Stepwise Threshold Clustering: A New Method for Genotyping MHC Loci Using Next-Generation Sequencing Technology

Comprehensive analysis of MHC class II genes in teleost fish genomes reveals dispensability of the peptide-loading DM system in a large part of vertebrates

(2013) Johannes M Dijkstra et al.   BMC EVOLUTIONARY BIOLOGY

MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout

(2013) Simone Sommer et al.   BMC GENOMICS

EVALUATING PATTERNS OF CONVERGENT EVOLUTION AND TRANS-SPECIES POLYMORPHISM AT MHC IMMUNOGENES IN TWO SYMPATRIC STICKLEBACK SPECIES

(2013) Tobias L. Lenz et al.   EVOLUTION

Nonparallelism in MHCIIβ diversity accompanies nonparallelism in pathogen infection of lake whitefish (Coregonus clupeaformis) species pairs as revealed by next-generation sequencing

(2013) Scott A. Pavey et al.   MOLECULAR ECOLOGY

MHC Class IIB Exon 2 Polymorphism in the Grey Partridge (Perdix perdix) Is Shaped by Selection, Recombination and Gene Conversion

(2013) Marta Promerová et al.   PLoS One

MHC VARIATION IS RELATED TO A SEXUALLY SELECTED ORNAMENT, SURVIVAL, AND PARASITE RESISTANCE IN COMMON YELLOWTHROATS

(2012) Peter O. Dunn et al.   EVOLUTION

MHC diversity, malaria and lifetime reproductive success in collared flycatchers

(2012) JACEK RADWAN et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

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

Major histocompatibility complex class II compatibility, but not class I, predicts mate choice in a bird with highly developed olfaction

(2012) M. Strandh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

mvabund- anRpackage for model-based analysis of multivariate abundance data

(2012) Yi Wang et al.   Methods in Ecology and Evolution

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher

(2011) Magdalena Zagalska-Neubauer et al.   BMC EVOLUTIONARY BIOLOGY

Next-generation sequencing for HLA typing of class I loci

(2011) Rachel L Erlich et al.   BMC GENOMICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Gene conversion rapidly generates major histocompatibility complex diversity in recently founded bird populations

(2011) LEWIS G. SPURGIN et al.   MOLECULAR ECOLOGY

Interspecific hybridization increases MHC class II diversity in two sister species of newts

(2011) KRYSTYNA NADACHOWSKA-BRZYSKA et al.   MOLECULAR ECOLOGY

jMHC: software assistant for multilocus genotyping of gene families using next-generation amplicon sequencing

(2011) MICHAŁ T. STUGLIK et al.   Molecular Ecology Resources

Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing

(2011) MARTA PROMEROVÁ et al.   Molecular Ecology Resources

MHC genotypes associate with resistance to a frog-killing fungus

(2011) A. E. Savage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distance-based multivariate analyses confound location and dispersion effects

(2011) David I. Warton et al.   Methods in Ecology and Evolution

A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies

(2010) Maxime Galan et al.   BMC GENOMICS

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

(2010) Osvaldo Zagordi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

The Threshold Bootstrap Clustering: A New Approach to Find Families or Transmission Clusters within Molecular Quasispecies

(2010) Mattia C. F. Prosperi et al.   PLoS One

MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer

(2010) H. V. Siddle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings

(2010) L. G. Spurgin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RSCA genotyping of MHC for high-throughput evolutionary studies in the model organism three-spined stickleback Gasterosteus aculeatus

(2009) Tobias L Lenz et al.   BMC EVOLUTIONARY BIOLOGY

VARIABLE PROGRESS TOWARD ECOLOGICAL SPECIATION IN PARAPATRY: STICKLEBACK ACROSS EIGHT LAKE-STREAM TRANSITIONS

(2009) Daniel Berner et al.   EVOLUTION

New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system

(2009) WIESŁAW BABIK et al.   Molecular Ecology Resources

Methods for MHC genotyping in non-model vertebrates

(2009) W. BABIK   Molecular Ecology Resources

INFERRING POPULATION HISTORY AND DEMOGRAPHY USING MICROSATELLITES, MITOCHONDRIAL DNA, AND MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) GENES

(2008) David H. Bos et al.   EVOLUTION

Simple approach to reduce PCR artefact formation leads to reliable genotyping of MHC and other highly polymorphic loci — Implications for evolutionary analysis

(2008) Tobias L. Lenz et al.   GENE

Parallel tagged sequencing on the 454 platform

(2008) Matthias Meyer et al.   Nature Protocols

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH