相关论文: A Statistical Approach to Identifying Significant …
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…
During mammalian embryo development, reprogramming of DNA methylation plays important roles in the erasure of parental epigenetic memory and the establishment of na\"{i}ve pluripogent cells. Multiple enzymes that regulate the processes of…
Identifying genes underlying cancer development is critical to cancer biology and has important implications across prevention, diagnosis and treatment. Cancer sequencing studies aim at discovering genes with high frequencies of somatic…
Copy number alterations (CNAs) are thought to account for 85% of the variation in gene expression observed among breast tumours. The expression of cis-associated genes is impacted by CNAs occurring at proximal loci of these genes, whereas…
With recent advances in sequencing technologies, large amounts of epigenomic data have become available and computational methods are contributing significantly to the progress of epigenetic research. As an orthogonal approach to methods…
DNA methylation datasets in cancer studies are comprised of measurements on a large number of genomic locations called cytosine-phosphate-guanine (CpG) sites with complex correlation structures. A fundamental goal of these studies is the…
Cancer development is associated with aberrant DNA methylation, including increased stochastic variability. Statistical tests for discovering cancer methylation biomarkers have focused on changes in mean methylation. To improve the power of…
This paper explores the transgenerational DNA methylation pattern (DNA methylation transmitted from one generation to the next) via a clustering approach. Beta regression is employed to model the transmission pattern from parents to their…
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 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…
Cancer arises from successive rounds of mutations which generate tumor cells with different genomic variation i.e. clones. For drug responsiveness and therapeutics, it is necessary to identify the clones in tumor sample accurately. Many…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…
Distinguishing the rare "driver" mutations that fuel cancer progression from the vast background of "passenger" mutations in the non-coding genome is a fundamental challenge in cancer biology. A primary mechanism that non-coding driver…
When considering a genetic disease with variable age at onset (ex: diabetes , familial amyloid neuropathy, cancers, etc.), computing the individual risk of the disease based on family history (FH) is of critical interest both for clinicians…
Genetic alterations initiate tumors and enable the evolution of drug resistance. The pro-cancer view of mutations is however incomplete, and several studies show that mutational load can reduce tumor fitness. Given its negative effect,…
Motivation: Despite being often perceived as the main contributors to cell fate and physiology, genes alone cannot predict cellular phenotype. During the process of gene expression, 95% of human genes can code for multiple proteins due to…
Epigenetics plays a crucial role in understanding the underlying molecular processes of several types of cancer as well as the determination of innovative therapeutic tools. To investigate the complex interplay between genetics and…
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…
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The…