Genetics

BRIDGE: A Multi-organ Histo-ST Foundation Model Enables Virtual Spatial Transcriptomics for Enhanced Few-shot Cancer Diagnosis

Recent studies have explored generating virtual spatial transcriptomics (ST) profiles from histological images, offering a promising alternative to laboratory-measured molecular profiling. However, existing approaches predominantly rely on single-organ models and require substantial organ-specific training data, restricting their accuracy under challenging few-shot conditions in clincical practice...

Cumulative-Goodness Free-Riding in Forward-Forward Networks: Real, Repairable, but Not Accuracy-Dominant

Forward-Forward (FF) training allows each layer to learn from a local goodness criterion. In cumulative-goodness variants, however, later layers can inherit a task that earlier layers have already partially separated. We formalize this phenomenon as layer free-riding: under the softplus FF criterion, the class-discrimination gradient reaching block $d$ decays exponentially with the positive margin...

DINORANKCLIP: DINOv3 Distillation and Injection for Vision-Language Pretraining with High-Order Ranking Consistency

Contrastive language-image pretraining (CLIP) suffers from two structural weaknesses: the symmetric InfoNCE loss discards the relative ordering among ...

Multimorbidity increases susceptibility to myocardial injury following cardiac surgery via dysregulated macrophage activation and the development of a cardiomyopathy phenotype

Background: People with Multiple Long-Term Conditions (MLTC) experience higher rates of organ failure and death following cardiac surgery. The aim of ...

Bridging genomes and peptidomes: hybrid sequencing reveals conserved bioactive peptides in crustaceans

Endogenous peptides are critical regulators of signaling and immunity but remain difficult to characterize in organisms with incomplete genomic annota...

Metastatic Site Prediction in Breast Cancer using Kirchhoff's Law and Omics Knowledge Graph

Predicting the anatomical site of metastasis from a primary tumour remains an unsolved problem in breast cancer (BRCA) and metastatic disease more bro...

Gene-Modulated Network Diffusion for Improved Modeling of Amyloid-β Spread in Alzheimer's Disease

Understanding the pathogenesis of amyloid-{beta} pathology in Alzheimer's Disease (AD) proves to be a challenge. In this work, we expand upon the appl...

Novel linkage disequilibrium-based genotype-by-environmental interaction method for genomic prediction of cotton yield and fibre quality traits

Genomic prediction (GP) across diverse environments has a potential to accelerate genetic gain in cotton breeding programs. A major challenge in GP is...

Evaluating Reference-Independent Pipelines for the Detection of Spreading Organisms in Metagenomic Datasets

The emergence of unidentified pathogens, or "Disease X," poses a significant threat to global health, necessitating the development of proactive surve...

Integrated Multi-Omics Analysis for the Identification of Disease-Associated Variations and Prognostic Biomarkers in Triple-Negative Breast Cancer (TNBC)

Background: Triple-negative breast cancer (TNBC) exhibits substantial molecular heterogeneity and lacks targeted receptor therapies. Single-omic appro...

Tumor cell specific total mRNA expression informed neural networks predicts cancer progression

Inferring tumor molecular phenotypes from high-dimensional multi-omic data is a fundamental challenge in computational biology. Current methods for es...

PEPR-GNN: Perturbation-Enhancer-Promoter-RNA Graph Neural Networks for Multiome Perturb-Seq modeling of regulomes

Cellular reprogramming is a complex interplay between perturbations and regulatory elements, culminating in gene expression changes. Current computati...

Extracting adverse event nature, severity, timelines and resulting interventions from clinical notes of patients receiving CAR-T therapy using large language models.

Chimeric Antigen Receptor T-cell (CAR-T) therapy, where genetically engineered patient T cells target tumor antigens, has transformed care for hematol...

A Pilot Evaluation of Open-Weight Large Language Models for Screening RNA-seq Metadata in Public Databases

Although the Gene Expression Omnibus and other public repositories are expanding rapidly, curation across these databases has not kept pace. Data reus...

EffectorGeneP: accurate gene annotation in pathogen genomes from infection transcriptomes

Accurate gene annotation is crucial for inference of biological knowledge from genomes. However, non-canonical genes such as orphan or single-exon gen...

Comparative single-cell transcriptomic roadmap of mammalian fetal ovarian development

Early ovarian development establishes the cellular basis of female reproduction, yet its cellular composition and developmental dynamics remain poorly...

Machine learning approaches for the identification and analysis of enterotoxin genes in Staphylococcus aureus genomes

Staphylococcus aureus produces a broad range of enterotoxins that act as superantigens, disrupting host immune responses and resulting in a myriad of ...

Combinatorial epigenomic patterns define regulatory programs underlying disease heterogeneity

Disease is a heterogeneous process that involves multiple organs and cell types. Understanding how genomic variation contributes to disease requires a...

Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data

Assays coupling high-throughput lineage tracing with single-cell transcriptomics are transforming studies of development and disease biology, revealin...

Functional Profiling of Thousands of Sequence-Diverse Protease Homologs with GROQ-seq

High-quality datasets that span broad sequence diversity are essential for understanding protein sequence-function relationships beyond local mutation...