90 citations · 280 across the 7 of their papers we have counts for
7 papers
Stochastic Neural Networks for Automatic Cell Tracking in Microscopy Image Sequences of Bacterial Colonies
Sorena Sarmadi, James J. Winkle, Razan N. Alnahhas +4
Our work targets automated analysis to quantify the growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deforma…
Modeling mechanical interactions in growing populations of rod-shaped bacteria
James J. Winkle, Oleg Igoshin, Matthew R. Bennett +2
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand,…
Effects of cell cycle noise on excitable gene circuits
Alan Veliz-Cuba, Chinmaya Gupta, Matthew R. Bennett +2
We assess the impact of cell cycle noise on gene circuit dynamics. For bistable genetic switches and excitable circuits, we find that transitions between metastable states most lik…
The validity of quasi steady-state approximations in discrete stochastic simulations
Jae Kyoung Kim, Krešimir Josić, Matthew R. Bennett
In biochemical networks, reactions often occur on disparate timescales and can be characterized as either "fast" or "slow." The quasi-steady state approximation (QSSA) utilizes tim…
Molecular mechanisms that regulate the coupled period of the mammalian circadian clock
Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett +1
In mammals, most cells in the brain and peripheral tissues generate circadian (~24hr) rhythms autonomously. These self-sustained rhythms are coordinated and entrained by a master c…
Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations
Chinmaya Gupta, José Manuel López, Robert Azencott +3
Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from t…
Transcriptional delay stabilizes bistable gene networks
Chinmaya Gupta, José Manuel López, William Ott +2
Transcriptional delay can significantly impact the dynamics of gene networks. Here we examine how such delay affects bistable systems. We investigate several stochastic models of b…