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The influence of DNA cis-regulatory elements on a gene's expression has been intensively studied. However, little is known about expressions driven by trans-acting DNA hotspots. DNA hotspots harboring copy number aberrations are recognized…
Transcription Factors (TFs) are proteins crucial for regulating gene expression. Effective regulation requires the TFs to rapidly bind to their correct target, enabling the cell to respond efficiently to stimuli such as nutrient…
We performed a gene co-expression analysis on Lung Squamous Cell Carcinoma data to find modules (groups) of genes that may highly impact the growth of these type of tumors. Additionally, we used cancer survival data to relate modules to…
Transcriptional repressor CTCF is an important regulator of chromatin 3D structure, facilitating the formation of topologically associating domains (TADs). However, its direct effects on gene regulation is less well understood. Here, we…
The emergence of acquired drug resistance in cancer represents a major barrier to treatment success. While research has traditionally focused on genetic sources of resistance, recent findings suggest that cancer cells can acquire transient…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
Background: MicroRNAs (miRNAs) play multiple roles in tumor biology [1]. Interestingly, reports from multiple groups suggest that miRNA targets may be coupled through competitive stoichiometric sequestration [2]. Specifically, computational…
We consider integrative modeling of multiple gene networks and diverse genomic data, including protein-DNA binding, gene expression and DNA sequence data, to accurately identify the regulatory target genes of a transcription factor (TF).…
Despite significant progress in structural and functional characterization of human genome, understanding of mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. We report that non-randomly distributed…
Cell stiffness is a key determinant of how cells deform, migrate, and adapt to mechanically restrictive environments, yet existing single-cell stiffness assays remain difficult to combine with molecular analysis and downstream functional…
DNA methylation is a well-studied genetic modification that regulates gene transcription of Eukaryotes. Its alternations have been recognized as a significant component of cancer development. In this study, we use the DNA methylation 450k…
Recent works have stressed the important role that random mutations have in the development of cancer phenotype. We challenge this current view by means of bioinformatic data analysis and computational modelling approaches. Not all the…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcripion factors should explain the different…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
Purpose of review: The epithelial-Mesenchymal Transition (EMT) and the generation of Cancer Stem Cells (CSC) are two fundamental aspects contributing to tumor growth, acquisition of resistance to therapy, formation of metastases, and tumor…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as…
By use of complex network dynamics and graph-based machine learning, we identified critical determinants of lineage-specific plasticity across the single-cell transcriptomics of pediatric high-grade glioma (pHGGs) subtypes: IDHWT…