Evidence map›Paper›PMID 41888873›Full record

ArticleGenome biology2026

ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.

Limin Jiang, Ivy Hurwitz, Lukasz S Wylezinski, Michael K Racke, Fengyao Yan, Fei Ye, Quanhu Sheng, Shuguang Leng, Cecilia P Chung, C Michael Stein and 8 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 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

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

18 authors.

Limin JiangDepartment of Public Health Sciences, University of Miami, Miami, FL, 33136, USA.
Ivy HurwitzCenter for Global Health, University of New Mexico, Albuquerque, NM, 87131, USA.
Lukasz S WylezinskiDecode Health, Inc., Nashville, TN, 37203, USA.
Michael K RackeQuest Diagnostics, Secaucus, NJ, 07094, USA.
Fengyao YanDepartment of Public Health Sciences, University of Miami, Miami, FL, 33136, USA.
Fei YeDepartment of Public Health Sciences, University of Miami, Miami, FL, 33136, USA.
Quanhu ShengDepartment of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37212, USA.
Shuguang LengDepartment of Internal Medicine, University of New Mexico, Albuquerque, NM, 87131, USA.
Cecilia P ChungDepartment of Rheumatology, University of Miami, Miami, FL, 33136, USA.
C Michael SteinDepartment of Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA.
Chung-I LiDepartment of Statistics, National Cheng Kung University, Tainan, 701401, Taiwan.
Naresh KumarDepartment of Public Health Sciences, University of Miami, Miami, FL, 33136, USA.
Michele CeccarelliDepartment of Public Health Sciences, University of Miami, Miami, FL, 33136, USA.
Steven F BakerInfectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, 87108, USA.
Douglas J PerkinsCenter for Global Health, University of New Mexico, Albuquerque, NM, 87131, USA.
Charles F SpurlockDecode Health, Inc., Nashville, TN, 37203, USA. chase@decodehealth.ai.
Leng HanDepartment of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. lenghan@iu.edu.
Yan GuoDepartment of Public Health Sciences, University of Miami, Miami, FL, 33136, USA. yxg835@med.miami.edu.

Funding

Tumor Biology Research ProgramP30CA240139 · NCI · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI Stephen D. Nimer · 2019 to 2026
$24.1M
Harnessing the Malarial Immunity Omics Landscape in Vaccinated and Unvaccinated Children for Improved Therapeutic StrategiesR01AI130473 · NIAID · UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR · PI Samuel Bonuke Anyona, Douglas Jay Perkins · 2018 to 2026
$5.6M
Impact of Macrophage Carbon Load and Epigenetic Aging on Lung Function Decline and MortalityR01ES035421 · NIEHS · UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR · PI Steven A Belinsky, Shuguang Leng · 2024 to 2026
$2.2M
Long non-coding RNA signatures to track treatment responses in multiple sclerosisR44AI145505 · NIAID · IQUITY LABS, INC · PI SPURLOCK, CHARLES FLOYD · 2019 to 2021
$1.1M
Long non-coding RNA signatures to distinguish relapsing-remitting multiple sclerosis from primary progressive and secondary progressive multiple sclerosisR43AI157674 · NIAID · DECODE HEALTH, INC. · PI SPURLOCK, CHARLES FLOYD · 2022 to 2022
$248k
NCI NIH HHS P30 CA240139NIAID NIH HHS R01 AI130473NIAID NIH HHS R43 AI157674NIAID NIH HHS R44 AI145505NIEHS NIH HHS R01 ES035421
6 · The paper itself

Abstract

HLA typing from sequencing data is crucial for studying immune gene families, but high allele similarity challenges existing tools. We present ImmuSeeker, comprehensive software for extracting HLA genotypes, expression, and diversity at gene, one-field, and two-field allele levels, with improved Bayesian zygosity inference and graphical phylogenetic visualization. ImmuSeeker was benchmarked against nine established tools using gold-standard HLA datasets, repeated RNA sequencing (RNA-seq) and Isoform Sequencing (Iso-Seq) data, and a longitudinal patient cohort, demonstrating superior accuracy, consistency, and analytical utility. ImmuSeeker provides a scalable, robust framework for comprehensive HLA typing and immune system analyses.

Indexed as

Histocompatibility TestingHLA AntigensMultigene FamilySoftwareAllelesBayes TheoremData MiningHumansPhylogenyHLA AntigensAutoimmune diseaseHLA-peptide-TCR bindingHLA typingPhylogenetic structures

Identifiers

PMID41888873
PMCPMC13154904

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.