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It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
The advent of digital pathology presents opportunities for computer vision for fast, accurate, and objective solutions for histopathological images and aid in knowledge discovery. This work uses deep learning to predict genomic biomarkers -…
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
Extrachromosomal DNA (ecDNA) can drive oncogene amplification, gene expression and intratumor heterogeneity, representing a major force in cancer initiation and progression. The phenomenon becomes even more intricate as distinct types of…
Variability in drug efficacy and adverse effects are observed in clinical practice. While the extent of genetic variability in classical pharmacokinetic genes is rather well understood, the role of genetic variation in drug targets is…
A mutation in a protein-coding gene in DNA can alter the protein structure coded by the same gene. Structurally altered proteins usually lose their functions and sometimes gain an undesirable function instead. These types of mutations and…
Recent works have stressed the important role that random mutations have in the development of cancer phenotype. We challenge this current view by means of bioinformatic data analysis and computational modelling approaches. Not all the…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
The pathogenesis of cancer in human is still poorly understood. With the rapid development of high-throughput sequencing technologies, huge volumes of cancer genomics data have been generated. Deciphering those data poses great…
Mammographic screening and prophylactic surgery such as risk-reducing salpingo oophorectomy (RRSO) can potentially reduce breast cancer risks among mutation carriers of BRCA families. The evaluation of these interventions is usually…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
Background Precise prediction of cancer types is vital for cancer diagnosis and therapy. Important cancer marker genes can be inferred through predictive model. Several studies have attempted to build machine learning models for this task…
The application of machine learning to transcriptomics data has led to significant advances in cancer research. However, the high dimensionality and complexity of RNA sequencing (RNA-seq) data pose significant challenges in pan-cancer…
Cancer cells evolve through random somatic mutations. "Beneficial" mutations which disrupt key pathways (e.g. cell cycle regulation) are subject to natural selection. Multiple mutations may lead to the same "beneficial" effect, in which…
The vast amount of sequencing data presently available allow the scientific community to explore a range of genetic variables that may drive and progress cancer. A myriad of predictive tools has been proposed, allowing researchers and…
Finding cancer driver genes has been a focal theme of cancer research and clinical studies. One of the recent approaches is based on network structural controllability that focuses on finding a control scheme and driver genes that can steer…
Multi-gene panel testing allows many cancer susceptibility genes to be tested quickly at a lower cost making such testing accessible to a broader population. Thus, more patients carrying pathogenic germline mutations in various…
The rapid growth of cancer genome structural information provides an opportunity for a better understanding of the mutational mechanisms of genomic alterations in cancer and the forces of selection that act upon them. Here we test the…
Cancers evolve from mutation of a single cell with sequential clonal and subclonal expansion of somatic mutation acquisition. Inferring clonal and subclonal structures from bulk or single cell tumor genomic sequencing data has a huge impact…