AIMC Topic: Saccharomyces cerevisiae Proteins
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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...
[PSI]-CIC: A Deep-Learning Pipeline for the Annotation of Sectored Saccharomyces cerevisiae Colonies.
Bulletin of mathematical biology
Dec 6, 2024
The prion phenotype in yeast manifests as a white, pink, or red color pigment. Experimental manipulations destabilize prion phenotypes, and allow colonies to exhibit (red) sectored phenotypes within otherwise completely white colonies. Further inve...
Graph-based machine learning model for weight prediction in protein-protein networks.
BMC bioinformatics
Nov 8, 2024
Proteins interact with each other in complex ways to perform significant biological functions. These interactions, known as protein-protein interactions (PPIs), can be depicted as a graph where proteins are nodes and their interactions are edges. The...
Deep-learning-based design of synthetic orthologs of SH3 signaling domains.
Cell systems
Aug 5, 2024
Evolution-based deep generative models represent an exciting direction in understanding and designing proteins. An open question is whether such models can learn specialized functional constraints that control fitness in specific biological contexts....
Automated quantification of vacuole fusion and lipophagy in from fluorescence and cryo-soft X-ray microscopy data using deep learning.
Autophagy
Oct 31, 2023
During starvation in the yeast vacuolar vesicles fuse and lipid droplets (LDs) can become internalized into the vacuole in an autophagic process named lipophagy. There is a lack of tools to quantitatively assess starvation-induced vacuole fusion and...
Computed structures of core eukaryotic protein complexes.
Science (New York, N.Y.)
Dec 10, 2021
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...
Multiprotein Complexes
Acyltransferases
Homologous Recombination
Chromosome Segregation
Ligases
DNA Repair
Protein Biosynthesis
Ribosomes
Ubiquitin
Protein Interaction Mapping
Saccharomyces cerevisiae Proteins
Computational Biology
Proteome
Membrane Proteins
Computer Simulation
Protein Conformation
Deep Learning
Saccharomyces cerevisiae
Protein Interaction Maps
Evolution, Molecular
Models, Molecular
Protein Abundance Prediction Through Machine Learning Methods.
Journal of molecular biology
Sep 23, 2021
Proteins are responsible for most physiological processes, and their abundance provides crucial information for systems biology research. However, absolute protein quantification, as determined by mass spectrometry, still has limitations in capturing...
A Deep Learning Framework for Identifying Essential Proteins by Integrating Multiple Types of Biological Information.
IEEE/ACM transactions on computational biology and bioinformatics
Feb 3, 2021
Computational methods including centrality and machine learning-based methods have been proposed to identify essential proteins for understanding the minimum requirements of the survival and evolution of a cell. In centrality methods, researchers are...
Using Weighted Extreme Learning Machine Combined With Scale-Invariant Feature Transform to Predict Protein-Protein Interactions From Protein Evolutionary Information.
IEEE/ACM transactions on computational biology and bioinformatics
Jan 10, 2020
Protein-Protein Interactions (PPIs) play an irreplaceable role in biological activities of organisms. Although many high-throughput methods are used to identify PPIs from different kinds of organisms, they have some shortcomings, such as high cost an...
Identification of self-interacting proteins by integrating random projection classifier and finite impulse response filter.
BMC genomics
Dec 27, 2019
BACKGROUND: Identification of protein-protein interactions (PPIs) is crucial for understanding biological processes and investigating the cellular functions of genes. Self-interacting proteins (SIPs) are those in which more than two identical protein...
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