Related papers: Alternative Splicing and Genomic Stability
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
Collagen is the most abundant extracellular-network-forming protein in animal biology and is important in both natural and artificial tissues, where it serves as a material of great mechanical versatility. This versatility arises from its…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
Our models for detecting the effect of adaptation on population genomic diversity are often predicated on a single newly arisen mutation sweeping rapidly to fixation. However, a population can also adapt to a new situation by multiple…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
We study the population dynamics of lytic viruses which replicate slowly in dividing host cells within an organism or cell culture, and find a range of viral replication rates that allows viruses to persist, avoiding extinction of host…
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…
Delay is an inherent feature of genetic regulatory networks. It represents the time required for the assembly of functional regulator proteins. The protein production process is complex, as it includes transcription, translocation,…
We propose an extended genetic algorithm (GA) with different local environmental conditions. Genetic entities, or configurations, are put on nodes in a ring structure, and location-dependent environmental conditions are applied for each…
Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts nucleotide sequences to enhance translational efficiency,…
Sex chromosomes have evolved repeatedly across the Tree of Life, yet their evolutionary fates differ strikingly. In sharp contrast to mammals and birds with degenerated, stable Y/W chromosomes, in most amphibians, teleosts, non avian…
In order to fulfill cell proliferation and differentiation through cellular hierarchy, stem cells can undergo either asymmetric or symmetric divisions. Recent studies pay special attention to the effect of different modes of stem cell…
In many models of genotypic evolution, the vector of genotype populations satisfies a system of linear ordinary differential equations. This system of equations models a competition between differential replication rates (fitness) and…
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such…
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space -…
DNA methylation (meDNA) is a suspected modulator of alternative splicing, while splicing in turn is involved in tumour formations nearly as frequently as DNA mutations. Yet, the impact of meDNA on tumorigenesis via its effect on splicing…
The preferred conditions for evolutionary innovation is a fundamental question, but little is known, in part because the question involves rare events. We focused on the potential role of polyploidy in the evolution of novel traits. There…