Molecular barcoding of native RNAs using nanopore sequencing and deep learning

Deep learning for time series classification: a review

(2019) Hassan Ismail Fawaz et al.   DATA MINING AND KNOWLEDGE DISCOVERY

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

(2019) Peng Ni et al.   BIOINFORMATICS

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

(2019) Haotian Teng et al.   GigaScience

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

(2019) Andrew M. Smith et al.   PLoS One

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

(2019) Maximilian Krause et al.   RNA

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

(2019) Rachael E. Workman et al.   NATURE METHODS

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Long reads: their purpose and place

(2018) Martin O Pollard et al.   HUMAN MOLECULAR GENETICS

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

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

(2018) Simon Ardui et al.   NUCLEIC ACIDS RESEARCH

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

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

(2018) Ryan R. Wick et al.   PLoS Computational Biology

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

(2017) Vladimír Boža et al.   PLoS One

Spliced synthetic genes as internal controls in RNA sequencing experiments

(2016) Simon A Hardwick et al.   NATURE METHODS

Deep learning

(2015) Yann LeCun et al.   NATURE

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

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

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS