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Structural variation shapes regulatory and evolutionary diversity at the HLA locus

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
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The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
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The genomic history of the Aegean palatial civilizations
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The genomic origins of the world’s first farmers
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High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
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The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers
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Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes
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Balancing selection and heterogeneity across the classical human leukocyte antigen loci: A meta-analytic review of 497 population studies
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EMBOSS: The European Molecular Biology Open Software Suite
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Associations of human leukocyte antigens with autoimmune diseases: challenges in identifying the mechanism
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Transcriptome and genome sequencing uncovers functional variation in humans
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Ancient human genomes suggest three ancestral populations for present-day Europeans
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Population genomics of Bronze Age Eurasia
inferredcites →https://doi.org/10.1038/ncomms14061openalex-snapshot
Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast
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Upper Palaeolithic genomes reveal deep roots of modern Eurasians
inferredcites →https://doi.org/10.1038/ng.3143openalex-snapshot
Variation at HLA-DRB1 is associated with resistance to enteric fever
inferredcites →https://doi.org/10.1038/ng0398-237openalex-snapshot
Recent origin of HLA-DRB1 alleles and implications for human evolution
inferredcites →https://doi.org/10.1038/nprot.2011.457openalex-snapshot
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
inferredcites →https://doi.org/10.1038/nri.2017.143openalex-snapshot
HLA variation and disease
inferredcites →https://doi.org/10.1038/s41467-018-03857-xopenalex-snapshot
Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans
inferredcites →https://doi.org/10.1038/s41467-021-21541-5openalex-snapshot
Accurate imputation of human leukocyte antigens with CookHLA
inferredcites →https://doi.org/10.1038/s41467-021-21975-xopenalex-snapshot
A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes
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Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak
inferredcites →https://doi.org/10.1038/s41467-023-40072-9openalex-snapshot
Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age
inferredcites →https://doi.org/10.1038/s41467-024-50583-8openalex-snapshot
The influence of HLA genetic variation on plasma protein expression
inferredcites →https://doi.org/10.1038/s41467-025-56749-2openalex-snapshot
Modeling and designing enhancers by introducing and harnessing transcription factor binding units
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Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance
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Ancient genomes indicate population replacement in Early Neolithic Britain
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Host genetics and infectious disease: new tools, insights and translational opportunities
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Nonhuman primate models of human viral infections
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A dynastic elite in monumental Neolithic society
inferredcites →https://doi.org/10.1038/s41586-020-2688-8openalex-snapshot
Population genomics of the Viking world
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A draft human pangenome reference
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Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations
inferredcites →https://doi.org/10.1038/s41586-023-06865-0openalex-snapshot
Population genomics of post-glacial western Eurasia
inferredcites →https://doi.org/10.1038/s41586-024-07509-7openalex-snapshot
Ancient genomes reveal insights into ritual life at Chichén Itzá
inferredcites →https://doi.org/10.1038/s41586-024-07651-2openalex-snapshot
Repeated plague infections across six generations of Neolithic Farmers
inferredcites →https://doi.org/10.1038/s41586-024-07708-2openalex-snapshot
Sources of gene expression variation in a globally diverse human cohort
inferredcites →https://doi.org/10.1038/s41586-024-07911-1openalex-snapshot
Recurrent evolution and selection shape structural diversity at the amylase locus
inferredcites →https://doi.org/10.1038/s41586-025-08816-3openalex-snapshot
Complete sequencing of ape genomes
inferredcites →https://doi.org/10.1038/s41586-025-09140-6openalex-snapshot
Complex genetic variation in nearly complete human genomes
inferredcites →https://doi.org/10.1038/s41586-025-09192-8openalex-snapshot
The spatiotemporal distribution of human pathogens in ancient Eurasia
inferredcites →https://doi.org/10.1038/s41586-025-09290-7openalex-snapshot
Structural variation in 1,019 diverse humans based on long-read sequencing
inferredcites →https://doi.org/10.1038/s41587-019-0217-9openalex-snapshot
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
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Accurate isoform discovery with IsoQuant using long reads
inferredcites →https://doi.org/10.1038/s41587-023-02024-yopenalex-snapshot
Detection of mosaic and population-level structural variants with Sniffles2
inferredcites →https://doi.org/10.1038/s41588-020-0579-4openalex-snapshot
Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci
inferredcites →https://doi.org/10.1038/s41588-021-00931-xopenalex-snapshot
A cross-population atlas of genetic associations for 220 human phenotypes
inferredcites →https://doi.org/10.1038/s41588-025-02362-4openalex-snapshot
Locityper enables targeted genotyping of complex polymorphic genes
inferredcites →https://doi.org/10.1038/s41590-023-01517-xopenalex-snapshot
CD4+ T cell calibration of antigen-presenting cells optimizes antiviral CD8+ T cell immunity
inferredcites →https://doi.org/10.1038/s41591-022-02078-6openalex-snapshot
Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection
inferredcites →https://doi.org/10.1038/s41591-024-02944-5openalex-snapshot
High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response
inferredcites →https://doi.org/10.1038/s41592-022-01753-3openalex-snapshot
Jasmine and Iris: population-scale structural variant comparison and analysis
inferredcites →https://doi.org/10.1038/s41598-024-82449-wopenalex-snapshot
Ancient DNA HLA typing reveals significant shifts in frequency in Europe since the Neolithic
inferredcites →https://doi.org/10.1038/s42003-023-05131-3openalex-snapshot
Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe
inferredcites →https://doi.org/10.1038/sj.ejhg.5200391openalex-snapshot
A linkage disequilibrium map of the MHC region based on the analysis of 14 loci haplotypes in 50 French families
inferredcites →https://doi.org/10.1038/sj.gene.6364272openalex-snapshot
Linkage disequilibrium and haplotype blocks in the MHC vary in an HLA haplotype specific manner assessed mainly by DRB1*03 and DRB1*04 haplotypes
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HLA‐DRB9— Possible Remnant of an Ancient Functional DRB Subregion
inferredcites →https://doi.org/10.1073/pnas.1518445113openalex-snapshot
Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome
inferredcites →https://doi.org/10.1073/pnas.1523951113openalex-snapshot
Early farmers from across Europe directly descended from Neolithic Aegeans
inferredcites →https://doi.org/10.1073/pnas.1818037116openalex-snapshot
Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society
inferredcites →https://doi.org/10.1073/pnas.1820210116openalex-snapshot
Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave
inferredcites →https://doi.org/10.1073/pnas.2310545121openalex-snapshot
Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France
inferredcites →https://doi.org/10.1086/519795openalex-snapshot
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
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NGSNGS: next-generation simulator for next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btaf332openalex-snapshot
SVbyEye: a visual tool to characterize structural variation among whole-genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btu548openalex-snapshot
OptiType: precision HLA typing from next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btv383openalex-snapshot
Bandage: interactive visualization of de novo genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/bty560openalex-snapshot
fastp: an ultra-fast all-in-one FASTQ preprocessor
inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
inferredcites →https://doi.org/10.1093/molbev/msab147openalex-snapshot
Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes
inferredcites →https://doi.org/10.1093/nar/gkac1011openalex-snapshot
The IPD-IMGT/HLA Database
inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
inferredcites →https://doi.org/10.1093/nar/gkj144openalex-snapshot
The UCSC Genome Browser Database: update 2006
inferredcites →https://doi.org/10.1093/nar/gkv416openalex-snapshot
The MEME Suite
inferredcites →https://doi.org/10.1101/2024.03.14.24304327openalex-snapshot
Genome-wide association study reveals a novel tuberculosis susceptibility locus in multiple East Asian and European populations
inferredcites →https://doi.org/10.1101/2024.12.13.24318019openalex-snapshot
The genetic architecture of gene expression in individuals of African and European ancestry
inferredcites →https://doi.org/10.1101/gr.278985.124openalex-snapshot
Full-resolution HLA and KIR gene annotations for human genome assemblies
inferredcites →https://doi.org/10.1109/ipdps.2019.00041openalex-snapshot
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems
inferredcites →https://doi.org/10.1111/j.1601-5223.1997.00047.xopenalex-snapshot
Presence of Solitary Exon 1 Sequences in the HLA-DR Region
inferredcites →https://doi.org/10.1111/tan.15020openalex-snapshot
Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures
inferredcites →https://doi.org/10.1126/sciadv.abd6535openalex-snapshot
Genetic ancestry changes in Stone to Bronze Age transition in the East European plain
inferredcites →https://doi.org/10.1126/science.1209202openalex-snapshot
The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans
inferredcites →https://doi.org/10.1126/science.aau1043openalex-snapshot
Characterizing mutagenic effects of recombination through a sequence-level genetic map
inferredcites →https://doi.org/10.1126/science.abf7117openalex-snapshot
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
inferredcites →https://doi.org/10.1126/science.abj6987openalex-snapshot
The complete sequence of a human genome
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-6-31openalex-snapshot
Automated generation of heuristics for biological sequence comparison
inferredcites →https://doi.org/10.1186/s12862-020-01669-6openalex-snapshot
Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution
inferredcites →https://doi.org/10.1186/s12915-019-0674-0openalex-snapshot
RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting
inferredcites →https://doi.org/10.1186/s13059-020-02168-zopenalex-snapshot
The design and construction of reference pangenome graphs with minigraph
inferredcites →https://doi.org/10.1186/s13059-022-02831-7openalex-snapshot
Strobealign: flexible seed size enables ultra-fast and accurate read alignment
inferredcites →https://doi.org/10.1186/s13059-022-02840-6openalex-snapshot
Truvari: refined structural variant comparison preserves allelic diversity
inferredcites →https://doi.org/10.1371/journal.pgen.1006852openalex-snapshot
The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods
inferredcites →https://doi.org/10.1371/journal.pgen.1008091openalex-snapshot
Expression estimation and eQTL mapping for HLA genes with a personalized pipeline
inferredcites →https://doi.org/10.1371/journal.pone.0199305openalex-snapshot
Clinical features of patients with homozygous complement C4A or C4B deficiency
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LDheatmap : An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms
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Evolution of the human HLA-DR region
inferredcites →https://doi.org/10.3389/fimmu.2023.1297589openalex-snapshot
High population frequencies of MICA copy number variations originate from independent recombination events

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.64898/2026.06.03.729980openalex-snapshot
Imputed graph-genotyped structural variants identify regulatory haplotypes associated with gene expression in Atlantic salmon
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