Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

(2022) Marta Byrska-Bishop et al.   CELL

SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction

(2021) Jerzy K. Kulski et al.   Frontiers in Genetics

Adaptive Admixture of HLA Class I Allotypes Enhanced Genetically Determined Strength of Natural Killer Cells in East Asians

(2021) Zhihui Deng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

The Need for a Human Pangenome Reference Sequence

(2021) Karen H. Miga et al.   Annual Review of Genomics and Human Genetics

Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

(2021) Jerzy K. Kulski et al.   Frontiers in Genetics

A diploid assembly-based benchmark for variants in the major histocompatibility complex

(2020) Chen-Shan Chin et al.   Nature Communications

State-of-the-art genome inference in the human MHC

(2020) Alexander T Dilthey   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Fast and accurate genomic analyses using genome graphs

(2019) Goran Rakocevic et al.   NATURE GENETICS

HLA*LA—HLA typing from linearly projected graph alignments

(2019) Alexander T Dilthey et al.   BIOINFORMATICS

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

(2019) Hannes P. Eggertsson et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Evolution of DNAase I Hypersensitive Sites in MHC Regulatory Regions of Primates

(2018) Yabin Jin et al.   GENETICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Evolution of DNAase I Hypersensitive Sites in MHC Regulatory Regions of Primates

(2018) Yabin Jin et al.   GENETICS

Genomes for all

(2018) Deanna M Church   NATURE BIOTECHNOLOGY

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Immune diversity sheds light on missing variation in worldwide genetic diversity panels

(2018) Laurent Abi-Rached et al.   PLoS One

Sequences of 95 humanMHChaplotypes reveal extreme coding variation in genes other than highly polymorphicHLA class IandII

(2017) Paul J. Norman et al.   GENOME RESEARCH

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

What has GWAS done for HLA and disease associations?

(2017) A. E. Kennedy et al.   International Journal of Immunogenetics

Graphtyper enables population-scale genotyping using pangenome graphs

(2017) Hannes P Eggertsson et al.   NATURE GENETICS

Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest

(2017) D J Pappas et al.   PHARMACOGENOMICS JOURNAL

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA

(2017) Chao Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Schizophrenia risk from complex variation of complement component 4

(2016) Aswin Sekar et al.   NATURE

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

(2016) Alexander T. Dilthey et al.   PLoS Computational Biology

Very long haplotype tracts characterized at high resolution from HLA homozygous cell lines

(2015) Paul J. Norman et al.   IMMUNOGENETICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

Class II HLA interactions modulate genetic risk for multiple sclerosis

(2015) Loukas Moutsianas et al.   NATURE GENETICS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

HLA Diversity in the 1000 Genomes Dataset

(2014) Pierre-Antoine Gourraud et al.   PLoS One

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Major Histocompatibility Complex Genomics and Human Disease

(2013) John Trowsdale et al.   Annual Review of Genomics and Human Genetics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Influence of HLA-C Expression Level on HIV Control

(2013) R. Apps et al.   SCIENCE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

(2008) Roger Horton et al.   IMMUNOGENETICS