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Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…
Today, skin cancer is considered as one of the most dangerous and common cancers in the world which demands special attention. Skin cancer may be developed in different types; including melanoma, actinic keratosis, basal cell carcinoma,…
In this paper, we examine the strength of deep learning technique for diagnosing lung cancer on medical image analysis problem. Convolutional neural networks (CNNs) models become popular among the pattern recognition and computer vision…
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…
The noval method for mutational disease prediction using bioinformatics tools and datasets for diagnosis the malignant mutations with powerful Artificial Neural Network (Backpropagation Network) for classifying these malignant mutations are…
According to official statistics, cancer is considered as the second leading cause of human fatalities. Among different types of cancer, brain tumor is seen as one of the deadliest forms due to its aggressive nature, heterogeneous…
Accurately inferring Gene Regulatory Networks (GRNs) is a critical and challenging task in biology. GRNs model the activatory and inhibitory interactions between genes and are inherently causal in nature. To accurately identify GRNs,…
Profiling of whole transcriptomes has become a cornerstone of molecular biology and an invaluable tool for the characterization of clinical phenotypes and the identification of disease subtypes. Analyses of these data are becoming ever more…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires…
The hierarchical organisation of cell identity is a fundamental feature of animal development with rich and well-characterized experimental phenomenology, yet the mechanisms driving its emergence remain unknown. The regulation of cell…
Predicting drug-gene associations is crucial for drug development and disease treatment. While graph neural networks (GNN) have shown effectiveness in this task, they face challenges with data sparsity and efficient contrastive learning…
Blood cancer can only be diagnosed properly if it is detected early. Each year, more than 1.24 million new cases of blood cancer are reported worldwide. There are about 6,000 cancers worldwide due to this disease. The importance of cancer…
It has been estimated that about 30% of the genes in the human genome are regulated by microRNAs (miRNAs). These are short RNA sequences that can down-regulate the levels of mRNAs or proteins in animals and plants. Genes regulated by miRNAs…
Tumor heterogeneity is a challenge to designing effective and targeted therapies. Glioma-type identification depends on specific molecular and histological features, which are defined by the official WHO classification CNS. These guidelines…
Increasing evidence has shown that gene-gene interactions have important effects on biological processes of human diseases. Due to the high dimensionality of genetic measurements, existing interaction analysis methods usually suffer from a…
Prostate cancer is one of the most common causes of cancer deaths in men. There is a growing demand for noninvasively and accurately diagnostic methods that facilitate the current standard prostate cancer risk assessment in clinical…
Tumor recurrence, driven by the evolution of drug resistance is a major barrier to therapeutic success in cancer. Resistance is often caused by genetic alterations such as point mutation, which refers to the modification of a single genomic…
Identifying cancer driver genes (CDGs) is essential for understanding cancer mechanisms and developing targeted therapies. Graph neural networks (GNNs) have recently been employed to identify CDGs by capturing patterns in biological…