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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…
Lung cancer is the leading cause of cancer death and morbidity worldwide. Many studies have shown machine learning models to be effective at detecting lung nodules from chest X-ray images. However, these techniques have yet to be embraced…
Heterogeneity is ubiquitous in stem cells (SC), cancer cells (CS), and cancer stem cells (CSC). SC and CSC heterogeneity is manifested as diverse sub-populations with self-renewing and unique regeneration capacity. Moreover, the CSC progeny…
According to the World Health Organization (WHO), cancer is the second leading cause of death worldwide, responsible for over 9.5 million deaths in 2018 alone. Brain tumors count for one out of every four cancer deaths. Therefore, accurate…
Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames and which have been termed long non-coding RNAs (lncRNAs). Despite the existence of several well-characterized…
The majority of cancer treatments end in failure due to Intra-Tumor Heterogeneity (ITH). ITH in cancer is represented by clonal evolution where different sub-clones compete with each other for resources under conditions of Darwinian natural…
An endogenous molecular-cellular network for both normal and abnormal functions is assumed to exist. This endogenous network forms a nonlinear stochastic dynamical system, with many stable attractors in its functional landscape. Normal or…
Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over…
Breast cancer is the second most responsible for all cancer types and has been the cause of numerous deaths over the years, especially among women. Any improvisation of the existing diagnosis system for the detection of cancer can…
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…
Prognostication for lung cancer, a leading cause of mortality, remains a complex task, as it needs to quantify the associations of risk factors and health events spanning a patient's entire life. One challenge is that an individual's…
Cancer is a complex disease characterized by uncontrolled cell growth. T cell receptors (TCRs), crucial proteins in the immune system, play a key role in recognizing antigens, including those associated with cancer. Recent advancements in…
Tumors are defined by their intense proliferation, but sometimes cancer cells turn senescent and stop replicating. In the stochastic cancer model in which all cells are tumorigenic, senescence is seen as the result of random mutations,…
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…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
Lung cancer is a major cause of cancer-related deaths, and early diagnosis and treatment are crucial for improving patients' survival outcomes. In this paper, we propose to employ convolutional neural networks to model the non-linear…
Lung cancer is the deadliest type of cancer worldwide and late detection is the major factor for the low survival rate of patients. Low dose computed tomography has been suggested as a potential screening tool but manual screening is…
DNA methylation is a well-studied genetic modification crucial to regulate the functioning of the genome. Its alterations play an important role in tumorigenesis and tumor-suppression. Thus, studying DNA methylation data may help biomarker…
Breast cancer is one of the main causes of cancer death worldwide. Early diagnostics significantly increases the chances of correct treatment and survival, but this process is tedious and often leads to a disagreement between pathologists.…
We propose a new multi-network-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multi-networks that we consider combine transcription factor…