Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree

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

(2016) Sanna Olsson et al.   Molecular Ecology Resources

Clues to the evolution of genome size and chromosome number in Tabebuia alliance (Bignoniaceae)

(2016) Rosane G. Collevatti et al.   PLANT SYSTEMATICS AND EVOLUTION

Genome sequence of the olive tree, Olea europaea

(2016) Fernando Cruz et al.   GigaScience

Biosynthesis and molecular actions of specialized 1,4-naphthoquinone natural products produced by horticultural plants

(2016) Joshua R Widhalm et al.   Horticulture Research

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins

(2016) Obed Ramírez-Sánchez et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

(2015) Christophe Plomion et al.   Molecular Ecology Resources

Translational genomics for plant breeding with the genome sequence explosion

(2015) Yang Jae Kang et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-Wide Mining, Characterization and Development of Microsatellite Markers in Gossypium Species

(2015) Qiong Wang et al.   Scientific Reports

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Louise Brousseau et al.   BMC GENOMICS

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Synthesis and Cytotoxicity on Human Leukemia Cells of Furonaphthoquinones Isolated from Tabebuia Plants

(2013) Ryuta Inagaki et al.   CHEMICAL & PHARMACEUTICAL BULLETIN

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

(2013) U. Hellsten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic analysis of intron size and abundance parameters in diverse lineages

(2013) Wu JiaYan et al.   Science China-Life Sciences

Wood colour in Lapacho (Tabebuia serratifolia): chemical composition and industrial implications

(2013) Manuela Romagnoli et al.   WOOD SCIENCE AND TECHNOLOGY

Use and valuation of native and introduced medicinal plant species in Campo Hermoso and Zetaquira, Boyacá, Colombia

(2013) Ana Lucía Cadena-González et al.   Journal of Ethnobiology and Ethnomedicine

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

Advances in plant genome sequencing

(2012) John P. Hamilton et al.   PLANT JOURNAL

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Crop genomics: advances and applications

(2011) Peter L. Morrell et al.   NATURE REVIEWS GENETICS

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Genome-Wide Distribution and Organization of Microsatellites in Plants: An Insight into Marker Development in Brachypodium

(2011) Humira Sonah et al.   PLoS One

Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant Genomes

(2011) Roger Barthelson et al.   PLoS One

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Temporal variation in pollen dispersal and breeding structure in a bee-pollinated Neotropical tree

(2010) A C Braga et al.   HEREDITY

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Network Analysis of Enzyme Activities and Metabolite Levels and Their Relationship to Biomass in a Large Panel of Arabidopsis Accessions

(2010) R. Sulpice et al.   PLANT CELL

A Novel Role for Minimal Introns: Routing mRNAs to the Cytosol

(2010) Jiang Zhu et al.   PLoS One

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

More genomic resources for less-studied crops

(2010) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Evaluating ipê (Tabebuia, Bignoniaceae) logging in Amazonia: Sustainable management or catalyst for forest degradation?

(2008) Mark Schulze et al.   BIOLOGICAL CONSERVATION

In vitro and in vivo anti-inflammatory effects of taheebo, a water extract from the inner bark of Tabebuia avellanedae

(2008) Se Eun Byeon et al.   JOURNAL OF ETHNOPHARMACOLOGY

Red Lapacho (Tabebuia impetiginosa)—A global ethnopharmacological commodity?

(2008) J. Rubén Gómez Castellanos et al.   JOURNAL OF ETHNOPHARMACOLOGY

BIOCHEMISTRY: Lifting the Veil on Traditional Chinese Medicine

(2008) R. Stone   SCIENCE