compbio-bioinfo

Genomic comparison and phenotypic characterization of Pseudomonas aeruginosa isolates across environmental and diverse clinical isolation sites

Pseudomonas aeruginosa is a clinically significant, opportunistic pathogen adept at thriving in both host-associated and environmental settings. We sought to define the extent to which P. aeruginosa isolates specialize across niches using a …

Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence

Prochlorococcus is a cyanobacterial genus that exhibits photosynthetic capacity and remarkable genetic diversity. We analyze how Prochlorococcus genomics relate to high vs. low light environment adaptations, applying traditional comparative genomics …

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 (antibiotics), warranting …

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 …

amR: an R package suite to predict antimicrobial resistance in bacterial pathogens

EB and AG are co-primary authors.

Phage-bacteria interactions

Computational prediction of bacterial susceptibility to phages and genomic signatures of phage-bacteria coevolution.

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 …