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Breast cancer is a relatively common cancer among gynecological cancers. Its diagnosis often relies on the pathology of cells in the lesion. The pathological diagnosis of breast cancer not only requires professionals and time, but also…

A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…

Thalassemia, a blood disorder and one of the most prevalent hereditary genetic disorders worldwide, is often caused by copy number variations (CNVs) in the hemoglobin genes. This disorder has incredible diversity, with a large number of…

Nuanced cancer patient care is needed, as the development and clinical course of cancer is multifactorial with influences from the general health status of the patient, germline and neoplastic mutations, co-morbidities, and environment. To…

Precise breast cancer classification on histopathological images has the potential to greatly improve the diagnosis and patient outcome in oncology. The data imbalance problem largely stems from the inherent imbalance within medical image…

Recently, there has been a resurgence of interest in rigorous algorithms for the inference of cancer progression from genomic data. The motivations are manifold: (i) growing NGS and single cell data from cancer patients, (ii) need for novel…

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…

Multi-omics data is increasingly being utilized to advance computational methods for cancer classification. However, multi-omics data integration poses significant challenges due to the high dimensionality, data complexity, and distinct…

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly…

Tumor samples are heterogeneous. They consist of different subclones that are characterized by differences in DNA nucleotide sequences and copy numbers on multiple loci. Heterogeneity can be measured through the identification of the…

Cardiac magnetic resonance imaging (CMR) has emerged as a valuable diagnostic tool for cardiac diseases. However, a limitation of CMR is its slow imaging speed, which causes patient discomfort and introduces artifacts in the images. There…

Recent analysis identified distinct genomic subtypes of lower-grade glioma tumors which are associated with shape features. In this study, we propose a fully automatic way to quantify tumor imaging characteristics using deep learning-based…

Biomarker identification is critical for precise disease diagnosis and understanding disease pathogenesis in omics data analysis, like using fold change and regression analysis. Graph neural networks (GNNs) have been the dominant deep…

Early detection is crucial for successful cancer treatment and increasing survivability rates, particularly in the most common forms. Ten different cancers have been identified in most of these advances that effectively use CNNs…

The application of machine learning to transcriptomics data has led to significant advances in cancer research. However, the high dimensionality and complexity of RNA sequencing (RNA-seq) data pose significant challenges in pan-cancer…

Cancer disease is one of the leading causes of death all over the world. Breast cancer, which is a common cancer disease especially in women, is quite common. The most important tool used for early detection of this cancer type, which…

The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of…

This study explores the use of graph neural networks (GNNs) with hierarchical pooling and multiple convolution layers for cancer classification based on RNA-seq data. We combine gene expression data from The Cancer Genome Atlas (TCGA) with…

Lifemapper (http://www.lifemapper.org) is a predictive electronic atlas of the Earth's biological biodiversity. Using a screensaver version of the GARP genetic algorithm for modeling species distributions, Lifemapper harnesses vast…

There is a growing need for unbiased clustering methods, ideally automated. We have developed a topology-based analysis tool called Two-Tier Mapper (TTMap) to detect subgroups in global gene expression datasets and identify their…