Related papers: On the basic computational structure of gene regul…
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional,…
A complexity-theoretic approach to studying biological networks is proposed. A simple graph representation is used where molecules (DNA, RNA, proteins and chemicals) are vertices and relations between them are directed and signed…
One of the characteristic features of genetic networks is their inherent robustness, that is, their ability to retain functionality in spite of the introduction of random errors. In this paper, we seek to better understand how robustness is…
Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and…
Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…
Robust systems, like the molecular networks of living cells are often resistant to single hits such as those caused by high-specificity drugs. Here we show that partial weakening of the Escherichia coli and Saccharomyces cerevisiae…
BACKGROUND: Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region of the regulated…
Various molecular interaction networks have been claimed to follow power-law decay for their global connectivity distribution. It has been proposed that there may be underlying generative models that explain this heavy-tailed behavior by…
Determining mechanistic models of gene regulation, especially underlying phenotypic variation, is a central goal of both mathematical biology and modern evolutionary biology. However, several challenges, involving both common…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
We analyze gene expression time-series data of yeast S. cerevisiae measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene…
Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of a process known as spontaneous immortalization. In this process a generic series of cell state transitions occur in…
Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
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…
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…
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 two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…