Related papers: An Algorithm for Cellular Reprogramming
Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to…
Cellular reprogramming, the conversion of one cell type to another, has fundamentally transformed our conception of cell types. Cellular reprogramming induces global changes in gene expression involving hundreds of transcription factors and…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
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…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…
Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
How to induce differentiated cells into pluripotent cells has elicited researchers' interests for a long time since pluripotent stem cells are able to offer remarkable potential in numerous subfields of biological research. However, the…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
We demonstrate that the algorithmic information content of a system is deeply connected to its potential dynamics, thus affording an avenue for moving systems in the information-theoretic space and controlling them in the phase space. To…
Cell tracking algorithms which automate and systematise the analysis of time lapse image data sets of cells are an indispensable tool in the modelling and understanding of cellular phenomena. In this study we present a theoretical framework…