Bacterial Infection

CBAM-Enhanced DenseNet121 for Multi-Class Chest X-Ray Classification with Grad-CAM Explainability

Pneumonia remains a leading cause of childhood mortality worldwide, with a heavy burden in low-resource settings such as Bangladesh where radiologist availability is limited. Most existing deep learning approaches treat pneumonia detection as a binary problem, overlooking the clinically critical distinction between bacterial and viral aetiology. This paper proposes CBAM-DenseNet121, a transfer-lea...

In-silico cell sorting revealed granulocyte-specific single-cell-type gene expression from peripheral blood bulk expression data and its application as host response biomarkers to discriminate bacterial and viral infections

Peripheral Blood transcriptome analysis evaluated the bulk transcript abundance (TA) covering all leukocyte cell populations. However, there are 2 main problems in using bulk expression as biomarkers: (1) A long list of differential expression genes (DEGs) was found, and (2) DEGs cannot be attributed to a host response of any specific cell-type. TA assays after conventional cell sorting, as the go...

FoundedPBI: Using Genomic Foundation Models to predict Phage-Bacterium Interactions

The scalability of phage therapy as a viable alternative or complement to antibiotics is limited by the labor-intensive experimental screening require...

A genetically encoded local learning rule enables physical learning in engineered bacteria

Training physical neural networks directly in matter remains difficult because most platforms do not implement weight storage and weight update within...

kinGEMs: A Robust and Scalable Framework forResource-Constraint Models through StochasticTuning of Deep Learning-Predicted KineticParameters

The construction of accurate enzyme-constrained genome-scale models (ecGEMs) remains a critical challenge in systems biology, limited by sparse kineti...

Non-perturbative Bacterial Identification Directly from Solid Agar Plates Using Raman

Raman spectroscopy is a promising tool for microbial identification, yet its implementation in microbiology and clinical workflow is still restricted ...

Integrated Artificial Intelligence and Quantum Chemistry Approach for the Rational Design of Novel Antibacterial Agents against Ralstonia solanacearum.

Antimicrobial resistance (AMR) in plant pathogenic bacteria poses a serious threat to global agriculture, necessitating the development of novel antib...

Rapid Bacterial Identification and Antibiotic Susceptibility Testing through Interferometry-based Surface Topography Measurement

Antimicrobial resistance poses a critical global health threat. For many bacterial infections, such as bacteremia, treatment can fail due to the time ...

GCN-Mamba: Graph Convolutional Network with Mamba for Antibacterial Synergy Prediction

The escalating crisis of antimicrobial resistance necessitates novel therapeutic strategies, among which drug combination therapy shows great promise ...

Bacterial proteome foundation model enhances functional prediction from enzymes to ecological interactions

Bacteria play fundamental roles in ecosystems, human health, and biotechnology. Although bacterial genome sequencing data have accumulated rapidly ove...

dAMN: a genome scale neural-mechanistic hybrid model to predict bacterial growth dynamics

This study presents dAMN, a hybrid neural-mechanistic model that integrates neural networks with genome-scale dynamic flux balance analysis (dFBA) to ...

Explainable AI for end-to-end pathogen target discovery and molecular design

Drug discovery is often constrained by target identification, a bottleneck especially acute in antimicrobial development and the fight against emergin...

Eubiota: Modular Agentic AI for Autonomous Discovery in the Gut Microbiome

The gut microbiome regulates many aspects of human biology, including immunity and inflammatory diseases, yet mechanistic discovery and translation re...

Cross hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH enables microbiome imaging with strain level taxonomic resolution

The spatial organization of microbial communities is a critical determinant of host-microbe interactions, yet species-level mapping remains challengin...

Predicting Multi-Drug Resistance in Bacterial Isolates Through Performance Comparison and LIME-based Interpretation of Classification Models

The rise of Antimicrobial Resistance, particularly Multi-Drug Resistance (MDR), presents a critical challenge for clinical decision-making due to limi...

Deep learning extracts MoA-specific signatures from high-throughput images of chemically and genetically perturbed Corynebacteria

Tuberculosis (TB) is the worldwide leading infectious killer due to a single pathogen and increasing antimicrobial resistance (AMR) makes it imperativ...

Bacterial protein function prediction via multimodal deep learning

Bacterial proteins are specialized with extensive functional diversity for survival in diverse and stressful environments. A significant portion of th...

Programmable RNA detection generates DNA barcodes for multiplexed phage-host interaction screening

Here, we introduce Detectrons, modular biosensors that couples programmable toehold switches with retron-mediated reverse transcription to transduce R...

Metagenomic strain tracking reveals patterns of bacterial spread and the impact of water chlorination

Bacterial infections are a major cause of morbidity and mortality among children under five in low- and middle-income countries (LMICs). Children in L...

Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial species

Pseudouridine ({Psi}) modifications are the most abundant RNA modifications; however, their distribution and functional significance in bacteria remai...