Related papers: Physics-based signal analysis of genome sequences:…

The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an…

Although there is substantial literature on identifying structural changes for continuous spatio-temporal processes, the same is not true for categorical spatio-temporal data. This work bridges that gap and proposes a novel spatio-temporal…

Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A wide range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together…

The increasing spread of COVID-19, caused by the virus SARS-CoV-2, raises concerns about the extent to which mutations have occurred across the viral genome. We present a partial replication of an earlier 2021 study by Wang, R. et al. that…

Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promoters and initiate transcription. Finding the exact location of these binding sites (aka motifs) is important in a variety…

Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get prepared for future waves of infections. The last three waves of…

The unscented transform uses a weighted set of samples called sigma points to propagate the means and covariances of nonlinear transformations of random variables. However, unscented transforms developed using either the Gaussian assumption…

Genome-wide association studies(GWAS) have proven to be highly useful in revealing the genetic basis of complex diseases. At present, most GWAS are studies of a particular single disease diagnosis against controls. However, in practice, an…

Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…

The coronavirus Covid-19 mutates quickly in the pandemic, leaves people struggling to verify and improve the effectiveness of the vaccine based on biochemistry. Is there any physical invariant in the variants of such kind of pathogen that…

The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…

Machine learning approaches in drug discovery, as well as in other areas of the chemical sciences, benefit from curated datasets of physical molecular properties. However, there is a lack of sufficiently large data collections that include…

Because of the recent advances of genome sequences, a large number of human genome sequences are available for the study of human genetics. Genome-wide association studies typically focus on associations between single-nucleotide…

In population genetics, there is often interest in inferring selection coefficients. This task becomes more challenging if multiple linked selected loci are considered simultaneously. For such a situation, we propose a novel generalized…

The COVID-19 outbreak resulted in multiple waves of infections that have been associated with different SARS-CoV-2 variants. Studies have reported differential impact of the variants on respiratory health of patients. We explore whether…

Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…

By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…

This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…

This manuscript delves into the intersection of genomics and phenotypic prediction, focusing on the statistical innovation required to navigate the complexities introduced by noisy covariates and confounders. The primary emphasis is on the…

The COVID-19 pandemic response relied heavily on statistical and machine learning models to predict key outcomes such as case prevalence and fatality rates. These predictions were instrumental in enabling timely public health interventions…