Improved genome inference in the MHC using a population reference graph

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

Short read alignment with populations of genomes

(2013) L. Huang et al.   BIOINFORMATICS

Adding unaligned sequences into an existing alignment using MAFFT and LAST

(2012) Kazutaka Katoh et al.   BIOINFORMATICS

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

Lapatinib-Induced Liver Injury Characterized by Class II HLA and Gilbert's Syndrome Genotypes

(2012) C F Spraggs et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors

(2012) W. Jiang et al.   GENOME RESEARCH

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Structural diversity and African origin of the 17q21.31 inversion polymorphism

(2012) Karyn Meltz Steinberg et al.   NATURE GENETICS

Structural haplotypes and recent evolution of the human 17q21.31 region

(2012) Linda M Boettger et al.   NATURE GENETICS

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Low-coverage sequencing: Implications for design of complex trait association studies

(2011) Y. Li et al.   GENOME RESEARCH

Cactus Graphs for Genome Comparisons

(2011) Benedict Paten et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

The HLA dictionary 2008: a summary of HLA-A, -B, -C, -DRB1/3/4/5, and -DQB1 alleles and their association with serologically defined HLA-A, -B, -C, -DR, and -DQ antigens

(2009) R. Holdsworth et al.   TISSUE ANTIGENS

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

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

(2008) Roger Horton et al.   IMMUNOGENETICS

IMGT(R), the international ImMunoGeneTics information system(R)

(2008) M.-P. Lefranc et al.   NUCLEIC ACIDS RESEARCH