Related papers: A New DNA Sequences Vector Space on a Genetic Code…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
(Abridged) We investigate the properties of galaxies between the blue and the red sequence (i.e., the transition region) by combining UV and NIR imaging to HI line observations for a volume-limited sample of nearby galaxies. We confirm the…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
An essential problem in domain adaptation is to understand and make use of distribution changes across domains. For this purpose, we first propose a flexible Generative Domain Adaptation Network (G-DAN) with specific latent variables to…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
HIV-1C is the most prevalent subtype of HIV-1 and accounts for over half of HIV-1 infections worldwide. Host genetic influence of HIV infection has been previously studied in HIV-1B, but little attention has been paid to the more prevalent…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…
We perform geometrization of genetics by representing genetic information by points of the 4-adic {\it information space.} By well known theorem of number theory this space can also be represented as the 2-adic space. The process of…
Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins.…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
We obtained GALEX FUV, NUV, and Spitzer/IRAC 3.6$\mu$m photometry for > 2000 galaxies, available for 90% of the S4G sample. We find a very tight "GALEX Blue Sequence (GBS)" in the (FUV-NUV) versus (NUV-[3.6]) color-color diagram which is…
Single-cell foundation models such as scGPT learn high-dimensional gene representations, but what biological knowledge these representations encode remains unclear. We systematically decode the geometric structure of scGPT internal…
Many DNA sequence variants influence phenotypes by altering gene expression. Our understanding of these variants is limited by sample sizes of current studies and by measurements of mRNA rather than protein abundance. We developed a…
Homologous proteins evolve from a common ancestral sequence, constrained by intricate patterns of co-evolving residues. Accurate reconstruction of evolutionary histories remains a challenge, primarily due to the inability of the existing…
We consider the impact of new exotic colored and/or charged matter interacting through the Higgs portal on Standard Model Higgs boson searches at the LHC. Such Higgs portal couplings can induce shifts in the effective Higgs-gluon-gluon and…
A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick…