Related papers: Revisiting the Neutral Dynamics Derived Limiting G…
We develop a physiological model of granulopoiesis which includes explicit modelling of the kinetics of the cytokine granulocyte colony-stimulating factor (G-CSF) incorporating both the freely circulating concentration and the concentration…
Big Bang Nucleosynthesis can provide, via constraints on the expansion rate at that time, limits on possible variations in Newton's Constant, $G$. The original analyses were performed before an independent measurement of the…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
We investigate the sensitivity of solar neutrino data to mixing of sterile neutrinos with masses $\gtrsim$ eV. For current data, we perform a Feldman-Cousins analysis to derive a robust limit on the sterile neutrino mixing. The solar…
We consider departures from hamiltonian dynamics in the evolution of neutral kaons due to their interactions with environment that generate entanglement among them. We propose a phenomenological model of stochastic re-scattering and…
CPT symmetry, the combination of Charge Conjugation, Parity and Time reversal, is a cornerstone of our model building strategy and therefore the repercussions of its potential violation will severely threaten the most extended tool we…
It has been recently claimed that it is possible to predict the rate of de novo mutation of each site in the human genome with almost perfect accuracy (Michaelson et al. (2012) Cell, 151, 1431-1442). We show that this claim is unwarranted.…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
The ratio of non-synonymous to synonymous substitutions $\omega(=d_{N}/d_{S})$ has been widely used as a measure of adaptive evolution in protein coding genes. Omega can be defined in terms of population genetics parameters as the fixation…
Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores we develop a maximum…
While Neutral Theory famously describes the number of discrete genetic differences in populations, we consider the number of genetic backgrounds under which such differences are observed - setting limits to the generalizability of their…
In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic…
In order to analyze data from cancer genome sequencing projects, we need to be able to distinguish causative, or "driver," mutations from "passenger" mutations that have no selective effect. Toward this end, we prove results concerning the…
Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed `volatility', to estimate selection pressures on protein…
Neutrinos with Standard Model interactions free-stream in the early Universe, leaving a distinct phase shift in the pattern of baryon acoustic oscillations (BAO). When isolated, this phase shift allows one to robustly infer the presence of…
A model is presented relating the evolution of genomic GC content over time to AT$\rightarrow$GC and GC$\rightarrow$AT mutation rates. By employing It\^o calculus it is shown that if mutation rates in asexually reproducing organisms are…
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
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…
Fine-tuning is widely used to adapt language models for specific goals, often leveraging real-world data such as patient records, customer-service interactions, or web content in languages not covered in pre-training. These datasets are…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…