Molecular Networks
The analysis of the mutational landscape of cancer, including mutual exclusivity and co-occurrence of mutations, has been instrumental in studying the disease. We hypothesized that exploring the interplay between co-occurrence, mutual…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
Mathematical modelling has become an established tool for studying the dynamics of biological systems. Current applications range from building models that reproduce quantitative data to identifying systems with predefined qualitative…
We present a protocol for building, validating and simulating models of signal transduction networks. These networks are challenging modelling targets due to the combinatorial complexity and sparse data, which have made it a major challenge…
An Elementary Flux Mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find…
Single-cell experiments show that gene expression is stochastic and bursty, a feature that can emerge from slow switching between promoter states with different activities. One source of long-lived promoter states is the slow binding and…
A variety of complex systems exhibit different types of relationships simultaneously that can be modeled by multiplex networks. A typical problem is to determine the community structure of such systems that, in general, depend on one or…
We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…
Development from egg to embryo to adult is a fascinating instance of biological self-organization for which genetics has supplied us with a parts list. It remains to find the principles organizing the assembly of those parts. In the last…
Plants depend on the signaling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular signaling network involves a negative feedback at the level of the Aux/IAA…
Whereas the relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single cell level has been vigorously studied, the relationship between the criticality of GRNs and system properties at a higher…
The impact of random fluctuations on the dynamical behavior a complex biological systems is a longstanding issue, whose understanding would shed light on the evolutionary pressure that nature imposes on the intrinsic noise levels and would…
Despite their dynamic nature, certain chromatin marks must be maintained over the long term. This is particulary true for histone 3 lysine 9 (H3K9) trimethylation, that is involved in the maintenance of healthy differentiated cellular…
In this review we address to what extent computational techniques can augment our ability to predict toxicity. The first section provides a brief history of empirical observations on toxicity dating back to the dawn of Sumerian…
Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time…
Genes are frequently regulated in complex manners, necessitating modelling approaches which go beyond simple (linear) gene-to-gene interactions and address the modularity of cis-regulatory regions and alternate transcription initiation…
A computational model of aquaporin regulation in cancer cells has been constructed as a Qualitative Network in the software BioModelAnalyzer (BMA). The model connects some important aquaporins expressed in human cancer to common phenotypes…
In the real world, most objects and data have multiple types of attributes and inter-connections. Such data structures are named "Heterogeneous Information Networks" (HIN) and have been widely researched. Biological systems are also…
In this work maximum entropy distributions in the space of steady states of metabolic networks are defined upon constraining the first and second moment of the growth rate. Inherent bistability of fast and slow phenotypes, akin to a Van-Der…
Many growing networks possess accelerating statistics where the number of links added with each new node is an increasing function of network size so the total number of links increases faster than linearly with network size. In particular,…