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Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…
Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution. We explored experimentally the effect of mutation supply and the strength of selective…
Bacterial growth environment strongly influences the efficacy of antibiotic treatment, with slow growth often being associated with decreased susceptibility. Yet in many cases the connection between antibiotic susceptibility and pathogen…
Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…
Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
With the recent advent of high-throughput genotyping techniques, genetic data for genome-wide association studies (GWAS) have become increasingly available, which entails the development of efficient and effective statistical approaches.…
Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these…
Replicability is central to scientific progress, and the partial conjunction (PC) hypothesis testing framework provides an objective tool to quantify it across disciplines. Existing PC methods assume independent studies. Yet many modern…
Bacteria develop resistance to antibiotics through various mechanisms, with the specific mechanism depending on the drug-bacteria pair. It remains unclear, however, which resistance mechanism best supports favorable treatment outcomes,…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
Genome-wide association studies (GWASs) have been extensively adopted to depict the underlying genetic architecture of complex diseases. Motivated by GWASs' limitations in identifying small effect loci to understand complex traits'…
New combinations of existing antibiotics are being investigated to combat bacterial resilience. This requires detection technologies with reasonable cost, accuracy, resolution, and throughput. Here, we present a multi -drug screening…
In the search for genetic factors that are associated with complex heritable human traits, considerable attention is now being focused on rare variants that individually have small effects. In response, numerous recent papers have proposed…
Genome-Wide Association Studies are typically conducted using linear models to find genetic variants associated with common diseases. In these studies, association testing is done on a variant-by-variant basis, possibly missing out on…
The evolution and emergence of antibiotic resistance is a major public health concern. The understanding of the within-host microbial dynamics combining mutational processes, horizontal gene transfer and resource consumption, is one of the…
A computationally simple genome-wide association study (GWAS) algorithm for estimating the main and epistatic effects of markers or single nucleotide polymorphisms (SNPs) is proposed. It is based on the intuitive assumption that changes of…
Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a…
Many DNA sequence variants influence phenotypes by altering gene expression. Our understanding of these variants is limited by sample sizes of current studies and by measurements of mRNA rather than protein abundance. We developed a…
Genetic variants in cis-regulatory elements or trans-acting regulators commonly influence the quantity and spatiotemporal distribution of gene transcription. Recent interest in expression quantitative trait locus (eQTL) mapping has…