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

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.

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Publication Details

Journal
Genome biology
Published
2026-03-26
DOI
https://doi.org/10.1186/s13059-026-04039-5
Primary Topic
vaccines and immunoinformatics approaches
Type
article
Field-Weighted Citation Impact
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article

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

Chung-I Li, Michael K. Racke, Fengyao Yan, Lukasz S. Wylezinski et al.
Genome biology
vaccines and immunoinformatics approaches
article

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

Chung-I Li, Michael K. Racke, Fengyao Yan, Lukasz S. Wylezinski, Cecilia P. Chung, Charles F. Spurlock, Ivy Hurwitz, Douglas J. Perkins, Leng Han, Steven F. Baker, Naresh Kumar, Michele Ceccarelli, Limin Jiang, Shuguang Leng, Quanhu Sheng, C. Michael Stein, Yan Guo, Fei Ye
article en

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.

Genome biology
Indiana University Health (US), Lovelace Respiratory Research Institute (US), deCODE Genetics (Iceland) (IS), University of Miami (US), University of New Mexico (US), Vanderbilt University (US), Tennessee Department of Health (US), Wagner College (US), Indiana University – Purdue University Indianapolis (US), Quest Diagnostics (United States) (US), Vanderbilt University Medical Center (US), National Cheng Kung University (TW)
Openalex Percentile: Top 7%
vaccines and immunoinformatics approaches
DOIOpen Access PDFOpenAlex
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