Related papers: A computational approach to regulatory element dis…
Some genes can promote or repress their own expressions, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the…
While coding regions in the genome have a direct interpretation in terms of protein products, significant fractions are non-coding and yet control essential biological functions. Unlike the genetic code, there is no "lookup table" that…
MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding and degrading target eukaryotic mRNAs. We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by…
Connectivity networks have recently become widely used in biology due to increasing amounts of information on the physical and functional links between individual proteins. This connectivity data provides valuable material for expanding our…
Despite the significant progress made in recent years, the computation of the complete set of elementary flux modes of large or even genome-scale metabolic networks is still impossible. We introduce a novel approach to speed up the…
Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the always increasing…
All cells respond to changes in both their internal milieu and the environment around them through the regulation of their genes. Despite decades of effort, there remain huge gaps in our knowledge of both the function of many genes (the…
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 the genome biology research, regulatory genome modeling is an important topic for many regulatory downstream tasks, such as promoter classification, transaction factor binding sites prediction. The core problem is to model how regulatory…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
We investigate the structural and dynamical properties of the transcriptional regulatory network of the yeast {\it Saccharomyces cerevisiae} and compare it with two unbiased ensembles: one obtained by reshuffling the edges and the other…
Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
Living cells are the product of gene expression programs that involve the regulated transcription of thousands of genes. The elucidation of transcriptional regulatory networks in thus needed to understand the cell's working mechanism, and…
BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the…
Motivation: Detecting local correlations in expression between neighbor genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to…
Microarray is one of the essential technologies used by the biologist to measure genome-wide expression levels of genes in a particular organism under some particular conditions or stimuli. As microarrays technologies have become more…
Transcription factors are proteins that regulate gene activity by activating or repressing gene transcription. A special class of transcriptional repressors operates via a short-range mechanism, making local DNA regions inaccessible to…
In synthetic biology, gene regulatory circuits are often constructed by combining smaller circuit components. Connections between components are achieved by transcription factors acting on promoters. If the individual components behave as…
During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially or simultaneously. These growth patterns are manifested in all types of bacteria and yeasts. The ubiquity of these growth…