Infectious Disease

Evolutionary Tree in Chemical Space of Natural Products

Natural products (NPs) are key to biological function and adaptation, with their distribution shaped by complex evolutionary and ecological forces. While it may seem reasonable to assume that closely related species produce chemically similar NPs, this assumption has not been systematically tested at a broad taxonomic scale. Here, we evaluate whether evolutionary (taxonomic) proximity correlates w...

Dietary Protein Source Shapes Gut Microbial Structure and Predicted Function: A Meta-Analysis with Machine Learning

Dietary proteins are major modulators of gut microbial ecology, yet the microbial signatures and functional consequences of plant-versus animal-based proteins remain poorly defined. Although digestibility and fermentation profiles differ by protein type, a systematic evaluation of how these differences shape microbial diversity, structure, and metabolic capacity is still lacking. This meta-analysi...

Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides

Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains...

Influ-BERT: A Domain-Adaptive Genomic Language Model for Advancing Influenza A Virus Research

Influenza A Virus (IAV) poses a persistent threat to global public health due to its broad host adaptability, frequent anti-genic variation, and poten...

Intra-genomic genes-to-genes correlation enables bacterial genome representation

The bacterial pan-genome consists of core genes shared by all members of a taxonomy and accessory genes found in only a subset. The correlation among ...

Accurate and robust classification of Mycobacterium bovis-infected cattle using peripheral blood RNA-seq data

The zoonotic bacterium, Mycobacterium bovis, causes bovine tuberculosis (bTB) and is closely related to Mycobacterium tuberculosis, the primary cause ...

Structure-based discovery of inhibitors of Mac1 domain of nonstructural protein-3 of SARS-CoV-2 by machine learning-augmented screening of chemical space

Significant efforts have been recently dedicated to the discovery of small molecule inhibitors against the Macrodomain 1 (Mac1) of nonstructural prote...

Deep Learning-Based Segmentation of 2D Projection-Derived Overlapping Prospore Membrane in Yeast

Quantitative morphological analysis is crucial for understanding cellular processes. While 3D Z-stack imaging offers high-resolution data, the complex...

Large-language-model-based antibiotic resistance gene prediction and resistomes mining in cyanobacterial blooms

The rapid spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a serious public health threat. Conventional ARG detection methods,...

Fourier transform infrared spectroscopy enables rapid species discrimination across Malassezia and strain-level typing in M. pachydermatis

Malassezia pachydermatis is a zoophilic yeast found on the skin and in the outer ear canal of many mammals. It normally maintains a commensal lifestyl...

Modulation of specific interactions within a viral fusion protein predicted from machine learning blocks membrane fusion

Enveloped viruses must enter host cells to initiate infections through a fusion process, during which the fusion proteins undergo significant and comp...

PRIME: A Multi-Agent Environment for Orchestrating Dynamic Computational Workflows in Protein Engineerings

Artificial intelligence (AI) is revolutionizing protein engineering, yet its practical application is often hindered by a fragmented toolchain and the...

Integrative Transcriptomic and Machine Learning Approaches to decipher Mitochondrial Gene Regulation in severe Plasmodium vivax Malaria

Mitochondria in Plasmodium vivax are functionally vital despite possessing a highly reduced genome and differing substantially from the human organell...

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...

High-throughput virus quantification using cytopathic effect area analysis by deep learning

Traditional infectivity-based virion quantification methods, such as 50% tissue culture infectious dose (TCID50) and plaque assays, are typically perf...

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 (...

Integrative Microbiome Profiling of Colorectal Cancer Across South Asian and Western Cohorts Using Interpretable Machine Learning

The incidence of colorectal cancer (CRC) cases has been steadily rising in South Asian countries compared to western countries. Microbiome dysbiosis h...

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...

Scalable and interpretable secretion system annotation with Sismis

Secretion systems play critical roles in bacterial growth, survival, and pathogenesis. Genes encoding secretion system components often co-occur toget...

Machine Learning-Guided Synthetic Microbial Communities Enable Functional and Sustainable Degradation of Persistent Environmental Pollutants

Persistent environmental pollutants demand the use of diverse microbial metabolic capabilities for effective degradation. While naturally occurring co...