The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny

Complete Chloroplast Genome of the Multifunctional Crop Globe Artichoke and Comparison with Other Asteraceae

(2015) Pasquale L. Curci et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World

(2014) Hideki Hirakawa et al.   DNA RESEARCH

Mapping yield-associated QTL in globe artichoke

(2014) Ezio Portis et al.   MOLECULAR BREEDING

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

(2014) Seungill Kim et al.   NATURE GENETICS

De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms

(2014) Y. Peng et al.   PLANT PHYSIOLOGY

Cytochrome P450s from Cynara cardunculus L. CYP71AV9 and CYP71BL5, catalyze distinct hydroxylations in the sesquiterpene lactone biosynthetic pathway

(2014) Kaouthar Eljounaidi et al.   PLANT SCIENCE

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

(2014) C. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

(2014) F. Denoeud et al.   SCIENCE

Novel insights from non-conserved microRNAs in plants

(2014) Zhengrui Qin et al.   Frontiers in Plant Science

Reconstructing the evolution and biogeographic history of tribe Cardueae (Compositae)

(2013) L. Barres et al.   AMERICAN JOURNAL OF BOTANY

Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa)

(2013) Tapan Kumar Mondal et al.   GENE

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley

(2013) Martin Mascher et al.   PLoS One

Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella

(2013) S. Chamala et al.   SCIENCE

In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus

(2012) Domenico Catalano et al.   BMC BIOINFORMATICS

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

(2012) Davide Scaglione et al.   BMC GENOMICS

The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis

(2012) Domenico De Paola et al.   BMC GENOMICS

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

(2012) Lucy W. Barrett et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa

(2012) Davide Scaglione et al.   PLANT BIOTECHNOLOGY JOURNAL

Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication

(2012) M. Abrouk et al.   PLANT CELL

The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

(2012) S. Evan Staton et al.   PLANT JOURNAL

Characterization and Evolution of microRNA Genes Derived from Repetitive Elements and Duplication Events in Plants

(2012) Jie Sun et al.   PLoS One

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

(2011) Paul D. Etter et al.   PLoS One

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

(2010) Anthony Mathelier et al.   BIOINFORMATICS

Cynara cardunculus L. genotypes as a crop for energy purposes in a Mediterranean environment

(2010) Anita Ierna et al.   BIOMASS & BIOENERGY

Potentiality of Cynara cardunculus L. as energy crop

(2010) E. Portis et al.   JOURNAL OF BIOTECHNOLOGY

Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

(2010) W. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database

(2009) Davide Scaglione et al.   BMC GENOMICS

The isolation and mapping of a novel hydroxycinnamoyltransferase in the globe artichoke chlorogenic acid pathway

(2009) Cinzia Comino et al.   BMC PLANT BIOLOGY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Globe artichoke: A functional food and source of nutraceutical ingredients

(2009) Vincenzo Lattanzio et al.   Journal of Functional Foods

Darwin's second “abominable mystery”: Why are there so many angiosperm species?

(2008) William L. Crepet et al.   AMERICAN JOURNAL OF BOTANY

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

The origin and evolution of plant cystatins and their target cysteine proteinases indicate a complex functional relationship

(2008) Manuel Martinez et al.   BMC EVOLUTIONARY BIOLOGY

Genetic diversity of globe artichoke landraces from Sicilian small-holdings: implications for evolution and domestication of the species

(2008) Rosario Mauro et al.   CONSERVATION GENETICS

MOLECULAR DEMOGRAPHIC HISTORY OF THE ANNUAL SUNFLOWERSHELIANTHUS ANNUUSANDH. PETIOLARIS-LARGE EFFECTIVE POPULATION SIZES AND RATES OF LONG-TERM GENE FLOW

(2008) Jared L. Strasburg et al.   EVOLUTION

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

(2008) R. S. Baucom et al.   GENOME RESEARCH

Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years

(2008) M. S. Barker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids

(2008) E. Lyons et al.   PLANT PHYSIOLOGY