Fungal Infection

Easy to use and low cost leaf disease quantification workflow using Ilastik

Accurate and reproducible assessment of foliar disease severity is essential for evaluating the performance of heterogeneous plant communities and understanding host-pathogen interactions. However, traditional visual scoring methods remain subjective, with limited precision, and difficult to scale in large phenotyping experiments. Here, we present a semi-automated image analysis workflow designed ...

Modifying integrated nursery management through the lens of mycorrhizal ecology improves radiata pine seedling performance and reshapes root mycobiome structure at operational industry scale

Early management decisions in operational forestry are critical for plantation success because it strongly influences seedling quality at planting. Beyond shaping seedling morphology, nursery inputs can also restructure root-associated fungal communities which has consequences for nutrient acquisition, stress tolerance and disease suppression after planting. In this study, we altered nutrient and ...

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...

Hybrid CNN and Multi-Head Attention Model for Analyzing Epigenetic Mechanisms and Gene Expression Across Fungal Phylogenetic Distances

Understanding gene expression is crucial for optimizing biological processes in bioeconomic processes, human health, and environmental regulation. Epi...

Advancing ab initio genome annotation with OrionGeno

The rapid expansion of eukaryotic genome sequencing has created an urgent demand for scalable and accurate gene annotation, particularly for large-sca...

GenPept-Curated-2025: A Benchmark Dataset for Antimicrobial Peptide Prediction with Homology-Controlled Partitioning

Antimicrobial peptides (AMPs) are promising therapeutic candidates against rising antimicrobial resistance, yet progress in AMP prediction is hampered...

Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

Eukaryotic genome annotation is currently bottlenecked by limitations in the generality, scalability and accuracy of computational methods. Deep learn...

OpenAc4C: A gateway to decode the landscape, regulation and pathogenesis of N4-acetylcytidine (ac4C) epitranscriptome

N4-acetylcytidine (ac4C) is an ancient and highly conserved chemical marker found in all domains of life. Recent advancements in sequencing techniques...

Plant Taxonomy Meets Plant Counting: A Fine-Grained, Taxonomic Dataset for Counting Hundreds of Plant Species

Visually cataloging and quantifying the natural world requires pushing the boundaries of both detailed visual classification and counting at scale. De...

Hidden Diversity in Yeast tRNAs: Comparative Genomics and Modification Mapping in a Eukaryotic Subphylum

tRNA are adapter molecules with an integral role in translation and further roles in stress adaptation. Processing of tRNA is tightly regulated and in...

kinGEMs: A Robust and Scalable Framework forResource-Constraint Models through StochasticTuning of Deep Learning-Predicted KineticParameters

The construction of accurate enzyme-constrained genome-scale models (ecGEMs) remains a critical challenge in systems biology, limited by sparse kineti...

Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales

Fungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens, and endophytes, yet their significance in marine environments is often u...

Genomic streamlining of seagrass-associated Colletotrichum sp. may be related to its adaptation to a marine monocot host

Colletotrichum spp. have a complicated history of association with land plants. Perhaps most well-known as plant pathogens for the devastating effect ...

REMAG: recovery of eukaryotic genomes from metagenomic data using contrastive learning

Metagenome-assembled genomes (MAGs) are central to exploring microbial communities. Yet, despite the relevance of protists and fungi to diverse ecosys...

A high-throughput method for measuring fungal growth rate on solid media using automated imaging and deep learning

Measuring the growth rate of filamentous fungi is an essential phenotype assay in fungal biology, enabling the comparison of nutrient-related fitness ...

Explainable AI for end-to-end pathogen target discovery and molecular design

Drug discovery is often constrained by target identification, a bottleneck especially acute in antimicrobial development and the fight against emergin...

MobileMold: A Smartphone-Based Microscopy Dataset for Food Mold Detection

Smartphone clip-on microscopes turn everyday devices into low-cost, portable imaging systems that can even reveal fungal structures at the microscopic...

Artefact-Aware Fungal Detection in Dermatophytosis: A Real-Time Transformer-Based Approach for KOH Microscopy

Dermatophytosis is commonly assessed using potassium hydroxide (KOH) microscopy, yet accurate recognition of fungal hyphae is hindered by artefacts, h...

Bootstrap resampling of mass spectral pairs with SpecReBoot reveals hidden molecular relationships

Mass spectral molecular networking (MN) has emerged as a key computational approach to organize and analyze the vast volumes of tandem mass spectromet...

NanoSimFormer: An end-to-end Transformer-based simulator for nanopore sequencing signal data

Nanopore sequencing has achieved a new standard of accuracy with the advent of R10.4.1 flow cell and high-performance Transformer-based basecalling mo...