Related papers: Modeling of Whole Genomic Sequencing Implementatio…
Machine learning provides a broad framework for addressing high-dimensional prediction problems in classification and regression. While machine learning is often applied for imaging problems in medical physics, there are many efforts to…
In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
The assessment of imaging biomarkers is critical for advancing precision medicine and improving disease characterization. Despite the availability of methods to derive disease heterogeneity metrics in imaging studies, a robust framework for…
One of the notable fields in studying the genetics of cancer is disease gene identification which affects disease treatment and drug discovery. Many researches have been done in this field. Genome-wide association studies (GWAS) are one of…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
This paper describes a novel approach to learning term-weighting schemes (TWSs) in the context of text classification. In text mining a TWS determines the way in which documents will be represented in a vector space model, before applying a…
Identifying measurable genetic indicators (or biomarkers) of a specific condition of a biological system is a key element of precision medicine. Indeed it allows to tailor diagnostic, prognostic and treatment choice to individual…
The overall aim of the software industry is to ensure delivery of high quality software to the end user. To ensure high quality software, it is required to test software. Testing ensures that software meets user specifications and…
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
Optimal biomarker combinations for treatment-selection can be derived by minimizing total burden to the population caused by the targeted disease and its treatment. However, when multiple biomarkers are present, including all in the model…
Environmental and genetic mutations can transform the cells in a co-operating healthy tissue into an ecosystem of individualistic tumour cells that compete for space and resources. Various selection forces are responsible for driving the…
Background. With the increasing interest in post-GWAS research which represents a transition from genome-wide association discovery to analysis of functional mechanisms, attention has been lately focused on the potential of including…
The last decade has seen an explosion in models that describe phenomena in systems medicine. Such models are especially useful for studying signaling pathways, such as the Wnt pathway. In this chapter we use the Wnt pathway to showcase…
DNA methylation is an important epigenetic mark that has been studied extensively for its regulatory role in biological processes and diseases. WGBS allows for genome-wide measurements of DNA methylation up to single-base resolutions, yet…
Background: While the importance of gene-gene interactions in human diseases has been well recognized, identifying them has been a great challenge, especially through association studies with millions of genetic markers and thousands of…
Genomic approaches have revolutionized medical research, providing valuable insights into human physiology and disease. Despite major benefits from large collections of genomes, the lack of diversity in genomic data represents a significant…
The prevailing method of analyzing GWAS data is still to test each marker individually, although from a statistical point of view it is quite obvious that in case of complex traits such single marker tests are not ideal. Recently several…
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…
Cooperation arises in nature at every scale, from within cells to entire ecosystems. In the framework of evolutionary game theory, public goods games (PGGs) are used to analyse scenarios where individuals can cooperate or defect, and can…
Prostate cancer is the second most common form of cancer, though most patients have a positive prognosis with many experiencing long-term survival with current treatment options. Yet, each treatment carries varying levels of intensity and…