Staphylococcus epidermidis is the leading cause of device-related infections, primarily due to its ability to form biofilms, surface-adherent bacterial communities that confer remarkable resistance to antibiotics and host defenses. Small basic protein, Sbp, is a 16-kDa protein expressed by S. epidermidis that has been shown to be crucial for biofilm formation, but little is known […]
Microbial-inspired antidotes to repurpose toxic compounds as antibiotics
Antibiotic-resistant (AMR) bacterial infections are a major global health threat. Despite the critical need for new antimicrobials, progress is constrained by protracted development timelines, as well as the requirement for chemical novelty to avoid cross-resistance. Repurposing therapeutics approved for indications other than infection offers a potential shortcut to rapidly develop new antibiotics that are outside […]
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification
Whole genome sequencing (WGS) offers a comprehensive, organism-agnostic method that effectively meets the need for efficient, reliable, and standardized responses to emerging threats from pathogens and pests. Here, we present PathogenSurveillance, an open-source and automated Nextflow pipeline for population genomic analyses of WGS data. It is designed with features tailored for biosurveillance and is suitable […]
Genome of the Predatory Volute Melo melo Provides Insights into Adaptive Gene Family Diversification in a Basal Neogastropod Lineage
Neogastropods represent one of the most diverse and ecologically specialized lineages of marine mollusks, yet many of their early-diverging families remain genomically underexplored. Here, we present the first high-contiguity genome of a volutid species, the tropical predatory snail Melo melo, assembled using PacBio HiFi long reads. The final assembly spans 2.29 Gb with high contiguity […]
CDR-aware masked language models for pairedantibodies enable state-of-the-art bindingprediction
Antibodies are a leading class of biologics, yet their architecture with conserved framework regions and hypervariable complementarity-determining regions (CDRs) poses unique challenges for computational modeling. We present a region-aware pretraining strategy for paired heavy (VH) and light (VL) sequences in variable domains using ESM2-3B and ESM C (600M) protein language models. We compare three masking […]