Genetics

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models

The rapid scaling of Genomic Foundation Models (GFMs) has created a critical need for standardized evaluation frameworks. Current benchmarking practices are often fragmented, relying on model-specific preprocessing and inconsistent metric implementations that hinder reproducible comparisons. We present GFMBench-API, a high-level Python interface designed to unify the evaluation lifecycle of GFMs. ...

Integrated Molecular and AI-Based Diagnostics for Banana Diseases: Development, Optimization, and Field Deployment of LAMP and Computer Vision Technologies

Banana and plantain (Musa spp.) production in Sub-Saharan Africa is severely constrained by multiple diseases, with Banana bunchy top virus (BBTV) representing the most devastating viral threat. Inadequate diagnostic infrastructure limits effective management, particularly for asymptomatic infections disseminated through informal planting material exchange. This study presents an integrated diagno...

Benchmarking Large Language Models for Predicting Therapeutic Antisense Oligonucleotide Efficacy

Antisense oligonucleotides (ASOs) are a promising class of therapeutic agents capable of selectively modulating gene expression and treating a wide ra...

Guide-Guard: Off-Target Predicting in CRISPR Applications

With the introduction of cyber-physical genome sequencing and editing technologies, such as CRISPR, researchers can more easily access tools to invest...

Parameter-free representations outperform single-cell foundation models on downstream benchmarks

Single-cell RNA sequencing (scRNA-seq) data exhibit strong and reproducible statistical structure. This has motivated the development of large-scale f...

Deep Agentic Variant Prioritisation for Expert Level Genetic Diagnosis Fast at Scale

Abstract. Genetic diagnosis remains a formidable challenge characterized by a diagnostic odyssey that spans years, with over half of rare disease pati...

Development and cross-tissue validation of a methylation profile score for the cortisol response to stress

Hypothalamic-pituitary-adrenal axis (HPA axis) dysregulation is a risk factor for poor mental and physical health. Animal studies indicate that DNA me...

Resolving Genome-to-Phenotype Links in Bacteria: Machine-Learned Inference from Downsampled k-mer Representations

Standard approaches to bacterial phenotyping often treat the entire genome as the fundamental unit of information, resulting in high-dimensional input...

Multi-modal tissue-aware graph neural network for in silico genetic discovery

Understanding how perturbations influence gene function in a tissue-specific manner is key to uncovering novel drug targets. However, current computat...

CLM-X: A multimodal single-cell foundation model with flexible multi-way Transformer for unified scRNA-seq and scATAC-seq analysis

Advances in single-cell multimodal profiling have enabled a more systematic analysis of cellular biology, yet the rapid accumulation of large-scale, h...

MGIDI selection and machine learning reveal harvest index driving traits in sodium azide-induced rice mutants with SSR-based genetic diversity

Sodium azide mutagenesis offers a powerful approach to generate genetic diversity for rice improvement, yet comprehensive characterization of mutant p...

A visualization framework for cell division activity and orientation in pre-anthesis ovaries of Prunus species

Fruit size and shape, which influence horticultural quality, are determined by the number and the size of the cells in the local region. In fruit tree...

Summary statistics and approximate bayesian computation are comparable to convolutional neural networks for inferring times to fixation

Detecting signatures of positive selection in genomes is a common application of population genetics and one of the most influential models for this t...

Biological Foundation Models Enable CRISPR Array Detection Without Metagenomic Assembly

Accurate identification of CRISPR arrays is essential for studying prokaryotic adaptive immunity, yet existing tools struggle with short-read sequenci...

Evaluating Single-Cell Perturbation Response Models Is Far from Straightforward

Predicting cellular responses to genetic and chemical perturbations remains a central challenge in single-cell biology and a key step toward building ...

RNAiSpline: A Deep learning model for siRNA efficacy prediction

RNA interference (RNAi) is a crucial biological post-transcriptional gene silencing mechanism where small interfering RNA (siRNA) guides RNA-induced s...

Comparing Modelling Architectures in the context of EGFR Status Classification in Non Small Cell Lung Cancer

Radiogenomics enables the non invasive characterisation of the genomic and molecular properties of tumours, with epidermal growth factor receptor (EGF...

A New Paradigm for Genome-wide DNA Methylation Prediction Without Methylation Input

DNA methylation (DNAm) is a key epigenetic modification that regulates gene expression and is pivotal in development and disease. However, profiling D...

Scaling Laws for Masked-Reconstruction Transformers on Single-Cell Transcriptomics

Neural scaling laws -- power-law relationships between loss, model size, and data -- have been extensively documented for language and vision transfor...

Programmable RNA detection generates DNA barcodes for multiplexed phage-host interaction screening

Here, we introduce Detectrons, modular biosensors that couples programmable toehold switches with retron-mediated reverse transcription to transduce R...