Hybridization ddRAD‐sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA

A roadmap for high-throughput sequencing studies of wild animal populations using non-invasive samples and hybridization capture

(2019) Lauren C. White et al.   Molecular Ecology Resources

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

(2019) Ethan Linck et al.   Molecular Ecology Resources

The origins and adaptation of European potatoes reconstructed from historical genomes

(2019) Rafal M. Gutaker et al.   Nature Ecology & Evolution

Expressed exome capture sequencing: A method for cost-effective exome sequencing for all organisms

(2018) Jonathan B. Puritz et al.   Molecular Ecology Resources

The rate and potential relevance of new mutations in a colonizing plant lineage

(2018) Moises Exposito-Alonso et al.   PLoS Genetics

Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections

(2018) Vanessa C. Bieker et al.   Botany Letters

Using herbaria to study global environmental change

(2018) Patricia L. M. Lang et al.   NEW PHYTOLOGIST

Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations

(2017) Julian M. Catchen et al.   Molecular Ecology Resources

African genomes illuminate the early history and transition to selfing inArabidopsis thaliana

(2017) Arun Durvasula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neandertal and Denisovan DNA from Pleistocene sediments

(2017) Viviane Slon et al.   SCIENCE

Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

(2017) Ethan B. Linck et al.   Ecology and Evolution

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes

(2016) Fátima Sánchez Barreiro et al.   Molecular Ecology Resources

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

(2016) Clemens L. Weiß et al.   Royal Society Open Science

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

(2016) Tomasz Suchan et al.   PLoS One

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Time to get moving: assisted gene flow of forest trees

(2015) Sally N. Aitken et al.   Evolutionary Applications

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

SNP genotyping and population genomics from expressed sequences - current advances and future possibilities

(2015) Pierre De Wit et al.   MOLECULAR ECOLOGY

Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries

(2015) María C. Ávila-Arcos et al.   Methods in Ecology and Evolution

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

The origin and evolution of maize in the Southwestern United States

(2015) Rute R. da Fonseca et al.   Nature Plants

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

(2014) Anna-Sapfo Malaspinas et al.   BIOINFORMATICS

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

(2014) B. Shapiro et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Comparative Population Genomics of the Ejaculate in Humans and the Great Apes

(2013) Jeffrey M. Good et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

DNA analysis of an early modern human from Tianyuan Cave, China

(2013) Q. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

(2011) María C. Ávila-Arcos et al.   Scientific Reports

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Implementing large-scale and long-term functional biodiversity research: The Biodiversity Exploratories

(2010) Markus Fischer et al.   BASIC AND APPLIED ECOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) H. A. Burbano et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Scale of Population Structure in Arabidopsis thaliana

(2010) Alexander Platt et al.   PLoS Genetics

Biogeography and Phylogeny of Cardamine (Brassicaceae)1

(2009) Tor Carlsen et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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