Gene regulatory network (GRN) modeling is a well-established theoretical framework for the study of cell-fate specification during developmental processes. Recently, dynamical models of GRNs have been taken as a basis for formalizing the metaphorical model of Waddingtons epigenetic landscape, providing a natural extension for the general protocol of GRN modeling. In this contribution we present...

Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. Here, we describe an extensive, quantitative perturbation analysis targeting the dorsal-ventral patter...

Gene regulatory network (GRN)-based morphogenetic models have recently gained an increasing attention. However, the relationship between microscopic properties of intracellular GRNs and macroscopic properties of morphogenetic systems has not been fully understood yet. Here we study a theoretical morphogenetic model using Kauffman’s NK random Boolean network (RBN) as a GRN and spring-mass-damper...

Design and implementation of robust network modules is essential for construction of complex biological systems through hierarchical assembly of 'parts' and 'devices'. The robustness of gene regulatory networks (GRNs) is ascribed chiefly to the underlying topology. The automatic designing capability of GRN topology that can exhibit robust behavior can dramatically change the current practice in...

Gene regulatory networks (GRNs) represent the interactions between genes and gene products, which drive the gene expression patterns that produce cellular phenotypes. GRNs display a number of characteristics that are beneficial for the development and evolution of organisms. For example, they are often robust to genetic perturbation, such as mutations in regulatory regions or loss of gene funct...

One of the exciting problems in systems biology research is to decipher how genome controls the development of complex biological system. The gene regulatory networks (GRNs) help in the identification of regulatory interactions between genes and offer fruitful information related to functional role of individual gene in a cellular system. Discovering GRNs lead to a wide range of applications, i...

Two major approaches are known in the field of stochastic dynamics of intra-cellular biochemical networks. The first one places the focus of attention on the fact that many biochemical constituents vitally important for the network functionality may be present only in small quantities within the cell, and therefore the regulatory process is essentially discrete and prone to relatively big fluct...

http://dx.doi.org/10.1016/B978-0-12-404729-7.00002-2 Copyright © 2015 Eric H. Davidson and Isabelle S. Peter. Published by Elsevier Inc. All rights reserved. 1. Introductory Overview of Developmental GRNs 42 1.1 GRN function and how GRNs are encoded in the genome 42 1.2 GRN hierarchy and modular organization 43 1.3 Models of GRN topology 44 2. Boolean Spatial Output 45 3. Regulatory States 48 4...

Reverse engineering genetic regulatory networks (GRNs) is greatly undetermined by the data available. We need to understand the plausibility of a recovered GRN, but little is known about the correlation between matching the target expression vector and recovery of the target GRN. Here, we explore this and related issues and claim that (i) evolved target GRNs are more reliably reconstructed by e...

Langerhans cells (LCs), residing in the epidermis, are able to induce potent immunogenic responses and also mediate immune tolerance. We propose that tolerogenic of LCs directed by signaling from epidermis involve counter-acting gene circuits coupled a core maturation module. base our analysis on recent genetic genomic findings facilitating understanding molecular mechanisms controlling these d...