相关论文: Hierarchical Bayesian analysis of somatic mutation…
Several diseases related to cell proliferation are characterized by the accumulation of somatic DNA changes, with respect to wildtype conditions. Cancer and HIV are two common examples of such diseases, where the mutational load in the…
Prostate cancer is among the most common cancer in males and its heterogeneity is well known. Its early detection helps making therapeutic decision. There is no standard technique or procedure yet which is full-proof in predicting cancer…
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…
The location, timing, and abundance of gene expression (both mRNA and proteins) within a tissue define the molecular mechanisms of cell functions. Recent technology breakthroughs in spatial molecular profiling, including imaging-based…
Spatial transcriptomics has revolutionized tissue analysis by simultaneously mapping gene expression, spatial topography, and histological context across consecutive tissue sections, enabling systematic investigation of spatial…
Cancer is often driven by specific combinations of an estimated two to nine gene mutations, known as multi-hit combinations. Identifying these multi-hit combinations of gene mutations that drive cancer is critical for understanding…
We calculate measures of hierarchy in gene and tissue networks of breast cancer patients. We find that the likelihood of metastasis in the future is correlated with increased values of network hierarchy for expression networks of…
Cancer is viewed as a multistep process whereby a normal cell is transformed into a cancer cell through the acquisition of mutations. We reduce the complexities of cancer progression to a simple set of underlying rules that govern the…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
Motivation: Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patterns along the…
We study the spatial evolutionary dynamics of solid tumors as they obtain additional driver mutations. We start with a cancer clone that expands uniformly in three dimensions giving rise to a spherical shape. We assume that cell division…
The Galleri (R) (GRAIL) multi-cancer early detection test measures circulating tumour DNA (ctDNA) to predict the presence of more than 50 different cancers, from a blood test. If sensitivity of the test to detect early-stage cancers is…
Cancer is responsible for millions of deaths worldwide every year. Although significant progress has been achieved in cancer medicine, many issues remain to be addressed for improving cancer therapy. Appropriate cancer patient…
Late diagnosis and high costs are key factors that negatively impact the care of cancer patients worldwide. Although the availability of biological markers for the diagnosis of cancer type is increasing, costs and reliability of tests…
Background: Radiotherapy outcomes are usually predicted using the Linear Quadratic model. However, this model does not integrate complex features of tumor growth, in particular cell cycle regulation. Methods: In this paper, we propose a…
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…
Network-based analyses of high-throughput genomics data provide a holistic, systems-level understanding of various biological mechanisms for a common population. However, when estimating multiple networks across heterogeneous…
Background: Current research suggests that a small set of "driver" mutations are responsible for tumorigenesis while a larger body of "passenger" mutations occurs in the tumor but does not progress the disease. Due to recent pharmacological…
Targeted therapies on the basis of genomic aberrations analysis of the tumor have shown promising results in cancer prognosis and treatment. Regardless of tumor type, trials that match patients to targeted therapies for their particular…
Cancer progression is driven by a small number of genetic alterations accumulating in a neoplasm. These few driver alterations reside in a cancer genome alongside tens of thousands of other mutations that are widely believed to have no role…