Related papers: High-throughput validation of ceRNA regulatory net…
Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with trait diversity and disease susceptibility, yet the functional properties of many genetic variants and their molecular…
RNA interference (RNAi) is a mechanism whereby small RNAs (siRNAs) directly control gene expression without assistance from proteins. This mechanism consists of interactions between RNAs and small RNAs both of which may be single or double…
Copy number alterations (CNAs) are thought to account for 85% of the variation in gene expression observed among breast tumours. The expression of cis-associated genes is impacted by CNAs occurring at proximal loci of these genes, whereas…
The focus of pancreatic cancer research has been shifted from pancreatic cancer cells towards their microenvironment, involving pancreatic stellate cells that interact with cancer cells and influence tumor progression. To quantitatively…
We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription…
The emerging field of epigenetics has recently unveiled a dynamic landscape in which gene expression is not determined solely by genetic sequences but also by intricate regulatory mechanisms. This review examines the interactions between…
MicroRNAs are small non-coding nucleotide sequences that regulate target protein expression at post-transcriptional levels. Biogenesis of microRNA is a highly regulated multi-step pathway. Regulation of miRNA biogenesis can be caused…
Reconstruction of gene regulatory networks or 'reverse-engineering' is a process of identifying gene interaction networks from experimental microarray gene expression profile through computation techniques. In this paper, we tried to…
MicroRNAs (miRNAs) critically modulate stem cell properties like pluripotency, but the fundamental mechanism remains largely unknown. This study systematically analyzes multiple-omics data and builds a systems physical network including…
The advent of large scale, high-throughput genomic screening has introduced a wide range of tests for diagnostic purposes. Prominent among them are tests using miRNA expression levels. Genomics and proteomics now provide expression levels…
Cancer disease occurs because of a disorder in the cellular regulatory mechanism, Which causes cellular malformation. The genes that start the malformation are called Cancer driver genes (CDGs) . Numerous computational methods have been…
MicroRNAs (miRNAs) are short sequences of ribonucleic acids that control the expression of target messenger RNAs (mRNAs) by binding them. Robust prediction of miRNA-mRNA pairs is of utmost importance in deciphering gene regulations but has…
Motivated by recent experimental work, we define and study a deterministic model of the complex miRNA-based regulatory circuit that putatively controls the early stage of myogenesis in human. We aim in particular at a quantitative…
miRNA and gene expression profiles have been proved useful for classifying cancer samples. Efficient classifiers have been recently sought and developed. A number of attempts to classify cancer samples using miRNA/gene expression profiles…
Background Precise prediction of cancer types is vital for cancer diagnosis and therapy. Important cancer marker genes can be inferred through predictive model. Several studies have attempted to build machine learning models for this task…
Background: Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide ``reverse engineering'' of such networks have been…
A wealth of new research has highlighted the critical roles of small RNAs (sRNAs) in diverse processes such as quorum sensing and cellular responses to stress. The pathways controlling these processes often have a central motif comprising…
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation. However, the experimental determination of miRNA sequence and structure is both expensive and time-consuming.…
Polygenic risk scores (PRSs) can significantly enhance breast cancer risk prediction when combined with clinical risk factor data. While many studies have explored the value-add of PRSs, little is known about the potential impact of…
Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. Little is known regarding the…