Transposon activation is a major driver in the genome evolution of cultivated olive trees ( Olea europaea L.)

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Tolerance of olive (Olea europaea ) cv Frantoio to Verticillium dahliae relies on both basal and pathogen-induced differential transcriptomic responses

(2017) María de la O Leyva-Pérez et al.   NEW PHYTOLOGIST

Genome of wild olive and the evolution of oil biosynthesis

(2017) Turgay Unver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptomic Analysis of L. Roots during the Early Infection Process

(2017) Jaime Jiménez-Ruiz et al.   Plant Genome

From Olive Fruits to Olive Oil: Phenolic Compound Transfer in Six Different Olive Cultivars Grown under the Same Agronomical Conditions

(2016) Nassima Talhaoui et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genome sequence and genetic diversity of European ash trees

(2016) Elizabeth S. A. Sollars et al.   NATURE

Genome sequence of the olive tree, Olea europaea

(2016) Fernando Cruz et al.   GigaScience

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Transcriptional analysis of adult cutting and juvenile seedling olive roots

(2015) Jaime Jiménez-Ruiz et al.   Tree Genetics & Genomes

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves

(2014) María de la O Leyva-Pérez et al.   DNA RESEARCH

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Olive domestication and diversification in the Mediterranean Basin

(2014) Concepcion M. Diez et al.   NEW PHYTOLOGIST

TEMP: a computational method for analyzing transposable element polymorphism in populations

(2014) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

A comprehensive evaluation of assembly scaffolding tools

(2014) Martin Hunt et al.   GENOME BIOLOGY

Population genetics of Mediterranean and Saharan olives: geographic patterns of differentiation and evidence for early generations of admixture

(2013) G. Besnard et al.   ANNALS OF BOTANY

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant

(2013) G. Besnard et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

On the origins and spread of Olea europaea L. (olive) domestication: evidence for shape variation of olive stones at Ugarit, Late Bronze Age, Syria—a window on the Mediterranean Basin and on the westward diffusion of olive varieties

(2013) Claire Newton et al.   VEGETATION HISTORY AND ARCHAEOBOTANY

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

(2012) Yongchao Liu et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Primary domestication and early uses of the emblematic olive tree: palaeobotanical, historical and molecular evidence from the Middle East

(2012) David Kaniewski et al.   BIOLOGICAL REVIEWS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

(2012) A. Boc et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

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

(2012) Ruibang Luo et al.   GigaScience

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)

(2011) Livia Donaire et al.   PLoS One

Artificial selection for a green revolution gene during japonica rice domestication

(2011) K. Asano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits

(2011) Angjelina Belaj et al.   Tree Genetics & Genomes

The IGF1 small dog haplotype is derived from Middle Eastern grey wolves

(2010) Melissa M Gray et al.   BMC BIOLOGY

MYB transcription factors in Arabidopsis

(2010) Christian Dubos et al.   TRENDS IN PLANT SCIENCE

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

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Physiological, biochemical and molecular changes occurring during olive development and ripening

(2008) Carlos Conde et al.   JOURNAL OF PLANT PHYSIOLOGY

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology