相关论文: How much non-coding DNA do eukaryotes require?

Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…

Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames and which have been termed long non-coding RNAs (lncRNAs). Despite the existence of several well-characterized…

Because genomes are products of natural processes rather than intelligent design, all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called rubbish DNA. Rubbish DNA consists…

Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron…

We study the length distribution of a particular class of DNA sequences known as 5'UTR exons. These exons belong to the messanger RNA of protein coding genes, but they are not coding (they are located upstream of the coding portion of the…

We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…

We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…

We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…

We derive theoretical upper and lower bounds on the maximum size of DNA codes of length n with constant GC-content w and minimum Hamming distance d, both with and without the additional constraint that the minimum Hamming distance between…

Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…

The origin and early evolution of eukaryotes are one of the major transitions in the evolution of life on earth. One of its most interesting aspects is the emergence of cellular organelles, their dynamics, their functions, and their…

We define the complexity of DNA sequences as the information content per nucleotide, calculated by means of some Lempel-Ziv data compression algorithm. It is possible to use the statistics of the complexity values of the functional regions…

In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of…

Increased biological complexity is generally associated with the addition of new genetic information, which must be integrated into the existing regulatory network that operates within the cell. General arguments on network control, as well…

With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this…

We formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. The model describes well a large amount of…

We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…

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…

The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes…

The nature of the quantitative distribution of the 64 DNA codons in the human genome has been an issue of debate for over a decade. Some groups have proposed that the quantitative distribution of the DNA codons ordered as a rank-frequency…