AIMC Topic: Nanopores
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S2Snet: deep learning for low molecular weight RNA identification with nanopore.
Briefings in bioinformatics
May 13, 2022
Ribonucleic acid (RNA) is a pivotal nucleic acid that plays a crucial role in regulating many biological activities. Recently, one study utilized a machine learning algorithm to automatically classify RNA structural events generated by a Mycobacteriu...
[Unsupervised deep learning for identifying the O -carboxymethyl guanine by nanopore sequencing].
Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi
Feb 25, 2022
O -carboxymethyl guanine(O -CMG) is a highly mutagenic alkylation product of DNA that causes gastrointestinal cancer in organisms. Existing studies used mutant porin A (MspA) nanopore assisted by Phi29 DNA polymerase to localize it. Recently, machi...
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.
Bioinformatics (Oxford, England)
Feb 7, 2022
MOTIVATION: DNA methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational methods have been developed to ...
Synthetic heparan sulfate standards and machine learning facilitate the development of solid-state nanopore analysis.
Proceedings of the National Academy of Sciences of the United States of America
Mar 16, 2021
The application of solid-state (SS) nanopore devices to single-molecule nucleic acid sequencing has been challenging. Thus, the early successes in applying SS nanopore devices to the more difficult class of biopolymer, glycosaminoglycans (GAGs), have...
Deep learning for nanopore ionic current blockades.
The Journal of chemical physics
Jan 28, 2021
DNA molecules can electrophoretically be driven through a nanoscale opening in a material, giving rise to rich and measurable ionic current blockades. In this work, we train machine learning models on experimental ionic blockade data from DNA nucleot...
Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning.
GigaScience
May 1, 2018
Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex elec...
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