The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants

Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza

(2021) Ying Ma et al.   Nature Communications

Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway

(2021) Jian Cheng et al.   Molecular Plant

The emerging role of biosynthetic gene clusters in plant defense and plant interactions

(2021) Guy Polturak et al.   PLoS Pathogens

Exploring Uncharted Territories of Plant Specialized Metabolism in the Postgenomic Era

(2020) Joseph R. Jacobowitz et al.   Annual Review of Plant Biology

Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae

(2020) Benjamin R Lichman et al.   CURRENT OPINION IN PLANT BIOLOGY

Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis

(2020) Fu-Xiang Wang et al.   DEVELOPMENTAL CELL

The delayed and geographically heterogeneous diversification of flowering plant families

(2020) Santiago Ramírez-Barahona et al.   Nature Ecology & Evolution

Mediation of JA signalling in glandular trichomes by the woolly/SlMYC1 regulatory module improves pest resistance in tomato

(2020) Bing Hua et al.   PLANT BIOTECHNOLOGY JOURNAL

Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana

(2020) John P Hamilton et al.   GigaScience

CAFE 5 models variation in evolutionary rates among gene families

(2020) Fábio K Mendes et al.   BIOINFORMATICS

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

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

(2019) Kai Dührkop et al.   NATURE METHODS

TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome

(2019) Weijia Su et al.   Molecular Plant

Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates

(2019) Arthur Zwaenepoel et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

(2019) Qing Zhao et al.   Molecular Plant

Cytochrome P450 enzymes: A driving force of plant diterpene diversity

(2019) Ulschan Bathe et al.   PHYTOCHEMISTRY

The Structure and Function of Major Plant Metabolite Modifications

(2019) Shouchuang Wang et al.   Molecular Plant

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

(2019) Shujun Ou et al.   Mobile DNA

Phylogeny and staminal evolution of Salvia (Lamiaceae, Nepetoideae) in East Asia

(2018) Guo-Xiong Hu et al.   ANNALS OF BOTANY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events

(2018) Irene Julca et al.   BMC BIOLOGY

Identification of New Compounds from Sage Flowers (Salvia officinalis L.) as Markers for Quality Control and the Influence of the Manufacturing Technology on the Chemical Composition and Antibacterial Activity of Sage Flower Extracts

(2018) Sebastian Gericke et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2018) Benoît Boachon et al.   Molecular Plant

Characterization of gossypol biosynthetic pathway

(2018) Xiu Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary history of the angiosperm flora of China

(2018) Li-Min Lu et al.   NATURE

A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae)

(2018) Sean R Johnson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SlMYC1 Regulates Type VI Glandular Trichome Formation and Terpene Biosynthesis in Tomato Glandular Cells

(2018) Jiesen Xu et al.   PLANT CELL

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

(2017) Sergey Koren et al.   GENOME RESEARCH

A (–)-kolavenyl diphosphate synthase catalyzes the first step of salvinorin A biosynthesis in Salvia divinorum

(2017) Xiaoyue Chen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Time to split Salvia s.l. (Lamiaceae) – New insights from Old World Salvia phylogeny

(2017) Maria Will et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The PhytoClust tool for metabolic gene clusters discovery in plant genomes

(2017) Nadine Töpfer et al.   NUCLEIC ACIDS RESEARCH

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

(2017) Satria A. Kautsar et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

(2017) Pascal Schläpfer et al.   PLANT PHYSIOLOGY

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Salvia united: The greatest good for the greatest number

(2017) BryanT. Drew et al.   TAXON

Targeted mutagenesis in the medicinal plant Salvia miltiorrhiza

(2017) Bin Li et al.   Scientific Reports

SmMYB36, a Novel R2R3-MYB Transcription Factor, Enhances Tanshinone Accumulation and Decreases Phenolic Acid Content in Salvia miltiorrhiza Hairy Roots

(2017) Kai Ding et al.   Scientific Reports

Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2016) Haibin Xu et al.   Molecular Plant

Genome sequence and genetic diversity of European ash trees

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

Carnosic acid biosynthesis elucidated by a synthetic biology platform

(2016) Codruta Ignea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast

(2016) Ulschan Scheler et al.   Nature Communications

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Cytochrome P450 promiscuity leads to a bifurcating biosynthetic pathway for tanshinones

(2015) Juan Guo et al.   NEW PHYTOLOGIST

To Gibberellins and Beyond! Surveying the Evolution of (Di)Terpenoid Metabolism

(2014) Jiachen Zi et al.   Annual Review of Plant Biology

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas

(2014) Adrien Favre et al.   BIOLOGICAL REVIEWS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Characterization of two genes for the biosynthesis of abietane-type diterpenes in rosemary (Rosmarinus officinalis) glandular trichomes

(2014) Kathleen Brückner et al.   PHYTOCHEMISTRY

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

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

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

(2014) W. Xiong 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

Molecular basis of natural variation and environmental control of trichome patterning

(2014) Marie-Theres Hauser   Frontiers in Plant Science

MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans

(2013) Yupeng Wang et al.   BIOINFORMATICS

PAMLX: A Graphical User Interface for PAML

(2013) B. Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

Evolution of a Complex Locus for Terpene Biosynthesis in Solanum

(2013) Y. Matsuba et al.   PLANT CELL

CYP76AH1 catalyzes turnover of miltiradiene in tanshinones biosynthesis and enables heterologous production of ferruginol in yeasts

(2013) J. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational identification of functional RNA homologs in metagenomic data

(2013) Eric P. Nawrocki et al.   RNA Biology

Discovery and functional characterization of two diterpene synthases for sclareol biosynthesis in Salvia sclarea (L.) and their relevance for perfume manufacture

(2012) Anne Caniard et al.   BMC PLANT BIOLOGY

Constituents from Salvia Species and Their Biological Activities

(2012) Yi-Bing Wu et al.   CHEMICAL REVIEWS

Phytochemical profile of Rosmarinus officinalis and Salvia officinalis extracts and correlation to their antioxidant and anti-proliferative activity

(2012) Vassiliki G. Kontogianni et al.   FOOD CHEMISTRY

Characterization of CYP76M5–8 Indicates Metabolic Plasticity within a Plant Biosynthetic Gene Cluster

(2012) Qiang Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanisms for cellular transport and release of allelochemicals from plant roots into the rhizosphere

(2012) L. A. Weston et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

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

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

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Carnosol: A promising anti-cancer and anti-inflammatory agent

(2011) Jeremy J. Johnson   CANCER LETTERS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Clustered Transcription Factor Genes Regulate Nicotine Biosynthesis in Tobacco

(2010) Tsubasa Shoji et al.   PLANT CELL

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

MYB transcription factors in Arabidopsis

(2010) Christian Dubos et al.   TRENDS IN PLANT SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

A Functional Genomics Approach to Tanshinone Biosynthesis Provides Stereochemical Insights

(2009) Wei Gao et al.   ORGANIC LETTERS

Cell Type-Specific Chromatin Decondensation of a Metabolic Gene Cluster in Oats

(2009) E. Wegel et al.   PLANT CELL

CYP76M7 Is an ent-Cassadiene C11 -Hydroxylase Defining a Second Multifunctional Diterpenoid Biosynthetic Gene Cluster in Rice

(2009) S. Swaminathan et al.   PLANT CELL

Bayesian Dating of Shallow Phylogenies with a Relaxed Clock

(2009) Richard P. Brown et al.   SYSTEMATIC BIOLOGY

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY