Related papers: Modeling competing endogenous RNAs networks
Circular RNAs (circRNAs) are a class of RNA with an important role in micro RNA (miRNA) regulation recently discovered in Human and various other eukaryotes as well as in archaea. Here, we have analyzed RNA-seq data obtained from {\it…
Understanding the insulin signaling cascade provides insights on the underlying mechanisms of biological phenomena such as insulin resistance, diabetes, Alzheimer's disease, and cancer. For this reason, previous studies utilized chemical…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
We investigate the dynamics of two models of biological networks with purely suppressive interactions between the units; species interacting via niche competition and neurons via inhibitory synaptic coupling. In both of these cases,…
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
In order to fully exploit the potential of molecular communication (MC) for intra-body communication, practically implementable cellular receivers are an important long-term goal. A variety of receiver architectures based on chemical…
Mean-field theory is a powerful tool for studying large neural networks. However, when the system is composed of a few neurons, macroscopic differences between the mean-field approximation and the real behavior of the network can arise.…
Realizations of low firing rates in neural networks usually require globally balanced distributions among excitatory and inhibitory links, while feasibility of temporal coding is limited by neuronal millisecond precision. We show that…
Cells make use of semi-flexible biopolymers such as actin or intermediate filaments to control their local viscoelastic response by dynamically adjusting the concentration and type of cross-linker molecules. The microstructure of the…
This paper studies the (discrete) \emph{chemical reaction network (CRN)} computational model that emerged in the last two decades as an abstraction for molecular programming. The correctness of CRN protocols is typically established under…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers,…
Membraneless droplets formed through liquid-liquid phase separation (LLPS) play a crucial role in mRNA storage, enabling organisms to swiftly respond to environmental changes. However, the mechanisms underlying mRNA integration and…
Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical…
1. In Bayesian Network Regression models, networks are considered the predictors of continuous responses. These models have been successfully used in brain research to identify regions in the brain that are associated with specific human…
Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic…
Molecular chaperones play a prominent role in signaling and transcriptional regulatory networks of the cell. Recent advances uncovered that chaperones act as genetic buffers stabilizing the phenotype of various cells and organisms and may…
The majority of mammalian genomic transcripts do not directly code for proteins and it is currently believed that most of these are not under evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and its strong…