AIMC Topic: Sequence Analysis, DNA

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Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model.

Journal of molecular biology
Enhancers are DNA regions that are responsible for controlling the expression of genes. Enhancers are usually found upstream or downstream of a gene, or even inside a gene's intron region, but are normally located at a distant location from the genes...

Ultra-fast deep-learned CNS tumour classification during surgery.

Nature
Central nervous system tumours represent one of the most lethal cancer types, particularly among children. Primary treatment includes neurosurgical resection of the tumour, in which a delicate balance must be struck between maximizing the extent of r...

Predicting pathogenic protein variants.

Science (New York, N.Y.)
Machine-learning algorithm uses structure prediction to spot disease-causing mutations.

Pharmacovariome scanning using whole pharmacogene resequencing coupled with deep computational analysis and machine learning for clinical pharmacogenomics.

Human genomics
BACKGROUND: This pilot study aims to identify and functionally assess pharmacovariants in whole exome sequencing data. While detection of known variants has benefited from pharmacogenomic-dedicated bioinformatics tools before, in this paper we have t...

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.

PLoS computational biology
The number of published metagenome assemblies is rapidly growing due to advances in sequencing technologies. However, sequencing errors, variable coverage, repetitive genomic regions, and other factors can produce misassemblies, which are challenging...

Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling.

Genome biology
BACKGROUND: Nanopore-based DNA sequencing relies on basecalling the electric current signal. Basecalling requires neural networks to achieve competitive accuracies. To improve sequencing accuracy further, new models are continuously proposed with new...

A Method for Predicting DNA Motif Length Based On Deep Learning.

IEEE/ACM transactions on computational biology and bioinformatics
A DNA motif is a sequence pattern shared by the DNA sequence segments that bind to a specific protein. Discovering motifs in a given DNA sequence dataset plays a vital role in studying gene expression regulation. As an important attribute of the DNA ...

Detecting genomic deletions from high-throughput sequence data with unsupervised learning.

BMC bioinformatics
BACKGROUND: Structural variation (SV), which ranges from 50 bp to [Formula: see text] 3 Mb in size, is an important type of genetic variations. Deletion is a type of SV in which a part of a chromosome or a sequence of DNA is lost during DNA replicati...

Operon Finder: A Deep Learning-based Web Server for Accurate Prediction of Prokaryotic Operons.

Journal of molecular biology
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...

RMSCNN: A Random Multi-Scale Convolutional Neural Network for Marine Microbial Bacteriocins Identification.

IEEE/ACM transactions on computational biology and bioinformatics
The abuse of traditional antibiotics has led to an increase in the resistance of bacteria and viruses. Similar to the function of antibacterial peptides, bacteriocins are more common as a kind of peptides produced by bacteria that have bactericidal o...