Geneious! Simplified Genome Skimming Methods for Phylogenetic Systematic Studies: A Case Study inOreocarya(Boraginaceae)

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

(2013) Shannon C.K. Straub et al.   Genome Biology and Evolution

Multiple origins for Hound’s tongues (Cynoglossum L.) and Navel seeds (Omphalodes Mill.) – The phylogeny of the borage family (Boraginaceae s.str.)

(2013) Maximilian Weigend et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke

(2013) Dan G. Bock et al.   NEW PHYTOLOGIST

STRAW: Species TRee Analysis Web server

(2013) Timothy I. Shaw et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Sequences Resolve Deep Relationships of the Grape Family

(2013) Jun Wen et al.   PLoS One

The potential of genomics in plant systematics

(2013) Douglas E. Soltis et al.   TAXON

Characterization of microsatellite markers isolated from members of Oreocarya (Boraginaceae)

(2013) Gerald E. Bresowar et al.   Conservation Genetics Resources

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

(2013) Gregory W. Stull et al.   Applications in Plant Sciences

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

(2012) Nolan Kane et al.   AMERICAN JOURNAL OF BOTANY

Targeted sequence capture as a powerful tool for evolutionary analysis1

(2012) Corrinne E. Grover et al.   AMERICAN JOURNAL OF BOTANY

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

(2012) Matthew Parks et al.   BMC EVOLUTIONARY BIOLOGY

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Making next-generation sequencing work for you: approaches and practical considerations for marker development and phylogenetics

(2012) Grant T. Godden et al.   Plant Ecology & Diversity

A Broad Phylogenetic Analysis of Boraginaceae: Implications for the Relationships of Mertensia

(2012) Mare Nazaire et al.   SYSTEMATIC BOTANY

Cat's Eyes and Popcorn Flowers: Phylogenetic Systematics of the Genus Cryptantha s. l. (Boraginaceae)

(2012) Kristen E. Hasenstab-Lehman et al.   SYSTEMATIC BOTANY

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines

(2010) J. B. WHITTALL et al.   MOLECULAR ECOLOGY

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

Heteroplasmy and stoichiometric complexity of plant mitochondrial genomes--though this be madness, yet there's method in't

(2009) M. Woloszynska   JOURNAL OF EXPERIMENTAL BOTANY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY