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Adaptation in response to selection on polygenic phenotypes may occur via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed…
Genome-wide association studies (GWAS) have identified many genetic factors underlying complex human traits. However, these factors have explained only a small fraction of these traits' genetic heritability. It is argued that many more…
Replication helps ensure that a genotype-phenotype association observed in a genome-wide association (GWA) study represents a credible association and is not a chance finding or an artifact due to uncontrolled biases. We discuss…
Phage therapy is an alternative treatment method for bacterial infections. It has shown particular promise in reducing bacterial load while preventing antibiotic resistance. Here, we develop a mathematical model of a bacterial infection…
One of the most important challenges in the analysis of high-throughput genetic data is the development of efficient computational methods to identify statistically significant Single Nucleotide Polymorphisms (SNPs). Genome-wide association…
Rapid detection of foodborne bacteria is critical for food safety and quality, yet traditional culture-based methods require extended incubation and specialized sample preparation. This study addresses these challenges by i) enhancing the…
The majority of common diseases are influenced by multiple genetic and environmental factors such as Cancer. Even though uncovering the main causes of disease is deemed difficult due to the complexity of gene-gene and gene-environment…
Due to the rise in antimicrobial resistance, identifying novel compounds with antibiotic potential is crucial for combatting this global health issue. However, traditional drug development methods are costly and inefficient. Recognizing the…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…
Although genome-wide association studies (GWAS) on complex traits have achieved great successes, the current leading GWAS approaches simply perform to test each genotype-phenotype association separately for each genetic variant. Curiously,…
Antibiotic resistance is a topical problem for both humans and animals and has been the subject of special monitoring for two decades. Several recent studies, including ours, have shown that this phenomenon is accentuated by the transfer of…
Common complex diseases are likely influenced by the interplay of hundreds, or even thousands, of genetic variants. Converging evidence shows that genetic variants with low marginal effects (LME) play an important role in disease…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Bacteria commonly inhabit porous environments such as host tissues, soil, and marine sediments, where complex geometries constrain and redirect their motion. Although bacterial motility has been studied in porous media, the roles of cell…
Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form…
Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human traits or diseases in the past decade. Nevertheless, much of the heritability of many traits is still unaccounted for. Commonly used…
Large case/control Genome-Wide Association Studies (GWAS) often include groups of related individuals with known relationships. When testing for associations at a given locus, current methods incorporate only the familial relationships…
Many common diseases are highly polygenic, modulated by a large number genetic factors with small effects on susceptibility to disease. These small effects are difficult to map reliably in genetic association studies. To address this…
Skin and soft tissue infections (SSTIs) are among the most frequently observed diseases in ambulatory and hospital settings. Resistance of diverse bacterial pathogens to antibiotics is a significant cause of severe SSTIs, and treatment…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…