Genome and evolution of the shade-requiring medicinal herb Panax ginseng

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng

(2018) Murukarthick Jayakodi et al.   BMC PLANT BIOLOGY

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

(2017) Dan Zhang et al.   Molecular Plant

Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species

(2017) Kyunghee Kim et al.   Scientific Reports

A refined Panax ginseng karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs

(2017) Nomar Espinosa Waminal et al.   Journal of Ginseng Research

Integrated Transcriptomic and Metabolomic Analysis of Five Panax ginseng Cultivars Reveals the Dynamics of Ginsenoside Biosynthesis

(2017) Yun Sun Lee et al.   Frontiers in Plant Science

Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax

(2017) Junki Lee et al.   Scientific Reports

Different chilling stresses stimulated the accumulation of different types of ginsenosides in Panax ginseng cells

(2016) Mingliang Jiang et al.   ACTA PHYSIOLOGIAE PLANTARUM

NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data

(2016) Young-Joo Seol et al.   Evolutionary Bioinformatics

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

(2016) Yi Zheng et al.   Molecular Plant

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

(2016) Massimo Iorizzo et al.   NATURE GENETICS

Phylogeny and diversification of Chinese Araliaceae based on nuclear and plastid DNA sequence data

(2016) Rong Li et al.   Journal of Systematics and Evolution

Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean ( Phaseolus vulgaris )

(2016) Dongying Gao et al.   G3-Genes Genomes Genetics

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Biosynthesis and biotechnological production of ginsenosides

(2015) Yu-Jin Kim et al.   BIOTECHNOLOGY ADVANCES

Recent advances in ginseng as cancer therapeutics: a functional and mechanistic overview

(2015) Alice S. T. Wong et al.   NATURAL PRODUCT REPORTS

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Leveraging transcript quantification for fast computation of alternative splicing profiles

(2015) Gael P. Alamancos et al.   RNA

Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

(2015) Kyunghee Kim et al.   Scientific Reports

Accumulation characteristics and correlation analysis of five ginsenosides with different cultivation ages from different regions

(2015) Dan Xiao et al.   Journal of Ginseng Research

Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species

(2015) Kyunghee Kim et al.   PLoS One

BRENDA in 2015: exciting developments in its 25th year of existence

(2014) Antje Chang et al.   NUCLEIC ACIDS RESEARCH

Major repeat components covering one-third of the ginseng (Panax ginsengC.A. Meyer) genome and evidence for allotetraploidy

(2014) Hong-Il Choi et al.   PLANT JOURNAL

Ginsenoside profiles and related gene expression during foliation in Panax ginseng Meyer

(2014) Yu-Jin Kim et al.   Journal of Ginseng Research

Investigation of ginsenosides in different tissues after elicitor treatment in Panax ginseng

(2014) Ji Yeon Oh et al.   Journal of Ginseng Research

A large and functionally diverse family of Fad2 genes in safflower (Carthamus tinctorius L.)

(2013) Shijiang Cao et al.   BMC PLANT BIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains

(2013) Yun-Dong Gao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The world ginseng market and the ginseng (Korea)

(2013) In-Ho Baeg et al.   Journal of Ginseng Research

Insilico profiling of microRNAs in Korean ginseng (Panax ginseng Meyer)

(2013) Ramya Mathiyalagan et al.   Journal of Ginseng Research

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Roles and mechanisms of ginseng in protecting heart

(2012) Si-dao Zheng et al.   Chinese Journal of Integrative Medicine

Karyotype analysis of Panax ginseng C.A.Meyer, 1843 (Araliaceae) based on rDNA loci and DAPI band distribution

(2012) Hyun Hee Kim et al.   Comparative Cytogenetics

Evolutionary relationship of Panax ginseng and P. quinquefolius inferred from sequencing and comparative analysis of expressed sequence tags

(2012) Hong-Il Choi et al.   GENETIC RESOURCES AND CROP EVOLUTION

Contribution of the different omega-3 fatty acid desaturase genes to the cold response in soybean

(2012) Ángela Román et al.   JOURNAL OF EXPERIMENTAL BOTANY

Enhancement of anti-inflammatory and antinociceptive actions of red ginseng extract by fermentation

(2012) Hyun-Joo Jung et al.   JOURNAL OF PHARMACY AND PHARMACOLOGY

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

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

Cytochrome P450 CYP716A53v2 Catalyzes the Formation of Protopanaxatriol from Protopanaxadiol During Ginsenoside Biosynthesis in Panax Ginseng

(2012) Jung-Yeon Han et al.   PLANT AND CELL PHYSIOLOGY

EST-SSR Marker Sets for Practical Authentication of All Nine Registered Ginseng Cultivars in Korea

(2012) Nam-Hoon Kim et al.   Journal of Ginseng Research

Effects of Panax ginseng in Neurodegenerative Diseases

(2012) Ik-Hyun Cho   Journal of Ginseng 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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

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

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

The Cyt P450 Enzyme CYP716A47 Catalyzes the Formation of Protopanaxadiol from Dammarenediol-II During Ginsenoside Biosynthesis in Panax ginseng

(2011) Jung-Yeon Han et al.   PLANT AND CELL PHYSIOLOGY

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization

(2010) Kuo-Chen Chou et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Current Evaluation of the Millennium Phytomedicine- Ginseng (I): Etymology, Pharmacognosy, Phytochemistry, Market and Regulations

(2009) Lee Jia et al.   CURRENT MEDICINAL CHEMISTRY

Regulation of ginsenoside and phytosterol biosynthesis by RNA interferences of squalene epoxidase gene in Panax ginseng

(2009) Jung-Yeon Han et al.   PHYTOCHEMISTRY

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

(2008) W. B. Barbazuk et al.   GENOME RESEARCH

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

(2008) Brian J Haas et al.   GENOME BIOLOGY

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology