Kim, et al., 

Molecular Systems Biology, (2023)

Mapping single‐cell responses to population‐level dynamics during antibiotic treatment

Many rod-shaped bacteria grow to long filaments without dividing under cell-wall targeting (beta lactam) antibiotic treatment. It was also known that a population of such bacteria would first keep on accumulating biomass before a population decay. But there was no quantitative framework to bridge these single cell- and population-level features. Here, led by my colleague Kyeri Kim, combining mathematical modeling and experiments we link the two. Specifically, we show that bacteria lyse typically when reaching a critical length. On the way to this critical length, the probability of lysis increases. The latter could be explained by a cell-wall damage accumulation process.

Şimşek, et al., 

Trends in Biotechnology, (2023)

Toward predictive engineering of gene circuits

In this invited Opinion article, we define what predictive engineering of gene circuits is. We dissect biological and environmental complexity into circuit and context complexities as confounding factors on the predictability in circuit engineering. We argue that predictive engineering of gene circuits is good for biotechnological applications such as target-specific drug delivery, metabolic engineering, microbiome engineering, and biomaterial synthesis. We argue that mechanistic modeling is useful to validate the predictability of an engineered gene circuit. We elaborate how machine learning can complement mechanistic modeling.

Lu, et al., 

Current Opinion in Chemical Biology, (2022)

Advances and challenges in programming pattern formation using living cells

In this invited Review article, led by my colleague Jia Lu, we discuss recent advances and pinpoint remaining challenges and opportunities in engineering spatial patterns using living bacteria.

Şimşek*, Dawson*, et al., 

The International Society for Microbial Ecology (ISME) Journal, (2022)

Spatial regulation of cell motility and its fitness effect in a surface-attached bacterial community

Partial migration is an ecological phenomenon widely known for animal populations in which only a subset of the individuals is motile while others are sessile. Here, we investigate partial migration in an example from surface attached bacteria (Proteus mirabilis). We show that a growing colony becomes partially migratory by generating motile individuals preferentially at the outer region (green). We provide evidence that the suppression of the motile phenotype in the central regions is triggered by nutrient depletion and uncovered a signaling mechanism (Rcs) through which this regulation occurs. Finally, we show that this partial migration strategy facilitates prolonged starvation survival.