(Q83224631)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

0 references

0 references

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

Katarzyna Knop

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

Nicholas Schurch

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

Geoffrey J. Barton

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

Gordon G Simpson

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

author name string

Anna V Sherwood

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

Katarzyna Mackinnon

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

Peter D Gould

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

Anthony Jw Hall

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

language of work or name

English

0 references

publication date

14 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

30 April 2020

edgeR

object named as

edgeR

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

tximport

object named as

tximport

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

1 reference

12 December 2020

Functional annotation of a full-length Arabidopsis cDNA collection

1 reference

12 December 2020

Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time

1 reference

12 December 2020

FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition.

1 reference

12 December 2020

Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway.

1 reference

12 December 2020

Proposed methods for testing and selecting the ERCC external RNA controls

1 reference

12 December 2020

Comprehensive splice-site analysis using comparative genomics

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

MEME SUITE: tools for motif discovery and searching

1 reference

12 December 2020

The Sequence Alignment/Map format and SAMtools

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

BLAST+: architecture and applications

1 reference

12 December 2020

The spen family protein FPA controls alternative cleavage and polyadenylation of RNA.

1 reference

12 December 2020

BEDTools: a flexible suite of utilities for comparing genomic features

1 reference

12 December 2020

Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro

1 reference

12 December 2020

Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs

1 reference

12 December 2020

Integrative genomics viewer

1 reference

12 December 2020

FIMO: scanning for occurrences of a given motif

1 reference

12 December 2020

Synthetic spike-in standards for RNA-seq experiments

1 reference

12 December 2020

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

1 reference

12 December 2020

The genetics of plant clocks

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Detecting differential usage of exons from RNA-seq data

1 reference

12 December 2020

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

1 reference

12 December 2020

Site identification in high-throughput RNA-protein interaction data

1 reference

12 December 2020

STAR: ultrafast universal RNA-seq aligner

1 reference

12 December 2020

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

1 reference

12 December 2020

Temperature-dependent regulation of flowering by antagonistic FLM variants.

1 reference

12 December 2020

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

1 reference

12 December 2020

Assessment of transcript reconstruction methods for RNA-seq

1 reference

12 December 2020

Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA.

1 reference

12 December 2020

RNA-methylation-dependent RNA processing controls the speed of the circadian clock

1 reference

12 December 2020

N6-methyladenosine-dependent regulation of messenger RNA stability

1 reference

12 December 2020

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.

1 reference

12 December 2020

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

1 reference

12 December 2020

The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Unique features of the m6A methylome in Arabidopsis thaliana.

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

External RNA Controls Consortium Beta Version Update

1 reference

12 December 2020

Chloroplast retrograde signal regulates flowering

1 reference

12 December 2020

Flexible expressed region analysis for RNA-seq with derfinder

1 reference

12 December 2020

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

1 reference

12 December 2020

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.

1 reference

12 December 2020

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

1 reference

12 December 2020

Detecting RNA modifications in the epitranscriptome: predict and validate

1 reference

12 December 2020

Salmon provides fast and bias-aware quantification of transcript expression

1 reference

12 December 2020

Mapping m6A at Individual-Nucleotide Resolution Using Crosslinking and Immunoprecipitation (miCLIP).

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention

1 reference

12 December 2020

Dynamic RNA Modifications in Gene Expression Regulation

1 reference

12 December 2020

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

1 reference

12 December 2020

Rethinking m6A Readers, Writers, and Erasers.

1 reference

12 December 2020

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

1 reference

12 December 2020

Light Controls Protein Localization through Phytochrome-Mediated Alternative Promoter Selection.

1 reference

12 December 2020

Molecular basis for the recognition of the human AAUAAA polyadenylation signal.

1 reference

12 December 2020

Highly parallel direct RNA sequencing on an array of nanopores.

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Earth BioGenome Project: Sequencing life for the future of life.

1 reference

12 December 2020

Minimap2: pairwise alignment for nucleotide sequences

1 reference

12 December 2020

Sequencing nothing: Exploring failure modes of nanopore sensing and implications for life detection

1 reference

12 December 2020

Characterization of mRNA polyadenylation in the apicomplexa

1 reference

12 December 2020

What Are 3' UTRs Doing?

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

1 reference

12 December 2020

The draft genomes of five agriculturally important African orphan crops

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

The m6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants

1 reference

12 December 2020

Deciphering the "m6A Code" via Antibody-Independent Quantitative Profiling

1 reference

12 December 2020

m6A enhances the phase separation potential of mRNA

1 reference

12 December 2020

Marking RNA: m6A writers, readers, and functions in Arabidopsis

1 reference

12 December 2020

Accurate detection of m6A RNA modifications in native RNA sequences

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Cutadapt removes adapter sequences from high-throughput sequencing reads

1 reference

2 April 2022

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.49658

Identifiers

DOI

10.7554/ELIFE.49658

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31931956%20AND%20SRC:MED&resulttype=core&format=json

30 April 2020

1 reference