In Silico Systems Biology

@inproceedings{Schneider2013InSS,
  title={In Silico Systems Biology},
  author={Maria Victoria Schneider},
  booktitle={Methods in Molecular Biology},
  year={2013}
}
  • M. Schneider
  • Published in Methods in Molecular Biology 2013
  • Biology
Here we provide a broad overview of the definition of the term “systems biology” as well as pinpoint specific events in biological research and beyond that are consistently cited to have contributed and led to the current science of in silico systems biology. Since there have been many reviews and historical accounts describing the term, it would be impossible to include all single references. However, we do attempt to provide a consensus vision of how the field has evolved and consequently the… 

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References

SHOWING 1-10 OF 63 REFERENCES

Differential network biology

TLDR
It is argued that differential network mapping, which allows for the interrogation of previously unexplored interaction spaces, will become a standard mode of network analysis in the future, just as differential gene expression and protein phosphorylation studies are already pervasive in genomic and proteomic analysis.

Modelling in molecular biology: describing transcription regulatory networks at different scales

  • T. SchlittA. Brazma
  • Computer Science
    Philosophical Transactions of the Royal Society B: Biological Sciences
  • 2006
TLDR
A new simple way of describing dynamic models called finite state linear model (FSLM) is introduced, which discusses the gap between the parts list and topology models on one hand, and network logic and dynamic models, on the other hand.

Gene Ontology: tool for the unification of biology

TLDR
The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.

Modular analysis of signal transduction networks

TLDR
The mechanisms that cells have developed to process information are described, and the decomposition of signalling networks into subsystems is discussed, and some simple criteria for the analysis of the resulting units are introduced.

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

TLDR
The subsystem approach is described, the first release of the growing library of populated subsystems is offered, and the SEED is the first annotation environment that supports this model of annotation.

Pathguide: a Pathway Resource List

TLDR
This meta-database provides an overview of more than 190 web-accessible biological pathway and network databases, which include databases on metabolic pathways, signaling pathways, transcription factor targets, gene regulatory networks, genetic interactions, protein–compound interactions, and protein–protein interactions.

Modeling and simulation of intracellular dynamics: choosing an appropriate framework

TLDR
A novel compact derivation is provided for the stochastic rate constant that forms the basis of the popular Gillespie algorithm and is argued that some of the arguments put forward are ignoring subtle differences and similarities that are important for answering the question in which conceptual framework one should investigate intracellular dynamics.

Interactome Networks and Human Disease

...