The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

The Structure of a Plant Tyrosinase from Walnut Leaves Reveals the Importance of “Substrate-Guiding Residues” for Enzymatic Specificity

(2015) Aleksandar Bijelic et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

(2015) Ming-Cheng Luo et al.   BMC GENOMICS

Histidine 352 (His352) and Tryptophan 355 (Trp355) Are Essential for Flax UGT74S1 Glucosylation Activity toward Secoisolariciresinol

(2015) Kaushik Ghose et al.   PLoS One

Cloning and functional expression inE. coliof a polyphenol oxidase transcript fromCoreopsis grandiflorainvolved in aurone formation

(2014) Cornelia Kaintz et al.   FEBS LETTERS

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

(2014) J. L. Wegrzyn et al.   GENETICS

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

(2014) Marco Biasini et al.   NUCLEIC ACIDS RESEARCH

Identification of UGT84A13 as a candidate enzyme for the first committed step of gallotannin biosynthesis in pedunculate oak (Quercus robur)

(2014) Juliane Mittasch et al.   PHYTOCHEMISTRY

Purification and characterization of tyrosinase from walnut leaves (Juglans regia)

(2014) Florime Zekiri et al.   PHYTOCHEMISTRY

Novel Roles for the Polyphenol Oxidase Enzyme in Secondary Metabolism and the Regulation of Cell Death in Walnut

(2014) S. Araji et al.   PLANT PHYSIOLOGY

Genome-wide identification and phylogenetic analysis of Family-1 UDP glycosyltransferases in maize (Zea mays)

(2014) Yanjie Li et al.   PLANTA

The Draft Genome Sequence of European Pear (Pyrus communis L. ‘Bartlett’)

(2014) David Chagné et al.   PLoS One

Crystallization and preliminary X-ray crystallographic analysis of polyphenol oxidase fromJuglans regia(jrPPO1)

(2014) Florime Zekiri et al.   Acta Crystallographica Section F-Structural Biology Communications

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The Shikimate Pathway and Aromatic Amino Acid Biosynthesis in Plants

(2012) Hiroshi Maeda et al.   Annual Review of Plant Biology

The polyphenol oxidase gene family in land plants: Lineage-specific duplication and expansion

(2012) Lan T Tran et al.   BMC GENOMICS

miR395 is a general component of the sulfate assimilation regulatory network in Arabidopsis

(2012) Colette A. Matthewman et al.   FEBS LETTERS

The genome of the pear (Pyrus bretschneideri Rehd.)

(2012) J. Wu et al.   GENOME RESEARCH

HPLC Determination of Phenolic Acids, Flavonoids and Juglone in Walnut Leaves

(2012) V. Nour et al.   JOURNAL OF CHROMATOGRAPHIC SCIENCE

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

(2012) Shaogui Guo et al.   NATURE GENETICS

InterPro in 2011: new developments in the family and domain prediction database

(2012) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Establishment of pomegranate (Punica granatum) hairy root cultures for genetic interrogation of the hydrolyzable tannin biosynthetic pathway

(2012) Nadia N. Ono et al.   PLANTA

A Measure of the Promiscuity of Proteins and Characteristics of Residues in the Vicinity of the Catalytic Site That Regulate Promiscuity

(2012) Sandeep Chakraborty et al.   PLoS One

An Automated Flow for Directed Evolution Based on Detection of Promiscuous Scaffolds Using Spatial and Electrostatic Properties of Catalytic Residues

(2012) Sandeep Chakraborty   PLoS One

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Defense mechanisms against herbivory in Picea: sequence evolution and expression regulation of gene family members in the phenylpropanoid pathway

(2011) Ilga Porth et al.   BMC GENOMICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

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

Phenolic response in green walnut husk after the infection with bacteria Xanthomonas arboricola pv. juglandis

(2011) M. Mikulic-Petkovsek et al.   PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY

Tannins in plant–herbivore interactions

(2011) Raymond V. Barbehenn et al.   PHYTOCHEMISTRY

Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints

(2011) Michaël Bekaert et al.   PLANT CELL

An evolutionary view of functional diversity in family 1 glycosyltransferases

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

A genome-wide phylogenetic reconstruction of family 1 UDP-glycosyltransferases revealed the expansion of the family during the adaptation of plants to life on land

(2011) Lorenzo Caputi et al.   PLANT JOURNAL

Characterizing the walnut genome through analyses of BAC end sequences

(2011) Jiajie Wu et al.   PLANT MOLECULAR BIOLOGY

Mechanism of gallic acid biosynthesis in bacteria (Escherichia coli) and walnut (Juglans regia)

(2011) Ryann M. Muir et al.   PLANT MOLECULAR BIOLOGY

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

(2010) Anthony Mathelier et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Molecular analysis of a UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT) gene from purple potato (Solanum tuberosum)

(2010) Chaoyang Hu et al.   MOLECULAR BIOLOGY REPORTS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Genome-Wide Comparative Gene Family Classification

(2010) Christian Frech et al.   PLoS One

Incidence of Venturia shoot blight in aspen (Populus tremuloides Michx.) varies with tree chemistry and genotype

(2009) Liza M. Holeski et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

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

(2009) G. Abrusan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cloning, Sequencing, Purification, and Crystal Structure of Grenache (Vitis vinifera) Polyphenol Oxidase

(2009) Victoria M. Virador et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

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

Antioxidant phenolic compounds from walnut kernels (Juglans regia L.)

(2008) Zijia Zhang et al.   FOOD CHEMISTRY

Walnut Polyphenols Prevent Liver Damage Induced by Carbon Tetrachloride andd-Galactosamine: Hepatoprotective Hydrolyzable Tannins in the Kernel Pellicles of Walnut

(2008) Hiroshi Shimoda et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: Problems and solutions

(2008) Andrey Zharkikh et al.   JOURNAL OF BIOTECHNOLOGY

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

Criteria for Annotation of Plant MicroRNAs

(2008) B. C. Meyers et al.   PLANT CELL

How to usefully compare homologous plant genes and chromosomes as DNA sequences

(2008) Eric Lyons et al.   PLANT JOURNAL

Plant ARGONAUTES

(2008) Hervé Vaucheret   TRENDS IN PLANT SCIENCE

Glycosyltransferases: Structures, Functions, and Mechanisms

(2007) L.L. Lairson et al.   Annual Review of Biochemistry

Phenolics from walnut (Juglans regia L.) kernels: Antioxidant activity and interactions with proteins

(2007) Diana O. Labuckas et al.   FOOD CHEMISTRY