相关论文: Gene & Genome Duplication in Acanthamoeba Polyphag…

De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…

Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…

Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms…

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…

The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…

Tandem duplications are an essential source of genetic novelty, and their variation in natural populations is expected to influence adaptive walks. Here, we describe evolutionary impacts of recently-derived, segregating tandem duplications…

A novel group of small non-coding RNA, known as microRNA (miRNA) is predicted to regulate as high as 90% of the coding genes in human. The diversity and abundance of miRNA targets offer an enormous level of combinatorial possibilities and…

The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…

Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…

Transfer Optimization is an incipient research area dedicated to solving multiple optimization tasks simultaneously. Among the different approaches that can address this problem effectively, Evolutionary Multitasking resorts to concepts…

Transfer RNAs (tRNAs) are essential components of the translational machinery. Their abundance and diversity shape decoding capacity and protein synthesis efficiency and accuracy. Because tRNA abundance is encoded in the genome through tDNA…

Recent evidence highlights the usefulness of DNA methylation (DNAm) biomarkers as surrogates for exposure to risk factors for non-communicable diseases in epidemiological studies and randomized trials. DNAm variability has been demonstrated…

Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…

Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…

The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…

Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…

Among all insect genomes, honeybee displays one of the most unusual patterns with interspersed long AT and GC-rich segments. Nearly 75% of the protein-coding genes are located in the AT-rich segments of the genome, but the biological…

Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…

We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of D. yakuba, and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing.…

In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies…