The promoter state of a gene and its expression levels are modulated by the amounts of transcription factors interacting with its regulatory regions. Hence, one may interpret a gene network as a communicating system in which the state of the promoter...
Network-based systems biology has become an important method for analyzing high-throughput gene expression data and gene function mining. Escherichia coli (E. coli) has long been a popular model organism for basic biological research. In this paper,...
Differential gene expression analyses to investigate multiple sclerosis (MS) molecular pathogenesis cannot detect genes harboring genetic and/or epigenetic modifications that change the gene functions without affecting their expression. Differential...
Caenorhabditis elegans (C. elegans) is a well-characterized metazoan, whose transcriptome has been profiled in different tissues, development stages, or other conditions. Large-scale transcriptomes can be reused for gene function annotation through s...
Gene networks have become a powerful tool for the comprehensive examination of gene expression patterns. Thanks to these networks generated by means of inference algorithms, it is possible to study different biological processes and even identify new...
Colorectal cancer (CRC) is a complex disease characterized by dynamically deregulated gene expression and crosstalk between signaling pathways. In this study, a new approach based on gene-function-based clusters was introduced to explore the CRC-asso...
Context: Inferring gene regulatory networks (GRN) from high-throughput gene expression data is a challenging task for which different strategies have been developed. Nevertheless, no ever-winning method exists, and each method has its advantages, int...
Gene expression classification remains a challenging task due to the high dimensionality and heterogeneity of available datasets. In this study, we present a comprehensive empirical analysis combining neural networks and Support Vector Machines (SVMs...
The evolving field of generative artificial intelligence (GenAI), particularly generative deep learning, is revolutionizing a host of scientific and technological sectors. One of the pivotal innovations within this domain is the emergence of generati...
Colorectal cancer (CRC) is driven in part by dysregulated Wnt, Ras-Raf-MAPK, TGF-β, and PI3K-Akt signaling. The progression of CRC is also promoted by molecular alterations and heterogeneous—yet interconnected—gene mutations, chromos...
Gene regulatory networks (GRN) govern cellular identity and function through precise control of gene transcription. Single-cell technologies have provided powerful means to dissect regulatory mechanisms within specific cellular states. However, exist...
Corynebacterium pseudotuberculosis is a Gram-positive bacterium that causes caseous lymphadenitis, a disease that predominantly affects sheep, goat, cattle, buffalo, and horses, but has also been recognized in other animals. This bacterium generates...
Recently, network controllability studies have proposed several frameworks for the control of large complex biological networks using a small number of life molecules. However, age-related changes in the brain have not been investigated from a contro...
The comprehensibility of good predictive models learned from high-dimensional gene expression data is attractive because it can lead to biomarker discovery. Several good classifiers provide comparable predictive performance but differ in their abilit...
Over the past decade, energy forecasting applications not only on the grid side of electric power systems but also on the customer side for load and demand prediction purposes have become ubiquitous after the advancements in the smart grid technologi...
Cytolytic immune activity in solid tissue can be quantified by transcript levels of two genes, GZMA and PRF1, which is named the CYT score. A previous study has investigated the molecular and genetic properties of tumors associated CYT, but a systema...
The power-generation mix of future grids will be quite diversified with the ever-increasing share of renewable energy technologies. Therefore, the prediction of electricity demand will become crucial for resource optimization and grid stability. Mach...
Self-expressiveness is a mathematical property that aims at characterizing the relationship between instances in a dataset. This property has been applied widely and successfully in computer-vision tasks, time-series analysis, and to infer underlying...
Studying relationships among gene products by expression profile analysis is a common approach in systems biology. Many studies have generalized the outcomes to the different levels of central dogma information flow and assumed a correlation of trans...
Transcriptomics has significantly grown as a functional genomics tool for understanding the expression of biological systems. The generated transcriptomics data can be utilised to produce a gene co-expression network that is one of the essential down...
The RNA-Seq and gene expression data of mature leaves under high temperature stress of Paeonia suffruticosa ‘Hu Hong’ were used to explore the key genes of heat tolerance of peony. The weighted gene co-expression network analysis (WGCNA)...
Background: Malaria results in more than 550,000 deaths each year due to drug resistance in the most lethal Plasmodium (P.) species P. falciparum. A full P. falciparum genome was published in 2002, yet 44.6% of its genes have unknown functions. Impro...
Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prior...
Discovering a genetic regulatory network (GRN) from time series gene expression data plays an essential role in the field of biomedical research. In its development, many methods have been proposed for inferring GRNs. Although most of them are effect...
Skin cutaneous melanoma (SCM) is a common malignant tumor of the skin and its pathogenesis still needs to be studied. In this work, we constructed a co-expression network and screened for hub genes by weighted gene co-expression network analysis (WGC...
There is an important urgency to detect cancer at early stages to treat it, to improve the patients’ lifespans, and even to cure it. In this work, we determined the entropic contributions of genes in cancer networks. We detected sudden changes in ent...
High-throughput microarrays contain a huge number of genes. Determining the relationships between all these genes is a time-consuming computation. In this paper, the authors provide a parallel algorithm for finding the Pearson’s correlation coe...
Plant height (PH) is a vital agronomic trait that significantly affects cotton yield and facilitates mechanized harvesting. Gaining insights into the genetic regulatory mechanisms governing plant height is fundamental to advancing cotton breeding. In...
Gene co-expression network analysis has been widely used in gene function annotation, especially for long noncoding RNAs (lncRNAs). However, there is a lack of effective cross-platform analysis tools. For biologists to easily build a gene co-expressi...
Background: The pathogenesis of ankylosing spondylitis (AS) remains undetermined. Ferroptosis is a newly discovered form of regulated cell death involved in multiple autoimmune diseases. Currently, there are no reports on the connection between ferro...
Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (...
Rhabdomyosarcoma is subclassified by the presence or absence of a recurrent chromosome translocation that fuses the FOXO1 and PAX3 or PAX7 genes. The fusion protein (FOXO1-PAX3/7) retains both binding domains and becomes a novel and potent transcript...
The extreme space environment accelerates aging and compromises human health. NASA has named five main hazards in space, including gravity changes. However, the contribution of each factor to the overall impact on biomolecular and cellular processes...
Abdominal aortic aneurysm (AAA) is a prevalent aortic disease that causes high mortality due to asymptomatic gradual expansion and sudden rupture. The underlying molecular mechanisms and effective pharmaceutical therapy for preventing AAA progression...
Idiopathic pulmonary fibrosis (IPF) is a severe fibrotic lung disease characterized by irreversible scarring of the lung parenchyma leading to dyspnea, progressive decline in lung function, and respiratory failure. We analyzed lung transcriptomic dat...
Alzheimer’s disease (AD) is the most widespread diagnosed cause of dementia in the elderly. It is a progressive neurodegenerative disease that causes memory loss as well as other detrimental symptoms that are ultimately fatal. Due to the urgent...
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Identifying characteristic genes of PTC are of great importance to reveal its potential genetic mechanisms. In this paper, we proposed a framework, as well as a measure name...
Feather follicle density plays an important role in appealing to consumers’ first impressions when making purchasing decisions. However, the molecular network that contributes to this trait remains largely unknown. The aim of this study was to...
Sporisorium scitamineum is a biotrophic fungus responsible for sugarcane smut disease. To investigate the key genes involved in S. scitamineum infection, we conducted RNA sequencing of sugarcane sprouts inoculated with S. scitamineum teliospores. A w...
Carotid intima-media thickness (CIMT) is a surrogate indicator for atherosclerosis and has been shown to predict cardiovascular risk in multiple large studies. Identification of molecular markers for carotid atheroma plaque formation can be critical...
Pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) relapses are still associated with a dismal outcome, justifying the search for new therapeutic targets and relapse biomarkers. Using single-cell RNA sequencing (scRNAseq) data from three paired sa...
Subtilases (SBTs), which belong to the serine peptidases, control plant development by regulating cell wall properties and the activity of extracellular signaling molecules, and affect all stages of the life cycle, such as seed development and germin...
The underlying mechanisms of eating disorders (EDs) are very complicated and still poorly understood. The pathogenesis of EDs may involve the interplay of multiple genes. To investigate the dysregulated gene pathways in EDs we analyzed gene expressio...
An effective feature extraction method is key to improving the accuracy of a prediction model. From the Gene Expression Omnibus (GEO) database, which includes 13,487 genes, we obtained microarray gene expression data for 238 samples from colorectal c...
The importance of gene expression data processing in solving the classification task is determined by its ability to discern intricate patterns and relationships within genetic information, enabling the precise categorization and understanding of var...
Drought severely affects the growth and production of pecan (Carya illinoinensis), while genes conferred drought adaptation are yet to be fully elucidated. Here, an in-depth exploration of the two different RNA-seq projects regarding drought stress (...
The development of hybrid models focused on gene expression data processing for the allocation of differentially expressed and mutually correlated genes is one of the current directions in modern bioinformatics. The solution to this problem can allow...
The ability to simulate gene expression and infer gene regulatory networks has vast potential applications in various fields, including medicine, agriculture, and environmental science. In recent years, machine learning approaches to simulate gene ex...
Ginseng, an important medicinal plant, is characterized by its main active component, ginsenosides. Among more than 40 ginsenosides, Rg1 is one of the ginsenosides used for measuring the quality of ginseng. Therefore, the identification and character...
High-throughput sequencing technologies have enabled the generation of single-cell RNA-seq (scRNA-seq) data, which explore both genetic heterogeneity and phenotypic variation between cells. Some methods have been proposed to detect the related genes...
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