Related papers: Predicting synthetic rescues in metabolic networks
Genome-Scale Metabolic Models (GEMs) describe the interactions between genes, proteins, and the biochemical reactions that underpin an organism's metabolism aiming to computationally simulate functions at the cellular level. While many…
Models of biochemical networks are usually presented as connected graphs where vertices indicate proteins and edges are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions…
There is a widening recognition that cancer cells are products of complex developmental processes. Carcinogenesis and metastasis formation are increasingly described as systems-level, network phenomena. Here we propose that malignant…
We propose a novel model-selection method for dynamic networks. Our approach involves training a classifier on a large body of synthetic network data. The data is generated by simulating nine state-of-the-art random graph models for dynamic…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
One central goal of systems biology is to infer biochemical regulations from large-scale OMICS data. Many aspects of cellular physiology and organism phenotypes could be understood as a result of the metabolic interaction network dynamics.…
Constraint based methods, such as the Flux Balance Analysis, are widely used to model cellular growth processes without relying on extensive information on the regulatory features. The regulation is instead substituted by an optimization…
The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes,…
Active nematics is an emerging paradigm for characterising biological systems. One aspect of particularly intense focus is the role active nematic defects play in these systems, as they have been found to mediate a growing number of…
Transformations to create more sustainable social-ecological systems are urgently needed. Structural change is a feature of transformations of social-ecological systems that is of critical importance but is little understood. Here, we…
Background: State-of-the art selection methods fail to identify weak but cumulative effects of features found in many high-dimensional omics datasets. Nevertheless, these features play an important role in certain diseases. Results: We…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
The design and synthesis of complex and large mimicked biochemical networks de novo is an unsolved problem in synthetic biology. To address this limitation without resorting to ad hoc computations and experiments, a predictive mathematical…
High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…
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…
In the context of epigenetic transformations in cancer metastasis, a puzzling effect was recently discovered, in which the elimination (knock-out) of an activating regulatory element leads to increased (rather than decreased) activity of…
We discuss how to use a Genetic Regulatory Network as an evolutionary representation to solve a typical GP reinforcement problem, the pole balancing. The network is a modified version of an Artificial Regulatory Network proposed a few years…
Biological networks, such as cellular metabolic pathways or networks of corticocortical connections in the brain, are intricately organized, yet remarkably robust toward structural damage. Whereas many studies have investigated specific…
Network science provides effective tools to model and analyze complex systems. However, the increasing size of real-world networks becomes a major hurdle in order to understand their structure and topological features. Therefore, mapping…
We propose a genetic algorithm (GA) based method for modifying n-best lists produced by a machine translation (MT) system. Our method offers an innovative approach to improving MT quality and identifying weaknesses in evaluation metrics.…