Evidence map›Paper›PMID 41742304›Full record

ArticleGenome biology2026

iPepGen: a modular, immunopeptidogenomic 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, Suzanne Coleman, Flavia E Popescu, Alexey I Nesvizhskii and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. 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. Article
  2. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Subina MehtaDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA.
Reid WagnerMinnesota Supercomputing Institute, University of Minnesota, Minneapolis, USA.
Katherine T DoDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA.
James E JohnsonMinnesota Supercomputing Institute, University of Minnesota, Minneapolis, USA.
Fengchao YuDepartment of Pathology, University of Michigan, Ann Arbor, USA.
Tyler JubenvilleMasonic Cancer Center, University of Minnesota, Minneapolis, USA.
Kyle RichardsDepartment of Pediatrics, University of Minnesota, Minneapolis, USA.
Suzanne ColemanMasonic Cancer Center, University of Minnesota, Minneapolis, USA.
Flavia E PopescuMasonic Cancer Center, University of Minnesota, Minneapolis, USA.
Alexey I NesvizhskiiDepartment of Pathology, University of Michigan, Ann Arbor, USA.
David A LargaespadaMasonic Cancer Center, University of Minnesota, Minneapolis, USA.
Pratik D JagtapDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA.
Timothy J GriffinDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA. tgriffin@umn.edu.

Funding

COMPUTATIONAL TOOLS FOR MASS SPECTROMETRY-BASED INTERACTOME DATAR01GM094231 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Alexey I Nesvizhskii · 2010 to 2026
$5.4M
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
Recurrent Tumor-Specific Alternately Processed Transcripts as a Source of Neoantigens for NF1-associated Malignant Peripheral Nerve Sheath Tumor ImmunopreventionUG3CA244687 · NCI · UNIVERSITY OF MINNESOTA · PI LARGAESPADA, DAVID ANDREW · 2019 to 2020
$1.5M
The immunoPeptidoGenomic (iPepGen) informatics resource forimmuno-oncology researchU01CA288888 · NCI · UNIVERSITY OF MINNESOTA · PI TIMOTHY J. GRIFFIN, Pratik D Jagtap · 2024 to 2026
$1.3M
A transformative next-generation Orbitrap Tribrid system for the UMN and Upper MidwestS10OD028717 · OD · UNIVERSITY OF MINNESOTA · PI GRIFFIN, TIMOTHY J. · 2020 to 2020
$1.2M
American Cancer Society RP-17-216-06-COUNNCI NIH HHS U01 CA288888NCI NIH HHS UG3 CA244687NIGMS NIH HHS R01 GM094231NIH HHS S10 OD028717NIH HHS S10OD028717NIH HHS U01CA288888NIH HHS UH3CA244687
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.

Indexed as

Antigens, NeoplasmNeoplasmsPeptidesSoftwareComputational BiologyGenomicsHumansImmunoinformaticsAntigens, NeoplasmPeptidesBioinformaticsGalaxyImmuno-oncologyImmunopeptidomicsMass spectrometryMulti-omicsNeoantigenNext-generation sequencingWorkflow

Identifiers

PMID41742304
PMCPMC13040755

What OpenQuestion 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 OpenQuestion graph.