High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites

Omics data input for metabolic modeling

(2016) Amit Rai et al.   CURRENT OPINION IN BIOTECHNOLOGY

RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis

(2016) Amit Rai et al.   Frontiers in Plant Science

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

(2015) Erik A. Visser et al.   BMC GENOMICS

RP-HPLC analysis of seco-iridoid glycoside swertiamarin from differentSwertiaspecies

(2015) Parthraj R. Kshirsagar et al.   NATURAL PRODUCT RESEARCH

Contents of therapeutic metabolites in Swertia chirayita correlate with the expression profiles of multiple genes in corresponding biosynthesis pathways

(2015) Jibesh Kumar Padhan et al.   PHYTOCHEMISTRY

High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome

(2015) Atsushi Fukushima et al.   PLoS One

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Xanthones fromSwertia mussotiias Multitarget-Directed Antidiabetic Agents

(2014) Huan-Huan Zheng et al.   ChemMedChem

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

(2014) Kenlee Nakasugi et al.   PLoS One

Phytochemical genomics — a new trend

(2013) Kazuki Saito   CURRENT OPINION IN PLANT BIOLOGY

Phylogenetic examination of crude drugs derived from Yunnanese Swertia plants

(2013) Nobuko Kakiuchi et al.   Journal of Natural Medicines

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Phytochemical Genomics on the Way

(2013) T. Muranaka et al.   PLANT AND CELL PHYSIOLOGY

Xanthones with Anti-Hepatitis B Virus Activity from Swertia mussotii

(2013) Tuan-Wu Cao et al.   PLANTA MEDICA

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

(2012) Nicole Gruenheit et al.   BMC GENOMICS

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

(2012) Jialei Duan et al.   BMC GENOMICS

Prevention of liver carcinogenesis by amarogentin through modulation of G 1 /S cell cycle check point and induction of apoptosis

(2012) Debolina Pal et al.   CARCINOGENESIS

Anti-diabetic Activity of Swertiamarin is due to an Active Metabolite, Gentianine, that Upregulates PPAR-γ Gene Expression in 3T3-L1 cells

(2012) Hitesh Vaidya et al.   PHYTOTHERAPY RESEARCH

Phenolic-Linked Biochemical Rationale for the Anti-Diabetic Properties ofSwertia chirayita(Roxb. ex Flem.) Karst.

(2012) Susanna Phoboo et al.   PHYTOTHERAPY RESEARCH

Constructing de Novo Biosynthetic Pathways for Chemical Synthesis inside Living Cells

(2011) Amy M. Weeks et al.   BIOCHEMISTRY

IPRStats: visualization of the functional potential of an InterProScan run

(2011) Ryan J Kelly et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Introgression of Swertia mussotii gene into Bupleurum scorzonerifolium via somatic hybridization

(2011) Junfeng Wang et al.   BMC PLANT BIOLOGY

Effects of Swertia japonica extract and its main compound swertiamarin on gastric emptying and gastrointestinal motility in mice

(2011) Yoshiyuki Kimura et al.   FITOTERAPIA

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

An evolutionary view of functional diversity in family 1 glycosyltransferases

(2011) Keiko Yonekura-Sakakibara et al.   PLANT JOURNAL

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

AFLP markers for identification of Swertia species (Gentianaceae)

(2010) A. Misra et al.   GENETICS AND MOLECULAR RESEARCH

Plant-derived medicines: A novel class of immunological adjuvants

(2010) Paul V Licciardi et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

A web-based resource for the Arabidopsis P450, cytochromes b5, NADPH-cytochrome P450 reductases, and family 1 glycosyltransferases (http://www.P450.kvl.dk)

(2009) Suzanne M. Paquette et al.   PHYTOCHEMISTRY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Development and mapping of Simple Sequence Repeat markers for pearl millet from data mining of Expressed Sequence Tags

(2008) S Senthilvel et al.   BMC PLANT BIOLOGY

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

(2008) D. E. Jarvis et al.   JOURNAL OF GENETICS