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

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Thomas Schlitt, Alvis Brazma

Abstract

Approaches to describe gene regulation networks can be categorized by increasing detail, as network parts lists, network topology models, network control logic models or dynamic models. We discuss the current state of the art for each of these approaches. We study the relationship between different topology models, and give examples how they can be used to infer functional annotations for genes of unknown function. We introduce a new simple way of describing dynamic models called finite state linear model (FSLM). We discuss the gap between the parts list and topology models on one hand, and network logic and dynamic models, on the other hand. The first two classes of models have reached a genome-wide scale, while for the other model classes high-throughput technologies are yet to make a major impact.

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Citations

Jun 2, 2007·Medical & Biological Engineering & Computing·Zhao WangChih-Chuan Liang
Mar 10, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·David T JonesJanet M Thornton
Nov 10, 2009·BMC Bioinformatics·Adaoha E C IhekwabaCorrado Priami
Oct 2, 2007·BMC Bioinformatics·Thomas Schlitt, Alvis Brazma
Aug 15, 2008·Computational Biology and Chemistry·K KhoshmaneshJ R Kanwar
Sep 11, 2007·International Journal of Medical Informatics·Fulvia FerrazziRiccardo Bellazzi
Nov 3, 2007·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ignacio PonzoniDavid Glass
Jul 19, 2006·Nature Reviews. Genetics·Alvis BrazmaUgis Sarkans

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