Related papers: Analysis of whole mitogenomes from ancient samples
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists due to its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina…
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…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
By profiting from recent developments in detector technologies, making it possible to access a stream of detection events with few-ns time resolutions, a new ptychographic workflow is established. This methodological framework, referred to…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Synthetic data generated by generative models can enhance the performance and capabilities of data-hungry deep learning models in medical imaging. However, there is (1) limited availability of (synthetic) datasets and (2) generative models…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
Modern spatial microscopy has provided developmental biology with powerful research tools. However, the recent significant technological breakthroughs have inevitably led to technical "bottlenecks" for the application of the new procedures…
Summary: Mapping ancient DNA to a reference genome is challenging as it involves numerous steps, is time-consuming and has to be repeated within a study to assess the quality of extracts and libraries; as a result, the mapping needs to be…
Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…
Neuroevolutionary algorithms, automatic searches of neural network structures by means of evolutionary techniques, are computationally costly procedures. In spite of this, due to the great performance provided by the architectures which are…
Modeling the 3D structures of cells and tissues is crucial in biology. Sequential cross-sectional images from electron microscopy provide high-resolution intracellular structure information. The segmentation of complex cell structures…
Filtered diode array spectrometers are routinely employed to infer the temporal evolution of spectral power from x-ray sources, but uniquely extracting spectral content from a finite set of broad, spectrally overlapping channel spectral…