相关论文: Hybrid Metabolic Network Completion

Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example are fragmentation methods, in which quantum chemical calculations are carried…

Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…

Time cost is a major challenge in achieving high-quality pluralistic image completion. Recently, the Retentive Network (RetNet) in natural language processing offers a novel approach to this problem with its low-cost inference capabilities.…

In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…

We have created a genome-scale network reconstruction of Escherichia coli metabolism. Existing reconstructions were improved in terms of annotation standards, to facilitate their subsequent use in dynamic modelling. The resultant network is…

Heterogeneous, interconnected, systems-level, molecular data have become increasingly available and key in precision medicine. We need to utilize them to better stratify patients into risk groups, discover new biomarkers and targets,…

Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flux Balance Analysis (FBA), by postulating that cells set…

Presented in this paper is a derivation of a 2D catalytic reaction-based model to solve combinatorial optimization problems (COPs). The simulated catalytic reactions, a computational metaphor, occurs in an artificial chemical reactor that…

Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…

With the rise of service-oriented computing, applications are more and more based on coordination of autonomous services. Envisioned over largely distributed and highly dynamic platforms, expressing this coordination calls for alternative…

The understanding of molecular cell biology requires insight into the structure and dynamics of networks that are made up of thousands of interacting molecules of DNA, RNA, proteins, metabolites, and other components. One of the central…

Understanding the structural complexity and predictability of complex networks is a central challenge in network science. Although recent studies have revealed a relationship between compression-based entropy and link prediction…

The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…

There exist several methods for simulating biological and physical systems as represented by chemical reaction networks. Systems with low numbers of particles are frequently modelled as discrete-state Markov jump processes and are typically…

Preference handling and optimization are indispensable means for addressing non-trivial applications in Answer Set Programming (ASP). However, their implementation becomes difficult whenever they bring about a significant increase in…

The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a modern multi-core desktop in reasonable…

Answer Set Programming (ASP) is a powerful tool for solving real-world problems. However, many problems involve numeric values and complex constraints beyond the capabilities of standard ASP solvers. Hybrid solvers like CLINGCON and…

Absolute concentration robustness (ACR) and concordance are novel concepts in the theory of robustness and stability within Chemical Reaction Network Theory. In this paper, we have extended Shinar and Feinberg's reaction network analysis…

An important application of Synthetic Biology is the engineering of the host cell system to yield useful products. However, an increase in the scale of the host system leads to huge design space and requires a large number of validation…

Motivation: Stochastic reaction networks are a widespread model to describe biological systems where the presence of noise is relevant, such as in cell regulatory processes. Unfortu-nately, in all but simplest models the resulting discrete…