A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China

Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims)

(2021) Zhiqiang Xia et al.   Horticulture Research

BcpLH organizes a specific subset of microRNAs to form a leafy head in Chinese cabbage (Brassica rapa ssp. pekinensis)

(2020) Wenqing Ren et al.   Horticulture Research

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

(2020) Minghui Kang et al.   Horticulture Research

Transcriptome-wide analysis of the AP2/ERF transcription factor gene family involved in the regulation of gypenoside biosynthesis in Gynostemma pentaphyllum

(2020) Shiqiang Xu et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

EasyCodeML: A visual tool for analysis of selection using CodeML

(2019) Fangluan Gao et al.   Ecology and Evolution

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

(2019) Qing Zhao et al.   Molecular Plant

Transcriptome analysis and targeted metabolic profiling for pathway elucidation and identification of a geraniol synthase involved in iridoid biosynthesis from Gardenia jasminoides

(2019) Peng Ye et al.   INDUSTRIAL CROPS AND PRODUCTS

Identification and characterization of a polysaccharide from the roots of Morinda officinalis, as an inducer of bone formation by up-regulation of target gene expression

(2019) Chunyan Yan et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

NextPolish: a fast and efficient genome polishing tool for long-read assembly

(2019) Jiang Hu et al.   BIOINFORMATICS

Transcriptome analysis reveals the molecular mechanisms of mucilage biosynthesis during Artemisia sphaerocephala seed development

(2019) Xiaoxu Han et al.   INDUSTRIAL CROPS AND PRODUCTS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

(2018) Damla Senol Cali et al.   BRIEFINGS IN BIOINFORMATICS

Morinda officinalis How. – A comprehensive review of traditional uses, phytochemistry and pharmacology

(2018) Jian-hua Zhang et al.   JOURNAL OF ETHNOPHARMACOLOGY

Simultaneous Analysis of Iridoid Glycosides and Anthraquinones in Morinda officinalis Using UPLC-QqQ-MS/MS and UPLC-Q/TOF-MSE

(2018) Xiangsheng Zhao et al.   MOLECULES

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

(2018) Jakob Franke et al.   CHEMBIOCHEM

Transcriptional Regulation of the Immune Receptor FLS2 Controls the Ontogeny of Plant Innate Immunity

(2018) Yanmin Zou et al.   PLANT CELL

The genome of the medicinal plant Andrographis paniculata provides insight into the biosynthesis of the bioactive diterpenoid neoandrographolide

(2018) Wei Sun et al.   PLANT JOURNAL

The Genome of Medicinal Plant Macleaya cordata Provides New Insights into Benzylisoquinoline Alkaloids Metabolism

(2017) Xiubin Liu et al.   Molecular Plant

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

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Anthraquinones As Pharmacological Tools and Drugs

(2016) Enas M. Malik et al.   MEDICINAL RESEARCH REVIEWS

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Chemical Components Isolated from the Roots of Morinda officinalis

(2015) Jianping Yong et al.   CHEMISTRY OF NATURAL COMPOUNDS

Effect of bajijiasu isolated from Morinda officinalis F. C. how on sexual function in male mice and its antioxidant protection of human sperm

(2015) Ze-Qing Wu et al.   JOURNAL OF ETHNOPHARMACOLOGY

Cyclic nucleotide gated channel gene family in tomato: genome-wide identification and functional analyses in disease resistance

(2015) Mumtaz A. Saand et al.   Frontiers in Plant Science

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

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

(2013) Moaine El Baidouri et al.   Genome Biology and Evolution

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

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

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

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

Coupling Deep Transcriptome Analysis with Untargeted Metabolic Profiling in Ophiorrhiza pumila to Further the Understanding of the Biosynthesis of the Anti-Cancer Alkaloid Camptothecin and Anthraquinones

(2013) Mami Yamazaki et al.   PLANT AND CELL PHYSIOLOGY

Phosphorylation of an ERF Transcription Factor by Arabidopsis MPK3/MPK6 Regulates Plant Defense Gene Induction and Fungal Resistance

(2013) X. Meng et al.   PLANT CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

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

Extraction of polysaccharides from Morinda officinalis by response surface methodology and effect of the polysaccharides on bone-related genes

(2011) MengYong Zhu et al.   CARBOHYDRATE POLYMERS

Anthraquinone compounds from Morinda officinalis inhibit osteoclastic bone resorption in vitro

(2011) Leilei Bao et al.   CHEMICO-BIOLOGICAL INTERACTIONS

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Structural characterization and anti-fatigue activity of polysaccharides from the roots of Morinda officinalis

(2008) Hua-lin Zhang et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

InterPro: the integrative protein signature database

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

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Brian J Haas et al.   GENOME BIOLOGY