Related papers: Optimized protocol for DNA extraction from ancient…
Efficient capture and detection of minute amount of deoxyribonucleic acid (DNA) molecules are pivotal for an array of modern gene technologies which are widely utilized in medical, forensic and defense applications, including DNA…
In this paper we introduce Shackleton as a generalized framework enabling the application of linear genetic programming -- a technique under the umbrella of evolutionary algorithms -- to a variety of use cases. We also explore here a novel…
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…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
Surface crack segmentation poses a challenging computer vision task as background, shape, colour and size of cracks vary. In this work we propose optimized deep encoder-decoder methods consisting of a combination of techniques which yield…
The main objective of this paper is to solve the optimization problem that is associated with the classification of DNA samples in PCR plates for Sanger sequencing. To achieve this goal, we design an integer linear programming model. Given…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Several of the next generation sequencers are limited in their sample preparation process by the need to make an absolute measurement of the number of template molecules in the library to be sequenced. As currently practiced, the practical…
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…
The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…
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…
Recent advances in DNA sequencing technology and DNA storage systems have rekindled the interest in deletion channels. Multiple recent works have looked at variants of sequence reconstruction over a single and over multiple deletion…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
In skeleton-based action recognition, graph convolutional networks (GCNs), which model human body skeletons using graphical components such as nodes and connections, have achieved remarkable performance recently. However, current…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic…
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
A probabilistic clustering algorithm is proposed for the analysis of forensic DNA mixtures in which individual cells are isolated and short tandem repeats are amplified using the polymerase chain reaction to generate single cell…