Related papers: Optimizing information flow in small genetic netwo…
It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a…
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…
Information theory has explained the organization of many biological phenomena, from the physiology of sensory receptive fields to the variability of certain DNA sequence ensembles. Some scholars have proposed that information should…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
In many biological networks the responses of individual elements are ambiguous. We consider a scenario in which many sensors respond to a shared signal, each with limited information capacity, and ask that the outputs together convey as…
In our previous publication, a framework for information flow in interaction networks based on random walks with damping was formulated with two fundamental modes: emitting and absorbing. While many other network analysis methods based on…
During development, highly ordered structures emerge as cells collectively coordinate with each other. While recent advances have clarified how individual cells process and respond to external signals, understanding collective cellular…
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…
Directed information transmission is paramount for many social, physical, and biological systems. For neural systems, scientists have studied this problem under the paradigm of feedforward networks for decades. In most models of feedforward…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Efficient coding theory posits that sensory circuits transform natural signals into neural representations that maximize information transmission subject to resource constraints. Local interneurons are thought to play an important role in…
The most common gene regulation mechanism is when a protein binds to a regulatory sequence to change RNA transcription. However, these sequences are short relative to the genome length, so finding them poses a challenging search problem.…
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…
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…
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,…
We study minimum-variance feedback-control design for a networked control system with retarded dynamics, where inter-agent communication is subject to latency. We prove that such a design can be solved efficiently for circular formations…
The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and…
MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals. They are known to play an important role in several biological processes and, together with transcription…
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…
It is now well established that the cell is a highly crowded environment. Yet, the effects of crowding on the dynamics of signaling pathways, gene regulation networks and metabolic networks are still largely unknown. Crowding can alter both…