Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads

Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics

(2013) Martin Danzer et al.   BMC GENOMICS

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

(2013) Chang Liu et al.   NUCLEIC ACIDS RESEARCH

HLA Haplotyping from RNA-seq Data Using Hierarchical Read Weighting

(2013) Hyunsung John Kim et al.   PLoS One

HLA Typing from 1000 Genomes Whole Genome and Whole Exome Illumina Data

(2013) Endre Major et al.   PLoS One

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

(2012) Kenneth Lo et al.   BMC Systems Biology

Widespread Impact of HLA Restriction on Immune Control and Escape Pathways of HIV-1

(2012) J. M. Carlson et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

High-throughput, high-fidelity HLA genotyping with deep sequencing

(2012) C. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting HLA class I expression to increase tumor immunogenicity

(2012) A. B. del Campo et al.   TISSUE ANTIGENS

HLA DNA typing: past, present, and future

(2012) H. Erlich   TISSUE ANTIGENS

Derivation of HLA types from shotgun sequence datasets

(2012) René L Warren et al.   Genome Medicine

Next-generation sequencing for HLA typing of class I loci

(2011) Rachel L Erlich et al.   BMC GENOMICS

Genetics of the HLA Region in the Prediction of Type 1 Diabetes

(2011) Janelle A. Noble et al.   Current Diabetes Reports

Human leucocyte antigen typing: techniques and technology, a critical appraisal

(2011) P. P. J. Dunn   International Journal of Immunogenetics

Pathogenesis of systemic lupus erythematosus revisited 2011: End organ resistance to damage, autoantibody initiation and diversification, and HLA-DR

(2011) Shu Man Fu et al.   JOURNAL OF AUTOIMMUNITY

Role of HLA class II genes in susceptibility and resistance to multiple sclerosis: Studies using HLA transgenic mice

(2011) David Luckey et al.   JOURNAL OF AUTOIMMUNITY

The uniqueome: a mappability resource for short-tag sequencing

(2010) Ryan Koehler et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

HLA and Autoimmune Digestive Disease: A Clinically Oriented Review for Gastroenterologists

(2008) Andrea Cassinotti et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

HLA typing demands for peptide-based anti-cancer vaccine

(2008) Dirk Nagorsen et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

The major histocompatibility complex class Ib molecule HLA-E at the interface between innate and adaptive immunity

(2008) L. C. Sullivan et al.   TISSUE ANTIGENS

T-cell allorecognition: a case of mistaken identity or déjà vu?

(2008) Julia K. Archbold et al.   TRENDS IN IMMUNOLOGY