Background: Mammalian preimplantation development is a complex process involving dramatic changes in the transcriptional architecture. However, it is still unclear about the crucial transcriptional network and key hub genes that regulate the proceeding of preimplantation embryos. Materials and Methods: Through single-cell RNAsequencing (RNA-seq) of both human and mouse preimplantation embryos, ...

Tryptophan is one of the 20 amino acids that link together to form proteins. For humans it is an essential amino acid, we must get it from our diet since we cannot synthesize it. E. coli bacterial cells, however, can synthesize the amino acid tryptophan when it is not provided from the environment (e.g. the gut where it lives). It would be wasteful to synthesize tryptophan when it is readily av...

Differential gene expression plays a critical role in the development and physiology of multicellular organisms. At a 'systems level' (e.g. at the level of a tissue, organ or whole organism), this process can be studied using gene regulatory network (GRN) models that capture physical and regulatory interactions between genes and their regulators. In the past years, significant progress has been...

Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: there are many ways to achieve the same function. Here we investigate the ability of regulatory networks to reproduce given expression levels within a simple model of gene regulation. We find an exponentially large space of regulatory networks compatible with...

Quantifying Gene Regulatory Networks

A fundamental question in biology is how cells change into specific cell types with unique roles throughout development. This process can be viewed as a program prescribing the system dynamics, governed by a network of genetic interactions. Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. Currently, there are limited tool...

Summary We develop DiffGraph, anRpackage that integrates four influential differential graphical models for identifying gene network rewiring under two different conditions from gene expression data. The input and output of different models are packaged in the same format, making it convenient for users to comparedifferent models using a wide range of datasets and carry out follow-up analysis. ...

Transcriptional delay can significantly impact the dynamics of gene networks. Here we examine how such delay affects bistable systems. We investigate several stochastic models of bistable gene networks and find that increasing delay dramatically increases the mean residence times near stable states. To explain this, we introduce a non-Markovian, analytically tractable reduced model. The model s...

The structural analysis of biological networks includes the ranking of the vertices based on the connection structure of a network. To support this analysis we discuss centrality measures which indicate the importance of vertices, and demonstrate their applicability on a gene regulatory network. We show that common centrality measures result in different valuations of the vertices and that nove...