Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe

Cell-penetrating corosolic acid liposome as a functional carrier for delivering chemotherapeutic drugs

(2020) Xuqian Li et al.   Acta Biomaterialia

Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants

(2020) Lingfeng Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A dual effect of ursolic acid to the treatment of multiple sclerosis through both immunomodulation and direct remyelination

(2020) Yuan Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

Formation and diversification of a paradigm biosynthetic gene cluster in plants

(2020) Zhenhua Liu et al.   Nature Communications

Robust predictions of specialized metabolism genes through machine learning

(2019) Bethany M. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ursolic Acid Isolated from the Leaves of Loquat (Eriobotrya japonica) Inhibited Osteoclast Differentiation through Targeting Exportin 5

(2019) Hui Tan et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Drivers of metabolic diversification: how dynamic genomic neighborhoods generate new biosynthetic pathways in the Brassicaceae

(2019) Zhenhua Liu et al.   NEW PHYTOLOGIST

The Rosa genome provides new insights into the domestication of modern roses

(2018) Olivier Raymond et al.   NATURE GENETICS

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

Whole-Genome Duplication and Plant Macroevolution

(2018) James W. Clark et al.   TRENDS IN PLANT SCIENCE

Oxidosqualene cyclase and CYP716 enzymes contribute to triterpene structural diversity in the medicinal tree banaba

(2018) Sandeep et al.   NEW PHYTOLOGIST

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Genome of wild olive and the evolution of oil biosynthesis

(2017) Turgay Unver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ancient CYP716 family is a major contributor to the diversification of eudicot triterpenoid biosynthesis

(2017) Karel Miettinen et al.   Nature Communications

Functional Characterization of CYP716 Family P450 Enzymes in Triterpenoid Biosynthesis in Tomato

(2017) Shuhei Yasumoto et al.   Frontiers in Plant Science

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

Multifunctional oxidosqualene cyclases and cytochrome P450 involved in the biosynthesis of apple fruit triterpenic acids

(2016) Christelle M. Andre et al.   NEW PHYTOLOGIST

Evolution of gene duplication in plants

(2016) Nicholas Panchy et al.   PLANT PHYSIOLOGY

Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism

(2016) Zhenhua Liu et al.   Nature Communications

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

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

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The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Rfam 12.0: updates to the RNA families database

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

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

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

(2014) Shengyi Liu et al.   Nature Communications

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

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

The evolutionary paths towards complexity: a metabolic perspective

(2013) Jing-Ke Weng   NEW PHYTOLOGIST

The genome of the pear (Pyrus bretschneideri Rehd.)

(2012) J. Wu et al.   GENOME RESEARCH

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(2012) Ben Langmead et al.   NATURE METHODS

CYP701A8: A Rice ent-Kaurene Oxidase Paralog Diverted to More Specialized Diterpenoid Metabolism

(2012) Q. Wang et al.   PLANT PHYSIOLOGY

The Rise of Chemodiversity in Plants

(2012) J.-K. Weng et al.   SCIENCE

Assembly of an Evolutionarily New Pathway for  -Pyrone Biosynthesis in Arabidopsis

(2012) J.-K. Weng et al.   SCIENCE

The genome of Prunus mume

(2012) Qixiang Zhang et al.   Nature Communications

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt 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

KNApSAcK Family Databases: Integrated Metabolite–Plant Species Databases for Multifaceted Plant Research

(2011) Farit Mochamad Afendi et al.   PLANT AND CELL PHYSIOLOGY

Medicago truncatulaCYP716A12 Is a Multifunctional Oxidase Involved in the Biosynthesis of Hemolytic Saponins

(2011) Maria Carelli et al.   PLANT CELL

An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods

(2010) G. Carrier et al.   AMERICAN JOURNAL OF BOTANY

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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

(2008) A. D. Johnson et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A Role for Gene Duplication and Natural Variation of Gene Expression in the Evolution of Metabolism

(2008) Daniel J. Kliebenstein   PLoS One