Related papers: MitoFREQ: A Novel Approach for Mitogenome Frequenc…
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations, and to look for genomic regions with…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
The fast and affordable sequencing of large clinical and environmental metagenomic datasets opens up new horizons in medical and biotechnological applications. It is believed that today we have described only about 1\% of the microorganisms…
Accurate mitotic figure classification is crucial in computational pathology, as mitotic activity informs cancer grading and patient prognosis. Distinguishing atypical mitotic figures (AMFs), which indicate higher tumor aggressiveness, from…
Motivation: Accurate classification of mitotic figures into normal and atypical types is crucial for tumor prognostication in digital pathology. However, developing robust deep learning models for this task is challenging due to the subtle…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…
Large-scale biobanks are being collected around the world in efforts to better understand human health and risk factors for disease. They often survey hundreds of thousands of individuals, combining questionnaires with clinical, genetic,…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
Populations of heterogeneous cells play an important role in many biological systems. In this paper we consider systems where each cell can be modelled by an ordinary differential equation. To account for heterogeneity, parameter values are…
Assessment of the density of mitotic figures (MFs) in histologic tumor sections is an important prognostic marker for many tumor types, including breast cancer. Recently, it has been reported in multiple works that the quantity of MFs with…
Mitotic activity is an important feature for grading several cancer types. Counting mitotic figures (MFs) is a time-consuming, laborious task prone to inter-observer variation. Inaccurate recognition of MFs can lead to incorrect grading and…
The integration of knowledge graphs and graph machine learning (GML) in genomic data analysis offers several opportunities for understanding complex genetic relationships, especially at the RNA level. We present a comprehensive approach for…
Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is…
In the complex landscape of hematologic samples such as peripheral blood or bone marrow, cell classification, delineating diverse populations into a hierarchical structure, presents profound challenges. This study presents LeukoGraph, a…
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic…
In genetic studies, haplotype data provide more refined information than data about separate genetic markers. However, large-scale studies that genotype hundreds to thousands of individuals may only provide results of pooled data, where…
Recent technological advancements have enabled detailed investigation of associations between the molecular architecture and tumor heterogeneity, through multi-source integration of radiological imaging and genomic (radiogenomic) data. In…
Identifying cancer driver genes is crucial for understanding tumor biology and developing precision therapies. However, existing computational methods often rely on single biological networks or population-level mutation patterns, limiting…
DNA samples are often pooled, either by experimental design, or because the sample itself is a mixture. For example, when population allele frequencies are of primary interest, individual samples may be pooled together to lower the cost of…
Y-chromosomal and mitochondrial DNA profiles have been used as evidence in courts for decades, yet the problem of evaluating the weight of evidence has not been adequately resolved. Both are lineage markers (inherited from just one parent),…