Related papers: Identifying lineage effects when controlling for p…
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…
Genome-wide association studies (GWAS) have identified hundreds of loci at very stringent levels of statistical significance across many different human traits. However, it is now clear that very large samples (n~10^4-10^5) are needed to…
Genome-Wide Association Studies (GWAS) help identify genetic variations in people with diseases such as Parkinson's disease (PD), which are less common in those without the disease. Thus, GWAS data can be used to identify genetic variations…
De novo therapeutic design is challenged by a vast chemical repertoire and multiple constraints, e.g., high broad-spectrum potency and low toxicity. We propose CLaSS (Controlled Latent attribute Space Sampling) - an efficient computational…
The evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore…
Understanding the genetic basis of complex traits is a longstanding challenge in the field of genomics. Genome-wide association studies (GWAS) have identified thousands of variant-trait associations, but most of these variants are located…
Motivation: Genome-wide association studies (GWAS) have successfully identified thousands of genetic risk loci for complex traits and diseases. Most of these GWAS loci lie in regulatory regions of the genome and the gene through which each…
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…
High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type…
The past decade has seen a rapid growth in omics technologies. Genome-wide association studies (GWAS) have uncovered susceptibility variants for a variety of complex traits. However, the functional significance of most discovered variants…
Antimicrobial resistance is becoming a major threat to public health throughout the world. Researchers are attempting to contrast it by developing both new antibiotics and patient-specific treatments. In the second case, whole-genome…
Background: Microbiota have evolved to acclimate themselves to many environments. Humanity is become ever increasingly medicated and many of those medications are antibiotics. Sadly, Microbiota are adapting to medication and with each…
For the vast majority of genome wide association studies (GWAS) published so far, statistical analysis was performed by testing markers individually. In this article we present some elementary statistical considerations which clearly show…
Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we…
In Genome-Wide Association Studies (GWAS) where multiple correlated traits have been measured on participants, a joint analysis strategy, whereby the traits are analyzed jointly, can improve statistical power over a single-trait analysis…
Traditional GWAS has advanced our understanding of complex diseases but often misses nonlinear genetic interactions. Deep learning offers new opportunities to capture complex genomic patterns, yet existing methods mostly depend on feature…
Methods to effectively detect multi-locus genetic association are becoming increasingly relevant in the genetic dissection of complex trait in humans. Current approaches typically consider a limited number of hypotheses, most of which are…
Disease-gene association through Genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms (SNPs) that correlate with specific diseases needs statistical analysis of associations.…
The paramount importance of replicating associations is well recognized in the genome-wide associaton (GWA) research community, yet methods for assessing replicability of associations are scarce. Published GWA studies often combine…
Bacteriophages (phages) are key regulators of bacterial populations and hold great promise for applications such as phage therapy, biocontrol, and industrial fermentation. The success of these applications depends on accurately determining…