分子网络
How to induce differentiated cells into pluripotent cells has elicited researchers' interests for a long time since pluripotent stem cells are able to offer remarkable potential in numerous subfields of biological research. However, the…
Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including nutrient uptake and persistence in bacteria,…
Despite the large quantity of information available, thorough researches in various biological databases are still needed in order to reconstruct and understand the steps that lead to known or new phenomena. By using protein-protein…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
Inputs to signaling pathways can have complex statistics that depend on the environment and on the behavioral response to previous stimuli. Such behavioral feedback is particularly important in navigation. Successful navigation relies on…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Recon 2 is a highly curated reconstruction of the human metabolic network. Whilst the network is state of the art, it has shortcomings, including the presence of unbalanced reactions involving generic metabolites. By replacing these generic…
We consider a generic proto-cell model consisting of any conservative chemical reaction network embedded within a membrane. The membrane results from the self-assembly of one of the chemical species (membrane precursor) and is…
Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…
We investigate the properties of large random conservative chemical reaction networks composed of elementary reactions endowed with either mass-action or saturating kinetics, assigning kinetic parameters in a thermodynamically-consistent…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…
Chromosomal aberrations are very frequent in leukemias and several recurring mutations capable of malignant transformation have been described. These mutations usually occur in hematopoietic stem cells (HSC), transforming them into leukemia…
Diabetes mellitus type II affects around 8 percent of the total adult population in the world. It is the fifth leading cause of death in high income countries and an epidemic in developing countries. We analyze protein-protein interaction…
Biochemical mechanisms with mass action kinetics are often modeled by systems of polynomial differential equations (DE). Determining directly if the DE system has multiple equilibria (multistationarity) is difficult for realistic systems,…
Background: Sphingolipids - as suggested by the prefix in their name - are mysterious molecules, which play surprisingly various roles in opposable cellular processes, like autophagy, apoptosis, proliferation and differentiation. Recently…
A recently experimentally observed biochemical "threshold filtering" mechanism by processes catalyzed by the enzyme malate dehydrogenase is explained in terms of a model that incorporates an unusual mechanism of inhibition of this enzyme…
Characterizing interactions between drugs is important to avoid potentially harmful combinations, to reduce off-target effects of treatments and to fight antibiotic resistant pathogens, among others. Here we present a network inference…
Omics technologies enable unbiased investigation of biological systems through massively parallel sequence acquisition or molecular measurements, bringing the life sciences into the era of Big Data. A central challenge posed by such omics…
Book review of Stochastic Chemical Kinetics. Theory and (Mostly) Systems Biological Applications, P. Erdi, G. Lente. Springer (2014)
Discovering patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary…