Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

(2021) Oguzhan Begik et al.   NATURE BIOTECHNOLOGY

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

(2021) Ploy N. Pratanwanich et al.   NATURE BIOTECHNOLOGY

The m6A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication

(2021) Sarah Elizabeth Martin et al.   RNA

Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions

(2021) Siwy Ling Yang et al.   Nature Communications

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

Causalcall: Nanopore Basecalling Using a Temporal Convolutional Network

(2020) Jingwen Zeng et al.   Frontiers in Genetics

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

Immunoglobulin expression and the humoral immune response is regulated by the non-canonical poly(A) polymerase TENT5C

(2020) Aleksandra Bilska et al.   Nature Communications

Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts

(2020) Hongxu Ding et al.   BIOINFORMATICS

GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis

(2020) Hasindu Gamaarachchi et al.   BMC BIOINFORMATICS

Profiling of circular RNA N 6 ‐methyladenosine in moso bamboo ( Phyllostachys edulis ) using nanopore‐based direct RNA sequencing

(2020) Yongsheng Wang et al.   Journal of Integrative Plant Biology

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

Detection of base analogs incorporated during DNA replication by nanopore sequencing

(2020) Daniela Georgieva et al.   NUCLEIC ACIDS RESEARCH

Decoding the epitranscriptional landscape from native RNA sequences

(2020) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms

(2020) Kerstin C. Maier et al.   GENOME RESEARCH

Determination of isoform-specific RNA structure with nanopore long reads

(2020) Jong Ghut Ashley Aw et al.   NATURE BIOTECHNOLOGY

Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy

(2020) Shubham Chandak et al.   BIOINFORMATICS

Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling

(2020) Adam D. Ewing et al.   MOLECULAR CELL

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

(2020) Sam Kovaka et al.   NATURE BIOTECHNOLOGY

Readfish enables targeted nanopore sequencing of gigabase-sized genomes

(2020) Alexander Payne et al.   NATURE BIOTECHNOLOGY

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

(2020) Isac Lee et al.   NATURE METHODS

Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

(2020) Alexander M. Price et al.   Nature Communications

Single-molecule sequencing detection of N6-methyladenine in microbial reference materials

(2019) Alexa B. R. McIntyre et al.   Nature Communications

NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data

(2019) Qian Liu et al.   BMC GENOMICS

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

(2019) Peng Ni et al.   BIOINFORMATICS

Adenine Methylation in Drosophila Is Associated with the Tissue-Specific Expression of Developmental and Regulatory Genes

(2019) Kinnary Shah et al.   G3-Genes Genomes Genetics

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

(2019) Maximilian Krause et al.   RNA

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

(2019) Adrian Viehweger et al.   GENOME RESEARCH

Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore

(2019) Degang Wu et al.   CELL

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing

(2019) Pay Giesselmann et al.   NATURE BIOTECHNOLOGY

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

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

Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution

(2019) Daniel A. Lorenz et al.   RNA

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes

(2019) Casslynn W. Q. Koh et al.   Nature Communications

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

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

(2018) Haotian Teng et al.   GigaScience

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Charting the unknown epitranscriptome

(2017) Eva Maria Novoa et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

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

(2017) Vladimír Boža et al.   PLoS One

Mass spectrometry of modified RNAs: recent developments

(2016) Collin Wetzel et al.   ANALYST

Nanocall: an open source basecaller for Oxford Nanopore sequencing data

(2016) Matei David et al.   BIOINFORMATICS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

De novo sequencing and variant calling with nanopores using PoreSeq

(2015) Tamas Szalay et al.   NATURE BIOTECHNOLOGY

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

DNA Base-Calling from a Nanopore Using a Viterbi Algorithm

(2012) Winston Timp et al.   BIOPHYSICAL JOURNAL

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Control of poly(A) tail length

(2010) Christian R. Eckmann et al.   Wiley Interdisciplinary Reviews-RNA

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY