stochastic model

Noisy foresight

Twenty years ago, I was just a boy with a crazy dream of building stochastic models of the noise affecting the expression of genes in living cells. Back in the 90s this idea sounded like an heresy. The dominant paradigm of the time was to consider that gene regulation was a qualitative and deterministic process […]

Noise in synthetic genetic oscillators

This paper focuses on characterizing the stochastic dynamics of previously described synthetic genetic oscillators. It is a very nice combination of experimental and computational work. The computational aspect includes both image analysis and parameter estimation. They breakdown the noise into different components including intrinsic noise, cell cycle noise, and parameter variability by looking at the expression […]

Modeling a Minimal CDK Network

This paper reports a computational analysis of the minimal CDK network engineered in fission yeast (doi:10.1038/nature09543). It had been observed that a Cdk-inhibitory mechanism working through tyrosine phosphorylation of the kinase subunit, which is essential for modern fission yeast, is dispensable in the minimal Cdk network. Developing both deterministic and stochastic models of the minimal Cdk […]

Leave it to chance or not

leave it to chance cover

Carolyn Beans wrote a blog post about our project to develop stochastic models of the regulatory network controlling cell division.  She was particularly interested in aspects of cell physiology that are affected by random events and how cells manage to remain healthy despite the vagaries of molecular interactions. Read her post on the NIGMS Biobeat […]

Stochastic modeling of the cell cycle goes on…

A couple of weeks ago, we received the renewal of the NIH grant funding our collaboration with John Tyson to develop stochastic models of the regulatory network controlling the cell cycle in yeast. This is the third funding cycle of this project that started in 2006. This renewal did not as smoothly as we had […]

Cell Cycle Model

cell cycle regulator mRNA

Cell cycle model: a noisy yet robust network A cell cycle model can help better understand the property of this complex regulatory network. The cell cycle is the process by which a growing cell replicates its genome and partitions the two copies of each chromosome to two daughter cells at division. It is of utmost […]

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Fifty years of genetic and molecular experiments have revealed a wealth of molecular interactions involved in the control of cell division. In light of the complexity of this control system, mathematical modeling has proved useful in analyzing biochemical hypotheses that can be tested experimentally. Stochastic modeling has been especially useful in understanding the intrinsic variability […]

Measurements modeling transcription noise makes the cover of Cell Cycle

The October issue of Cell Cycle includes an article reporting our efforts to measure and model the transcriptional noise affecting the the regulatory network controlling the cell cycle in the baker yeast (Saccharomyces cerevisiae). The journal cover page features an image derived from this work.   Cell Cycle. 2013 Sep 4;12(19). [Epub ahead of print] Measurement […]