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We construct a model of cell reprogramming (the conversion of fully differentiated cells to a state of pluripotency, known as induced pluripotent stem cells, or iPSCs) which builds on key elements of cell biology viz. cell cycles and cell…
We investigate the intergenerational shape dynamics of single Caulobacter crescentus cells using a novel combination of imaging techniques and theoretical modeling. We determine the dynamics of cell pole-to-pole lengths, cross-sectional…
We study a one-dimensional three-state run-and-tumble model motivated by the bacterium Caulobacter crescentus which displays a cell cycle between two non-proliferation mobile phase and a proliferating sedentary phase. Our model implements…
Cell size is a fundamental determinant of cellular physiology, influencing processes such as growth, division, and function. In this study, we develop a segmented mathematical framework to investigate how different control mechanisms…
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…
The regulatory mechanisms driving progression of the yeast cell cycle appears to be comprised of an interacting network of transcription factors (TFs), cyclin-dependent kinases (CDK) and ubiquitin ligases. From a systems perspective the…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Cell functional diversity is a significant determinant on how biological processes unfold. Most accounts of diversity involve a search for sequence or expression differences. Perhaps there are more subtle mechanisms at work. Using the…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…
Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell's fate, such as disease therapeutics and stem cell reprogramming. Here we develop a novel network control…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
Single-cell data provide high-dimensional measurements of the transcriptional states of cells, but extracting insights into the regulatory functions of genes, particularly identifying transcriptional mechanisms affected by biological…
Biological functions in living cells are controlled by protein interaction and genetic networks. These molecular networks should be dynamically stable against various fluctuations which are inevitable in the living world. In this paper, we…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are…
The biological processes that execute complex multiple functions, such as cell cycle, must ensure the order of sequential events and keep the dynamic robustness against various fluctuations. Here, we examine the dynamic mechanism and the…