AIMC Topic: Base Sequence

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BAT-Net: An enhanced RNA Secondary Structure prediction via bidirectional GRU-based network with attention mechanism.

Computational biology and chemistry Sep 1, 2022
BACKGROUND: RNA Secondary Structure (RSS) has drawn growing concern, both for their pivotal roles in RNA tertiary structures prediction and critical effect in penetrating the mechanism of functional non-coding RNA. Computational techniques that can r...
Base Sequence Protein Structure, Secondary Neural Networks, Computer RNA
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Automated filtering of genome-wide large deletions through an ensemble deep learning framework.

Methods (San Diego, Calif.) Aug 28, 2022
Computational methods based on whole genome linked-reads and short-reads have been successful in genome assembly and detection of structural variants (SVs). Numerous variant callers that rely on linked-reads and short reads can detect genetic variati...
Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Humans Deep Learning Genome, Human Sequence Analysis Base Sequence
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Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks.

Proceedings of the National Academy of Sciences of the United States of America Aug 26, 2022
Taxonomic classification, that is, the assignment to biological clades with shared ancestry, is a common task in genetics, mainly based on a genome similarity search of large genome databases. The classification quality depends heavily on the databas...
Base Sequence Genome DNA DNA Barcoding, Taxonomic Software Algorithms Deep Learning Genomics
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Development and Application of Two Inducible Expression Systems for Streptococcus suis.

Microbiology spectrum Jun 27, 2022
Streptococcus suis is an important zoonotic bacterial pathogen posing a threat to the pig industry as well as public health, for which the mechanisms of growth and cell division remain largely unknown. Developing convenient genetic tools that can ach...
Streptococcus suis Base Sequence Promoter Regions, Genetic Isopropyl Thiogalactoside Cell Division Swine Bacterial Proteins Animals
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EMDLP: Ensemble multiscale deep learning model for RNA methylation site prediction.

BMC bioinformatics Jun 8, 2022
BACKGROUND: Recent research recommends that epi-transcriptome regulation through post-transcriptional RNA modifications is essential for all sorts of RNA. Exact identification of RNA modification is vital for understanding their purposes and regulato...
Methylation Base Sequence Natural Language Processing RNA Deep Learning
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Deep learning modeling mA deposition reveals the importance of downstream cis-element sequences.

Nature communications May 17, 2022
The N-methyladenosine (mA) modification is deposited to nascent transcripts on chromatin, but its site-specificity mechanism is mostly unknown. Here we model the mA deposition to pre-mRNA by iM6A (intelligent mA), a deep learning method, demonstratin...
Methylation Base Sequence Regulatory Sequences, Nucleic Acid Codon, Terminator Deep Learning
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iProm-Zea: A two-layer model to identify plant promoters and their types using convolutional neural network.

Genomics May 6, 2022
A promoter is a short DNA sequence near the start codon, responsible for initiating the transcription of a specific gene in the genome. The accurate recognition of promoters is important for achieving a better understanding of transcriptional regulat...
Base Sequence Promoter Regions, Genetic TATA Box Algorithms Zea mays Neural Networks, Computer
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PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest.

Interdisciplinary sciences, computational life sciences Apr 30, 2022
Promoters short DNA sequences play vital roles in initiating gene transcription. However, it remains a challenge to identify promoters using conventional experiment techniques in a high-throughput manner. To this end, several computational predictors...
Base Sequence Promoter Regions, Genetic Machine Learning
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DeepBtoD: Improved RNA-binding proteins prediction via integrated deep learning.

Journal of bioinformatics and computational biology Apr 21, 2022
RNA-binding proteins (RBPs) have crucial roles in various cellular processes such as alternative splicing and gene regulation. Therefore, the analysis and identification of RBPs is an essential issue. However, although many computational methods have...
Base Sequence Binding Sites RNA Computational Biology RNA-Binding Proteins Deep Learning Protein Binding
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Nucleosome positioning based on DNA sequence embedding and deep learning.

BMC genomics Apr 13, 2022
BACKGROUND: Nucleosome positioning is the precise determination of the location of nucleosomes on DNA sequence. With the continuous advancement of biotechnology and computer technology, biological data is showing explosive growth. It is of practical ...
Nucleosomes Drosophila melanogaster Caenorhabditis elegans Plant Extracts Base Sequence Animals Deep Learning
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