Universal precautions

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...

Feature-Mask-Based Strategies for Subtype-Specific Freezing of Gait Detection using CNNs

Freezing of gait (FOG), a disabling symptom of Parkinson’s disease, varies in manifestations and motion contexts. Its heterogeneity motivates subtype categorization such as manifestation-specific subtypes (akinesia, trembling or shuffling) or motion-specific subtypes (gait-initiation, walking or turning). Despite numerous promising deep learning FOG detection studies, few consider FOG heterogeneit...

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 ...

Decoding pathogen ecological memory from chemical-stress phenotypes

Can standardized chemical stress reveal an ecological “memory” of host origin in plant pathogens? We profiled six coffee-associated Colletotrichum iso...

H3BERTa: A CDR-H3 specific language model for antibody repertoire analysis

Antibodies are central to immune defense and therapeutic design, yet predicting which sequences confer functional activity remains challenging. Deep l...

Iterative immunogen optimization to focus immune responses on a conserved, subdominant viral epitope

Designing effective vaccination strategies against genetically diverse viruses, such as HIV or influenza, is hindered by the ability of these pathogen...

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 ...

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....

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...

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...

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...

From minutes to bounds: A probabilistic UV-C control and a shape-only morphological fingerprint for postharvest Colletotrichum

Postharvest losses in high-value horticultural crops such as cacao and coffee are often driven by Colletotrichum spp. and other latent fruit pathogens...

Integrating and refining the predictions of ensembled plant effector detection programs using machine learning

Effectors are pathogen proteins that facilitate infection by manipulating plant immunity. Computational programs have been developed that identify eff...

vir2vec: A Viral Genome-Wide Viral Embedding

Genomic language models (gLMs) have recently emerged as powerful numerical surrogates for DNA, but existing architectures are largely focused on human...

Viral Sentry AI (VirSentAI) - Automated Zoonotic Surveillance & Drug Repurposing Agent

Zoonotic viruses capable of jumping from animal reservoirs into human populations represent a persistent and unpredictable menace to global health. To...

Evaluating Deep Learning Based Structure Prediction Methods on Antibody-Antigen Complexes

AlphaFold2 significantly improved the prediction of protein complex structures. However, its accuracy is lower for interactions without coevolutionary...

Moremi Bio Agent: Using Neisseria meningitidis Reference Data For The Double Blinded Validation of A General Purpose Biology-Trained Reasoning Model for Pathogen and Antigen Discovery

Antibodies serve as vital diagnostic and therapeutic agents due to their exceptional specificity toward antigenic targets. Mapping antibody–antigen in...

Efficient Classification of Pulmonary Pneumonia and Tuberculosis Alongside Normal and Non-X-ray Images with Minimal Resources and Maximum Accuracy

Pneumonia, primarily caused by Streptococcus pneumoniae, and tuberculosis (TB), caused by Mycobacterium tuberculosis, continue to present significant ...