Research

From sequence to signature: Uncovering multiscale AMR features across bacterial pathogens with supervised machine learning

Since the clinical introduction of antibiotics in the 1940s, antimicrobial resistance (AMR) has become an increasingly dire threat to global public health. Pathogens acquire AMR much faster than we discover new drugs, warranting new methods to better …

Integrative transcriptome-based drug repurposing in tuberculosis

Tuberculosis (TB) remains the second leading cause of infectious disease mortality worldwide, killing over one million people annually. Rising antibiotic resistance has created an urgent need for host-directed therapeutics (HDTs) — preferably by …

Unlocking antimicrobial resistance with multiomics and machine learning

The global antimicrobial resistance (AMR) emergency is driven by complex and evolving molecular mechanisms. Cutting-edge machine learning methods and multiomics technologies can help to combat this crisis by predicting novel AMR biomarkers and …

Modeling the START transition in the budding yeast cell cycle

Budding yeast, *Saccharomyces cerevisiae*, is widely used as a model organism to study the genetics underlying eukaryotic cellular processes and growth critical to cancer development, such as cell division and cell cycle progression. The budding …

The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history

Bacterial phage shock protein (PSP) systems stabilize the bacterial cell membrane and protect against envelope stress. These systems have been associated with virulence, but despite their critical roles, PSP components are not well characterized …

The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition

Sulfur is an indispensable element for proliferation of bacterial pathogens. Prior studies indicated that the human pathogen, Staphylococcus aureus utilizes glutathione (GSH) as a source of nutrient sulfur; however, mechanisms of GSH acquisition are …

MolEvolvR BTS: When and how to build a web-app and software package?

We recently developed a web application, MolEvolvR, to characterize proteins using molecular evolution and phylogeny. This session will serve as a behind-the-scenes (BTS) sneak peek into what MolEvolvR does, how it does it, and its origin story. The …

Feedback in the β-catenin destruction complex imparts bistability and cellular memory

Positive feedback within the β-catenin destruction complex gives rise to bistability and memory in response to Wnt stimulation, imparting signal transduction accuracy and insulation.

Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria

DciA Helicase Operators Exhibit Diversity across Bacterial Phyla

Despite the fundamental importance of DNA replication for life, this process remains understudied in bacteria outside Escherichia coli and Bacillus subtilis. In particular, most bacteria do not encode the helicase-loading proteins that are essential in E. coli and B. subtilis for DNA replication. Instead, most bacteria encode a DciA homolog that likely constitutes the predominant mechanism of helicase operation in bacteria. However, it is still unknown how DciA structure and function compare across diverse phyla that encode DciA proteins. In this study, we performed computational evolutionary analyses to uncover tremendous diversity among DciA homologs. These studies provide a significant advance in our understanding of an essential component of the bacterial DNA replication machinery.