The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success

High‐throughput methods for efficiently building massive phylogenies from natural history collections

(2021) Ryan A. Folk et al.   Applications in Plant Sciences

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

(2020) Gregory W. Stull et al.   AMERICAN JOURNAL OF BOTANY

Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis

(2020) Michelle L. Gaynor et al.   Journal of Systematics and Evolution

Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes

(2019) Thomas L. P. Couvreur et al.   Frontiers in Plant Science

Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

(2019) Grace E. Brewer et al.   Frontiers in Plant Science

The Limits of Hyb-Seq for Herbarium Specimens: Impact of Preservation Techniques

(2019) Laura L. Forrest et al.   Frontiers in Ecology and Evolution

aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data

(2018) Julie M Allen et al.   Evolutionary Bioinformatics

Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above

(2018) Tamara Villaverde et al.   NEW PHYTOLOGIST

Genome skimming herbarium specimens for DNA barcoding and phylogenomics

(2018) Chun-Xia Zeng et al.   Plant Methods

Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

(2018) Mohammad Vatanparast et al.   Applications in Plant Sciences

A comparative analysis of library prep approaches for sequencing low input translatome samples

(2018) Yang Song et al.   BMC GENOMICS

Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications

(2018) Peter W. Inglis et al.   PLoS One

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci

(2017) Heather R. Kates et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize

(2017) Amani Abdel-Latif et al.   Plant Methods

Using Herbarium-Derived DNAs to Assemble a Large-Scale DNA Barcode Library for the Vascular Plants of Canada

(2017) Maria L. Kuzmina et al.   Applications in Plant Sciences

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

(2016)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Retrieval of hundreds of nuclear loci from herbarium specimens

(2016) Michelle L. Hart et al.   TAXON

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

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

Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline

(2015) Freek T. Bakker et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

Dates and Times Made Easy withlubridate

(2015) Garrett Grolemund et al.   Journal of Statistical Software

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exome Sequencing from Nanogram Amounts of Starting DNA: Comparing Three Approaches

(2014) Vera N. Rykalina et al.   PLoS One

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

(2013) Martijn Staats et al.   PLoS One

Enhancing PCR Amplification of DNA from Recalcitrant Plant Specimens Using a Trehalose-Based Additive

(2013) Tharangamala Samarakoon et al.   Applications in Plant Sciences

Assessment of age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA

(2012) Roy H.J. Erkens et al.   BLUMEA

How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens

(2012) Tiina Särkinen et al.   PLoS One

The notes from nature tool for unlocking biodiversity records from museum records through citizen science

(2012) Andrew Hill et al.   ZooKeys

A general and simple method for obtainingR2from generalized linear mixed-effects models

(2012) Shinichi Nakagawa et al.   Methods in Ecology and Evolution

DNA Damage in Plant Herbarium Tissue

(2011) Martijn Staats et al.   PLoS One

Two micro-scale protocols for the isolation of DNA from polysaccharide-rich plant tissue

(2010) Lara D. Shepherd et al.   JOURNAL OF PLANT RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS