References

Ackermann, Martin. 2015. “A Functional Perspective on Phenotypic Heterogeneity in Microorganisms.” Nature Reviews Microbiology 13 (8): 497–508. https://doi.org/10.1038/nrmicro3491.

Allaire, JJ. 2022. Quarto: R Interface to Quarto Markdown Publishing System. https://github.com/quarto-dev/quarto-r.

Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2023. Rmarkdown: Dynamic Documents for r. https://CRAN.R-project.org/package=rmarkdown.

Altman, N. S. 1992. “An Introduction to Kernel and Nearest-Neighbor Nonparametric Regression.” The American Statistician 46 (3): 175–85. https://doi.org/10.1080/00031305.1992.10475879.

Andersson, Dan I. 2005. “The Ways in Which Bacteria Resist Antibiotics.” International Journal of Risk and Safety in Medicine 17 (3-4): 111–16.

Andrews, J. M. 2002. “Determination of Minimum Inhibitory Concentrations.” Journal of Antimicrobial Chemotherapy 49 (6): 1049–49. https://doi.org/10.1093/jac/dkf083.

Andrews, Jennifer M. 2001. “Determination of Minimum Inhibitory Concentrations.” Journal of Antimicrobial Chemotherapy 48 (suppl_1): 5–16. https://doi.org/10.1093/jac/48.suppl_1.5.

Balaban, Nathalie Q., Jack Merrin, Remy Chait, Lukasz Kowalik, and Stanislas Leibler. 2004. “Bacterial Persistence as a Phenotypic Switch.” Science 305 (5690): 1622–25. https://doi.org/10.1126/science.1099390.

Bezanson, Jeff, Alan Edelman, Stefan Karpinski, and Viral B Shah. 2017. “Julia: A Fresh Approach to Numerical Computing.” SIAM Review 59 (1): 65–98. https://doi.org/10.1137/141000671.

Bos, Julia, Qiucen Zhang, Saurabh Vyawahare, Elizabeth Rogers, Susan M. Rosenberg, and Robert H. Austin. 2015. “Emergence of Antibiotic Resistance from Multinucleated Bacterial Filaments.” Proceedings of the National Academy of Sciences 112 (1): 178–83. https://doi.org/10.1073/pnas.1420702111.

Brinkmann, Ron. 2008. The Art and Science of Digital Compositing, Second Edition: Techniques for Visual Effects, Animation and Motion Graphics (the Morgan Kaufmann Series in ... Morgan Kaufmann Series in Computer Graphics). 2nd ed. San Francisco, CA, USA: Morgan Kaufmann Publishers Inc.

Bruggeman, Frank J., Jorrit J. Hornberg, Fred C. Boogerd, and Hans V. Westerhoff. 2007. “Introduction to Systems Biology.” In, 1–19. Birkhäuser Basel. https://doi.org/10.1007/978-3-7643-7439-6_1.

Caicedo, Juan C, Sam Cooper, Florian Heigwer, Scott Warchal, Peng Qiu, Csaba Molnar, Aliaksei S Vasilevich, et al. 2017. “Data-Analysis Strategies for Image-Based Cell Profiling.” Nature Methods 14 (9): 849–63. https://doi.org/10.1038/nmeth.4397.

Campos, Manuel, Ivan V. Surovtsev, Setsu Kato, Ahmad Paintdakhi, Bruno Beltran, Sarah E. Ebmeier, and Christine Jacobs-Wagner. 2014. “A Constant Size Extension Drives Bacterial Cell Size Homeostasis.” Cell 159 (6): 1433–46. https://doi.org/10.1016/j.cell.2014.11.022.

Cayron, Julien, Annick Dedieu, and Christian Lesterlin. 2020. “Bacterial Filament Division Dynamics Allows Rapid Post-Stress Cell Proliferation.” http://dx.doi.org/10.1101/2020.03.16.993345.

Convery, Neil, and Nikolaj Gadegaard. 2019. “30 Years of Microfluidics.” Micro and Nano Engineering 2 (March): 76–91. https://doi.org/10.1016/j.mne.2019.01.003.

Datseris, George, Jonas Isensee, Sebastian Pech, and Tamás Gál. 2020. “DrWatson: The Perfect Sidekick for Your Scientific Inquiries.” Journal of Open Source Software 5 (54): 2673. https://doi.org/10.21105/joss.02673.

Dever, L. A., and T. S. Dermody. 1991. “Mechanisms of bacterial resistance to antibiotics.” Archives of Internal Medicine 151 (5): 886–95.

“Editorial Board.” 2014. Journal of Global Antimicrobial Resistance 2 (2): ii. https://doi.org/10.1016/S2213-7165(14)00044-7.

Elowitz, Michael B., Arnold J. Levine, Eric D. Siggia, and Peter S. Swain. 2002. “Stochastic Gene Expression in a Single Cell.” Science 297 (5584): 1183–86. https://doi.org/10.1126/science.1070919.

Firke, Sam. 2021. Janitor: Simple Tools for Examining and Cleaning Dirty Data. https://github.com/sfirke/janitor.

Friedman, Nir, Shuki Vardi, Michal Ronen, Uri Alon, and Joel Stavans. 2005. “Precise Temporal Modulation in the Response of the SOS DNA Repair Network in Individual Bacteria.” Edited by B’en’edicte Michel. PLoS Biology 3 (7): e238. https://doi.org/10.1371/journal.pbio.0030238.

Gillies, Sean et al. 2007--. “Shapely: Manipulation and Analysis of Geometric Objects.” toblerity.org. https://github.com/Toblerity/Shapely.

Hagberg, Aric, Pieter Swart, and Daniel S Chult. 2008. “Exploring Network Structure, Dynamics, and Function Using NetworkX.” Los Alamos National Lab.(LANL), Los Alamos, NM (United States).

Harris, Charles R., K. Jarrod Millman, Stéfan J van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, et al. 2020. “Array Programming with NumPy.” Nature 585: 357–62. https://doi.org/10.1038/s41586-020-2649-2.

Harris, Leigh K., and Julie A. Theriot. 2016. “Relative Rates of Surface and Volume Synthesis Set Bacterial Cell Size.” Cell 165 (6): 1479–92. https://doi.org/10.1016/j.cell.2016.05.045.

Heinrich, Kristina, David J. Leslie, and Kristina Jonas. 2015. “Modulation of Bacterial Proliferation as a Survival Strategy.” In, 127–71. Elsevier. https://doi.org/10.1016/bs.aambs.2015.02.004.

Hester, Jim, Hadley Wickham, and Gábor Csárdi. 2021. Fs: Cross-Platform File System Operations Based on Libuv. https://CRAN.R-project.org/package=fs.

Hotelling, Harold. 1936. “Relations Between Two Sets of Variates.” Biometrika 28 (3/4): 321. https://doi.org/10.2307/2333955.

Hunter, John D. 2007. “Matplotlib: A 2D Graphics Environment.” Computing in Science & Engineering 9 (3): 90–95.

Hvitfeldt, Emil, and Max Kuhn. 2022. Embed: Extra Recipes for Encoding Predictors. https://CRAN.R-project.org/package=embed.

Jaimes-Lizcano, Yuly A., Dayton D. Hunn, and Kyriakos D. Papadopoulos. 2014. “Filamentous Escherichia Coli Cells Swimming in Tapered Microcapillaries.” Research in Microbiology 165 (3): 166–74. https://doi.org/10.1016/j.resmic.2014.01.007.

Joseleau-Petit, Daniel̀e, Daniel Vinella, and Richard D’Ari. 1999. “Metabolic Alarms and Cell Division in Escherichia Coli.” Journal of Bacteriology 181 (1): 9–14. https://doi.org/10.1128/jb.181.1.9-14.1999.

Justice, S. S., D. A. Hunstad, P. C. Seed, and S. J. Hultgren. 2006. “Filamentation by Escherichia Coli Subverts Innate Defenses During Urinary Tract Infection.” Proceedings of the National Academy of Sciences 103 (52): 19884–89. https://doi.org/10.1073/pnas.0606329104.

Justice, Sheryl S., David A. Hunstad, Lynette Cegelski, and Scott J. Hultgren. 2008. “Morphological Plasticity as a Bacterial Survival Strategy.” Nature Reviews Microbiology 6 (2): 162–68. https://doi.org/10.1038/nrmicro1820.

Kassambara, Alboukadel. 2020. Ggpubr: Ggplot2 Based Publication Ready Plots. https://rpkgs.datanovia.com/ggpubr/.

Kay, Matthew. 2022. Ggdist: Visualizations of Distributions and Uncertainty. https://CRAN.R-project.org/package=ggdist.

Kroemer, G, L Galluzzi, P Vandenabeele, J Abrams, E S Alnemri, E H Baehrecke, M V Blagosklonny, et al. 2008. “Classification of Cell Death: Recommendations of the Nomenclature Committee on Cell Death 2009.” Cell Death & Differentiation 16 (1): 3–11. https://doi.org/10.1038/cdd.2008.150.

Kuhn, Max, and Hadley Wickham. 2022. Tidymodels: Easily Install and Load the Tidymodels Packages. https://CRAN.R-project.org/package=tidymodels.

Lambert, P. 2005. “Bacterial Resistance to Antibiotics: Modified Target Sites.” Advanced Drug Delivery Reviews 57 (10): 1471–85. https://doi.org/10.1016/j.addr.2005.04.003.

McInnes, Leland, John Healy, and James Melville. 2018. “Umap: Uniform Manifold Approximation and Projection for Dimension Reduction.” arXiv Preprint arXiv:1802.03426.

McKinney, Wes et al. 2010. “Data Structures for Statistical Computing in Python.” In Proceedings of the 9th Python in Science Conference, 445:51–56. Austin, TX.

Meldrum, Deirdre. 2005. “Faculty Opinions Recommendation of Bacterial Persistence as a Phenotypic Switch.” https://doi.org/10.3410/f.1021664.264823.

Miller, C. 2004. “SOS Response Induction by -Lactams and Bacterial Defense Against Antibiotic Lethality.” Science 305 (5690): 1629–31. https://doi.org/10.1126/science.1101630.

Million-Weaver, Samuel, and Manel Camps. 2014. “Mechanisms of Plasmid Segregation: Have Multicopy Plasmids Been Overlooked?” Plasmid 75 (September): 27–36. https://doi.org/10.1016/j.plasmid.2014.07.002.

Moger-Reischer, Roy Z., and Jay T. Lennon. 2019. “Microbial Ageing and Longevity.” Nature Reviews Microbiology 17 (11): 679–90. https://doi.org/10.1038/s41579-019-0253-y.

Mückl, Andrea, Matthaeus Schwarz-Schilling, Katrin Fischer, and Friedrich C. Simmel. 2018. “Filamentation and Restoration of Normal Growth in Escherichia Coli Using a Combined CRISPRi sgRNA/Antisense RNA Approach.” Edited by Mark Isalan. PLOS ONE 13 (9): e0198058. https://doi.org/10.1371/journal.pone.0198058.

Müller, Kirill. 2020. Here: A Simpler Way to Find Your Files. https://CRAN.R-project.org/package=here.

Neidhardt, Frederick C. 1999. “Bacterial Growth: Constant Obsession with dN/Dt.” Journal of Bacteriology 181 (24): 7405–8. https://doi.org/10.1128/JB.181.24.7405-7408.1999.

Pearson, Karl. 1901. “LIII. On Lines and Planes of Closest Fit to Systems of Points in Space.” The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science 2 (11): 559–72. https://doi.org/10.1080/14786440109462720.

Pedersen, Thomas Lin. 2020. Patchwork: The Composer of Plots. https://CRAN.R-project.org/package=patchwork.

Pérez, Fernando, and Brian E Granger. 2007. “IPython: A System for Interactive Scientific Computing.” Computing in Science & Engineering 9 (3).

R Core Team. 2022. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.

Rackauckas, Christopher, and Qing Nie. 2017a. “Adaptive Methods for Stochastic Differential Equations via Natural Embeddings and Rejection Sampling with Memory.” Discrete and Continuous Dynamical Systems. Series B 22 (7): 2731.

———. 2017b. “Differentialequations.jl–a Performant and Feature-Rich Ecosystem for Solving Differential Equations in Julia.” Journal of Open Research Software 5 (1).

———. 2018. “Stability-Optimized High Order Methods and Stiffness Detection for Pathwise Stiff Stochastic Differential Equations.” arXiv:1804.04344 [Math]. http://arxiv.org/abs/1804.04344.

Robinson, David, and Julia Silge. 2022. Tidytext: Text Mining Using Dplyr, Ggplot2, and Other Tidy Tools. https://github.com/juliasilge/tidytext.

Rocklin, Matthew. 2015. “Dask: Parallel Computation with Blocked Algorithms and Task Scheduling.” In Proceedings of the 14th Python in Science Conference. 130-136. Citeseer.

Roostalu, Johanna, Arvi Jõers, Hannes Luidalepp, Niilo Kaldalu, and Tanel Tenson. 2008. “Cell Division in Escherichia Colicultures Monitored at Single Cell Resolution.” BMC Microbiology 8 (1). https://doi.org/10.1186/1471-2180-8-68.

San Millan, Alvaro, Jose Antonio Escudero, Danna R. Gifford, Didier Mazel, and R. Craig MacLean. 2016. “Multicopy Plasmids Potentiate the Evolution of Antibiotic Resistance in Bacteria.” Nature Ecology & Evolution 1 (1). https://doi.org/10.1038/s41559-016-0010.

Sato, Kazuhito, and Taiji Nakae. 1991. “Outer Membrane Permeability of Acinetobacter Calcoaceticus and Its Implication in Antibiotic Resistance.” Journal of Antimicrobial Chemotherapy 28 (1): 35–45. https://doi.org/10.1093/jac/28.1.35.

Schaechter, M., O. MaalOe, and N. O. Kjeldgaard. 1958. “Dependency on Medium and Temperature of Cell Size and Chemical Composition During Balanced Growth of Salmonella Typhimurium.” Journal of General Microbiology 19 (3): 592–606. https://doi.org/10.1099/00221287-19-3-592.

Schaechter, M., J. P. Williamson, J. R. Hood, and A. L. Koch. 1962. “Growth, Cell and Nuclear Divisions in Some Bacteria.” Journal of General Microbiology 29 (3): 421–34. https://doi.org/10.1099/00221287-29-3-421.

Schermelleh, Lothar, Alexia Ferrand, Thomas Huser, Christian Eggeling, Markus Sauer, Oliver Biehlmaier, and Gregor P. C. Drummen. 2019. “Super-Resolution Microscopy Demystified.” Nature Cell Biology 21 (1): 72–84. https://doi.org/10.1038/s41556-018-0251-8.

Schloerke, Barret, Di Cook, Joseph Larmarange, Francois Briatte, Moritz Marbach, Edwin Thoen, Amos Elberg, and Jason Crowley. 2021. GGally: Extension to Ggplot2. https://CRAN.R-project.org/package=GGally.

Schneider, Caroline A, Wayne S Rasband, and Kevin W Eliceiri. 2012. “NIH Image to ImageJ: 25 Years of Image Analysis.” Nature Methods 9 (7): 671–75. https://doi.org/10.1038/nmeth.2089.

Sievert, Carson, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec, and Pedro Despouy. 2021. Plotly: Create Interactive Web Graphics via Plotly.js. https://CRAN.R-project.org/package=plotly.

Sliusarenko, Oleksii, Jennifer Heinritz, Thierry Emonet, and Christine Jacobs-Wagner. 2011. “High-Throughput, Subpixel Precision Analysis of Bacterial Morphogenesis and Intracellular Spatio-Temporal Dynamics: Quantitative Analysis of Spatio-Temporal Dynamics.” Molecular Microbiology 80 (3): 612–27. https://doi.org/10.1111/j.1365-2958.2011.07579.x.

Smith, Kevin, Filippo Piccinini, Tamas Balassa, Krisztian Koos, Tivadar Danka, Hossein Azizpour, and Peter Horvath. 2018. “Phenotypic Image Analysis Software Tools for Exploring and Understanding Big Image Data from Cell-Based Assays.” Cell Systems 6 (6): 636–53. https://doi.org/10.1016/j.cels.2018.06.001.

Sofroniew, Nicholas, Talley Lambert, Kira Evans, Juan Nunez-Iglesias, Grzegorz Bokota, Gonzalo Peña-Castellanos, Philip Winston, et al. 2021. Napari/Napari: 0.4.12rc2. Zenodo. https://doi.org/10.5281/ZENODO.3555620.

Specht, Elizabeth A., Esther Braselmann, and Amy E. Palmer. 2017. “A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging.” Annual Review of Physiology 79 (1): 93–117. https://doi.org/10.1146/annurev-physiol-022516-034055.

Taheri-Araghi, Sattar, Serena Bradde, John T. Sauls, Norbert S. Hill, Petra Anne Levin, Johan Paulsson, Massimo Vergassola, and Suckjoon Jun. 2017. “Cell-Size Control and Homeostasis in Bacteria.” Current Biology 27 (9): 1392. https://doi.org/10.1016/j.cub.2017.04.028.

Trevors, J.T. 2012. “Can Dead Bacterial Cells Be Defined and Are Genes Expressed After Cell Death?” Journal of Microbiological Methods 90 (1): 25–28. https://doi.org/10.1016/j.mimet.2012.04.004.

TURING, A. M. 1950. “I.COMPUTING MACHINERY AND INTELLIGENCE.” Mind LIX (236): 433–60. https://doi.org/10.1093/mind/lix.236.433.

Ursell, Tristan, Timothy K. Lee, Daisuke Shiomi, Handuo Shi, Carolina Tropini, Russell D. Monds, Alexandre Colavin, et al. 2017. “Rapid, Precise Quantification of Bacterial Cellular Dimensions Across a Genomic-Scale Knockout Library.” BMC Biology 15 (1): 17. https://doi.org/10.1186/s12915-017-0348-8.

Ushey, Kevin. 2022. Renv: Project Environments. https://rstudio.github.io/renv/.

van der Walt, Stéfan, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, and Tony Yu. 2014. “Scikit-Image: Image Processing in Python.” PeerJ 2 (June): e453. https://doi.org/10.7717/peerj.453.

Van Rossum, Guido. 2020. The Python Library Reference, Release 3.8.2. Python Software Foundation.

Van Rossum, Guido, and Fred L. Drake. 2009. Python 3 Reference Manual. Scotts Valley, CA: CreateSpace.

Van Valen, David A., Takamasa Kudo, Keara M. Lane, Derek N. Macklin, Nicolas T. Quach, Mialy M. DeFelice, Inbal Maayan, Yu Tanouchi, Euan A. Ashley, and Markus W. Covert. 2016. “Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.” Edited by Martin Meier-Schellersheim. PLOS Computational Biology 12 (11): e1005177. https://doi.org/10.1371/journal.pcbi.1005177.

Verschaffel, Lieven, Brian Greer, and Erik de Corte. 2002. “Everyday Knowledge and Mathematical Modeling of School Word Problems.” In, 257–76. Springer Netherlands. https://doi.org/10.1007/978-94-017-3194-2_16.

Wang, Jue D., and Petra A. Levin. 2009. “Metabolism, Cell Growth and the Bacterial Cell Cycle.” Nature Reviews Microbiology 7 (11): 822–27. https://doi.org/10.1038/nrmicro2202.

Wang, Ying, Hong Wu, Xiaoran Jiang, and Guo-Qiang Chen. 2014. “Engineering Escherichia Coli for Enhanced Production of Poly(3-Hydroxybutyrate-Co-4-Hydroxybutyrate) in Larger Cellular Space.” Metabolic Engineering 25 (September): 183–93. https://doi.org/10.1016/j.ymben.2014.07.010.

Wang, Ying, Jin Yin, and Guo-Qiang Chen. 2014. “Polyhydroxyalkanoates, Challenges and Opportunities.” Current Opinion in Biotechnology 30 (December): 59–65. https://doi.org/10.1016/j.copbio.2014.06.001.

Webber, M. A. 2003. “The Importance of Efflux Pumps in Bacterial Antibiotic Resistance.” Journal of Antimicrobial Chemotherapy 51 (1): 9–11. https://doi.org/10.1093/jac/dkg050.

White, John Myles, Bogumił Kamiński, Powerdistribution, Milan Bouchet-Valat, Sean Garborg, Jacob Quinn, Simon Kornblith, et al. 2021. JuliaData/DataFrames.jl: V1.2.2. Zenodo. https://doi.org/10.5281/ZENODO.3376177.

Wickham, Hadley. 2019. Stringr: Simple, Consistent Wrappers for Common String Operations. https://CRAN.R-project.org/package=stringr.

———. 2022. Tidyverse: Easily Install and Load the Tidyverse. https://CRAN.R-project.org/package=tidyverse.

Wickham, Hadley, Winston Chang, Robert Flight, Kirill Müller, and Jim Hester. 2021. Sessioninfo: R Session Information. https://CRAN.R-project.org/package=sessioninfo.

Wright, G. 2005. “Bacterial Resistance to Antibiotics: Enzymatic Degradation and Modification.” Advanced Drug Delivery Reviews 57 (10): 1451–70. https://doi.org/10.1016/j.addr.2005.04.002.

Xie, Yihui. 2022. Knitr: A General-Purpose Package for Dynamic Report Generation in r. https://yihui.org/knitr/.

Yin, Huabing, and Damian Marshall. 2012. “Microfluidics for Single Cell Analysis.” Current Opinion in Biotechnology 23 (1): 110–19. https://doi.org/10.1016/j.copbio.2011.11.002.