Targeted sequence capture as a powerful tool for evolutionary analysis1

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

(2011) Philippa C Griffin et al.   BMC BIOLOGY

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterations

(2011) Michal R. Schweiger et al.   CANCER AND METASTASIS REVIEWS

High-throughput approaches for plant epigenomic studies

(2011) Robert J Schmitz et al.   CURRENT OPINION IN PLANT BIOLOGY

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

(2011) R. D. George et al.   GENOME RESEARCH

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The hairy problem of epigenetics in evolution

(2011) Christina L. Richards et al.   NEW PHYTOLOGIST

Differential regulation of a MYB transcription factor is correlated with transgenerational epigenetic inheritance of trichome density in Mimulus guttatus

(2011) Alison G. Scoville et al.   NEW PHYTOLOGIST

Efficient and Cost Effective Population Resequencing by Pooling and In-Solution Hybridization

(2011) Vikas Bansal et al.   PLoS One

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform

(2011) Dale J. Hedges et al.   PLoS One

High-quality DNA sequence capture of 524 disease candidate genes

(2011) P. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome

(2011) Cyrille Saintenac et al.   GENOME BIOLOGY

History in a single hair

(2010) Howard Wolinsky   EMBO REPORTS

Epigenetics meets next-generation sequencing

(2010) Peter J. Park   Epigenetics

Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples

(2010) K. E. Varley et al.   GENOME RESEARCH

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Tackling the epigenome: challenges and opportunities for collaboration

(2010) John S Satterlee et al.   NATURE BIOTECHNOLOGY

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

The population genomics of plant adaptation

(2010) Mathieu Siol et al.   NEW PHYTOLOGIST

Repeat subtraction-mediated sequence capture from a complex genome

(2010) Yan Fu et al.   PLANT JOURNAL

High-throughput method for analyzing methylation of CpGs in targeted genomic regions

(2010) Shivani Nautiyal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

(2010) C. T. Hittinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

(2010) J. Gordon Burleigh et al.   SYSTEMATIC BIOLOGY

Genetic perspectives on crop domestication

(2010) Briana L. Gross et al.   TRENDS IN PLANT SCIENCE

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

Cross species analysis of microarray expression data

(2009) Y. Lu et al.   BIOINFORMATICS

Perspective: conservation genetics enters the genomics era

(2009) John C. Avise   CONSERVATION GENETICS

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

(2009) E. Hodges et al.   GENOME RESEARCH

A SNP discovery method to assess variant allele probability from next-generation resequencing data

(2009) Y. Shen et al.   GENOME RESEARCH

Enabling technologies of genomic-scale sequence enrichment for targeted high-throughput sequencing

(2009) Daniel Summerer   GENOMICS

Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics

(2009) J. G. Gibbons et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA Chip Analysis in Diverse Organisms with Unsequenced Genomes

(2009) Ross N. Nazar et al.   MOLECULAR BIOTECHNOLOGY

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Massively parallel exon capture and library-free resequencing across 16 genomes

(2009) Emily H Turner et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

High-throughput, high-accuracy array-based resequencing

(2009) J. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next-generation sequencing technologies and their implications for crop genetics and breeding

(2009) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Characterizing natural variation using next-generation sequencing technologies

(2009) Yoav Gilad et al.   TRENDS IN GENETICS

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

Molecular insights into the evolution of crop plants

(2008) Jutta C. Burger et al.   AMERICAN JOURNAL OF BOTANY

Using supernetworks to distinguish hybridization from lineage-sorting

(2008) Barbara R Holland et al.   BMC EVOLUTIONARY BIOLOGY

Epigenome Sequencing Comes of Age

(2008) Jian-Kang Zhu   CELL

Multilocus phylogeography and phylogenetics using sequence-based markers

(2008) Patrícia H. Brito et al.   GENETICA

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Variation in Constraint Versus Positive Selection as an Explanation for Evolutionary Rate Variation Among Anthocyanin Genes

(2008) Mark D. Rausher et al.   JOURNAL OF MOLECULAR EVOLUTION

Selecting Single-Copy Nuclear Genes for Plant Phylogenetics: A Preliminary Analysis for the Senecioneae (Asteraceae)

(2008) Inés Álvarez et al.   JOURNAL OF MOLECULAR EVOLUTION

Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids

(2008) P. Roxanne Steele et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

A comprehensive assay for targeted multiplex amplification of human DNA sequences

(2008) S. Krishnakumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

The Epigenetic Landscape of Plants

(2008) X. Zhang   SCIENCE

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources

The role of hybridization in evolution

(2003) N. H. Barton   MOLECULAR ECOLOGY