The Amaryllidaceae alkaloids: biosynthesis and methods for enzyme discovery

Metabolomics Beyond Spectroscopic Databases: A Combined MS/NMR Strategy for the Rapid Identification of New Metabolites in Complex Mixtures

(2015) Kerem Bingol et al.   ANALYTICAL CHEMISTRY

Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)

(2015) Rina Kamenetsky et al.   BMC GENOMICS

Genome assembly using Nanopore-guided long and error-free DNA reads

(2015) Mohammed-Amin Madoui et al.   BMC GENOMICS

Expanding the Imine Reductase Toolbox by Exploring the Bacterial Protein-Sequence Space

(2015) Dennis Wetzl et al.   CHEMBIOCHEM

Unlocking the Diversity of Alkaloids in Catharanthus roseus: Nuclear Localization Suggests Metabolic Channeling in Secondary Metabolism

(2015) Anna Stavrinides et al.   CHEMISTRY & BIOLOGY

Two elephants in the room

(2015) Kerem Bingol et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

Dimeric CRISPR RNA-Guided FokI-dCas9 Nucleases Directed by Truncated gRNAs for Highly Specific Genome Editing

(2015) Nicolas Wyvekens et al.   HUMAN GENE THERAPY

Plant aldo-keto reductases (AKRs) as multi-tasking soldiers involved in diverse plant metabolic processes and stress defense: A structure-function update

(2015) Debashree Sengupta et al.   JOURNAL OF PLANT PHYSIOLOGY

Cytochrome P450-Catalyzed Regio- and Stereoselective Phenol Coupling of Fungal Natural Products

(2015) Laura S. Mazzaferro et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum)

(2015) Hikaru Tsukazaki et al.   MOLECULAR BREEDING

Efficient Virus-Mediated Genome Editing in Plants Using the CRISPR/Cas9 System

(2015) Zahir Ali et al.   Molecular Plant

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects

(2015) Lloyd W. Sumner et al.   NATURAL PRODUCT REPORTS

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

DNA-binding-domain fusions enhance the targeting range and precision of Cas9

(2015) Mehmet Fatih Bolukbasi et al.   NATURE METHODS

Successful test launch for nanopore sequencing

(2015) Nicholas J Loman et al.   NATURE METHODS

Cytotoxic activities of Amaryllidaceae alkaloids against gastrointestinal cancer cells

(2015) Ivo Doskočil et al.   Phytochemistry Letters

Elucidating steroid alkaloid biosynthesis inVeratrum californicum:production of verazine in Sf9 cells

(2015) Megan M. Augustin et al.   PLANT JOURNAL

Genome-guided investigation of plant natural product biosynthesis

(2015) Franziska Kellner et al.   PLANT JOURNAL

Comparison of CRISPR/Cas9 expression constructs for efficient targeted mutagenesis in rice

(2015) Masafumi Mikami et al.   PLANT MOLECULAR BIOLOGY

De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes

(2015) Hemalatha Rajkumar et al.   PLoS One

Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system

(2015) Kabin Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The nature of chemical innovation: new enzymes by evolution

(2015) Frances H. Arnold   QUARTERLY REVIEWS OF BIOPHYSICS

Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone

(2015) Warren Lau et al.   SCIENCE

Targeted mutagenesis in soybean using the CRISPR-Cas9 system

(2015) Xianjun Sun et al.   Scientific Reports

A geminivirus-based guide RNA delivery system for CRISPR/Cas9 mediated plant genome editing

(2015) Kangquan Yin et al.   Scientific Reports

Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review

(2015) Engy A. Mahrous et al.   Journal of Advanced Research

De Novo Assembly and Annotation of the Chinese Chive (Allium tuberosum Rottler ex Spr.) Transcriptome Using the Illumina Platform

(2015) Shu-Mei Zhou et al.   PLoS One

Efficient CRISPR/Cas9-mediated Targeted Mutagenesis in Populus in the First Generation

(2015) Di Fan et al.   Scientific Reports

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

(2014) Ruolin Liu et al.   BMC BIOINFORMATICS

The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms

(2014) Peter A Larsen et al.   BMC GENOMICS

A first look at the Oxford Nanopore MinION sequencer

(2014) Alexander S. Mikheyev et al.   Molecular Ecology Resources

Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity

(2014) John P Guilinger et al.   NATURE METHODS

Tobacco rattle virus–based virus-induced gene silencing in Nicotiana benthamiana

(2014) Muthappa Senthil-Kumar et al.   Nature Protocols

Regulation of metabolic gene clusters inArabidopsis thaliana

(2014) Hans-Wilhelm Nützmann et al.   NEW PHYTOLOGIST

Evolution of alkaloid biosynthesis in the genus Narcissus

(2014) Strahil Berkov et al.   PHYTOCHEMISTRY

CRISPR/Cas9-Mediated Targeted Mutagenesis in the Liverwort Marchantia polymorpha L.

(2014) Shigeo S. Sugano et al.   PLANT AND CELL PHYSIOLOGY

The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation

(2014) Hui Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Comparative assessments of CRISPR-Cas nucleases’ cleavage efficiency in planta

(2014) Ross A. Johnson et al.   PLANT MOLECULAR BIOLOGY

CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum

(2014) Junping Gao et al.   PLANT MOLECULAR BIOLOGY

Hairy Root Transformation Using Agrobacterium rhizogenes as a Tool for Exploring Cell Type-Specific Gene Expression and Function Using Tomato as a Model

(2014) M. Ron et al.   PLANT PHYSIOLOGY

Efficient Gene Editing in Tomato in the First Generation Using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated9 System

(2014) C. Brooks et al.   PLANT PHYSIOLOGY

Targeted Genome Editing of Sweet Orange Using Cas9/sgRNA

(2014) Hongge Jia et al.   PLoS One

Cloning and Characterization of a Norbelladine 4′-O-Methyltransferase Involved in the Biosynthesis of the Alzheimer’s Drug Galanthamine in Narcissus sp. aff. pseudonarcissus

(2014) Matthew B. Kilgore et al.   PLoS One

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

Genomic Signatures of Specialized Metabolism in Plants

(2014) L. Chae et al.   SCIENCE

The rise of operon-like gene clusters in plants

(2014) Svetlana Boycheva et al.   TRENDS IN PLANT SCIENCE

Vanillin formation from ferulic acid in Vanilla planifolia is catalysed by a single enzyme

(2014) Nethaji J. Gallage et al.   Nature Communications

Functional genetics for all: engineered nucleases, CRISPR and the gene editing revolution

(2014) Anna F Gilles et al.   EvoDevo

Towards a Molecular Understanding of the Biosynthesis of Amaryllidaceae Alkaloids in Support of Their Expanding Medical Use

(2013) Adam Takos et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Amaryllidaceae and Sceletium alkaloids

(2013) Zhong Jin   NATURAL PRODUCT REPORTS

Targeted genome modification of crop plants using a CRISPR-Cas system

(2013) Qiwei Shan 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

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

(2013) Wenzhi Jiang et al.   NUCLEIC ACIDS RESEARCH

The effect of Amaryllidaceae alkaloids haemanthamine and haemanthidine on cell cycle progression and apoptosis in p53-negative human leukemic Jurkat cells

(2013) Radim Havelek et al.   PHYTOMEDICINE

Analysing complex Triticeae genomes – concepts and strategies

(2013) Manuel Spannagl et al.   Plant Methods

De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing

(2013) Ren Wang et al.   PLoS One

Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes

(2013) M. Itkin et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

Physiological and comparative proteomic analyses in response to nitrogen application in an Amaryllidaceae plant, Lycoris aurea

(2012) Qiaomei Ru et al.   ACTA PHYSIOLOGIAE PLANTARUM

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceae

(2012) Nina Rønsted et al.   BMC EVOLUTIONARY BIOLOGY

Aldo–keto reductases in retinoid metabolism: Search for substrate specificity and inhibitor selectivity

(2012) Sergio Porté et al.   CHEMICO-BIOLOGICAL INTERACTIONS

Laccase-catalyzed oxidative phenolic coupling of vanillidene derivatives

(2012) Mihaela-Anca Constantin et al.   GREEN CHEMISTRY

Functional Identification of Valerena-1,10-diene Synthase, a Terpene Synthase Catalyzing a Unique Chemical Cascade in the Biosynthesis of Biologically Active Sesquiterpenes inValeriana officinalis

(2012) Yun-Soo Yeo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular and analysis of a phenylalanine ammonia-lyase gene (LrPAL2) from Lycoris radiata

(2012) Yumei Jiang et al.   MOLECULAR BIOLOGY REPORTS

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

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

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Why biosynthetic genes for chemical defense compounds cluster

(2012) Adam M. Takos et al.   TRENDS IN PLANT SCIENCE

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

(2012) Nicholas Furnham et al.   PLoS Computational Biology

Small-Volume Nuclear Magnetic Resonance Spectroscopy

(2011) Raluca M. Fratila et al.   Annual Review of Analytical Chemistry

Convergent Evolution in Plant Specialized Metabolism

(2011) Eran Pichersky et al.   Annual Review of Plant Biology

Genome Engineering With Zinc-Finger Nucleases

(2011) Dana Carroll   GENETICS

A Stereoselective Hydroxylation Step of Alkaloid Biosynthesis by a Unique Cytochrome P450 inCatharanthus roseus

(2011) Lesley-Ann Giddings et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genomic clustering of cyanogenic glucoside biosynthetic genes aids their identification inLotus japonicusand suggests the repeated evolution of this chemical defence pathway

(2011) Adam M. Takos et al.   PLANT JOURNAL

A P450-centric view of plant evolution

(2011) David Nelson et al.   PLANT JOURNAL

The involvement of Narcissus hispanicus Gouan in the origin of Narcissus bujei and of cultivated trumpet daffodils (Amaryllidaceae)

(2010) B. J.M. Zonneveld   ANALES DEL JARDIN BOTANICO DE MADRID

LC–high resolution MS in environmental analysis: from target screening to the identification of unknowns

(2010) Martin Krauss et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Characterization of two methylenedioxy bridge-forming cytochrome P450-dependent enzymes of alkaloid formation in the Mexican prickly poppy Argemone mexicana

(2010) Maria Luisa Díaz Chávez et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

LC-MS-SPE-NMR for the Isolation and Characterization ofneo-Clerodane Diterpenoids fromTeucrium luteumsubsp.flavovirens⊥

(2010) Amaya Castro et al.   JOURNAL OF NATURAL PRODUCTS

Molecular cloning and characterization of a phenylalanine ammonia-lyase gene (LrPAL) from Lycoris radiata

(2010) Yumei Jiang et al.   MOLECULAR BIOLOGY REPORTS

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A subfamilial classification for the expanded asparagalean families Amaryllidaceae, Asparagaceae and Xanthorrhoeaceae

(2009) MARK W. CHASE et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Gene expression and characterization of a stress-induced tyrosine decarboxylase fromArabidopsis thaliana

(2009) Thomas Lehmann et al.   FEBS LETTERS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

OsTGAP1, a bZIP Transcription Factor, Coordinately Regulates the Inductive Production of Diterpenoid Phytoalexins in Rice

(2009) Atsushi Okada et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Amaryllidaceae and Sceletium alkaloids

(2009) Zhong Jin   NATURAL PRODUCT REPORTS

Medium- and short-chain dehydrogenase/reductase gene and protein families

(2008) K. L. Kavanagh et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Chemistry, Biology, and Medicinal Potential of Narciclasine and its Congeners

(2008) Alexander Kornienko et al.   CHEMICAL REVIEWS

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

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

Antimicrobial and Antioxidative Activities of Bioactive Constituents from Hydnophytum formicarum Jack.

(2008) Supaluk Prachayasittikul et al.   MOLECULES

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The systematic value of nuclear DNA content for all species of Narcissus L. (Amaryllidaceae)

(2008) B. J. M. Zonneveld   PLANT SYSTEMATICS AND EVOLUTION

Towards a universal product ion mass spectral library – reproducibility of product ion spectra across eleven different mass spectrometers

(2008) Chris Hopley et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY