AIMC Topic: Eukaryota
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Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.
BMC bioinformatics
Dec 15, 2016
BACKGROUND: MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays...
Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules.
BMC bioinformatics
Mar 18, 2016
BACKGROUND: It is generally acknowledged that a functional understanding of a biological system can only be obtained by an understanding of the collective of molecular interactions in form of biological networks. Protein networks are one particular n...
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins.
Bioinformatics (Oxford, England)
Jun 16, 2015
MOTIVATION: Molecular recognition of N-terminal targeting peptides is the most common mechanism controlling the import of nuclear-encoded proteins into mitochondria and chloroplasts. When experimental information is lacking, computational methods can...
An improved Artificial Protozoa Optimizer for CNN architecture optimization.
Neural networks : the official journal of the International Neural Network Society
Jul 1, 2025
In this paper, we propose a novel neural architecture search (NAS) method called MAPOCNN, which leverages an enhanced version of the Artificial Protozoa Optimizer (APO) to optimize the architecture of Convolutional Neural Networks (CNNs). The APO is ...
VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.
Briefings in bioinformatics
Nov 22, 2024
This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus ide...
Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning.
FEMS microbiology ecology
Jul 12, 2024
Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composit...
IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning.
GigaScience
Jan 2, 2024
BACKGROUND: The virome obtained through virus-like particle enrichment contains a mixture of prokaryotic and eukaryotic virus-derived fragments. Accurate identification and classification of these elements are crucial to understanding their roles and...
The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics.
Proceedings of the National Academy of Sciences of the United States of America
Feb 15, 2022
Intricate networks of single-celled eukaryotes (protists) dominate carbon flow in the ocean. Their growth, demise, and interactions with other microorganisms drive the fluxes of biogeochemical elements through marine ecosystems. Mixotrophic protists ...
Tiara: deep learning-based classification system for eukaryotic sequences.
Bioinformatics (Oxford, England)
Jan 3, 2022
MOTIVATION: With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding ...
SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning.
Briefings in bioinformatics
Sep 2, 2021
MOTIVATION: mRNA location corresponds to the location of protein translation and contributes to precise spatial and temporal management of the protein function. However, current assignment of subcellular localization of eukaryotic mRNA reveals import...
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