AIMC Topic: Sequence Analysis, DNA

Clear Filters Showing 211 to 220 of 274 articles

Coding genomes with gapped pattern graph convolutional network.

Bioinformatics (Oxford, England) Mar 29, 2024
MOTIVATION: Genome sequencing technologies reveal a huge amount of genomic sequences. Neural network-based methods can be prime candidates for retrieving insights from these sequences because of their applicability to large and diverse datasets. Howe...
Genome Algorithms Animals Genomics Sequence Analysis, DNA Neural Networks, Computer Software Humans
View on PubMed DOI

NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data.

Bioinformatics (Oxford, England) Mar 4, 2024
MOTIVATION: Structural variants (SVs) play a causal role in numerous diseases but can be difficult to detect and accurately genotype (determine zygosity) with short-read genome sequencing data (SRS). Improving SV genotyping accuracy in SRS data, part...
Software High-Throughput Nucleotide Sequencing Deep Learning Genome, Human Humans Genotype Genomic Structural Variation Sequence Analysis, DNA
View on PubMed DOI

Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2024
This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a non-gradient neural network. Biological sequences can be viewed as data components with higher non-f...
Humans Neural Networks, Computer Computational Biology Sequence Analysis, DNA DNA Algorithms Deep Learning DNA Barcoding, Taxonomic
View on PubMed DOI

Achieving pan-microbiome biological insights via the dbBact knowledge base.

Nucleic acids research Jul 21, 2023
16S rRNA amplicon sequencing provides a relatively inexpensive culture-independent method for studying microbial communities. Although thousands of such studies have examined diverse habitats, it is difficult for researchers to use this vast trove of...
Microbiota Knowledge Bases Bacteria DNA, Bacterial RNA, Ribosomal, 16S Sequence Analysis, DNA
View on PubMed DOI

Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.

Briefings in bioinformatics Mar 19, 2023
Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair res...
Chromatin Immunoprecipitation Chromatin Immunoprecipitation Sequencing DNA-Binding Proteins Binding Sites Software Deep Learning Sequence Analysis, DNA Algorithms
View on PubMed DOI

Deep Learning on Chromatin Accessibility.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
DNA accessibility has been a powerful tool in locating active regulatory elements in a cell type, but dissecting the combinatorial logic within these regulatory elements has been a continued challenge in the field. Deep learning models have been show...
Deep Learning Chromatin Genomics DNA Sequence Analysis, DNA High-Throughput Nucleotide Sequencing
View on PubMed DOI

Deep learning-assisted genome-wide characterization of massively parallel reporter assays.

Nucleic acids research Nov 11, 2022
Massively parallel reporter assay (MPRA) is a high-throughput method that enables the study of the regulatory activities of tens of thousands of DNA oligonucleotides in a single experiment. While MPRA experiments have grown in popularity, their small...
DNA Genome, Human Regulatory Sequences, Nucleic Acid Deep Learning Sequence Analysis, DNA Humans
View on PubMed DOI

DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome.

Bioinformatics (Oxford, England) Oct 14, 2022
MOTIVATION: Metagenomics is the study of microbiomes using DNA sequencing. A microbiome consists of an assemblage of microbes that is associated with a 'theater of activity' (ToA). An important question is, to what degree does the taxonomic and funct...
Sequence Analysis, DNA Metagenome Algorithms Microbiota Deep Learning Metagenomics
View on PubMed DOI

DeNovoCNN: a deep learning approach to de novo variant calling in next generation sequencing data.

Nucleic acids research Sep 23, 2022
De novo mutations (DNMs) are an important cause of genetic disorders. The accurate identification of DNMs from sequencing data is therefore fundamental to rare disease research and diagnostics. Unfortunately, identifying reliable DNMs remains a major...
High-Throughput Nucleotide Sequencing Deep Learning Exome Sequencing Sequence Analysis, DNA
View on PubMed DOI

MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach.

Briefings in bioinformatics Sep 20, 2022
Structural variations (SVs) play important roles in human genetic diversity; deletions and insertions are two common types of SVs that have been proven to be associated with genetic diseases. Hence, accurately detecting and genotyping SVs is signific...
Humans Genome, Human Sequence Analysis, DNA Deep Learning Software High-Throughput Nucleotide Sequencing Genotyping Techniques Genotype
View on PubMed DOI
Popular Topics
Recent Journals