The chromosome‐scale reference genome of Rubus chingii Hu provides insight into the biosynthetic pathway of hydrolyzable tannins

Discovery and characterization of tannase genes in plants: roles in hydrolysis of tannins

(2020) Xinlong Dai et al.   NEW PHYTOLOGIST

Phenolic Composition, Mineral Content, and Beneficial Bioactivities of Leaf Extracts from Black Currant (Ribes nigrum L.), Raspberry (Rubus idaeus), and Aronia (Aronia melanocarpa)

(2020) Monika Staszowska-Karkut et al.   Nutrients

Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal

(2020) Graham J Etherington et al.   GigaScience

Identification of Ellagitannins in the Unripe Fruit of Rubus Chingii Hu and Evaluation of its Potential Antidiabetic Activity

(2019) Yue Chen et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Rubus chingii Hu: A Review of the Phytochemistry and Pharmacology

(2019) Guohua Yu et al.   Frontiers in Pharmacology

The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution

(2019) Qing-gang Zhu et al.   Horticulture Research

OUP accepted manuscript

(2018)   BIOINFORMATICS

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

(2018) Damla Senol Cali et al.   BRIEFINGS IN BIOINFORMATICS

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

(2018) Rubina Jibran et al.   Horticulture Research

Studies on the anti-aging activity of a glycoprotein isolated from Fupenzi (Rubus chingii Hu.) and its regulation on klotho gene expression in mice kidney

(2018) Hua-jin Zeng et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

(2018) Robert VanBuren et al.   GigaScience

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

(2018) Maojun Wang et al.   NATURE GENETICS

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

(2017) Nicolas Daccord et al.   NATURE GENETICS

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

Identification of UDP-glycosyltransferases involved in the biosynthesis of astringent taste compounds in tea (Camellia sinensis)

(2016) Lilan Cui et al.   JOURNAL OF EXPERIMENTAL BOTANY

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

The genome of black raspberry (Rubus occidentalis)

(2016) Robert VanBuren et al.   PLANT JOURNAL

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Bioactivities and extraction optimization of crude polysaccharides from the fruits and leaves of Rubus chingii Hu

(2015) Tian-Tian Zhang et al.   CARBOHYDRATE POLYMERS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

BAHD or SCPL acyltransferase? What a dilemma for acylation in the world of plant phenolic compounds

(2015) Thibaut Bontpart et al.   NEW PHYTOLOGIST

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Comprehensive identification of walnut polyphenols by liquid chromatography coupled to linear ion trap–Orbitrap mass spectrometry

(2013) Jorge Regueiro et al.   FOOD CHEMISTRY

DNA tool kit goes live online

(2013) Ewen Callaway   NATURE

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

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

New genes as drivers of phenotypic evolution

(2013) Sidi Chen et al.   NATURE REVIEWS GENETICS

Pfam: the protein families database

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

The genome of the pear (Pyrus bretschneideri Rehd.)

(2012) J. Wu et al.   GENOME RESEARCH

Purification and Characterization of a Novel Galloyltransferase Involved in Catechin Galloylation in the Tea Plant (Camellia sinensis)

(2012) Yajun Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Antithrombotic activity of fractions and components obtained from raspberry leaves (Rubus chingii)

(2011) Na Han et al.   FOOD CHEMISTRY

The Blackberry Fruit: A Review on Its Composition and Chemistry, Metabolism and Bioavailability, and Health Benefits

(2011) Lydia Kaume et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Identification and functional characterization of cDNAs coding for hydroxybenzoate/hydroxycinnamate glucosyltransferases co-expressed with genes related to proanthocyanidin biosynthesis

(2011) F. Khater et al.   JOURNAL OF EXPERIMENTAL BOTANY

Phenolic Compounds in Cherry (Prunus avium) Heartwood with a View to Their Use in Cooperage

(2010) Miriam Sanz et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY