Related papers: Beta sheet propensity and the genetic code
In addition to natural selection, adaptive evolution requires genetic variation to proceed. Yet the G-matrix may have limited 'genetic degrees of freedom', with certain combinations of trait values unavailable to evolution. Such limitations…
One of the key phenomena in the adaptive immune response to infection and immunization is affinity maturation, during which antibody genes are mutated and selected, typically resulting in a substantial increase in binding affinity to the…
A quantum mechanical model on histone modification is proposed. Along with the methyl / acetate or other groups bound to the modified residues the torsion angles of the nearby histone chain are supposed to participate in the quantum…
Atomic migration from metallic contacts, and subsequent filament formation, is recognised as a prevailing mechanism leading to resistive switching in memristors based on two-dimensional materials (2DMs). This study presents a detailed…
A rigorous methodology is proposed to study cell division data consisting in several observed genealogical trees of possibly different shapes. The procedure takes into account missing observations, data from different trees, as well as the…
We extend classical results on simple varieties of trees (asymptotic enumeration, average behavior of tree parameters) to trees counted by their number of leaves. Motivated by genome comparison of related species, we then apply these…
There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiome-gut-brain axis.…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
In a (two-type) Wright-Fisher diffusion with directional selection and two-way mutation, let $x$ denote today's frequency of the beneficial type, and given $x$, let $h(x)$ be the probability that, among all individuals of today's…
Background: Acceleration of adaptation dynamics by stress-induced hypermutation has been found experimentally. Evolved evolvability is a prominent explanation. We investigate a more generally applicable explanation by a physical constraint.…
A mutator is an allele that increases the mutation rate throughout the genome by disrupting some aspect of DNA replication or repair. Mutators that increase the mutation rate by the order of 100 fold have been observed to spontaneously…
Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…
Our goal is to produce validation data that can be used as an efficient (pre) test set for structural stuck-at faults. In this paper, we detail an original test-oriented mutation sampling technique used for generating such data and we…
The cell cortex is a thin layer beneath the plasma membrane that gives animal cells mechanical resistance and drives most of their shape changes, from migration, division to multicellular morphogenesis. It is mainly composed of actin…
Epigenetic observations are represented by the total number of reads from a given pool of cells and the number of methylated reads, making it reasonable to model this data by a binomial distribution. There are numerous factors that can…
The design and the implementation of a genetic algorithm are described. The applicability domain is on structure-activity relationships expressed as multiple linear regressions and predictor variables are from families of structure-based…
Mendelian randomization uses genetic variants to make causal inferences about the effect of a risk factor on an outcome. With fine-mapped genetic data, there may be hundreds of genetic variants in a single gene region any of which could be…
We consider transformations between attractor basins of binary cylindrical cellular automata resulting from mutations. A t-point mutation of a state consists in toggling t sites in that state. Results of such mutations are described by a…
The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code…
We define the beta diffusion tree, a random tree structure with a set of leaves that defines a collection of overlapping subsets of objects, known as a feature allocation. A generative process for the tree structure is defined in terms of…