相关论文: How much non-coding DNA do eukaryotes require?
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
Diatoms, a major group of microalgae, play a critical role in global carbon cycling and primary production. Despite their ecological significance, comprehensive genomic resources for diatoms are limited. To address this, we have annotated…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
We previously proposed the existence of DNA to DNA transcription in eukaryotic cells, but the mechanism by which single-stranded DNA (ssDNA) transcript is produced and released from the genome remains unknown. We once speculated that the…
The first level of folding of DNA in eukaryotes is provided by the so called '10 nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging bead on a string…
The mean length and the variability of coding sequences for 48 genomes of bacteria and archaea were analyzed. It was found that the plotted data can be described by an angular area. This suggests the followings: a) The variability of a…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution,…
In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…
Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data…
Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
Networks exhibiting "accelerating" growth have total link numbers growing faster than linearly with network size and can exhibit transitions from stationary to nonstationary statistics and from random to scale-free to regular statistics at…
Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…
The volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the…
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly…
Eukarya and Bacteria are the most evolutionarily distant domains of life, which is reflected by differences in their cellular structure and physiology. For example, Eukarya feature membrane-bound organelles such as nuclei and mitochondria,…
The NEMO-3 experiment measured the half-life of the $2\nu\beta\beta$ decay and searched for the $0\nu\beta\beta$ decay of $^{116}$Cd. Using $410$ g of $^{116}$Cd installed in the detector with an exposure of $5.26$ y, ($4968\pm74$) events…