modeling

Synthetic Biology Summer Schools

For graduate students interested in getting intensive training in synthetic biology, there are several summer schools worth considering: CSHL Summer School in Synthetic Biology: This program spans 2 weeks and combines lectures and intensive lab experience. Application deadline is April 15th.  SSBSS 2017:The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential […]

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 […]

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 […]

DNA Design

genocad dna design software

DNA Design: CAD of Gene Expression Systems We are developing DNA design strategies relying on design rules that accelerate the development of expression vectors and reduce costly errors. Most bioinformatics software packages include sequence editors that facilitate the design and assembly of new DNA sequences. Automatic recognition of sequence features, identification of restriction sites, and […]

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 […]

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines […]

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 […]