相关论文: How much non-coding DNA do eukaryotes require?
The availability of high-throughput parallel methods for sequencing microbial communities is increasing our knowledge of the microbial world at an unprecedented rate. Though most attention has focused on determining lower-bounds on the…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…
We have considered as a theoretical possibility for the development of a nanobiochip the operation principle of which is based on measuring conductance in single-stranded and double-stranded DNA. Calculations have demonstrated that in the…
Half-lives of radionuclides span more than 50 orders of magnitude. We characterize the probability distribution of this broad-range data set at the same time that explore a method for fitting power-laws and testing goodness-of-fit. It is…
Functional annotation of microbial genomes is often biased toward protein-coding genes, leaving a vast, unexplored landscape of non-coding RNAs (ncRNAs) that are critical for regulating bacterial and archaeal physiology, stress response and…
We model long range correlations of nucleotides in the human DNA sequence using the long range one dimensional Ising model. We show that for distances between $10^3$ and $10^6$ bp the correlations show an universal behaviour and may be…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
Network Medicine has improved the mechanistic understanding of disease, offering quantitative insights into disease mechanisms, comorbidities, and novel diagnostic tools and therapeutic treatments. Yet, most network-based approaches rely on…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
We describe the distribution of Guanine and Cytosine (GC) content in the third codon position (GC3) distributions in different species, analyze evolutionary trends and discuss differences between genes and organisms with distinct GC3…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
A measurement of neutrinoless double beta decay in one isotope does not allow to determine the underlying physics mechanism. We discuss the discrimination of mechanisms for neutrinoless double beta decay by comparing ratios of half life…
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. However, analogous equilibrium models do not perform as well in…
Spatial fluctuations of guanine and cytosine base content (GC%) are studied by spectral analysis for the complete set of human genomic DNA sequences. We find that (i) the 1/f^alpha decay is universally observed in the power spectra of all…
In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
Motivated by recent intensive experimental efforts on searching for neutrinoless double-beta decays, we perform a detailed analysis of the physics potential of the experiments based on $^{76}\mathrm{Ge}$. Assuming no signals, current and…
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic…
We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…