CathaCyc, a Metabolic Pathway Database Built from Catharanthus roseus RNA-Seq Data

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Regulatory network operations in the Pathway Tools software

(2012) Suzanne M Paley et al.   BMC BIOINFORMATICS

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

(2012) Fernando Geu-Flores et al.   NATURE

ORCAE: online resource for community annotation of eukaryotes

(2012) Lieven Sterck et al.   NATURE METHODS

Characterization of the plastidial geraniol synthase from Madagascar periwinkle which initiates the monoterpenoid branch of the alkaloid pathway in internal phloem associated parenchyma

(2012) Andrew J. Simkin et al.   PHYTOCHEMISTRY

Functional characterization of amyrin synthase involved in ursolic acid biosynthesis in Catharanthus roseus leaf epidermis

(2012) Fang Yu et al.   PHYTOCHEMISTRY

The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway

(2012) Michele Fabris et al.   PLANT JOURNAL

Integration of deep transcript and targeted metabolite profiles for eight cultivars of opium poppy

(2012) Isabel Desgagné-Penix et al.   PLANT MOLECULAR BIOLOGY

Molecular characterization of the pentacyclic triterpenoid biosynthetic pathway in Catharanthus roseus

(2012) Lili Huang et al.   PLANTA

De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosynthesis of Active Metabolites

(2012) Miao He et al.   PLoS One

Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species

(2012) Elsa Góngora-Castillo et al.   PLoS One

Transcriptional machineries in jasmonate-elicited plant secondary metabolism

(2012) Nathan De Geyter et al.   TRENDS IN PLANT SCIENCE

De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients

(2011) Hua Wenping et al.   GENOMICS

Identification of phenolic compounds in isolated vacuoles of the medicinal plant Catharanthus roseus and their interaction with vacuolar class III peroxidase: an H2O2 affair?

(2011) Federico Ferreres et al.   JOURNAL OF EXPERIMENTAL BOTANY

Combinatorial biosynthesis in plants: A (p)review on its potential and future exploitation

(2011) Jacob Pollier et al.   NATURAL PRODUCT REPORTS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

The JAZ Proteins: A Crucial Interface in the Jasmonate Signaling Cascade

(2011) Laurens Pauwels et al.   PLANT CELL

Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

(2011) M. Van Bel et al.   PLANT PHYSIOLOGY

Emerging trends in research on spatial and temporal organization of terpenoid indole alkaloid pathway in Catharanthus roseus: a literature update

(2011) Priyanka Verma et al.   PROTOPLASMA

Spatial organization of the vindoline biosynthetic pathway in Catharanthus roseus

(2010) Grégory Guirimand et al.   JOURNAL OF PLANT PHYSIOLOGY

Production of Plant Bioactive Triterpenoid Saponins: Elicitation Strategies and Target Genes to Improve Yields

(2010) Anna C. A. Yendo et al.   MOLECULAR BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants

(2010) P. Zhang et al.   PLANT PHYSIOLOGY

Homolog of tocopherol C methyltransferases catalyzes N methylation in anticancer alkaloid biosynthesis

(2010) D. K. Liscombe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FrameDP: sensitive peptide detection on noisy matured sequences

(2009) J. Gouzy et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Production and metabolic engineering of terpenoid indole alkaloids in cell cultures of the medicinal plant Catharanthus roseus (L.) G. Don (Madagascar periwinkle)

(2009) Mei-Liang Zhou et al.   BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

(2009) Patrick May et al.   BMC GENOMICS

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

A Dynamic Interface for Capsaicinoid Systems Biology

(2009) M. Mazourek et al.   PLANT PHYSIOLOGY

Jasmonate-inducible gene: what does it mean?

(2009) Laurens Pauwels et al.   TRENDS IN PLANT SCIENCE

Alkaloid Biosynthesis: Metabolism and Trafficking

(2008) Jörg Ziegler et al.   Annual Review of Plant Biology

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

InterPro: the integrative protein signature database

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

The Leaf Epidermome of Catharanthus roseus Reveals Its Biochemical Specialization

(2008) J. Murata et al.   PLANT CELL

Opium poppy and Madagascar periwinkle: model non-model systems to investigate alkaloid biosynthesis in plants

(2008) Peter J. Facchini et al.   PLANT JOURNAL