Infectious Disease

Viral protease-Initiated Pyroptosis Activator mRNA therapy as a Universal Antiviral Strategy

Although therapeutic drugs targeting gasdermin (GSDM)-mediated pyroptosis have made remarkable progress in treating various diseases, their potential for antiviral therapy remains largely unexplored. Inspired by the autoinhibitory mechanism of GSDM proteins and the clinical success of mRNA vaccines, herein we propose a concept of viral protease-initiated pyroptosis (VIP) mRNA therapy as a universa...

Confidence-based Prediction of Antibiotic Resistance at the Patient Level

Rapid and accurate diagnostics of bacterial infections are necessary for efficient treatment of antibiotic-resistant pathogens. Cultivation-based methods, such as antibiotic susceptibility testing (AST), are limited by bacterial growth rates and seldom yield results before treatment needs to start, increasing patient risk and contributing to antibiotic overprescription. Here, we present a deep-lea...

Predicting Future SARS-CoV-2 Mutations using Deep Learning

SARS-CoV-2 continues to spread over the world steadily as opposed to many earlier estimations that it would disappear in less than two years. Even tho...

A Global Discovery of Antimicrobial Peptides in Deep-Sea Microbiomes Driven by an ESM-2 and Transformer-based Dual-Engine Framework

The escalating global threat of multidrug-resistant pathogens underscores the urgent demand for innovative strategies in antimicrobial peptide (AMP) d...

Extending digital biology: bacterial survival and morphological heterogeneity under antibiotic stress

The morphology of bacteria is modified by antibiotic stress while also serving to survive the antibiotic. However associating morphological descriptor...

Harnessing Interpretable Deep Learning to Predict Meropenem Resistance in Klebsiella pneumoniae

Antimicrobial resistance represents an escalating global healthcare threat, complicating treatment and increasing both morbidity and mortality. Deep l...

The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum

Saccharomycotina yeasts are a highly diverse and widely distributed subphylum of ascomycete fungi that exhibit diversity in their asexual growth morph...

Decode-gLM: Tools to Interpret, Audit, and Steer Genomic Language Models

While genomic language models are enabling the de novo design of entire genomes, they remain challenging to interpret, limiting their trustworthiness....

Graph attention with structural features improves the generalizability of identifying functional sequences at a protein interface

Accurate prediction of the set of sequences compatible with a protein-protein interface is an unsolved problem in biology. While supervised sequence-b...

Machine Learning Driven Simulations of the SARS-CoV-2 Fitness Landscape from Deep Mutational Scanning Experiments

Predicting protein variant effects is a key challenge in preparing for pathogenic viral strains, understanding mutation-linked diseases, and designing...

TEIP: A Compact, Open-Source Framework for Predicting Tumor Epitope Immunogenicity in Glioblastoma Using Deep Learning and Multi-Modal Biological Features

This work introduces a modular, open-source computational pipeline for glioblastoma (GBM) vaccine design that integrates omics-based OIP5 target disco...

Skin lipid chemistry influences host-microbiome-pathogen interactions in snake fungal disease (ophidiomycosis)

Within host-microbiome-pathogen systems, the host chemical microenvironment is often overlooked despite its inherent role in host physiology. We used ...

Deep learning challenge to generate apo RNA conformations with cryptic binding site

RNA plays vital roles in diverse biological processes, thus drawing much attention as potential therapeutic target. Notably, cryptic ligand binding si...

Development of a metabolic signature of post-weaning diarrhoea in pigs

In the agricultural sector, antibiotics have been used to improve swine growth performance. This application is banned nowadays, due to increased risk...

Microcompartments in archaeal ancestors of eukaryotes: a bioenergetic engine that could have fuelled eukaryogenesis

Eukaryotic intracellular compartmentalization is a key innovation in the evolution of complex cellular life. While microcompartments enable metabolic ...

Scoring gene importance by interpreting single-cell foundation models

Determining a gene’s functional significance within a cellular context has long been a challenge, as absolute expression level is an unreliable indica...

Generative design and construction of functional plasmids with a DNA language model

DNA language models offer a new paradigm for sequence design, yet their ability to generate functional genomic sequences remains underexplored. Plasmi...

Deep learning analyses of DNA sequences resolve the retention of the Duffy-null resistance to Plasmodium vivax malaria in Africa

P. vivax, the most geographically widespread human malaria parasite with millions of clinical cases per year, is however quasi absent in sub-Saharan A...

Substrate-enhanced filamentation of 3-methylcrotonyl-CoA carboxylase in Legionella pneumophila

3-Methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent carboxylase that metabolizes the amino acid leucine. MCC is present in bacteria, fungi, p...

Colon-Specific Epigenetic Clocks from Minimal Features Reveal Disease-Driven Aging

Epigenetic clocks estimate chronological and biological age from DNA methylation patterns, but conventional models typically train on hundreds of thou...