Evidence map›Paper›PMID 42415949›Full record

ArticleNAR genomics and bioinformatics2026

QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing.

Michael Piechotta, Wei Guo, Isabel S Naarmann-de Vries, Felix Kallenborn, Swastik Mishra, Francesca Tuorto, Bertil Schmidt, Christoph Dieterich

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in NAR genomics and bioinformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Michael PiechottaKlaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Im Neuenheimer Feld 669, Heidelberg 69120, Baden-Württemberg, Germany.
Wei GuoCenter for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg 69120, Baden-Württemberg, Germany.
Isabel S Naarmann-de VriesKlaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Im Neuenheimer Feld 669, Heidelberg 69120, Baden-Württemberg, Germany.
Felix KallenbornInstitute of Computer Science, Johannes Gutenberg University, Staudingerweg 9, Mainz 55128, Rheinland-Pfalz, Germany.ORCID https://orcid.org/0000-0003-4516-6357
Swastik MishraKlaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Im Neuenheimer Feld 669, Heidelberg 69120, Baden-Württemberg, Germany.
Francesca TuortoCenter for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg 69120, Baden-Württemberg, Germany.ORCID https://orcid.org/0000-0003-1625-1181
Bertil SchmidtInstitute of Computer Science, Johannes Gutenberg University, Staudingerweg 9, Mainz 55128, Rheinland-Pfalz, Germany.ORCID https://orcid.org/0000-0003-2597-8331
Christoph DieterichKlaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Im Neuenheimer Feld 669, Heidelberg 69120, Baden-Württemberg, Germany.ORCID https://orcid.org/0000-0001-9468-6311

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Transfer RNAs (tRNAs) are essential for protein synthesis and are extensively modified to ensure their structure and function. Direct RNA sequencing with Oxford Nanopore Technologies enables positional modification analysis but is challenged by tRNAs' short length, redundancy, and dense modifications. We present QutRNA2, a scalable workflow that includes GPU-accelerated local alignment, statistical filtering, pairwise error profile comparison, and customizable visualization. Achieving up to 25-fold speed gains over CPU methods, QutRNA2 identifies enzyme-dependent modifications in nuclear- and mitochondrial-encoded tRNAs, demonstrated in high-volume human and mouse samples. This open-source solution provides a comprehensive, multiplexing-compatible framework for tRNA analysis, addressing a key gap in current tools. QutRNA2 is released under Apache-2.0 license and is available at https://github.com/dieterich-lab/QutRNA2.

Indexed as

Nanopore SequencingRNA Processing, Post-TranscriptionalRNA, TransferSequence Analysis, RNASoftwareAnimalsHumansMiceRNA, Transfer

Identifiers

PMID42415949
PMCPMC13338716

What Socratic holds

Textmetadata
LicenceCC BY-NC
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 Socratic graph.