Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales

Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement

(2017) Kelly J. Vining et al.   Molecular Plant

The Apostasia genome and the evolution of orchids

(2017) Guo-Qiang Zhang et al.   NATURE

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

(2017) Hélène Badouin et al.   NATURE

Transcriptome sequencing provides insights into the metabolic pathways of patchouli alcohol and pogostone in Pogostemon cablin (Blanco) Benth.

(2016) Yang He et al.   Genes & Genomics

Genome sequence and genetic diversity of European ash trees

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

Draft genome assembly and annotation of Glycyrrhiza uralensis , a medicinal legume

(2016) Keiichi Mochida et al.   PLANT JOURNAL

Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis

(2016) Yang He et al.   Scientific Reports

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

The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb

(2015) Liang Yan et al.   Molecular Plant

Genome-guided investigation of plant natural product biosynthesis

(2015) Franziska Kellner et al.   PLANT JOURNAL

Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)

(2015) Guanghui Zhang et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette 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

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

(2013) Ray Ming et al.   GENOME BIOLOGY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

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

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom

(2011) Feng Chen et al.   PLANT JOURNAL

Genetic diversity analysis among and within populations of Pogostemon cablin from China with ISSR and SRAP markers

(2010) You-Gen Wu et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

(2010) Bastian Schäferhoff et al.   BMC EVOLUTIONARY BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS