Related papers: Hybrid Metabolic Network Completion
Purpose: Proton magnetic resonance spectroscopic imaging ($^1$H MRSI) enables the mapping of whole-brain metabolites concentrations in-vivo. However, a long-standing problem for its clinical applicability is the metabolic quantification,…
Synthetic lethal reaction/gene-sets are sets of reactions/genes where only the simultaneous removal of all reactions/genes in the set abolishes growth of an organism. In silico, synthetic lethal sets can be identified by simulating the…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial…
A metabolic model can be represented as bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a…
The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-based models in particular play a key role in the attempt to…
In many key applications of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect changes in metabolic processes, usually represented in the form of pathways. As an alternative, a broader point of view…
We introduce an approach to detecting inconsistencies in large biological networks by using Answer Set Programming (ASP). To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we…
A key step in the origin of life is the emergence of a primitive metabolism. This requires the formation of a subset of chemical reactions that is both self-sustaining and collectively autocatalytic. A generic theory to study such processes…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
Associative network models featuring multi-tasking properties have been introduced recently and studied in the low load regime, where the number $P$ of simultaneously retrievable patterns scales with the number $N$ of nodes as $P\sim \log…
We study a simplified, solvable model of a fully-connected metabolic network with constrained quenched disorder to mimic the conservation laws imposed by stoichiometry on chemical reactions. Within a spin-glass type of approach, we show…
We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high-throughput metabolite profiling data. For this, we generate synthetic metabolic…
Genome-scale metabolic models (GEMs) are essential tools for systems biology and rational chassis design, but conventional top-down reconstruction depends heavily on sequence homology and often leaves unknown enzymes and metabolic dark…
In many networks, including networks of protein-protein interactions, interdisciplinary collaboration networks, and semantic networks, connections are established between nodes with complementary rather than similar properties. While…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Answer set programming (ASP) is a paradigm for modeling knowledge intensive domains and solving challenging reasoning problems. In ASP solving, a typical strategy is to preprocess problem instances by rewriting complex rules into simpler…