Related papers: The style of genetic computing
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
How intracellular and extracellular signals are integrated by transcription factors is essential for understanding complex cellular patterns at the population level. In this Letter, by using a synthetic genetic oscillator coupled to a…
By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…
Gene Regulatory Networks (GRNs) consisting of combinations of transcription factors (TFs) and their cis promoters are assumed to be sufficient to direct the development of organisms. Mutations in GRNs are assumed to be the primary drivers…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are…
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…
This paper presents an intracellular feedback control strategy, to regulate the gene expression process dynamics. For this purpose, two types of genetic circuits are designed in order to compare concentrations of the input transcription…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
Deciphering how DNA sequence encodes gene regulation remains a central challenge in biology. Advances in machine learning and functional genomics have enabled sequence-to-function (seq2func) models that predict molecular regulatory readouts…
The ability to learn and respond to recurrent events depends on the capacity to remember transient biological signals received in the past. Moreover, it may be desirable to remember or ignore these transient signals conditioned upon other…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
Appropriate regulation of gene expression is essential to ensure that protein synthesis occurs in a selective manner. The control of transcription is the most dominant type of regulation mediated by a complex of molecules such as…