Related papers: Gene Copy Number and Cell Cycle Arrest
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Cancer cells are widely known to be protected from apoptosis, which is a major hurdle to successful anti-cancer therapy. Over-expression of several anti-apoptotic proteins, or mutations in pro-apoptotic factors, has been recognized to…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
How DNA repair enzymes find the relatively rare sites of damage is not known in great detail. Recent experiments and molecular data suggest that the individual repair enzymes do not work independently of each other, but rather interact with…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Cancer is a disease involving many genes, consequently it has been difficult to design anticancer drugs that are efficacious over a broad range of cancers. The robustness of cellular responses to gene knockout and the need to reduce…
Cancer cells exhibit significant alterations in their metabolism, characterised by a reduction in oxidative phosphorylation (OXPHOS) and an increased reliance on glycolysis, even in the presence of oxygen. This metabolic shift, known as the…
A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor reoccurs. Genome sequencing and…
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…
Previous divide-and-conquer segmentation analyses of DNA sequences do not provide a satisfactory stopping criterion for the recursion. This paper proposes that segmentation be considered as a model selection process. Using the tools in…
We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
Cancer progression involves the sequential accumulation of genetic alterations that cumulatively shape the tumour phenotype. In prostate cancer, tumours can follow divergent evolutionary trajectories that lead to distinct subtypes, but the…
Background: In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined by a regulatory…
Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…
Cell-cell communication is often achieved by secreted signaling molecules that bind membrane-bound receptors. A common class of such receptors are G-protein coupled receptors, where extracellular binding induces changes on the membrane…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…