AIMC Topic: Sequence Analysis, DNA

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Discovering differential genome sequence activity with interpretable and efficient deep learning.

PLoS computational biology Aug 9, 2021
Discovering sequence features that differentially direct cells to alternate fates is key to understanding both cellular development and the consequences of disease related mutations. We introduce Expected Pattern Effect and Differential Expected Patt...
Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Genome, Human Deep Learning Transcription Factors Humans Neural Networks, Computer
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iEnhancer-RD: Identification of enhancers and their strength using RKPK features and deep neural networks.

Analytical biochemistry Aug 5, 2021
Enhancers are regulatory elements involved in gene expression.It is a part of DNA, which can enhance the transcription rate of gene. However, the identification of enhancer by biological experimental methods is time-consuming and expensive. Therefore...
Sequence Analysis, DNA DNA Enhancer Elements, Genetic Humans Neural Networks, Computer Computational Biology
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A deep learning model for predicting next-generation sequencing depth from DNA sequence.

Nature communications Jul 19, 2021
Targeted high-throughput DNA sequencing is a primary approach for genomics and molecular diagnostics, and more recently as a readout for DNA information storage. Oligonucleotide probes used to enrich gene loci of interest have different hybridization...
DNA Genomics High-Throughput Nucleotide Sequencing Polymorphism, Single Nucleotide Humans Base Sequence Deep Learning Sequence Analysis, DNA DNA Probes
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Analysis of DNA Sequence Classification Using CNN and Hybrid Models.

Computational and mathematical methods in medicine Jul 15, 2021
In a general computational context for biomedical data analysis, DNA sequence classification is a crucial challenge. Several machine learning techniques have used to complete this task in recent years successfully. Identification and classification o...
Base Sequence Databases, Nucleic Acid Deep Learning Computational Biology DNA, Viral Pandemics Sequence Analysis, DNA Humans COVID-19 High-Throughput Nucleotide Sequencing Neural Networks, Computer SARS-CoV-2
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Gene Position Index Mutation Detection Algorithm Based on Feedback Fast Learning Neural Network.

Computational intelligence and neuroscience Jul 6, 2021
In the detection of genome variation, the research on the internal correlation of reference genome is deepening; the detection of variation in genome sequence has become the focus of research, and it has also become an effective path to find new gene...
Neural Networks, Computer Software Gene Order Algorithms Feedback Sequence Analysis, DNA Mutation
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Ultrasensitive detection of circulating tumour DNA via deep methylation sequencing aided by machine learning.

Nature biomedical engineering Jun 15, 2021
The low abundance of circulating tumour DNA (ctDNA) in plasma samples makes the analysis of ctDNA biomarkers for the detection or monitoring of early-stage cancers challenging. Here we show that deep methylation sequencing aided by a machine-learning...
Circulating Tumor DNA Humans Machine Learning Case-Control Studies Female Lung Neoplasms Biomarkers, Tumor DNA Methylation Adult Sequence Analysis, DNA Early Detection of Cancer Male High-Throughput Nucleotide Sequencing Middle Aged
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Using deep learning to identify recent positive selection in malaria parasite sequence data.

Malaria journal Jun 14, 2021
BACKGROUND: Malaria, caused by Plasmodium parasites, is a major global public health problem. To assist an understanding of malaria pathogenesis, including drug resistance, there is a need for the timely detection of underlying genetic mutations and ...
Selection, Genetic Plasmodium vivax Genome Size Sequence Analysis, DNA Plasmodium falciparum Genome, Protozoan Deep Learning
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DNAscent v2: detecting replication forks in nanopore sequencing data with deep learning.

BMC genomics Jun 9, 2021
BACKGROUND: Measuring DNA replication dynamics with high throughput and single-molecule resolution is critical for understanding both the basic biology behind how cells replicate their DNA and how DNA replication can be used as a therapeutic target f...
Nanopore Sequencing High-Throughput Nucleotide Sequencing Nanopores Software Deep Learning Sequence Analysis, DNA
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MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly.

BMC bioinformatics Jun 2, 2021
BACKGROUND: The increasing use of whole metagenome sequencing has spurred the need to improve de novo assemblers to facilitate the discovery of unknown species and the analysis of their genomic functions. MetaVelvet-SL is a short-read de novo metagen...
Software Algorithms High-Throughput Nucleotide Sequencing Metagenomics Metagenome Deep Learning Genomics Sequence Analysis, DNA
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Feasibility of predicting allele specific expression from DNA sequencing using machine learning.

Scientific reports May 19, 2021
Allele specific expression (ASE) concerns divergent expression quantity of alternative alleles and is measured by RNA sequencing. Multiple studies show that ASE plays a role in hereditary diseases by modulating penetrance or phenotype severity. Howev...
Feasibility Studies Alleles Gene Expression Regulation Humans Genome, Human Machine Learning Models, Genetic ROC Curve Sequence Analysis, DNA Polymorphism, Single Nucleotide Bias
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