Related papers: BAK1 Gene Variation: the doubts remain
The spectral problem of the Heisenberg XXZ spin-$\frac{1}{2}$ chain on the segment is investigated within a modified algebraic Bethe ansatz framework. We consider in this work the most general boundaries allowed by integrability. The…
A simple explanation for the symmetry of the genetic code has been suggested. An alternative to the wobble hypothesis has been proposed. The facts revealed in this study offer a new insight into physical mechanisms of the functioning of the…
The X-chromosome is often excluded from genome-wide association studies because of analytical challenges. Some of the problems, such as the random, skewed or no X-inactivation model uncertainty, have been investigated. Other considerations…
In addition to variation in terms of single nucleotide polymorphisms (SNPs), whole regions ranging from several kilobases up to a megabase in length differ in copy number among individuals. These differences are referred to as Copy Number…
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…
The modified algebraic Bethe ansatz, introduced by Cramp\'e and the author [8], is used to characterize the spectral problem of the Heisenberg XXZ spin-$\frac{1}{2}$ chain on the segment with lower and upper triangular boundaries. The…
A principal component analysis of a multiple sequence alignement of hemagglutinin sequences of subtype H1 has been performed, the sequences being encoded using the amino-acid property that maximizes the weight of the major component. In the…
This paper introduces a novel Bayesian approach to detect changes in the variance of a Gaussian sequence model, focusing on quantifying the uncertainty in the change point locations and providing a scalable algorithm for inference. Such a…
The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard…
GWAS in humans are revealing the genetic architecture of biomedical and anthropomorphic traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to…
We present the first in a series of papers describing the X-ray properties of a sample of 18 Seyfert 1 galaxies, using data obtained by \asca. The imaging data reveal a number of serendipitous hard X-ray sources in some source fields, but…
Following transmission, HIV-1 evolves into a diverse population, and next generation sequencing enables us to detect variants occurring at low frequencies. Studying viral evolution at the level of whole genomes was hitherto not possible…
Recent studies have shown that hybridization between modern and archaic humans was commonplace in the history of our species. After admixture, some individuals with admixed autosomes carried the modern Homo Sapiens uniparental DNAs, while…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
How mutations accumulate in genomes is the central question of molecular evolution theories, however our understanding of this process is far from complete. Drake's rule is a notoriously universal property of genomes from microbes to…
We once proposed that cell-type-associated chromatin configurations determine cell types and that cancer cell type is determined by cancer-associated chromatin configuration (CACC). In this paper, we hypothesize that flexible…
Human T-cell leukemia virus type 1 (HTLV-1) causes adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy (HAM) after a long latent period in a fraction of infected individuals. These HTLV-1-infected cells typically have phenotypes…
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 evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore…
Present day data allow significant reconsideration of ideas on mechanisms underlying the degeneracy in the genetic code. Here a hypothesis is presented which links the degeneracy to possible conformational alterations in the codon-anticodon…