Related papers: Physics-based signal analysis of genome sequences:…
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…
The SARS-CoV-2 pandemic has led to a significant emergence of highly mutated forms of viruses with a great ability to adapt to the human host. Some mutations resulted in changes in the amino acid sequences of viral proteins, including the…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
This work presents a new approach for classification of genomic sequences from measurements of complex networks and information theory. For this, it is considered the nucleotides, dinucleotides and trinucleotides of a genomic sequence. For…
Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been…
Coronavirus (COVID-19) emerged towards the end of 2019. World Health Organization (WHO) was identified it as a global epidemic. Consensus occurred in the opinion that using Computerized Tomography (CT) techniques for early diagnosis of…
COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…
With the rapid spread of the novel coronavirus (COVID-19) across the globe and its continuous mutation, it is of pivotal importance to design a system to identify different known (and unknown) variants of SARS-CoV-2. Identifying particular…
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…
In silico methods evaluating the mutation effects of missense mutations are providing an important approach for understanding mutations in personal genomes and identifying disease-relevant biomarkers. However, existing methods, including…
As the major target of many vaccines and neutralizing antibodies against SARS-CoV-2, the spike (S) protein is observed to mutate over time. In this paper, we present statistical approaches to tackle some challenges associated with the…
The availability of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus data post-COVID has reached exponentially to an enormous magnitude, opening research doors to analyze its behavior. Various studies are conducted by…
Whole-genome sequencing (WGS) has revealed numerous non-coding short variants whose functional impacts remain poorly understood. Despite recent advances in deep-learning genomic approaches, accurately predicting and prioritizing clinically…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
We introduce ScannerBit, the statistics and sampling module of the public, open-source global fitting framework GAMBIT. ScannerBit provides a standardised interface to different sampling algorithms, enabling the use and comparison of…
The identification of genetic signal regions in the human genome is critical for understanding the genetic architecture of complex traits and diseases. Numerous methods based on scan algorithms (i.e. QSCAN, SCANG, SCANG-STARR) have been…
DNA sequencing allows for the determination of the genetic code of an organism, and therefore is an indispensable tool that has applications in Medicine, Life Sciences, Evolutionary Biology, Food Sciences and Technology, and Agriculture. In…
With recent advances in sequencing technology it has become affordable and practical to sequence genomes to very high depth-of-coverage, allowing researchers to discover low-frequency variants in the genome. However, due to the errors in…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
In cryptanalysis, security of ciphers vis-a-vis attacks is gauged against three criteria of complexities, i.e., computations, memory and time. Some features may not be so apparent in a particular domain, and their analysis in a transformed…