Modeling DNA Sequence-Based cis-Regulatory Gene Networks

Modeling DNA sequence-based cis-regulatory gene networks.

Gene network analysis requires computationally based models which represent the functional architecture of regulatory interactions, and which provide directly testable predictions. The type of model that is useful is constrained by the particular features of developmentally active cis-regulatory systems. These systems function by processing diverse regulatory inputs, generating novel regulatory...

Multigenome DNA sequence conservation identifies Hox cis-regulatory elements.

To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced approximately 0.5% of the C. br...

Modeling gene regulatory networks: Classical models, optimal perturbation for identification of network

Deep understanding of molecular biology has allowed emergence of new technologies like DNA decryption.  On the other hand, advancements of molecular biology have made manipulation of genetic systems simpler than ever; this promises extraordinary progress in biological, medical and biotechnological applications.  This is not an unrealistic goal since genes which are regulated by gene regulatory ...

Systems Level Modeling of Gene Regulatory Networks

Modeling gene regulatory networks using Petri Nets

Petri nets (PNs) are a qualitative approach to modeling the gene regulatory networks (GRNs) capable of characterising the dynamical properties of complex systems while also describing their structure with PN graphs. In this paper we show how to construct basic building blocks for GRNs using PNs. We present solutions to some of the known weaknesses of using conventional PNs for descrbing GRNs by...