Fangwei Si
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View article: Power-law memory governs bacterial adaptation and learning in fluctuating environments
Power-law memory governs bacterial adaptation and learning in fluctuating environments Open
How do single-celled organisms adapt and learn to survive in dynamic environments without a nervous system? Here, we provide experimental evidence and a theoretical model demon-strating learning-like behavior by single bacterial cells in f…
View article: Tools and methods for high-throughput single-cell imaging with the mother machine
Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Author Response: Tools and methods for high-throughput single-cell imaging with the mother machine
Author Response: Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Tools and methods for high-throughput single-cell imaging with the mother machine
Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Reviewer #1 (Public Review): Tools and methods for high-throughput single-cell imaging with the mother machine
Reviewer #1 (Public Review): Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Tools and methods for high-throughput single-cell imaging with the mother machine
Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Reviewer #2 (Public Review): Tools and methods for high-throughput single-cell imaging with the mother machine
Reviewer #2 (Public Review): Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Author Response: Tools and methods for high-throughput single-cell imaging with the mother machine
Author Response: Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Tools and methods for high-throughput single-cell imaging with the mother machine
Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Tools and methods for high-throughput single-cell imaging with the mother machine
Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Tools and methods for high-throughput single-cell imaging with the mother machine
Tools and methods for high-throughput single-cell imaging with the mother machine Open
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of mi…
View article: Effects of antibiotics on bacterial cell morphology and their physiological origins
Effects of antibiotics on bacterial cell morphology and their physiological origins Open
Characterizing the physiological response of bacterial cells to antibiotic treatment is crucial for the design of antibacterial therapies and for understanding the mechanisms of antibiotic resistance. While the effects of antibiotics are c…
View article: Quantitative Examination of Five Stochastic Cell-Cycle and Cell-Size Control Models for Escherichia coli and Bacillus subtilis
Quantitative Examination of Five Stochastic Cell-Cycle and Cell-Size Control Models for Escherichia coli and Bacillus subtilis Open
We examine five quantitative models of the cell-cycle and cell-size control in Escherichia coli and Bacillus subtilis that have been proposed over the last decade to explain single-cell experimental data generated with high-throughput meth…
View article: Quantitative examination of five stochastic cell-cycle and cell-size control models for<i>Escherichia coli</i>and<i>Bacillus subtilis</i>
Quantitative examination of five stochastic cell-cycle and cell-size control models for<i>Escherichia coli</i>and<i>Bacillus subtilis</i> Open
We examine five quantitative models of the cell-cycle and cell-size control in Escherichia coli and Bacillus subtilis that have been proposed over the last decade to explain single-cell experimental data generated with high-throughput meth…
View article: Single-cell data and correlation analysis support the independent double adder model in both<i>Escherichia coli</i>and<i>Bacillus subtilis</i>
Single-cell data and correlation analysis support the independent double adder model in both<i>Escherichia coli</i>and<i>Bacillus subtilis</i> Open
The reference point for cell-size control in the cell cycle is a fundamental biological question. We previously reported that we were unable to reproduce the conclusions of Witz et al. ’s eLife paper (Witz, van Nimwegen, and Julou 2019) en…
View article: Comment on ‘Initiation of chromosome replication controls both division and replication cycles in<i>E. coli</i>through a double-adder mechanism’
Comment on ‘Initiation of chromosome replication controls both division and replication cycles in<i>E. coli</i>through a double-adder mechanism’ Open
Witz et al . recently performed single-cell mother machine experiments to track growth and the replication cycle in E. coli . They analyzed the correlation structure of selected parameters using both their data and published data, and conc…
View article: Mother machine image analysis with MM3
Mother machine image analysis with MM3 Open
The mother machine is a microfluidic device for high-throughput time-lapse imaging of microbes. Here, we present MM3, a complete and modular image analysis pipeline. MM3 turns raw mother machine images, both phase contrast and fluorescence…
View article: Mechanistic origin of cell-size control and homeostasis in bacteria
Mechanistic origin of cell-size control and homeostasis in bacteria Open
Evolutionarily divergent bacteria share a common phenomenological strategy for cell-size homeostasis under steady-state conditions. In the presence of inherent physiological stochasticity, cells following this “adder” principle gradually r…
View article: Role of membrane-tension gated Ca2+ flux in cell mechanosensation
Role of membrane-tension gated Ca2+ flux in cell mechanosensation Open
Eukaryotic cells are sensitive to mechanical forces they experience from the environment. The process of mechanosensation is complex, and involves elements such as the cytoskeleton and active contraction from myosin motors. Ultimately, mec…
View article: Role of Membrane-tension Gated Ca Flux in Cell Mechanosensation
Role of Membrane-tension Gated Ca Flux in Cell Mechanosensation Open
Eukaryotic cells are sensitive to mechanical forces that they experience from the environment. The process of mechanosensation is complex, and involves elements such as the cytoskeleton and active contraction from myosin motors. Ultimately…
View article: Invariance of initiation mass and predictability of cell size in<i>Escherichia coli</i>
Invariance of initiation mass and predictability of cell size in<i>Escherichia coli</i> Open
Summary It is generally assumed that the allocation and synthesis of total cellular resources in microorganisms are uniquely determined by the growth conditions. Adaptation to a new physiological state leads to a change in cell size via re…
View article: To Grow is Not Enough: Impact of Noise on Cell Environmental Response and Fitness
To Grow is Not Enough: Impact of Noise on Cell Environmental Response and Fitness Open
Quantitative single cell measurements have shown that cell cycle duration (the time between cell divisions) for diverse cell types is a noisy variable. The underlying distribution is mean scalable with a universal shape for many cell types…
View article: To grow is not enough: impact of noise on cell environmental response and fitness
To grow is not enough: impact of noise on cell environmental response and fitness Open
Quantitative single cell measurements have shown that cell cycle duration (the time between cell divisions) for diverse cell types is a noisy variable. This work highlights how this noise may impact cell fitness through adaptability.