AIMC Topic: Gene Expression Regulation, 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 ...
Regulation and induction of fungal secondary metabolites: a comprehensive review.
Archives of microbiology
Jul 1, 2025
Fungal secondary metabolites (SMs) represent a vast reservoir of bioactive compounds with immense therapeutic, agricultural, and industrial potential. These small molecules, including antibiotics, immunosuppressants, and anticancer agents, are synthe...
Divergence in a eukaryotic transcription factor's co-TF dependence involves multiple intrinsically disordered regions.
Nature communications
Jun 18, 2025
Combinatorial control by transcription factors (TFs) is central to eukaryotic gene regulation, yet its mechanism, evolution, and regulatory impact are not well understood. Here we use natural variation in the yeast phosphate starvation (PHO) response...
Closed-loop cycles of experiment design, execution, and learning accelerate systems biology model development in yeast.
Proceedings of the National Academy of Sciences of the United States of America
Aug 16, 2019
One of the most challenging tasks in modern science is the development of systems biology models: Existing models are often very complex but generally have low predictive performance. The construction of high-fidelity models will require hundreds/tho...
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...
Gene Expression Regulation, Fungal
Tandem Mass Spectrometry
Chromatography, Liquid
Genes, Fungal
Plant Diseases
Microbial Sensitivity Tests
Camellia sinensis
RNA, Messenger
Fungal Proteins
Oxidation-Reduction
Phenazines
Antifungal Agents
Plant Structures
Culture Media
Down-Regulation
Up-Regulation
Homeostasis
Mycelium
Ascomycota
Nanotechnology
Energy Metabolism
Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast.
Nucleic acids research
Feb 22, 2016
Understanding telomere length maintenance mechanisms is central in cancer biology as their dysregulation is one of the hallmarks for immortalization of cancer cells. Important for this well-balanced control is the transcriptional regulation of the te...
Network stratification analysis for identifying function-specific network layers.
Molecular bioSystems
Feb 16, 2016
A major challenge of systems biology is to capture the rewiring of biological functions (e.g. signaling pathways) in a molecular network. To address this problem, we proposed a novel computational framework, namely network stratification analysis (Ne...
Transcription, Genetic
Cluster Analysis
Models, Biological
Gene Expression Regulation, Fungal
Liver Neoplasms
Carcinoma, Hepatocellular
Protein Interaction Maps
Gene Regulatory Networks
Computational Biology
Gene Expression Regulation, Neoplastic
Signal Transduction
Neural Networks, Computer
Algorithms
Disease Progression
Humans
Gene Expression Profiling
Detection of overlapping protein complexes in gene expression, phenotype and pathways of Saccharomyces cerevisiae using Prorank based Fuzzy algorithm.
Gene
Jan 22, 2016
Proteins show their functional activity by interacting with other proteins and forms protein complexes since it is playing an important role in cellular organization and function. To understand the higher order protein organization, overlapping is an...
Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.
BMC bioinformatics
Jan 11, 2016
BACKGROUND: A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental and intracellular signals, and it further transmits signals that control cellular responses, including a tightly con...
The pan-genome of Saccharomyces cerevisiae.
FEMS yeast research
Nov 1, 2019
Understanding genotype-phenotype relationship is fundamental in biology. With the benefit from next-generation sequencing and high-throughput phenotyping methodologies, there have been generated much genome and phenome data for Saccharomyces cerevisi...
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