Infectious Disease

omicML: An Integrative Bioinformatics and Machine Learning Framework for Transcriptomic Biomarker Identification

Transcriptomic biomarker discovery has been a challenge due to variation in datasets and platforms, complexity in statistical and computational methods, integration of multiple programming languages, and intricacy of ML workflow to evaluate biomarkers. Standard workflows necessitate several stages (quality control, normalization, differential expression), typically executed in R or Python, resulti...

Deciphering the Antigenic Evolution of Seasonal Influenza A Viruses with PREDAC-Transformer: From Antigenic Clustering to Key Site Identification

Seasonal influenza viruses undergo continuous antigenic drift due to mutations in the hemagglutinin (HA) protein, rendering vaccines ineffective and posing a significant global public health challenge. Existing computational models can predict antigenic relationships but generally lack interpretability, making it difficult to reveal the molecular determinants driving antigenic changes. To address ...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV

Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission event...

A study on edge devices for image classification of the Tasmanian devil (Sarcophilus harrisii) for vaccine delivery

A target-specific bait dispenser is required for oral bait vaccination of the endangered Tasmanian devil (Sarcophilus harrisii) against the deadly dev...

The promise of AlphaFold for gene structure annotation

As sequencing technology improves, more genomes become available. Most lack annotation, automated methods are error prone, and few genomes are ever ma...

A natural history of AMR in Klebsiella pneumoniae: Global diversity, predictors, and predictions of evolutionary pathways

Antimicrobial resistance (AMR) is a substantial and growing global health burden. Understanding, and predicting, its evolution in specific pathogens w...

Machine learning–assisted selection of informative loci for strain-level phylogenetics of Neisseria gonorrhoeae

Epidemiological surveillance of Neisseria gonorrhoeae is hindered by the limitations of existing molecular typing methods, such as NG-MAST and MLST, w...

Leveraging Deep Learning and MD Simulations to Decipher the Molecular Basis of Attenuated Activity in Glycocin F

The escalating crisis of multi-drug resistant bacteria demand a new generation of antibiotics. Glycocin F (GccF), a potent bacteriocin, is a promising...

Multivariate analysis of glycogenes reveals coordinated regulation of immunoglobulin glycosylation in an immortalized human B cell system

While neutralizing ability has traditionally been considered the most important antibody function, appreciation has grown for Fc-mediated ‘extra-neutr...

PlasmoFP: leveraging deep learning to predict protein function of uncharacterized proteins across the malaria parasite genus

The first malaria parasite Plasmodium falciparum genome published in 2002 jump-started functional studies, but a large fraction of all predicted prote...

ppLM-CO:Pre-trained Protein Language Model for Codon Optimization

Messenger ribonucleic acid (mRNA) vaccines represent a major advancement in synthetic biology, yet their efficacy remains limited by how efficiently t...

Integrating theory and machine learning to reveal determinants of plasmid copy number

Plasmids are extrachromosomal mobile genetic elements whose copy numbers (PCNs) critically influence microbial evolution, antibiotic resistance and pa...

Leveraging Multimodal Large Language Models to Extract Mechanistic Insights from Biomedical Visuals: A Case Study on COVID-19 and Neurodegenerative Diseases

The COVID-19 pandemic has intensified concerns about its long-term neurological impact, with growing evidence linking SARS-CoV-2 infection to neurodeg...

A validated set of neural gene reporter mice and chemical tracers tools for mapping knee innervating neurons

Joint pain is an increasing concern for our aging population, as current therapies to slow joint disease progression or reduce pain are largely ineffe...

Structural constraints acting on the SARS-CoV-2 spike protein reveal limited space for viral adaptation

The SARS-CoV-2 pandemic resulted in an unprecedented scientific response. The enormous scale of global genome sequencing, protein structural determina...

Benchmarking Large Language Models for Pathogen–Disease Classification in Post-Acute Infection Syndromes

Post-Acute Infection Syndromes (PAIS) are medical conditions that persist following acute infections from pathogens such as SARS-CoV-2, Epstein-Barr v...

A lettuce receptor-like kinase recognizes the highly conserved heptapeptide motif within microbial NEP1-like proteins

Plants rely on cell surface immune receptors to detect microbial patterns and initiate effective defense responses. Although the Asteraceae family is ...

Morphology-Guided Deep Learning for Nanoparticle Agglomeration Diagnostic Assays

Affordable, accurate, and rapid point-of-care diagnostic tests remain elusive due to inherent trade-offs between performance and cost. Conventional nu...

USP-ddG: A Unified Structural Paradigm with Data Efficacy and Mixture-of-Experts for Predicting Mutational Effects on Protein-Protein Interactions

Accurately estimating changes in binding free energy (ΔΔG) is essential for understanding protein-protein interactions (PPIs) and guiding rational pro...

Covary: A translation-aware framework for alignment-free phylogenetics using machine learning

In large-scale phylogenetic analysis, incorporating translation awareness is critical to account for the genotypic and phenotypic dimensions underlyin...