AIMC Topic: Base Sequence

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A machine learning approach for accurate and real-time DNA sequence identification.

BMC genomics Jul 9, 2021
BACKGROUND: The all-electronic Single Molecule Break Junction (SMBJ) method is an emerging alternative to traditional polymerase chain reaction (PCR) techniques for genetic sequencing and identification. Existing work indicates that the current spect...
Machine Learning DNA Base Sequence
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Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications.

Nature communications Jun 29, 2021
Recent studies suggest that epi-transcriptome regulation via post-transcriptional RNA modifications is vital for all RNA types. Precise identification of RNA modification sites is essential for understanding the functions and regulatory mechanisms of...
RNA Processing, Post-Transcriptional DNA Methylation RNA Humans Base Sequence Neural Networks, Computer Computational Biology
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Nature communications Jun 2, 2021
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene ...
Base Sequence Mice Genome, Human Computational Biology Polymorphism, Genetic Animals Promoter Regions, Genetic Deep Learning A549 Cells Neurodegenerative Diseases High-Throughput Nucleotide Sequencing Humans Neural Networks, Computer Transcription Initiation, Genetic Enhancer Elements, Genetic Microsatellite Repeats Transcription Initiation Site
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i4mC-EL: Identifying DNA N4-Methylcytosine Sites in the Mouse Genome Using Ensemble Learning.

BioMed research international May 29, 2021
As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) plays a crucial role in controlling gene replication, expression, cell cycle, DNA replication, and differentiation. The accurate identification of 4mC sites is necessary to und...
Genetic Techniques Cytosine Data Mining Computational Biology Base Sequence Animals Genome Epigenesis, Genetic ROC Curve Bayes Theorem DNA Methylation Area Under Curve Mice Internet DNA Machine Learning Algorithms Reproducibility of Results
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MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics.

BMC bioinformatics May 7, 2021
BACKGROUND: Cis-regulatory elements (CREs) are DNA sequence segments that regulate gene expression. Among CREs are promoters, enhancers, Boundary Elements (BEs) and Polycomb Response Elements (PREs), all of which are enriched in specific sequence mot...
Support Vector Machine Base Sequence Nucleotide Motifs Position-Specific Scoring Matrices Algorithms
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A convolutional neural network for the prediction and forward design of ribozyme-based gene-control elements.

eLife Apr 16, 2021
Ribozyme switches are a class of RNA-encoded genetic switch that support conditional regulation of gene expression across diverse organisms. An improved elucidation of the relationships between sequence, structure, and activity can improve our capaci...
RNA, Catalytic Neural Networks, Computer Structure-Activity Relationship Sequence Analysis, RNA Ligands Gene Expression Regulation Nucleic Acid Conformation Models, Genetic High-Throughput Nucleotide Sequencing Base Sequence Saccharomyces cerevisiae Machine Learning Escherichia coli Computer-Aided Design Aptamers, Nucleotide
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Prediction of PCR amplification from primer and template sequences using recurrent neural network.

Scientific reports Apr 5, 2021
We have developed a novel method to predict the success of PCR amplification for a specific primer set and DNA template based on the relationship between the primer sequence and the template. To perform the prediction using a recurrent neural network...
Reproducibility of Results DNA Primers Computational Biology Base Sequence Neural Networks, Computer Algorithms Polymerase Chain Reaction Templates, Genetic
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A two-stream convolutional neural network for microRNA transcription start site feature integration and identification.

Scientific reports Mar 11, 2021
MicroRNAs (miRNAs) play important roles in post-transcriptional gene regulation and phenotype development. Understanding the regulation of miRNA genes is critical to understand gene regulation. One of the challenges to study miRNA gene regulation is ...
Computational Biology Cell Line MicroRNAs Human Embryonic Stem Cells Neural Networks, Computer Base Sequence Reproducibility of Results Algorithms Transcription Initiation Site Humans Deep Learning
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CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores.

Genome medicine Feb 22, 2021
BACKGROUND: Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to identify beyond...
Humans Base Sequence Deep Learning RNA Splicing Introns Exons Genome-Wide Association Study Genetic Variation
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Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species.

PLoS computational biology Feb 18, 2021
N6-methyladenine (6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for under-standing of 6mA's biological functions. However, the existing ...
Base Sequence Species Specificity Fragaria Rosa Databases, Nucleic Acid Binding Sites Adenine DNA Methylation DNA Oryza Neural Networks, Computer Deep Learning Computational Biology DNA, Plant Arabidopsis
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