The chromosome-level genome assembly of Gentiana dahurica (Gentianaceae) provides insights into gentiopicroside biosynthesis

The chromosome‐scale high‐quality genome assembly of Panax notoginseng provides insight into dencichine biosynthesis

(2021) Zijiang Yang et al.   PLANT BIOTECHNOLOGY JOURNAL

Immunosuppressive gentianellane-type sesterterpenoids from the traditional Uighur medicine Gentianella turkestanorum

(2021) Kai Guo et al.   PHYTOCHEMISTRY

A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis

(2021) Minghui Kang et al.   Nature Communications

UHPLC-QQQ-MS/MS assay for the quantification of dianthrones as potential toxic markers of Polygonum multiflorum Thunb: applications for the standardization of traditional Chinese medicines (TCMs) with endogenous toxicity

(2021) Jian-Bo Yang et al.   Chinese Medicine

Secoiridoids and triterpenoids from the traditional Tibetan medicine Gentiana veitchiorum and their immunosuppressive activity

(2021) Kai Guo et al.   PHYTOCHEMISTRY

Gentianelloids A and B: Immunosuppressive 10,11-seco-Gentianellane Sesterterpenoids from the Traditional Uighur Medicine Gentianella turkestanorum

(2020) Kai Guo et al.   JOURNAL OF ORGANIC CHEMISTRY

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

Gardenia jasminoides Ellis: Ethnopharmacology, phytochemistry, and pharmacological and industrial applications of an important traditional Chinese medicine

(2020) Liping Chen et al.   JOURNAL OF ETHNOPHARMACOLOGY

Monoterpene indole alkaloids with diverse skeletons from the stems of Rauvolfia vomitoria and their acetylcholinesterase inhibitory activities

(2020) Guanqun Zhan et al.   PHYTOCHEMISTRY

Cytochrome P450 family: Genome-wide identification provides insights into the rutin synthesis pathway in Tartary buckwheat and the improvement of agricultural product quality

(2020) Wenjun Sun et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism

(2019) Satoko Yoshida et al.   CURRENT BIOLOGY

High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant

(2018) Ai-Xiang Dong et al.   GigaScience

Gene Discovery in Gelsemium Highlights Conserved Gene Clusters in Monoterpene Indole Alkaloid Biosynthesis

(2018) Jakob Franke et al.   CHEMBIOCHEM

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

(2017) Sergey Koren et al.   GENOME RESEARCH

The Medicinal Herb Panax notoginseng Genome Provides Insights into Ginsenoside Biosynthesis and Genome Evolution

(2017) Dan Zhang et al.   Molecular Plant

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

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

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Genome of wild olive and the evolution of oil biosynthesis

(2017) Turgay Unver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Olga Dudchenko et al.   SCIENCE

Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea , a Producer of Anticancer and Antimalarial Cardenolides

(2017) Genevieve M. Hoopes et al.   G3-Genes Genomes Genetics

De novo sequencing transcriptome of endemic Gentiana straminea (Gentianaceae) to identify genes involved in the biosynthesis of active ingredients

(2016) Dangwei Zhou et al.   GENE

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

Discovery and metabolic engineering of iridoid/secoiridoid and monoterpenoid indole alkaloid biosynthesis

(2016) Antje M. K. Thamm et al.   PHYTOCHEMISTRY REVIEWS

Metabolite Diversity in Alkaloid Biosynthesis: A Multilane (Diastereomer) Highway for Camptothecin Synthesis in Camptotheca acuminata

(2016) Radin Sadre et al.   PLANT CELL

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens

(2015) Xiaodong Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The resurrection genome ofBoea hygrometrica: A blueprint for survival of dehydration

(2015) Lihong Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

An insight into the genes involved in secoiridoid biosynthesis in Gentiana macrophylla by RNA-seq

(2014) Wenping Hua et al.   MOLECULAR BIOLOGY REPORTS

7-Deoxyloganetic acid synthase catalyzes a key 3 step oxidation to form 7-deoxyloganetic acid in Catharanthus roseus iridoid biosynthesis

(2014) Vonny Salim et al.   PHYTOCHEMISTRY

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

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

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

(2014) F. Denoeud et al.   SCIENCE

The seco-iridoid pathway from Catharanthus roseus

(2014) Karel Miettinen et al.   Nature Communications

Network Analysis of the MVA and MEP Pathways for Isoprenoid Synthesis

(2013) Eva Vranová et al.   Annual Review of Plant Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

A 7-Deoxyloganetic Acid Glucosyltransferase Contributes a Key Step in Secologanin Biosynthesis in Madagascar Periwinkle

(2013) K. Asada et al.   PLANT CELL

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Transcriptome Analysis Reveals Putative Genes Involved in Iridoid Biosynthesis in Rehmannia glutinosa

(2012) Peng Sun et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis

(2012) Fernando Geu-Flores et al.   NATURE

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

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

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

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

The flowering world: a tale of duplications

(2009) Yves Van de Peer et al.   TRENDS IN PLANT SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY