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Tumour heterogeneity is increasingly recognized as a major obstacle to therapeutic success across neuro-oncology. Gliomas are characterised by distinct combinations of genetic and epigenetic alterations, resulting in complex interactions…
Cancer remains a global challenge due to its growing clinical and economic burden. Its uniquely personal manifestation, which makes treatment difficult, has fuelled the quest for personalized treatment strategies. Thus, genomic profiling is…
Molecular systems often remain trapped for long times around some local minimum of the potential energy function, before switching to another one -- a behavior known as metastability. Simulating transition paths linking one metastable state…
A major challenge in biomedical data science is to identify the causal genes underlying complex genetic diseases. Despite the massive influx of genome sequencing data, identifying disease-relevant genes remains difficult as individuals with…
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…
It is obvious that both epigenetic and non-epigenetic actors contribute to tumorigenesis in chondrosarcomas and more generally in other cancers. Thus, the main altered pathways in chondrosarcomas are now well established and include both…
The analysis of cancer genomic data has long suffered "the curse of dimensionality". Sample sizes for most cancer genomic studies are a few hundreds at most while there are tens of thousands of genomic features studied. Various methods have…
Accurate diagnostic tests are essential for effective screening and treatment. However, individual biomarkers often fail to provide sufficient diagnostic accuracy, as they typically capture only one aspect of the complex disease process.…
Accurate diagnosis of breast cancer in histopathology images is challenging due to the heterogeneity of cancer cell growth as well as of a variety of benign breast tissue proliferative lesions. In this paper, we propose a practical and…
Genome-wide gene expression profiles, as measured with microarrays or RNA-Seq experiments, have revolutionized biological and biomedical research by providing a quantitative measure of the entire mRNA transcriptome. Typically, researchers…
Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with trait diversity and disease susceptibility, yet the functional properties of many genetic variants and their molecular…
Spatial transcriptomics is a technology that captures gene expression levels at different spatial locations, widely used in tumor microenvironment analysis and molecular profiling of histopathology, providing valuable insights into…
This paper presents a new modeling strategy for joint unsupervised analysis of multiple high-throughput biological studies. As in Multi-study Factor Analysis, our goals are to identify both common factors shared across studies and…
Cancer is one of the most feared diseases in the world it has increased disturbingly and breast cancer occurs in one out of eight women, the prediction of malignancies plays essential roles not only in revealing human genome, but also in…
In cancer genomics, it is of great importance to distinguish driver mutations, which contribute to cancer progression, from causally neutral passenger mutations. We propose a random-effect regression approach to estimate the effects of…
Mitogen-activated protein kinase (MAPK) signaling pathways play an essential role in the transduction of environmental stimuli to the nucleus, thereby regulating a variety of cellular processes, including cell proliferation, differentiation…
A major task in genetic studies is to identify genes related to human diseases and traits to understand functional characteristics of genetic mutations and enhance patient diagnosis. Besides marginal analyses of individual genes,…
The cellular composition of the tumor microenvironment can directly impact cancer progression and the efficacy of therapeutics. Understanding immune cell activity, the body's natural defense mechanism, in the vicinity of cancerous cells is…
Spatial variable genes (SVGs) reveal critical information about tissue architecture, cellular interactions, and disease microenvironments. As spatial transcriptomics (ST) technologies proliferate, accurately identifying SVGs across diverse…
The integration of multi-modal data, such as pathological images and genomic data, is essential for understanding cancer heterogeneity and complexity for personalized treatments, as well as for enhancing survival predictions. Despite the…