Genomics
Background Despite its status as a model organism, the development of Caenorhabditis elegans is not necessarily archetypical for nematodes. The phylum Nematoda is divided into the Chromadorea (indcludes C. elegans) and the Enoplea. Compared…
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study non- model organisms. However, when the reference transcriptome used to calculate differential expression is incomplete, significant error in…
GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the…
The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds…
GC-content, the ratio of guanine and cytosine bases in an entire nucleotide sequence, and palindromic sequences are unique for every organism due to genomic evolution. The goals of our research was to establish a correlation between…
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…
Connectivity networks have recently become widely used in biology due to increasing amounts of information on the physical and functional links between individual proteins. This connectivity data provides valuable material for expanding our…
Withdrawn by arXiv administrators due to content entirely plagiarized from other authors (not in arXiv).
Growing evidence suggests that many vertebrate lineages are evolving at significantly different rates. As a first approximation of evolutionary rates, we assessed the amount of neutral (dS) and non-neutral (dN) substitutions that have…
Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very…
Darwin introduced the concept of the "living fossil" to describe species belonging to lineages that have experienced little evolutionary change, and suggested that species in more slowly evolving lineages are more prone to extinction (1).…
Tandem repeats are ubiquitous in the genome of organisms and their mutated forms play a vital role in pathogenesis. In this study, tandem repeats in Gastric Intrinsic Factor (GIF) of gastric parietal cells have been investigated using an in…
Pattern analysis of tandem repeats in gene is an indispensable computational approach to the understanding of the gene expression and pathogenesis of diseases. This research applied a computational motif model and database techniques to…
Mirtrons are a special type of pre-miRNA which originate from intronic regions and are spliced directly from the transcript instead of being processed by Drosha. The splicing mechanism is better understood for the processing of mRNA for…
High-throughput sequencing of RNA transcripts (RNA-seq) has become the method of choice for detection of differential expression (DE). Concurrent with the growing popularity of this technology there has been a significant research effort…
We have recently used genetic programming to automatically generate an improved version of Langmead's DNA read alignment tool Bowtie2 Sect.5.3 RN/12/09. We find it runs more than four times faster than the Bioinformatics sequencing tool…
Regulatory relationships of 686 intronic miRNA and 784 intergenic miRNAs with mRNAs of 51 intronic miRNA coding genes were established. Interaction features of studied miRNAs with 5'UTR, CDS and 3'UTR of mRNA of each gene were revealed.…
Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced…