AIMC Topic: Prokaryotic Cells
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Accurate prediction of absolute prokaryotic abundance from DNA concentration.
Cell reports methods
Apr 28, 2025
Quantification of the absolute microbial abundance in a human stool sample is crucial for a comprehensive understanding of the microbial ecosystem, but this information is lost upon metagenomic sequencing. While several methods exist to measure absol...
DeepReg: a deep learning hybrid model for predicting transcription factors in eukaryotic and prokaryotic genomes.
Scientific reports
Apr 21, 2024
Deep learning models (DLMs) have gained importance in predicting, detecting, translating, and classifying a diversity of inputs. In bioinformatics, DLMs have been used to predict protein structures, transcription factor-binding sites, and promoters. ...
Operon Finder: A Deep Learning-based Web Server for Accurate Prediction of Prokaryotic Operons.
Journal of molecular biology
Dec 14, 2022
Operons are groups of consecutive genes that transcribe together under the regulation of a common promoter. They influence protein regulation and various physiological pathways, making their accurate detection desirable. The detection of operons thro...
Predicting essential genes of 41 prokaryotes by a semi-supervised method.
Analytical biochemistry
Aug 19, 2020
Essential genes are vitally important to the survival and reproduction of organisms. Many machine learning methods have been widely employed to predict essential genes and have obtained satisfactory results. However, most of these methods are supervi...
ProNA2020 predicts protein-DNA, protein-RNA, and protein-protein binding proteins and residues from sequence.
Journal of molecular biology
Mar 4, 2020
The intricate details of how proteins bind to proteins, DNA, and RNA are crucial for the understanding of almost all biological processes. Disease-causing sequence variants often affect binding residues. Here, we described a new, comprehensive system...
AGONOTES: A Robot Annotator for Argonaute Proteins.
Interdisciplinary sciences, computational life sciences
Nov 18, 2019
The argonaute protein (Ago) exists in almost all organisms. In eukaryotes, it functions as a regulatory system for gene expression. In prokaryotes, it is a type of defense system against foreign invasive genomes. The Ago system has been engineered fo...
Prediction and functional analysis of prokaryote lysine acetylation site by incorporating six types of features into Chou's general PseAAC.
Journal of theoretical biology
Oct 23, 2018
Lysine acetylation is one of the most important types of protein post-translational modifications (PTM) that are widely involved in cellular regulatory processes. To fully understand the regulatory mechanism of acetylation, identification of acetylat...
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.
Journal of biomedical semantics
Nov 23, 2017
BACKGROUND: High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires integrative tools and methods...
Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks.
PloS one
Feb 3, 2017
Accurate computational identification of promoters remains a challenge as these key DNA regulatory regions have variable structures composed of functional motifs that provide gene-specific initiation of transcription. In this paper we utilize Convolu...
MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins.
Bioinformatics (Oxford, England)
Jul 4, 2016
MOTIVATION: Two-component systems (TCS) are the main signalling pathways of prokaryotes, and control a wide range of biological phenomena. Their functioning depends on interactions between TCS proteins, the specificity of which is poorly understood.
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