Allergy

Characterizing spatial functional microniches with SpaceTravLR

The advent of spatial omics has revolutionized our understanding of tissue biology; however, these technologies remain largely descriptive and do not capture how changes in gene regulation propagate across spatial neighborhoods. While in-silico perturbation methods and foundation models aim to model the impact of genetic perturbations, these methods are limited to single-cell approaches that lack ...

Predictive power of different Akkermansia phylogroups in clinical response to PD-1 blockade against non-small cell lung cancer

Immune checkpoint blockade has emerged as a promising form of cancer therapy. However, only some patients respond to checkpoint inhibitors, while a significant proportion of patients do not, calling for the discovery of reliable biomarkers. Recent studies reported the importance of the gut microbiome in the clinical response to PD-1 blockade against non-small cell lung cancer (NSCLC), highlighting...

A unified language model bridging de novo and fragment-based 3D molecule design delivers potent CBL-B inhibitors for cancer treatment

The rational design of small molecules is central to drug discovery, yet current artificial intelligence (AI) methodologies for generating three-dimen...

IMMUNIA: A Multi-LLM Reasoning Agent for Immunoregulatory Surfaceome Discovery

Biomarker discovery for immunotherapy often requires reasoning across complex immune contexts. We present IMMUNIA, a multi-large-language-model (multi...

From Tasks to Topology: Dorsal and Ventral Streams Emerge in Optimized Neural Networks

The primate visual system is organized into dorsal and ventral pathways, classically linked to visuomotor control and perception. A long-standing ques...

Targeting peptide–MHC complexes with designed T cell receptors and antibodies

Class I major histocompatibility complexes (MHCs), expressed on the surface of all nucleated cells, present peptides derived from intracellular protei...

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...

A transcription factor-responsive enhancer discovery platform for targeted immunotherapy

Synthetic enhancers with high specificity are crucial for therapeutic gene control. Although existing experimental screens and machine learning-based ...

A Computational Pipeline for Glioblastoma Vaccine Development: Integrating Novel Omics-Driven OIP5 Target Discovery to Create a Deep Learning-Based Immunogenicity Framework for Personalized Immunotherapy

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

Successful Predictive Modeling of Pollen Fitness Phenotypes Is Enabled by Measures of Expression Specificity

The ability to predict phenotypes from genotypes in multicellular organisms remains limited despite rapid advances in genotyping and phenotyping metho...

Assessing Inflammatory Protein Biomarkers in COPD Subjects with and without Alpha-1 Antitrypsin Deficiency

Individuals homozygous for the Alpha-1 Antitrypsin (AAT) Z allele (Pi*ZZ) exhibit heterogeneity in COPD risk. COPD occurrence in non-smokers with AAT ...

Automated Detection of Faciobrachial Dystonic Seizures Related Events in LGI1 Autoimmune Encephalitis Patients with Wearables

To evaluate the potential of wrist-worn wearable devices to detect and quantify Faciobrachial Dystonic Seizures (FBDS) and related events associated w...

Proteome-wide autoantibody screening and holistic autoantigenomic analysis unveil COVID-19 signature of autoantibody landscape

This study presents “aUToAntiBody Comprehensive Database (UT-ABCD)”, a comprehensive catalog of autoantibody profiles in 284 human individuals. The su...

CNNeoPP: A Deep Learning Pipeline for Personalized Neoantigen Prediction and Liquid Biopsy Applications

Neoantigens have emerged as promising targets for personalized cancer immunotherapy. However, accurate identification of immunogenic neoantigens remai...

Activation status of immune cells in the airway is a defining feature of severe fungal asthma

Airborne fungi are potent inducers of respiratory disease and cause the debilitating conditions severe asthma with fungal sensitisation (SAFS) and all...

ROC Analysis of Biomarker Combinations in Fragile X Syndrome-Specific Clinical Trials: Evaluating Treatment Efficacy via Exploratory Biomarkers

Fragile X Syndrome (FXS) is a rare neurodevelopmental disorder caused by a trinucleotide repeat expansion on the 5’ untranslated region of the FMR1 ge...

An exploratory machine learning study on paediatric abdominal pain phenotyping and prediction

The exact mechanisms underlying paediatric abdominal pain (AP) remain unclear due to patient heterogeneity. This study aimed to identify AP phenotypes...

The Golgi Apparatus as an Arbiter of Oncofetal Reprogramming: A Systematic Review and Meta-Analysis Linking Embryonic Germ Layer Origin to the Post-Translational Modification Landscape of Cancer

Post-translational modifications (PTMs) represent a fourth dimension of the genetic code, orchestrated by the Golgi apparatus and central to the biolo...

Artificial Intelligence (AI)-Powered H&E Whole-Slide Image Analysis of Tertiary Lymphoid Structure (TLS) Independently Predicts Survival in Patients with Non-Small Cell Lung Cancer (NSCLC) Receiving Immunotherapy

Tertiary lymphoid structures (TLSs) within the tumor microenvironment have emerged as potential indicators of treatment response to immune checkpoint ...

Machine Learning-Based Reconstruction of 2D MRI for Quantitative Morphometry in Epilepsy

Structural neuroimaging analyses require ‘research quality’ images, acquired with costly MRI acquisitions. Isotropic (3D-T1) images are desirable for ...