Infectious Disease

YeastSAM: A Deep Learning Model for Accurate Segmentation of Budding Yeast Cells

An essential step for quantitative image analysis is cell segmentation, which is the process of defining the outline of individual cells in microscopy images. Segmentation of budding yeast is challenging due to their asymmetric cell division and mother-bud morphology. As a result, a dividing cell is frequently misidentified as two separate cells, causing errors in downstream analysis. Here, we ove...

Intracellular acidification by bacteria-derived valeric acid is a mechanism of trans-kingdom ecology against Candida parapsilosis colonization

In hematopoietic cell transplant patients, intestinal Candida parapsilosis expansion and translocation cause life-threatening candidemia, yet how commensal intestinal bacteria prevent Candida expansion remains incompletely defined. Here, we trained a machine learning model on supernatant metabolomic profiles of commensal bacteria to identify bacteria-derived inhibitors of fungal growth, with valer...

Machine learning based lineage prediction from AMR phenotypes for Escherichia coli ST131 clade C surveillance across infection types

Rising antimicrobial resistance (AMR) in Escherichia coli bloodstream infections (BSIs) in high-income settings has typically been dominated by one cl...

Breaking the culture habit: metagenomic diagnosis of companion animal skin infections

Skin infections have been described as the primary cause for presentation in veterinary small animal practices and they frequently result in prescript...

A deep reinforcement learning platform for antibiotic discovery

Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here ...

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 ...

Instruction-tuned extraction of virus-host interactions from integrated scientific evidence

Viral infectious diseases continue to pose a major threat to global health. Understanding protein-protein interactions (PPIs) and RNA-protein interact...

Efficacy and safety evaluation of artificial intelligence-identified antimicrobial peptides for use against avian pathogenic Escherichia coli in the poultry industry

The overuse of antibiotics in both veterinary and human medicine has resulted in the emergence of antibiotic-resistant bacteria, prompting a search fo...

AFMnanoSALQ: An Accurate Detection Framework for Semi-Automatic Labeling and Quantitative Analysis of α-Hemolysin Nanopores Using Intensity-Height Cues in HS-AFM Data

High-Speed Atomic Force Microscopy (HS-AFM) enables imaging of biological structures and dynamics with nanometer spatial and millisecond temporal reso...

Deep Generative Optimization of mRNA Codon Sequences for Enhanced mRNA Translation and Therapeutic Efficacy

Messenger RNA (mRNA) therapeutics show immense promise, but their efficacy is limited by suboptimal protein expression. Here, we present RiboDecode, a...

Capturing the Mutational Dynamics of SARS-CoV-2 with Graphs

The rapid evolution of SARS-CoV-2 presents significant challenges for modeling viral dynamics, driven by lineage diversification and region-specific m...

An AI for an AI: identifying zoonotic potential of avian influenza viruses via genomic machine learning

Avian influenza remains a serious risk to human health via zoonotic transmission, as well as a feasible pandemic threat. Although limited zoonotic cas...

DLRNA-BERTa: A transformer approach for RNA-drug binding affinity prediction

RNA-based therapies are a rapidly expanding field, offering treatments for a wide range of diseases, including many rare conditions. To date, 24 RNA t...

Discovery of RdRp Thumb-1 as a novel broad-spectrum antiviral family of targets and MDL-001 as a potent broad-spectrum inhibitor thereof

Multiple positive-sense, single-stranded RNA (+ssRNA) viruses cause human diseases, ranging from mild colds to deadly pandemics. These viruses share a...

Early detection of ampicillin susceptibility in Enterococcus faecium with MALDI-TOF MS and machine learning

Enterococcus faecium can cause severe infections and is often resistant to the first-line antibiotic ampicillin. Consequently, clinicians usually pres...

High-throughput cell-free profiling of SARS-CoV-2 RBD variants enables rapid and quantitative in vitro affinity landscape mapping

SARS-CoV-2 variants continue to threaten public health, necessitating the study of cumulative and epistatic effects of receptor-binding domain (RBD) m...

Illuminating the Virosphere’s Dark Matter using Hierarchical Deep Learning

Systematic discovery of novel viruses is essential for pandemic preparedness, understanding tumor-associated viruses, developing viral delivery system...

Improved sensory representations as a result of temporal adaptation

Human perception is robust under challenging conditions, for example when sensory inputs change over time. Temporal adaptation in the form of reduced ...

A Machine Learning Approach Reveals CRISPR-Cas I-F as a Genomic Marker of Antibiotic Susceptibility in Uropathogenic E. coli

Antimicrobial resistance (AMR) in Escherichia coli is a critical global health challenge, particularly in urinary tract infections, where first-line t...

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...