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Convolutional neural networks (CNNs) have shown great promise in improving computer aided detection (CADe). From classifying tumors found via mammography as benign or malignant to automated detection of colorectal polyps in CT colonography,…
The prediction plays the important role in detecting efficient protection and therapy of cancer. The prediction of mutations in gene needs a diagnostic and classification, which is based on the whole database (big dataset), to reach…
The discovery of important biomarkers is a significant step towards understanding the molecular mechanisms of carcinogenesis; enabling accurate diagnosis for, and prognosis of, a certain cancer type. Before recommending any diagnosis,…
Graphical models are commonly used to discover associations within gene or protein networks for complex diseases such as cancer. Most existing methods estimate a single graph for a population, while in many cases, researchers are interested…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Cancer, a leading cause of death globally, occurs due to genomic changes and manifests heterogeneously across patients. To advance research on personalized treatment strategies, the effectiveness of various drugs on cells derived from…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
A central goal in cancer genomics is to identify the somatic alterations that underpin tumor initiation and progression. This task is challenging as the mutational profiles of cancer genomes exhibit vast heterogeneity, with many alterations…
In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to the discovery of biological pathways associated to the disease. As a cancer progresses, its signalling…
Cancers are the leading cause of death in many countries. Early diagnosis plays a crucial role in having proper treatment for this debilitating disease. The automated classification of the type of cancer is a challenging task since…
Complex gene interactions play a significant role in cancer progression, driving cellular behaviors that contribute to tumor growth, invasion, and metastasis. Gene co-expression networks model the functional connectivity between genes under…
Networks (graphs) in psychology are often restricted to settings without interventions. Here we consider a framework borrowed from biology that involves multiple interventions from different contexts (observations and experiments) in a…
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…
Invasive ductal carcinoma is a prevalent, potentially deadly disease associated with a high rate of morbidity and mortality. Its malignancy is the second leading cause of death from cancer in women. The mammogram is an extremely useful…
Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the always increasing…
The dysregulation of transcripts is characterized as one of the main mechanisms in tumor pathogenesis. The recent discovery developed a new hypothesis, competitive endogenous RNAs (ceRNAs), which could regulate other RNA transcripts via…
The Cancer Genome Atlas (TCGA) provides researchers with clinicopathological data and genomic characterizations of various carcinomas. These data sets include expression microarrays for genes and microRNAs -- short, non-coding strands of…
In the current technological era, the medical profession has emerged as one of the researchers' favorite subject areas, and cancer is one of them. Because there is now no effective treatment for this illness, it is a matter of concern. Only…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…