Evidence map›Paper›PMID 40395503›Full record

ArticleBioinformatics advances2025

Yizhou Peter Huang, Lauren Harmon, Eve Deering-Gardner, Xiaotu Ma, Josiah Harsh, Zhaoyu Xue, Hong Wen, Marcel Ramos, Sean Davis, Timothy J Triche

Abstract read
In one paragraph

Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

  • Update of
    2024
5 · Who and what money

Authors and funding

10 authors.

Yizhou Peter HuangMichigan State University, East Lansing, MI 48824, United States.ORCID https://orcid.org/0009-0004-5689-0193
Lauren HarmonDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, United States.
Eve Deering-GardnerDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, United States.ORCID https://orcid.org/0009-0009-4133-8343
Xiaotu MaComputational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, United States.ORCID https://orcid.org/0000-0002-6233-2145
Josiah HarshDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, United States.
Zhaoyu XueDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, United States.ORCID https://orcid.org/0000-0001-7288-8780
Hong WenDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, United States.ORCID https://orcid.org/0000-0001-8739-4572
Marcel RamosBiostatistics and Computational Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, United States.ORCID https://orcid.org/0000-0002-3242-0582
Sean DavisBiomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.ORCID https://orcid.org/0000-0002-8991-6458
Timothy J TricheMichigan State University, East Lansing, MI 48824, United States.ORCID https://orcid.org/0000-0001-5665-946X

Funding

Exploiting Public Metagenomic Data to Uncover Cancer-Microbiome RelationshipsR01CA230551 · NCI · GRADUATE SCHOOL OF PUBLIC HEALTH AND HEALTH POLICY · PI Levi Waldron · 2020 to 2026
$3.9M
The roles of genetics, hormones, and gender in sexually dimorphic immune responseR01AI171984 · NIAID · VAN ANDEL RESEARCH INSTITUTE · PI KRAWCZYK, CONNIE, PROKOP, JEREMY WILLIAM · 2022 to 2024
$1.4M
Dissecting the role of germline genetic variation and viral exposures as determinants of hematological disease predispositionR03CA290259 · NCI · VAN ANDEL RESEARCH INSTITUTE · PI TRICHE, TIMOTHY J. · 2024 to 2024
$336k
Determinants of susceptibility to pediatric acute myeloid leukemiaF99CA294248 · NCI · VAN ANDEL RESEARCH INSTITUTE · PI HARMON, LAUREN MARIE · 2024 to 2025
$104k
NCI NIH HHS F99 CA294248NCI NIH HHS R01 CA230551NCI NIH HHS R03 CA290259NIAID NIH HHS R01 AI171984
6 · The paper itself

Abstract

Motivation: The National Cancer Institute Genomic Data Commons (GDC) provides controlled access to sequencing data from thousands of subjects, enabling large-scale study of impactful genetic alterations such as simple and complex germline and structural variants. However, efficient analysis requires significant computational resources and expertise, especially when calling variants from raw sequence reads. To solve these problems, we developed Results: Here, we demonstrate population-scale genomic and transcriptomic analyses with minimal compute burden using Availability and implementation:

Identifiers

PMID40395503
PMCPMC12089696

What OpenQuestion holds

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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.