Evidence map›Paper›PMID 38585946›Full record

ArticlebioRxiv : the preprint server for biology2025

Identification of non-canonical peptides with moPepGen.

Chenghao Zhu, Lydia Y Liu, Annie Ha, Takafumi N Yamaguchi, Helen Zhu, Rupert Hugh-White, Julie Livingstone, Yash Patel, Thomas Kislinger, Paul C Boutros

Open access · greenAbstract 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, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors at 2 institutions in 2 countries.

Chenghao ZhuDepartment of Human Genetics, University of California, Los Angeles, CA, USA.ORCID 0000-0003-1674-4533
Lydia Y LiuDepartment of Human Genetics, University of California, Los Angeles, CA, USA.ORCID 0000-0001-6026-3169
Annie HaDepartment of Medical Biophysics, University of Toronto, Toronto, Canada.ORCID 0000-0002-8740-4125
Takafumi N YamaguchiDepartment of Human Genetics, University of California, Los Angeles, CA, USA.ORCID 0000-0003-1082-3871
Helen ZhuDepartment of Medical Biophysics, University of Toronto, Toronto, Canada.
Rupert Hugh-WhiteDepartment of Human Genetics, University of California, Los Angeles, CA, USA.ORCID 0000-0003-3351-8925
Julie LivingstoneDepartment of Human Genetics, University of California, Los Angeles, CA, USA.ORCID 0000-0002-8424-3768
Yash PatelDepartment of Human Genetics, University of California, Los Angeles, CA, USA.ORCID 0000-0003-3113-7010
Thomas KislingerDepartment of Medical Biophysics, University of Toronto, Toronto, Canada.ORCID 0000-0003-3525-5540
Paul C BoutrosDepartment of Human Genetics, University of California, Los Angeles, CA, USA.ORCID 0000-0003-0553-7520
University Health Network · CAUniversity of California, Los Angeles · US

Funding

Women's CancersP30CA016042 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Robert Damoiseaux · 1985 to 2026
$134.5M
UCLA SPORE IN PROSTATE CANCERP50CA092131 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI REITER, ROBERT E · 2002 to 2023
$42.6M
Advancing method benchmarking and data sharing through crowd-sourced competitions in cancer researchU24CA248265 · NCI · SAGE BIONETWORKS · PI BOUTROS, PAUL CHRISTOPHER, VARMA, SUSHEEL · 2020 to 2024
$4.1M
The Evolution of Sarcoma Drug Sensitivity through Time and SpaceR01CA244729 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BOUTROS, PAUL CHRISTOPHER, SORAGNI, ALICE · 2020 to 2024
$3.4M
Virginia-UCLA-Toronto Biomarker Characterization CenterU2CCA271894 · NCI · OLD DOMINION UNIVERSITY · PI OLIVER John SEMMES · 2022 to 2026
$3.2M
Development of Protein Biomarkers in Post-DRE Urine for use in Liquid Biopsy of Prostate CancerU01CA214194 · NCI · EASTERN VIRGINIA MEDICAL SCHOOL · PI BOUTROS, PAUL CHRISTOPHER, KISLINGER, THOMAS · 2016 to 2021
$2.5M
NCI NIH HHS P30 CA016042NCI NIH HHS P50 CA092131NCI NIH HHS R01 CA244729NCI NIH HHS U01 CA214194NCI NIH HHS U24 CA248265NCI NIH HHS U2C CA271894
6 · The paper itself

Abstract

Proteogenomics is limited by challenges of modeling the complexities of gene expression. We create moPepGen, a graph-based algorithm that comprehensively generates non-canonical peptides in linear time. moPepGen works with multiple technologies, in multiple species and on all types of genetic and transcriptomic data. In human cancer proteomes, it enumerates previously unobservable noncanonical peptides arising from germline and somatic genomic variants, noncoding open reading frames, RNA fusions and RNA circularization.

Identifiers

PMID38585946
PMCPMC10996593
OpenAlexW4393363301

What OpenQuestion 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 OpenQuestion graph.