Universal precautions

Bat anthropogenic roosting ecology influences taxonomic and geographic predictions of zoonotic risk

The ability of wildlife to live in anthropogenic structures is widely observed across many animal species. As proximity to humans is an important risk factor for pathogen transmission, anthropogenic roosting may have important consequences for predicting virus spillover and spillback of viruses. For bats, the influence of roosting in anthropogenic structures on predicting virus hosting ability and...

Predicting antifolate resistance in the unculturable fungal pathogen Pneumocystis jirovecii

Pneumocystis jirovecii is a fungal pathogen causing Pneumocystis pneumonia in humans, mainly in immunocompromised individuals. Infections by P. jirovecii are treated using the antifolate combination drug trimethoprim-sulfamethoxazole (TMP-SMX), targeting the dihydrofolate reductase (DHFR) and the dihydropteroate synthase (DHPS). In recent years, there has been an increase of treatment failure, wit...

Novel Machine Learning-based Approach to Identify Viral Biomarkers of Human Respiratory Emissions from Oral and Nasal Metagenomes

Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental samp...

T-cell receptor specificity landscape revealed through de novo peptide design

T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (...

ppIRIS: deep learning for proteome-wide prediction of bacterial protein-protein interactions

Protein–protein interactions (PPIs) are central to cellular processes and host–pathogen dynamics, yet bacterial interactomes remain poorly mapped, esp...

Geno2pheno[bNAbs]: Interpretable and accurate HIV antibody resistance prediction

Antiretroviral therapy (ART) is a life saving option for people living with HIV-1 (PLWH) and is effective against many viral strains. The most common ...

A comparative study of plant phenotyping workflows based on three-dimensional reconstruction from multi-view images

With the world facing escalating food demand, limited agricultural land, and environmental change, there is a growing need for data-driven sustainable...

Predicting Clinical Outcomes in Helicobacter pylori-positive Patients using Supervised Learning through the Integration of Demographic and Genomic Features

Helicobacter pylori (H. pylori) infection is widespread globally and is linked to outcomes ranging from chronic gastritis to gastric cancer. However, ...

Unveiling the Human Nasopharyngeal Microbiome Compendium: Systematic Characterization of Community Architecture and Function Through a Comprehensive Meta-Analysis

The nasopharyngeal microbiome acts as a dynamic interface between the human body and environmental exposures, modulating immune responses and helping ...

Hyperspectral image analysis for classification of multiple infections in wheat

Plant diseases can cause heavy yield losses in arable crops resulting in major economic losses. Effective early disease recognition is paramount for m...

Robust and accurate diagnosis of infectious skin diseases from histopathology images by integrating deep learning and explainable AI

Accurate diagnosis of infectious skin diseases remains a major challenge, particularly for neglected tropical diseases such as mycetoma, where precise...

Application and Characterization of the Multiple Instance Learning Framework in Flow Cytometry

For decades, flow cytometry has allowed for single-cell profiling based on selected biomarkers and is widely used in both clinical and research settin...

Decoding emergent properties of microbial community functions through sub-community observations and interpretable machine learning

The functions of microbial communities, including substrate conversion and pathogen suppression, arise not as a simple sum of individual species’ capa...

SmartHisto: Bayesian Active Learning for Histology Images

Accurate and efficient characterization of biological images is crucial for advancing systems biology and medical research. Recent advancements in dee...

Adaptive transcriptional strategies underpin the host-specific virulence of the generalist oomycete Phytophthora capsici during early crown infection

Phytophthora capsici is a destructive, broad-host-range oomycete responsible for substantial losses in global agriculture. While most transcriptomic s...

Pathogen and pest communities in agroecosystems across climate gradients: Anticipating future challenges in the highland tropics

Tropical cropping systems must adapt to the current and future geographic distribution of pathogen and pest communities. An important research gap is ...

Structurally Informed Fitness Landscapes for Surveillance of Emerging PRRSV Variants

Antibodies play a central role in neutralizing pathogens through direct interference with viral entry and recruitment of effector immune cells. Howeve...

Coenzyme A depletion causes antibiotic tolerance in Pseudomonas aeruginosa

The widespread use of antibiotics promotes both resistance and tolerance. While resistance enables bacterial growth in the presence of drugs, toleranc...

From sequence to signature: Machine learning uncovers multiscale feature landscapes that predict AMR across ESKAPE pathogens

Since the clinical introduction of antibiotics in the 1940s, antimicrobial resistance (AMR) has become an increasingly dire threat to global public he...

Generating Synthetic MR Perfusion Maps from DWI and FLAIR in Acute Ischemic Stroke using Deep Learning

Magnetic resonance imaging (MRI) is critical for acute stroke triage, but time-consuming, and often requires contrast injection for perfusion imaging....