Related papers: On the codon assignment of chain termination signa…
The well-quasi-ordering (i.e., a well-founded quasi-ordering such that all antichains are finite) that defines well-structured transition systems (WSTS) is shown not to be the weakest hypothesis that implies decidability of the coverability…
Somatic mutations in cancer cells affect various genomic elements disrupting important cell functions. In particular, mutations in DNA binding sites recognized by transcription factors can alter regulator binding affinities and expression…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Size-Change Termination (SCT) is a method of proving program termination based on the impossibility of infinite descent. To this end we use a program abstraction in which transitions are described by Monotonicity Constraints over (abstract)…
The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci and the genome-wide patterns of polymorphism show signatures consistent with…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
Progress in the behavioral analysis of software product lines at the family level benefits from further development of the underlying semantical theory. Here, we propose a behavioral equivalence for feature transition systems (FTS)…
A simple yet effective way of modeling survival data with cure fraction is by considering Box-Cox transformation cure model (BCTM) that unifies mixture and promotion time cure models. In this article, we numerically study the statistical…
This work develops a rate-distortion-based approach to stochastic Chase decoding of algebraic codes over binary memoryless symmetric (BMS) channels, replacing the heuristics traditionally used to determine flip probabilities with…
Mutational robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of mutational robustness in the budding yeast by genome wide dosage suppressor analysis of 53…
We describe the theory of quantum convolutional error correcting codes. These codes are aimed at protecting a flow of quantum information over long distance communication. They are largely inspired by their classical analogs which are used…
The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…
In evolutionary dynamics, a key measure of a mutant trait's success is the probability that it takes over the population given some initial mutant-appearance distribution. This "fixation probability" is difficult to compute in general, as…
In this work, a unique set of generators for a cyclic code over a finite chain ring has been established. The minimal spanning set and rank of the code have also been determined. Further, sufficient as well as necessary conditions for a…
Contention resolution schemes have proven to be an incredibly powerful concept which allows to tackle a broad class of problems. The framework has been initially designed to handle submodular optimization under various types of constraints,…
Reduction of costs in biological signalling seems an evolutionary advantage, but recent experiments have shown signalling codes shifted to signals of high cost with a underutilisation of low cost signals. Here I show that errors in the…
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…
The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly non-random. The three main concepts on origin and evolution of the code are the stereochemical theory; the coevolution theory; and…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…