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Barcoding and demultiplexing Oxford Nanopore native RNA sequencing reads with deep residual learning

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s10618-019-00619-1openalex-snapshot

Deep learning for time series classification: a review

inferredcites →https://doi.org/10.1016/j.cpc.2010.04.018openalex-snapshot

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

inferredcites →https://doi.org/10.1016/j.tig.2018.05.008openalex-snapshot

The Third Revolution in Sequencing Technology

inferredcites →https://doi.org/10.1021/ac60214a047openalex-snapshot

Smoothing and Differentiation of Data by Simplified Least Squares Procedures.

inferredcites →https://doi.org/10.1038/nature14539openalex-snapshot

Deep learning

inferredcites →https://doi.org/10.1038/nmeth.3958openalex-snapshot

Spliced synthetic genes as internal controls in RNA sequencing experiments

inferredcites →https://doi.org/10.1038/nmeth.4577openalex-snapshot

Highly parallel direct RNA sequencing on an array of nanopores

inferredcites →https://doi.org/10.1038/s41467-019-11713-9openalex-snapshot

Accurate detection of m6A RNA modifications in native RNA sequences

inferredcites →https://doi.org/10.1038/s41592-019-0617-2openalex-snapshot

Nanopore native RNA sequencing of a human poly(A) transcriptome

inferredcites →https://doi.org/10.1038/s41592-019-0697-zopenalex-snapshot

Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome

inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot

Minimap2: pairwise alignment for nucleotide sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btz276openalex-snapshot

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

inferredcites →https://doi.org/10.1093/bioinformatics/btz586openalex-snapshot

SquiggleKit: a toolkit for manipulating nanopore signal data

inferredcites →https://doi.org/10.1093/gigascience/giy037openalex-snapshot

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

inferredcites →https://doi.org/10.1093/hmg/ddy177openalex-snapshot

Long reads: their purpose and place

inferredcites →https://doi.org/10.1093/nar/gky066openalex-snapshot

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

inferredcites →https://doi.org/10.1101/843136openalex-snapshot

RNA modifications detection by comparative Nanopore direct RNA sequencing

inferredcites →https://doi.org/10.1109/caipt.2017.8320684openalex-snapshot

A review of deep learning in image recognition

inferredcites →https://doi.org/10.1109/cvpr.2016.90openalex-snapshot

Deep Residual Learning for Image Recognition

inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot

Matplotlib: A 2D Graphics Environment

inferredcites →https://doi.org/10.1109/mcse.2011.37openalex-snapshot

The NumPy Array: A Structure for Efficient Numerical Computation

inferredcites →https://doi.org/10.1186/s13059-018-1462-9openalex-snapshot

From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy

inferredcites →https://doi.org/10.1209/0295-5075/4/9/004openalex-snapshot

Recurrence Plots of Dynamical Systems

inferredcites →https://doi.org/10.1261/rna.071332.119openalex-snapshot

tailfindr : alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

inferredcites →https://doi.org/10.1371/journal.pcbi.1006583openalex-snapshot

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

inferredcites →https://doi.org/10.1371/journal.pone.0178751openalex-snapshot

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

inferredcites →https://doi.org/10.1371/journal.pone.0216709openalex-snapshot

Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing

inferredcites →https://doi.org/10.21105/joss.00729openalex-snapshot

PyCM: Multiclass confusion matrix library in Python

inferredcites →https://doi.org/10.25080/majora-92bf1922-00aopenalex-snapshot

Data Structures for Statistical Computing in Python

inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot

Scikit-learn: Machine Learning in Python

inferredcites →https://doi.org/10.5281/zenodo.1244151openalex-snapshot

johannfaouzi/pyts: Release of 0.7.3 version

inferredcites →https://doi.org/10.5555/3026877.3026899openalex-snapshot

TensorFlow: A system for large-scale machine learning

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.cis.2021.102561openalex-snapshot

Solid-state and polymer nanopores for protein sensing: A review

inferred← citeshttps://doi.org/10.1038/s41467-020-19151-8openalex-snapshot

Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures

inferred← citeshttps://doi.org/10.1038/s41587-021-00915-6openalex-snapshot

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

inferred← citeshttps://doi.org/10.1101/2020.06.09.20126219openalex-snapshot

Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing

inferred← citeshttps://doi.org/10.1109/embc44109.2020.9176358openalex-snapshot

Locating patterns in Nanopore currents using time-warped signal representation of consensus nucleotides for demultiplexing and motif detection

inferred← citeshttps://doi.org/10.3389/fgene.2020.00211openalex-snapshot

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets

inferred← citeshttps://doi.org/10.3390/bios10100140openalex-snapshot

Machine Learning to Improve the Sensing of Biomolecules by Conical Track-Etched Nanopore

inferred← citeshttps://doi.org/10.3390/fishes8050271openalex-snapshot

Decoding the Transcriptome of Sharks, Rays, and Chimaeras: Insights into Their Physiology, Morphology, Evolution, and Biomedical Applications

inferred← citeshttps://doi.org/10.3390/v12080841openalex-snapshot

Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing

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