Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers

Low-Coverage, Whole-Genome Sequencing of Artocarpus camansi (Moraceae) for Phylogenetic Marker Development and Gene Discovery

(2016) Elliot M. Gardner et al.   Applications in Plant Sciences

Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications

(2015) Lei Huang et al.   Annual Review of Genomics and Human Genetics

Widespread mistaken identity in tropical plant collections

(2015) Zoë A. Goodwin et al.   CURRENT BIOLOGY

Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins

(2015) David L. Remington   EVOLUTION

Symphonia globulifera, a Widespread Source of Complex Metabolites with Potent Biological Activities

(2015) Yann Fromentin et al.   PLANTA MEDICA

ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome

(2015) Rosario Carmona et al.   Frontiers in Plant Science

High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species

(2014) Louise Brousseau et al.   BMC GENOMICS

Genomic data integration for ecological and evolutionary traits in non-model organisms

(2014) Denis Tagu et al.   BMC GENOMICS

Structural variation and genome complexity: is dispensable really dispensable?

(2014) Fabio Marroni et al.   CURRENT OPINION IN PLANT BIOLOGY

Sma3s: A Three-Step Modular Annotator for Large Sequence Datasets

(2014) A. Munoz-Merida et al.   DNA RESEARCH

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinaster Aiton, Pinaceae)

(2014) J.-P. Jaramillo-Correa et al.   GENETICS

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

Signatures of diversifying selection at EST-SSR loci and association with climate in naturalEucalyptuspopulations

(2014) Donna Bradbury et al.   MOLECULAR ECOLOGY

Comparative Phylogeography in Rainforest Trees from Lower Guinea, Africa

(2014) Myriam Heuertz et al.   PLoS One

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

(2014) Daren C. Card et al.   PLoS One

Genetic Differentiation Revealed by Selective Loci of Drought-Responding EST-SSRs between Upland and Lowland Rice in China

(2014) Hui Xia et al.   PLoS One

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

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

Gene Prediction and Annotation inPenstemon(Plantaginaceae): A Workflow for Marker Development from Extremely Low-Coverage Genome Sequencing

(2014) Paul D. Blischak et al.   Applications in Plant Sciences

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa

(2013) K B Budde et al.   HEREDITY

Characterization and high cross-species transferability of microsatellite markers from the floral transcriptome ofAspidistra saxicola(Asparagaceae)

(2013) Danni Huang et al.   Molecular Ecology Resources

Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs

(2013) Christophe Dufresnes et al.   Molecular Ecology Resources

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

(2013) Nabila Tabbasam et al.   PLANT SYSTEMATICS AND EVOLUTION

Mate Pair Sequencing of Whole-Genome-Amplified DNA Following Laser Capture Microdissection of Prostate Cancer

(2012) S. J. Murphy et al.   DNA RESEARCH

Phylogeography of a species complex of lowland Neotropical rain forest trees (Carapa, Meliaceae)

(2012) Caroline Scotti-Saintagne et al.   JOURNAL OF BIOGEOGRAPHY

Recent population decline and selection shape diversity of taxol-related genes

(2012) C. BURGARELLA et al.   MOLECULAR ECOLOGY

Phylogeographical patterns shed light on evolutionary process in South America

(2012) A. C. Turchetto-Zolet et al.   MOLECULAR ECOLOGY

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

(2012) Aureliano Bombarely et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The draft genome of sweet orange (Citrus sinensis)

(2012) Qiang Xu et al.   NATURE GENETICS

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

(2012) Tiina Särkinen et al.   PLoS One

Always Look on Both Sides: Phylogenetic Information Conveyed by Simple Sequence Repeat Allele Sequences

(2012) Stéphanie Barthe et al.   PLoS One

Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology

(2012) Florian Leese et al.   PLoS One

The genomics of speciation-with-gene-flow

(2012) Jeffrey L. Feder et al.   TRENDS IN GENETICS

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Development and characterization of microsatellite loci in Pericopsis elata (Fabaceae) using a cost-efficient approach

(2011) Claire Micheneau et al.   AMERICAN JOURNAL OF BOTANY

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

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads

(2010) Juan Falgueras et al.   BMC BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Antiplasmodial benzophenone derivatives from the root barks of Symphonia globulifera (Clusiaceae)

(2010) Guillaume Marti et al.   PHYTOCHEMISTRY

From Conservation Genetics to Conservation Genomics

(2009) Craig R. Primmer   Annals of the New York Academy of Sciences

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

Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L.)

(2009) Ram Sharma et al.   BMC PLANT BIOLOGY

Stability Predicts Genetic Diversity in the Brazilian Atlantic Forest Hotspot

(2009) A. C. Carnaval et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

THE COMPLEX BIOGEOGRAPHIC HISTORY OF A WIDESPREAD TROPICAL TREE SPECIES

(2008) Christopher W. Dick et al.   EVOLUTION

GSTand its relatives do not measure differentiation

(2008) LOU JOST   MOLECULAR ECOLOGY

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design

(2007) BRANT C. FAIRCLOTH   Molecular Ecology Resources