Related papers: Relationship between promoter sequence and its str…
Current-day genomes bear the mark of the evolutionary processes. One of the strongest indications is the sequence homology among families of proteins that perform similar biological functions in different species. The number of proteins in…
Prokaryotes living at extreme environmental temperatures exhibit pronounced signatures in the amino acid composition of their proteins and nucleotide compositions of their genomes reflective of adaptation to their thermal environments.…
The previously formulated model for the evolution of the genetic code was shown to clarify why base triplets of some precursor amino acids differ by a single base from product amino acid codons, while others show less homology. First, the…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
Locating the promoter region in DNA sequences is of paramount importance in the field of bioinformatics. This is a problem widely studied in the literature, however, not yet fully resolved. Some researchers have presented remarkable results…
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the…
Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions (called gene expression "noise" or phenotype "fluctuation"). In yeast and Escherichia coli, positive…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
We propose a conformity-driven reproductive ability in which an individual $i$ is more (less) likely to imitate a neighbor $j$'s strategy if $j$'s strategy is majority (minority) in $i$'s neighborhood. The results on the evolutionary…
We survey results on neural network expressivity described in "On the Expressive Power of Deep Neural Networks". The paper motivates and develops three natural measures of expressiveness, which all display an exponential dependence on the…
Recent genome-wide measurements of binding preferences of ~200 transcription regulators in the vicinity of transcription start sites in yeast, have provided a unique insight into the cis- regulatory code of a eukaryotic genome (Venters et…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
We study the emergence of cooperation in structured populations with any arrangement of cooperators and defectors on the evolutionary graph. Using structure coefficients defined for configurations describing such arrangements of any number…
We have analysed an effect of the Bak-Sneppen predator-prey food-chain self-organization on nucleotide content of evolving species. In our model, genomes of the species under consideration have been represented by their nucleotide genomic…
In previous papers it was demonstrated that lower performance groups have a larger size-dependent cumulative advantage for receiving citations than top-performance groups. Furthermore, regardless of performance, larger groups have less…
Mentoring is a key component of scientific achievements, contributing to overall measures of career success for mentees and mentors. A common success metric in the scientific enterprise is acquiring a large research group, which is believed…
Strong monads are important for several applications, in particular, in the denotational semantics of effectful languages, where strength is needed to sequence computations that have free variables. Strength is non-trivial: it can be…
Stronger selection implies faster evolution---that is, the greater the force, the faster the change. This apparently self-evident proposition, however, is derived under the assumption that genetic variation within a population is primarily…