AIMC Topic: Genes, Fungal
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Machine learning reveals genes impacting oxidative stress resistance across yeasts.
Nature communications
Jul 1, 2025
Reactive oxygen species (ROS) are highly reactive molecules encountered by yeasts during routine metabolism and during interactions with other organisms, including host infection. Here, we characterize the variation in resistance to the ROS-inducing ...
Landscape of essential growth and fluconazole-resistance genes in the human fungal pathogen Cryptococcus neoformans.
PLoS biology
May 22, 2025
Fungi can cause devastating invasive infections, typically in immunocompromised patients. Treatment is complicated both by the evolutionary similarity between humans and fungi and by the frequent emergence of drug resistance. Studies in fungal pathog...
Identifying longevity associated genes by integrating gene expression and curated annotations.
PLoS computational biology
Nov 30, 2020
Aging is a complex process with poorly understood genetic mechanisms. Recent studies have sought to classify genes as pro-longevity or anti-longevity using a variety of machine learning algorithms. However, it is not clear which types of features are...
Hierarchy and levels: analysing networks to study mechanisms in molecular biology.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Feb 24, 2020
Network representations are flat while mechanisms are organized into a hierarchy of levels, suggesting that the two are fundamentally opposed. I challenge this opposition by focusing on two aspects of the ways in which large-scale networks constructe...
Gene Essentiality Analyzed by Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of .
mBio
Oct 30, 2018
Knowing the full set of essential genes for a given organism provides important information about ways to promote, and to limit, its growth and survival. For many non-model organisms, the lack of a stable haploid state and low transformation efficien...
Effects and inhibition mechanism of phenazine-1-carboxamide on the mycelial morphology and ultrastructure of Rhizoctonia solani.
Pesticide biochemistry and physiology
Oct 24, 2017
The purpose of this research was to explore the effect of phenazine-1-carboxamide (PCN) on Rhizoctonia solani and to elucidate its mechanisms of action. The toxicity of PCN to R. solani was measured using a growth rate method. The results indicated t...
Investigating the antifungal activity and mechanism of a microbial pesticide Shenqinmycin against Phoma sp.
Pesticide biochemistry and physiology
Aug 30, 2017
Tea white scab (TWS) is a major disease affecting tea trees in mid-elevation regions and often occurs during rainy seasons with low temperatures. This disease is caused by the fungal pathogen Phoma sp. TWS can infect young stems, tender leaves, and t...
Tandem Mass Spectrometry
Nanotechnology
Energy Metabolism
Plant Diseases
Gene Expression Regulation, Fungal
Fungal Proteins
Chromatography, Liquid
Homeostasis
Microbial Sensitivity Tests
Camellia sinensis
Genes, Fungal
Down-Regulation
Mycelium
RNA, Messenger
Oxidation-Reduction
Up-Regulation
Phenazines
Ascomycota
Culture Media
Antifungal Agents
Plant Structures
Semi-Supervised Multi-View Learning for Gene Network Reconstruction.
PloS one
Dec 7, 2015
The task of gene regulatory network reconstruction from high-throughput data is receiving increasing attention in recent years. As a consequence, many inference methods for solving this task have been proposed in the literature. It has been recently ...
Integrating biological knowledge based on functional annotations for biclustering of gene expression data.
Computer methods and programs in biomedicine
Mar 18, 2015
Gene expression data analysis is based on the assumption that co-expressed genes imply co-regulated genes. This assumption is being reformulated because the co-expression of a group of genes may be the result of an independent activation with respect...
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.
Database : the journal of biological databases and curation
Mar 8, 2015
Enzymes active on components of lignocellulosic biomass are used for industrial applications ranging from food processing to biofuels production. These include a diverse array of glycoside hydrolases, carbohydrate esterases, polysaccharide lyases and...
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