzu K. Belete, Daniel A. Charlebois, Gabor Balazsi. bioRxiv, doi: 10.1101/369371 (2018).

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16.

Efflux pump control alters synthetic gene circuit function. Junchen Diao, Daniel A. Charlebois, Dmitry Nevozhay, Zoltan Bodi,Csaba Pal, Gabor Balazsi. ACS Synthetic Biology, 5: 619-631 (2016).

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15.

Effect and evolution of gene expression noise on the fitness landscape. Daniel A. Charlebois. Physical Review E, 92: 022713 (2015).

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14.

Coherent feedforward transcriptional regulatory motifs enhance drug resistance. Daniel A. Charlebois, Gabor Balazsi, Mads Kaern. Physical Review E, 89: 052708 (2014).

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13.

An accelerated method for simulating population dynamics. Daniel A. Charlebois, Mads Kaern. Communications in Computational Physics, 14: 461-476 (2013).

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12.

Book review on "Number-crunching: Taming unruly computational problems from mathematical physics to science fiction" by Paul J. Nahin. Daniel A. Charlebois. Physics in Canada, 69: 72-73 (2013).

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11.

Computational investigations of noise-mediated cell population dynamics. Daniel A. Charlebois. PhD Thesis. University of Ottawa (2013).

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10.

What all the noise is about: The physical basis of cellular individuality. Daniel A. Charlebois, Mads Kaern. Canadian Journal of Physics, doi: 10.1139/p2012-091 (2012).

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9.

Gene express noise facilitates adaptation and drug resistance independently of mutation. Daniel A. Charlebois, Nezar Abdennur, Mads Kaern. Physical Review Letters, 107, doi: 10.1103/PhysRevLett.107.218101 (2011).

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8.

An algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. Daniel A. Charlebois, Jukka Intosalmi, Dawn Fraser, Mads Kaern. Communications in Computational Physics, 9: 89-112 (2011).

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7.

Stochastic gene expression and the processing and propagation of noise signal in genetic networks. Daniel A. Charlebois, Theodore J. Perkins, Mads Kaern. Information Processing and Biological Systems, Andre S. Ribeiro and Samuli Niiranen (Eds.), Springer-Verlag, pgs. 89-112, ISBN: 978-3-642-19620-1 (2011).

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6.

An algorithm for the stochastic simulation of gene expression and cell population dynamics. Daniel A. Charlebois. MSc Thesis. University of Ottawa (2010).

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5.

Dynamics of stochastic gene rings. Daniel A. Charlebois. CUPJ, 8: 13-16 (2010).

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4.

A biophysicist ponders the application of hidden metric spaces to genetic networks. Daniel Charlebois. Nature, 458: 811 (2009).

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3.

The human side of Einstein. Daniel Charlebois. CUPJ, 8: 37 (2008).

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2.

CellLine, a stochastic cell lineage simulator. Andre S. Ribeiro, Daniel A. Charlebois, Jason Lloyd-Price. Bioinformatics, 23: 3409-3411 (2007).

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1.

Effects of microarray noise on inference efficiency of a stochastic model of gene networks. Daniel A. Charlebois, Andre S. Ribeiro, Antti Lehmussola, Jason Lloyd-Price, Olli Yli-Harja, Stuart A. Kauffman. WSEAS Transactions on Biology and Biomedicine, 4: 15-21 (2007).

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