Evidence map›Paper›PMID 41497629›Full record

ArticlebioRxiv : the preprint server for biology2025

tRNA isodecoder analysis using Nanopore ionic current signals and deep learning.

Stuart Akeson, Pooria Daneshvar Kakhaki, Neda Ghohabi Esfahani, Julia L Reinsch, Margaret L Barry, Maddy Zamecnik, Talia Tzadikario, Robin L Abu-Shumays, David M Garcia, Kristin S Koutmou and 1 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

11 authors.

Stuart AkesonDepartment of Bioengineering, Northeastern University, Boston, MA 02115, USA.ORCID 0009-0008-8008-2486
Pooria Daneshvar KakhakiDepartment of Electrical & Computer Engineering, Northeastern University, Boston, MA 02115, USA.ORCID 0009-0001-3030-836X
Neda Ghohabi EsfahaniDepartment of Bioengineering, Northeastern University, Boston, MA 02115, USA.ORCID 0000-0003-0539-4603
Julia L ReinschInstitute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.ORCID 0009-0004-6102-6594
Margaret L BarryInstitute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
Maddy ZamecnikDepartment of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.ORCID 0009-0003-9612-666X
Talia TzadikarioDepartment of Bioengineering, Northeastern University, Boston, MA 02115, USA.
Robin L Abu-ShumaysBiomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA.ORCID 0000-0003-1485-080X
David M GarciaInstitute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
Kristin S KoutmouDepartment of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.ORCID 0000-0002-7763-9262
Miten JainDepartment of Bioengineering, Northeastern University, Boston, MA 02115, USA.ORCID 0000-0002-4571-3982

Funding

Prion-based regulation of RNA-modifying enzyme activitiesR35GM143125 · NIGMS · UNIVERSITY OF OREGON · PI GARCIA, DAVID M. · 2021 to 2025
$1.9M
Graduate Training Grant in GeneticsT32GM149387 · NIGMS · UNIVERSITY OF OREGON · PI Karen J Guillemin · 2023 to 2026
$1.6M
MFB: Integrating LC-MS/MS and Nanopore Sequencing Platforms to Enable the Direct and Quantatative Detection of RNA ModificationsR01HG013876 · NHGRI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Kristin S Koutmou · 2024 to 2026
$1.2M
NHGRI NIH HHS R01 HG013876NIGMS NIH HHS R35 GM143125NIGMS NIH HHS T32 GM149387
6 · The paper itself

Abstract

We describe application of Nanopore direct tRNA sequencing and ionic current signal for isodecoder-level analysis of bacterial and yeast tRNA. The computational advance is the application of deep learning for predicting tRNA isodecoders directly from raw nanopore ionic current signals. We then combined ionic current analysis with a pairwise sequence alignment strategy to improve tRNA sequence alignments. We applied this strategy to Nanopore data for

Indexed as

Deep learningIonic current analysisIsodecoder classificationNanopore direct tRNA sequencingtRNA modifications

Identifiers

PMID41497629
PMCPMC12767535

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

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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.