Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

(2019) Daniel P. Depledge et al.   Nature Communications

Long-read direct RNA sequencing by 5’-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts

(2019) Feng Jiang et al.   RNA Biology

Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling

(2019) Miguel Angel Garcia-Campos et al.   CELL

m6A enhances the phase separation potential of mRNA

(2019) Ryan J. Ries et al.   NATURE

DART-seq: an antibody-free method for global m6A detection

(2019) Kate D. Meyer   NATURE METHODS

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

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing

(2018) Angel Mojarro et al.   BMC BIOINFORMATICS

Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex

(2018) Marcello Clerici et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex

(2018) Marcello Clerici et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ambiguous splice sites distinguish circRNA and linear splicing in the human genome

(2018) Roozbeh Dehghannasiri et al.   BIOINFORMATICS

Characterization of mRNA polyadenylation in the apicomplexa

(2018) Ashley T. Stevens et al.   PLoS One

What Are 3′ UTRs Doing?

(2018) Christine Mayr   Cold Spring Harbor Perspectives in Biology

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA

(2018) Michael A. Schon et al.   GENOME RESEARCH

N6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis

(2018) Stephen J. Anderson et al.   Cell Reports

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

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

The draft genomes of five agriculturally important African orphan crops

(2018) Yue Chang et al.   GigaScience

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

Short poly(A) tails are a conserved feature of highly expressed genes

(2017) Sarah Azoubel Lima et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of factors required for m6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

(2017) Kamil Růžička et al.   NEW PHYTOLOGIST

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

(2017) Runxuan Zhang et al.   NUCLEIC ACIDS RESEARCH

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

Novel Stress-Inducible Antisense RNAs of Protein-Coding Loci Are Synthesized by RNA-Dependent RNA Polymerase

(2017) Akihiro Matsui et al.   PLANT PHYSIOLOGY

Molecular basis for the recognition of the human AAUAAA polyadenylation signal

(2017) Yadong Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Short poly(A) tails are a conserved feature of highly expressed genes

(2017) Sarah Azoubel Lima et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

N 6 -Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis

(2016) Lisha Shen et al.   DEVELOPMENTAL CELL

The m 6 A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells

(2016) Shuibin Lin et al.   MOLECULAR CELL

Flexible expressed region analysis for RNA-seq withderfinder

(2016) Leonardo Collado-Torres et al.   NUCLEIC ACIDS RESEARCH

Chloroplast retrograde signal regulates flowering

(2016) Peiqiang Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

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

PTGBase: an integrated database to study tandem duplicated genes in plants

(2015) Jingyin Yu et al.   Database-The Journal of Biological Databases and Curation

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3′ processing

(2014) Serena L. Chan et al.   GENES & DEVELOPMENT

Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33

(2014) Lars Schönemann et al.   GENES & DEVELOPMENT

Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs

(2014) Nicholas J. Schurch et al.   PLoS One

Unique features of the m6A methylome in Arabidopsis thaliana

(2014) Guan-Zheng Luo et al.   Nature Communications

Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types

(2014) Zheng Xia et al.   Nature Communications

The RNA Helicases AtMTR4 and HEN2 Target Specific Subsets of Nuclear Transcripts for Degradation by the Nuclear Exosome in Arabidopsis thaliana

(2014) Heike Lange et al.   PLoS Genetics

RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

(2013) Jean-Michel Fustin et al.   CELL

Temperature-dependent regulation of flowering by antagonistic FLM variants

(2013) David Posé et al.   NATURE

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA

(2013) N. Liu et al.   RNA

Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA

(2013) Céline Duc et al.   PLoS Genetics

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns

(2012) Mélanie Rigal et al.   EMBO JOURNAL

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

(2012) Alexander Sherstnev et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Spen Family Protein FPA Controls Alternative Cleavage and Polyadenylation of RNA

(2010) Csaba Hornyik et al.   DEVELOPMENTAL CELL

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

(2010) Jonathan Houseley et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Delayed fluorescence as a universal tool for the measurement of circadian rhythms in higher plants

(2009) Peter D. Gould et al.   PLANT JOURNAL

uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts

(2008) Minghui Jiang et al.   BMC BIOINFORMATICS