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We consider applying Bayesian Variable Selection Regression, or BVSR, to genome-wide association studies and similar large-scale regression problems. Currently, typical genome-wide association studies measure hundreds of thousands, or…
Breast cancer has long been a prominent cause of mortality among women. Diagnosis, therapy, and prognosis are now possible, thanks to the availability of RNA sequencing tools capable of recording gene expression data. Molecular subtyping…
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…
Breast cancer(BC) is a prevalent type of malignant tumor in women. Early diagnosis and treatment are vital for enhancing the patients' survival rate. Downsampling in deep networks may lead to loss of information, so for compensating the…
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…
Breast cancer is one of the most threatening diseases in women's life; thus, the early and accurate diagnosis plays a key role in reducing the risk of death in a patient's life. Mammography stands as the reference technique for breast…
Genetic studies have identified associations between gene mutations and clear cell renal cell carcinoma (ccRCC). Because the complete gene mutational landscape cannot be characterized through biopsy and sequencing assays for each patient,…
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,…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
Background and Objective: Breast cancer, which accounts for 23% of all cancers, is threatening the communities of developing countries because of poor awareness and treatment. Early diagnosis helps a lot in the treatment of the disease. The…
Molecular subtyping of breast cancer is crucial for personalized treatment and prognosis. Traditional classification approaches rely on either histopathological images or gene expression profiling, limiting their predictive power. In this…
The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however,…
Histone modification is a vital epigenetic mechanism for transcriptional control in eukaryotes. High-throughput techniques have enabled whole-genome analysis of histone modifications in recent years. However, most studies assume one…
Significant advances in biotechnology have allowed for simultaneous measurement of molecular data points across multiple genomic and transcriptomic levels from a single tumor/cancer sample. This has motivated systematic approaches to…
Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the genetic toolkit in Drosophila melanogaster. Despite their widespread use, the organization of balancer chromosomes has not been…
The diverse, specialized genes in today's lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is controlled by a complex network of interactions, and…
Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in amoeba. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as point mutation…
Diagnosis of breast cancer has been well studied in the past. Multiple linear programming models have been devised to approximate the relationship between cell features and tumour malignancy. However, these models are less capable in…
Undoubtedly breast cancer identifies itself as one of the most widespread and terrifying cancers across the globe. Millions of women are getting affected each year from it. Breast cancer remains the major one for being the reason of largest…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…