Related papers: Multiple Genome Analytics Framework: The Case of A…
The variance component tests used in genomewide association studies of thousands of individuals become computationally exhaustive when multiple traits are analysed in the context of omics studies. We introduce two high-throughput algorithms…
The classical Sankoff algorithm for the simultaneous folding and alignment of homologous RNA sequences is highly influential, but it suffers from two major limitations in efficiency and modeling power. First, it takes $O(n^6)$ for two…
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…
SARS-CoV-2 lineages are defined according to placement in a phylogenetic tree, but approximated by a list of mutations based on sequences collected from clinical sampling. Wastewater lineage abundance is generally found under the assumption…
Meta-analysis of multiple genome-wide association studies (GWAS) is effective for detecting single or multi marker associations with complex traits. We develop a flexible procedure ("STAMP") based on mixture models to perform region based…
Wastewater surveillance has proven to be a useful tool to monitor pathogens such as SARS-CoV-2 as it is a nonintrusive way to survey the potential disease burden of the population contributing to a sewershed. With the expansion of this…
Gathering observational data for medical decision-making often involves uncertainties arising from both type I (false positive)and type II (false negative) errors. In this work, we develop a statistical model to study how medical…
Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…
The intricate relationship between genetic variation and human diseases has been a focal point of medical research, evidenced by the identification of risk genes regarding specific diseases. The advent of advanced genome sequencing…
The integration of knowledge graphs and graph machine learning (GML) in genomic data analysis offers several opportunities for understanding complex genetic relationships, especially at the RNA level. We present a comprehensive approach for…
Comparative analyses of graph structured datasets underly diverse problems. Examples of these problems include identification of conserved functional components (biochemical interactions) across species, structural similarity of large…
Predicting the binding of viral peptides to the major histocompatibility complex with machine learning can potentially extend the computational immunology toolkit for vaccine development, and serve as a key component in the fight against a…
Identifying similar documents within extensive volumes of data poses a significant challenge. To tackle this issue, researchers have developed a variety of effective distributed computing techniques. With the advancement of computing power…
Because of the rapid spread of COVID-19 to almost every part of the globe, huge volumes of data and case studies have been made available, providing researchers with a unique opportunity to find trends and make discoveries like never…
The SARS-CoV-2 spike (S) protein facilitates viral infection, and has been the focus of many structure determination efforts. Its flexible loop regions are known to be involved in protein binding and may adopt multiple conformations. This…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
The main goal of the multitasking optimization paradigm is to solve multiple and concurrent optimization tasks in a simultaneous way through a single search process. For attaining promising results, potential complementarities and synergies…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
Pattern matching is a fundamental tool for answering complex graph queries. Unfortunately, existing solutions have limited capabilities: they do not scale to process large graphs and/or support only a restricted set of search templates or…
With the advancement of high-throughput biotechnologies, we increasingly accumulate biomedical data about diseases, especially cancer. There is a need for computational models and methods to sift through, integrate, and extract new…