A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways

A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways

(2019) Dongyan Zhao et al.   GigaScience

Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation

(2018) Ramasamy Yasodha et al.   DNA RESEARCH

Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae

(2018) Benoît Boachon et al.   Molecular Plant

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2016) Haibin Xu et al.   Molecular Plant

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Large-scale transcriptional profiling of lignified tissues in Tectona grandis

(2015) Esteban Galeano et al.   BMC PLANT BIOLOGY

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biosynthesis of Lycosantalonol, a cis-Prenyl Derived Diterpenoid

(2014) Jiachen Zi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Investigation of terpene diversification across multiple sequenced plant genomes

(2014) Alexander M. Boutanaev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biosynthesis, function and metabolic engineering of plant volatile organic compounds

(2013) Natalia Dudareva et al.   NEW PHYTOLOGIST

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics

(2010) Michael S. Barker et al.   Evolutionary Bioinformatics

Apollo: a community resource for genome annotation editing

(2009) E. Lee et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE