The development of accurate and reliable dynamical modeling procedures that describe the time evolution of gene expression levels is a prerequisite to understanding and controlling the transcription process. We focused on data from DNA microarray time series for 20 Drosophila genes involved in muscle development during the embryonic stage. Genes with similar expression profiles were clustered o...

Cellular injury caused by stimuli plays an important role in the progression of various diseases including acute and chronic kidney diseases. The dynamic transcriptional regulation responding to underlies mechanism injury. In this study, we investigated regulatory elements their activities tubular epithelial cells. We captured chromatin accessibility gene expression with ATAC-seq RNA sequencing...

A fundamental problem in functional genomics is to determine the structure and dynamics of genetic networks based on expression data. We describe a new strategy for solving this problem and apply it to recently published data on early Drosophila melanogaster development. Our method is orders of magnitude faster than current fitting methods and allows us to fit different types of rules for expre...

The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own expression or the production of protein in another network. Engineered control of cellular function through the design and manipulation of such networks lies within t...

To infect their hosts, DNA viruses must successfully initiate the expression of viral genes that control subsequent viral gene expression and manipulate the host environment. Viral genes that are immediately expressed upon infection play critical roles in the early infection process. In this study, we investigated the expression and regulation of five canonical regulatory immediate-early (IE) g...

Previous gene expression profiling studies of neuropathic pain (NP) following spinal cord injury (SCI) have predominantly been performed in animal models. The present study aimed to investigate gene alterations in patients with spinal cord injury and to further examine the mechanisms underlying NP following SCI. The GSE69901 gene expression profile was downloaded from the public Gene Expression...

The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a much broader array of conditions. However, the process of adaptation by exploratory dynamics within the lifetime of a cell is not well understood. Here we demon...

Lung cancer is a prevalent cancer with a high death rate. Underlying mechanisms have been found to be highly correlated with epigenetics, especially with DNA methylation. With methylation array and other regulation data, we constructed a TF-gene regulation network and a TF-pathway network. Through those networks, we identified lung cancer related genes that were found by previous studies, and s...

Boolean Networks are emerging as a simple yet powerful formalism to model and study Gene Regulatory Networks. Nevertheless, the most widely used Boolean Network-based models do not include any post-transcriptional regulation mechanism. In this paper we discuss how the post-transcriptional regulation mechanism mediated by miRNAs can be included in a Boolean Network based model. This contribution...

Understanding the control of gene expression remains one of the main challenges in the post-genomic era. Accordingly, a plethora of methods exists to identify variations in gene expression levels. These variations underlay almost all relevant biological phenomena, including disease and adaptation to environmental conditions. However, computational tools to identify how regulation changes are sc...