Evidence map›Paper›PMID 40631152›Full record

ArticlebioRxiv : the preprint server for biology2025

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome.

Megan D Schertzer, Stella H Park, Jiayu Su, Gloria M Sheynkman, David A Knowles

Abstract readPreprint
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

5 authors.

Megan D SchertzerNew York Genome Center, New York, NY.ORCID 0000-0003-4997-8221
Stella H ParkNew York Genome Center, New York, NY.ORCID 0009-0008-0933-8602
Jiayu SuDepartment of Systems Biology, Columbia University, New York, NY.ORCID 0000-0002-8997-9272
Gloria M SheynkmanDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA.ORCID 0000-0002-4223-9947
David A KnowlesNew York Genome Center, New York, NY.ORCID 0000-0002-7408-146X

Funding

IMAT-ITCR Collaboration: A Cytoscape Toolkit to Model Proteoform-Resolved Cancer NetworksR33CA281919 · NCI · UNIVERSITY OF VIRGINIA · PI Gloria Sheynkman · 2024 to 2026
$1.3M
A CRISPR/Cas13 approach for identifying individual transcript isoform function in cancerR21CA272345 · NCI · NEW YORK GENOME CENTER · PI KNOWLES, DAVID ARTHUR · 2022 to 2023
$699k
Measuring allele and isoform-specific RBP binding to improve predictive models of RNA splicingF32GM142213 · NIGMS · NEW YORK GENOME CENTER · PI SCHERTZER, MEGAN · 2021 to 2022
$134k
NCI NIH HHS R21 CA272345NCI NIH HHS R33 CA281919NIGMS NIH HHS F32 GM142213
6 · The paper itself

Abstract

Long-read sequencing (LRS) has revealed a far greater diversity of RNA isoforms than earlier technologies, increasing the critical need to determine which, and how many, isoforms per gene are biologically meaningful. To define the space of relevant isoforms from LRS, many existing analysis pipelines rely on arbitrary expression cutoffs, but a single threshold cannot accommodate the broad variability in isoform complexity across genes, cell-types, and disease states captured by LRS. To address this, we propose using

Identifiers

PMID40631152
PMCPMC12236620

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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.