Evidence map›Paper›PMID 33835447›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2021

RNA Editing Detection in HPC Infrastructures.

Claudio Lo Giudice, Luigi Mansi, Tiziano Flati, Silvia Gioiosa, Giovanni Chillemi, Pietro Libro, Tiziana Castrignanò, Graziano Pesole, Ernesto Picardi

Erratum issuedAbstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. ncRNA Editing: Functional Characterization and Computational Resources.Methods in molecular biology (Clifton, N.J.) · 2025
    Article
  2. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Claudio Lo GiudiceDepartment of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.
Luigi MansiDepartment of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.
Tiziano FlatiSCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy.
Silvia GioiosaSCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy.
Giovanni ChillemiSCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy.
Pietro LibroDepartment of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy.
Tiziana CastrignanòDepartment of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy.
Graziano PesoleDepartment of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.
Ernesto PicardiDepartment of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy. ernesto.picardi@uniba.it.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

RNA editing by A-to-I deamination is a relevant co/posttranscriptional modification carried out by ADAR enzymes. In humans, it has pivotal cellular effects and its deregulation has been linked to a variety of human disorders including neurological and neurodegenerative diseases and cancer. Despite its biological relevance, the detection of RNA editing variants in large transcriptome sequencing experiments (RNAseq) is yet a challenging computational task. To drastically reduce computing times we have developed a novel REDItools version able to identify A-to-I events in huge amount of RNAseq data employing High Performance Computing (HPC) infrastructures.Here we show how to use REDItools v2 in HPC systems.

Indexed as

Computing MethodologiesAnimalsComputational BiologyDatabases, GeneticDatasets as TopicGenomicsHigh-Throughput Nucleotide SequencingHumansNeoplasmsNervous System DiseasesNeurodegenerative DiseasesRNA EditingSequence Analysis, RNASoftwareTranscriptomeA-to-I editingBioinformaticsDeep sequencingDNAseqGenomicsHPCMPIRNA editingRNAseqTranscriptomics

Identifiers

PMID33835447

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.