Related papers: A new method for identifying vertebrates using onl…
More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (i.e. cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a…
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…
Dangerous damage to mitochondrial DNA (mtDNA) can be ameliorated during mammalian development through a highly debated mechanism called the mtDNA bottleneck. Uncertainty surrounding this process limits our ability to address inherited mtDNA…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The…
Precise segmentation and anatomical identification of the vertebrae provides the basis for automatic analysis of the spine, such as detection of vertebral compression fractures or other abnormalities. Most dedicated spine CT and MR scans as…
Y-chromosomal and mitochondrial DNA profiles have been used as evidence in courts for decades, yet the problem of evaluating the weight of evidence has not been adequately resolved. Both are lineage markers (inherited from just one parent),…
In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…
The ability to locate and annotate mitochondrial genes is an important practical issue, given the rapidly increasing number of mitogenomes appearing in the public databases. Unfortunately, tRNA genes in Metazoan mitochondria have proved to…
We propose a novel convolutional method for the detection and identification of vertebrae in whole spine MRIs. This involves using a learnt vector field to group detected vertebrae corners together into individual vertebral bodies and…
DNA methylation is an intensely studied epigenetic mark implicated in many biological processes of direct clinical relevance. While sequencing based technologies are increasingly allowing high resolution measurements of DNA methylation,…
Mitochondrial genetic material is widely used for phylogenetic reconstruction and as a barcode for species identification. Here we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the…
High quality ancient DNA (aDNA) is essential for molecular paleontology. Due to DNA degradation and contamination by environmental DNA (eDNA), current research is limited to fossils less than 1 million years old. The study successfully…
We perform a statistical study of the distances between successive occurrencies of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the dinucleotide CG…
Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly mitochondria, is increasingly being recognised as an…
DNA detection is of great significance in the point-of-care diagnostics. The stiffness of DNA, varying with its sequence and mechanochemical environment, could be a potential marker for DNA identification. The steric configurations of DNA…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…