Related papers: Sequence Dependence of Transcription Factor-Mediat…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…
We present a statistical-mechanical analysis of the positioning of nucleosomes along one of the chromosomes of yeast DNA as a function of the strength of the binding potential and of the chemical potential of the nucleosomes. We find a…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…
Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from…
The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…
Recent experimental data indicate that the elastic wormlike rod model of DNA that works well on long length scales may break down on shorter scales relevant to biology. According to Noy and Golestanian (Phys. Rev. Lett. 109, 228101, 2012)…
We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…
In biological cells, DNA replication is carried out by the replisome, a protein complex encompassing multiple DNA polymerases. DNA replication is semi-discontinuous: a DNA polymerase synthesizes one (leading) strand of the DNA continuously,…
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…