Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs

(2018) Valérie Laucou et al.   PLoS One

Precise detection of de novo single nucleotide variants in human genomes

(2018) Laura Gómez-Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Firefly genomes illuminate parallel origins of bioluminescence in beetles

(2018) Timothy R Fallon et al.   eLife

Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci inDrosophila melanogaster

(2017) Daniel E. Khost et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Reduction of heterozygosity (ROH) as a method to detect mosaic structural variation

(2017) Fabio Marroni et al.   PLANT BIOTECHNOLOGY JOURNAL

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

(2017) Yuki Yoshida et al.   PLOS BIOLOGY

How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes

(2017) Andrea Minio et al.   Frontiers in Plant Science

Molecular and Evolutionary Mechanisms of Cuticular Wax for Plant Drought Tolerance

(2017) Dawei Xue et al.   Frontiers in Plant Science

Whole-genome sequencing and SNV genotyping of ‘Nebbiolo’ (Vitis vinifera L.) clones

(2017) Giorgio Gambino et al.   Scientific Reports

Fast genotyping of known SNPs through approximatek-mer matching

(2016) Ariya Shajii et al.   BIOINFORMATICS

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Ultrastructural leave features of grapevine cultivars (Vitis vinifera L. ssp. vinifera)

(2016) Christoph Konlechner et al.   OENO One

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

P-MITE: a database for plant miniature inverted-repeat transposable elements

(2013) Jiongjiong Chen et al.   NUCLEIC ACIDS RESEARCH

The Formation and Function of Plant Cuticles

(2013) T. H. Yeats et al.   PLANT PHYSIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Plant fatty acyl reductases: Enzymes generating fatty alcohols for protective layers with potential for industrial applications

(2012) Owen Rowland et al.   PLANT SCIENCE

Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L.

(2012) Grégory Carrier et al.   PLoS One

Large-scale parentage analysis in an extended set of grapevine cultivars (Vitis vinifera L.)

(2012) Thierry Lacombe et al.   THEORETICAL AND APPLIED GENETICS

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

High throughput analysis of grape genetic diversity as a tool for germplasm collection management

(2011) V. Laucou et al.   THEORETICAL AND APPLIED GENETICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.)

(2010) Francesco Emanuelli et al.   BMC PLANT BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Rapid Genomic Characterization of the Genus Vitis

(2010) Sean Myles et al.   PLoS One

The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin

(2010) Guido Cipriani et al.   THEORETICAL AND APPLIED GENETICS

A banned variety was the mother of several major wine grapes

(2009) H. V. Hunt et al.   Biology Letters

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Cutin deficiency in the tomato fruit cuticle consistently affects resistance to microbial infection and biomechanical properties, but not transpirational water loss

(2009) Tal Isaacson et al.   PLANT JOURNAL

CYP704B1 Is a Long-Chain Fatty Acid  -Hydroxylase Essential for Sporopollenin Synthesis in Pollen of Arabidopsis

(2009) A. A. Dobritsa et al.   PLANT PHYSIOLOGY

Variation of linalool and geraniol content within two pairs of aromatic and non-aromatic grapevine clones

(2008) E. DUCHÊNE et al.   AUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH

A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping

(2008) Guido Cipriani et al.   BMC PLANT BIOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE