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High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
Sex difference in allele frequency is an emerging topic that is critical to our understanding of ascertainment bias, as well as data quality particularly of the largely overlooked X chromosome. To detect sex difference in allele frequency…
Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
The research community continues to seek increasingly more advanced synthetic data generators to reliably evaluate the strengths and limitations of machine learning methods. This work aims to increase the availability of datasets…
Over the last 20 years, there has been an explosion of genomic data collected for disease association, functional analyses, and other large-scale discoveries. At the same time, there have been revolutions in cloud computing that enable…
In the last decade the broad scope of complex networks has led to a rapid progress. In this area a particular interest has the study of community structures. The analysis of this type of structure requires the formalization of the intuitive…
Computational analysis methods including machine learning have a significant impact in the fields of genomics and medicine. High-throughput gene expression analysis methods such as microarray technology and RNA sequencing produce enormous…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
A number of signal processing and statistical methods can be used in analyzing either pieces of text or DNA sequences. These techniques can be used in a number of ways, such as determining authorship of documents, finding genes in DNA, and…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
The amount of sequence data obtained from ancient samples has dramatically expanded in the last decade, and so have the types of questions that can now be addressed using ancient DNA. In the field of human history, while ancient DNA has…