Related papers: Alternative Splicing and Genomic Stability
In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Molecular biology features numerous complexes of proteins that coordinate in an interlocking fashion to fulfill different functions. Adaptive evolution explains some of this complexity, but needn't be the default when neutral explanations…
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
In many adult tissues, stem cells and differentiated cells are not homogeneously distributed : stem cells are arranged in periodic "niches", and differentiated cells are constantly produced and migrate out of these niches. In this article,…
Subdivision schemes are iterative methods for the design of smooth curves and surfaces. Any linear subdivision scheme can be identified by a sequence of Laurent polynomials, also called subdivision symbols, which describe the linear rules…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
Learning ensembles by bagging can substantially improve the generalization performance of low-bias, high-variance estimators, including those evolved by Genetic Programming (GP). To be efficient, modern GP algorithms for evolving (bagging)…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
We present different bit-string models of haploid asexual populations in which individuals may exchange part of their genome with other individuals (parasex) according to a given probability. We study the advantages of this parasex…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
Theory of splicing is an abstract model of the recombinant behaviour of DNAs. In a splicing system, two strings to be spliced are taken from the same set and the splicing rule is from another set. Here we propose a generalised splicing (GS)…
Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work - for which…
Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…
Biopolymer length regulation is a complex process that involves a large number of subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length…
We propose a mechanism to explain what occurs when a mixture of grains of different sizes and different shapes (i.e. different repose angles) is poured into a quasi-two-dimensional cell. Specifically, we develop a model that displays…
Here I describe a view of the evolution of cellular automata that allows to operate on larger structures. Instead of calculating the next state of all cells in one step, the method here developed uses a time slice that can proceed at…
Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in…