Evidence map›Paper›PMID 40291680›Full record

ArticlebioRxiv : the preprint server for biology2025

A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.

Subina Mehta, Reid Wagner, Katherine T Do, James E Johnson, Fengchao Yu, Tyler Jubenville, Kyle Richards, Susan Coleman, Flavia E Popescu, Alexey I Nesvizhskii and 3 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

5 · Who and what money

Authors and funding

13 authors.

Subina MehtaORCID 0000-0001-9818-0537
Reid Wagner
Katherine T DoORCID 0000-0002-1230-8577
James E Johnson
Fengchao YuORCID 0000-0002-7695-3698
Tyler JubenvilleORCID 0009-0003-9578-4847
Kyle RichardsORCID 0000-0002-7155-3281
Susan ColemanORCID 0000-0002-7578-7747
Flavia E Popescu
Alexey I NesvizhskiiORCID 0000-0002-2806-7819
David A Largaespada
Pratik D JagtapORCID 0000-0003-0984-0973
Timothy J GriffinORCID 0000-0001-6801-2559

Funding

Recurrent Tumor-Specific Alternately Processed Transcripts as a Source of Neoantigens for NF1-associated Malignant Peripheral Nerve Sheath Tumor ImmunopreventionUH3CA244687 · NCI · UNIVERSITY OF MINNESOTA · PI LARGAESPADA, DAVID ANDREW · 2021 to 2023
$2.1M
NCI NIH HHS UH3 CA244687
6 · The paper itself

Abstract

Characterizing tumor-specific neoantigen peptides, derived from genomic or transcriptomic aberrations and presented to the immune system, is critical for immuno-oncology studies. To this end, the modular iPepGen immunopeptidogenomics pipeline provides these functions: (1) Neoantigen prediction and protein database generation from genomic or transcriptomic sequencing data; (2) Peptide identification (3) Verification from immunopeptidomic mass spectral data; (4) Neoantigen classification and visualization; (5) Candidate prioritization for further study. Easy access via a publicly available, scalable cloud-based gateway coupled with online, interactive training materials streamlines the adoption by cancer researchers who require immunopeptidogenomic analysis tools but lack advanced computational expertise and resources.

Identifiers

PMID40291680
PMCPMC12026984

What OpenQuestion holds

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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.