Multi-Omics-Based Discovery of Plant Signaling Molecules

Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity

(2021) Jiancai Li et al.   SCIENCE

Why and How to Dig into Plant Metabolite–Protein Interactions

(2021) Jhon Venegas-Molina et al.   TRENDS IN PLANT SCIENCE

Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity

(2021) Dapeng Li et al.   Annual Review of Plant Biology

Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway

(2021) Jian Cheng et al.   Molecular Plant

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

(2021) Wenbing Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field

(2021) Selma Cadot et al.   Microbiome

The chromosome-level Hemerocallis citrina Borani genome provides new insights into the rutin biosynthesis and the lack of colchicine

(2021) Zhixing Qing et al.   Horticulture Research

Microbiota-root-shoot-environment axis and stress tolerance in plants

(2021) Shiji Hou et al.   CURRENT OPINION IN PLANT BIOLOGY

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

(2021) Saleh Alseekh et al.   NATURE METHODS

Multi‐omics assisted identification of the key and species‐specific regulatory components of drought‐tolerant mechanisms in Gossypium stocksii

(2021) Dongliang Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

(2021) Ling Xu et al.   Nature Communications

The emerging role of biosynthetic gene clusters in plant defense and plant interactions

(2021) Guy Polturak et al.   PLoS Pathogens

A novel form of bivalent chromatin associates with rapid induction of camalexin biosynthesis genes in response to a pathogen signal in Arabidopsis

(2021) Kangmei Zhao et al.   eLife

A Pathogen-Responsive Gene Cluster for Highly Modified Fatty Acids in Tomato

(2020) Ju Eun Jeon et al.   CELL

Genome mining as a biotechnological tool for the discovery of novel marine natural products

(2020) Leixia Chu et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Building near-complete plant genomes

(2020) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

Ethylene signaling in plants

(2020) Brad M. Binder   JOURNAL OF BIOLOGICAL CHEMISTRY

Mass-spectrometry-based draft of the Arabidopsis proteome

(2020) Julia Mergner et al.   NATURE

FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis

(2020) Lei Gao et al.   Nature Chemistry

Multiview learning for understanding functional multiomics

(2020) Nam D. Nguyen et al.   PLoS Computational Biology

Discovery and engineering of colchicine alkaloid biosynthesis

(2020) Ryan S. Nett et al.   NATURE

Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome

(2020) Jiawen Cui et al.   Plant Methods

Regulation of Lignin Biosynthesis by Post-translational Protein Modifications

(2020) Daniel B. Sulis et al.   Frontiers in Plant Science

Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis

(2020) Christopher J. Harbort et al.   Cell Host & Microbe

Coumarin Communication Along the Microbiome–Root–Shoot Axis

(2020) Max J.J. Stassen et al.   TRENDS IN PLANT SCIENCE

Plant Single-Cell Metabolomics—Challenges and Perspectives

(2020) Leonardo Perez de Souza et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Single-Cell Transcriptome Analysis in Plants: Advances and Challenges

(2020) Rahul Shaw et al.   Molecular Plant

Modulation of Arabidopsis root growth by specialized triterpenes

(2020) Yuechen Bai et al.   NEW PHYTOLOGIST

The Age of Coumarins in Plant–Microbe Interactions

(2019) Ioannis A Stringlis et al.   PLANT AND CELL PHYSIOLOGY

A specialized metabolic network selectively modulates Arabidopsis root microbiota

(2019) Ancheng C. Huang et al.   SCIENCE

Maize synthesized benzoxazinoids affect the host associated microbiome

(2019) Enoch Narh Kudjordjie et al.   Microbiome

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

Identification of key enzymes responsible for protolimonoid biosynthesis in plants: Opening the door to azadirachtin production

(2019) Hannah Hodgson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isochorismate-derived biosynthesis of the plant stress hormone salicylic acid

(2019) Dmitrij Rekhter et al.   SCIENCE

NMR Spectroscopy for Metabolomics Research

(2019) Abdul-Hamid Emwas et al.   Metabolites

A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

(2019) Jiorgos Kourelis et al.   BMC GENOMICS

CETSA in integrated proteomics studies of cellular processes

(2019) Nayana Prabhu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

A noncanonical vacuolar sugar transferase required for biosynthesis of antimicrobial defense compounds in oat

(2019) Anastasia Orme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

METLIN: A Technology Platform for Identifying Knowns and Unknowns

(2018) Carlos Guijas et al.   ANALYTICAL CHEMISTRY

Plant Secondary Metabolite Diversity and Species Interactions

(2018) André Kessler et al.   Annual Review of Ecology Evolution and Systematics

N-hydroxy-pipecolic acid is a mobile metabolite that induces systemic disease resistance inArabidopsis

(2018) Yun-Chu Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health

(2018) Ioannis A. Stringlis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota

(2018) Lingfei Hu et al.   Nature Communications

Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding

(2018) Hong-Kyu Choi   Genes & Genomics

Review of recent developments in GC–MS approaches to metabolomics-based research

(2018) David J. Beale et al.   Metabolomics

Gene-guided discovery and engineering of branched cyclic peptides in plants

(2018) Roland D. Kersten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Challenges, progress and promises of metabolite annotation for LC–MS-based metabolomics

(2018) Romanas Chaleckis et al.   CURRENT OPINION IN BIOTECHNOLOGY

Plant genome sequences: past, present, future

(2018) Paul Julian Kersey   CURRENT OPINION IN PLANT BIOLOGY

The Combined Use of Proteomics and Transcriptomics Reveals a Complex Secondary Metabolite Network in Peperomia obtusifolia

(2017) Andrea N. L. Batista et al.   JOURNAL OF NATURAL PRODUCTS

The PhytoClust tool for metabolic gene clusters discovery in plant genomes

(2017) Nadine Töpfer et al.   NUCLEIC ACIDS RESEARCH

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

(2017) Satria A. Kautsar et al.   NUCLEIC ACIDS RESEARCH

A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants

(2017) Jennifer H. Wisecaver et al.   PLANT CELL

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

(2017) Pascal Schläpfer et al.   PLANT PHYSIOLOGY

Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution

(2017) Ancheng C. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy

(2017) Robert A. Quinn et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

(2017) Kamlesh K. Meena et al.   Frontiers in Plant Science

Abscisic Acid Signaling and Abiotic Stress Tolerance in Plants: A Review on Current Knowledge and Future Prospects

(2017) Kanchan Vishwakarma et al.   Frontiers in Plant Science

epiGBS: reference-free reduced representation bisulfite sequencing

(2016) Thomas P van Gurp et al.   NATURE METHODS

Plant metabolic clusters - from genetics to genomics

(2016) Hans-Wilhelm Nützmann et al.   NEW PHYTOLOGIST

Delineation of metabolic gene clusters in plant genomes by chromatin signatures

(2016) Nan Yu et al.   NUCLEIC ACIDS RESEARCH

Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs)

(2016) Dhiraj P. Murale et al.   Proteome Science

Plant metabolism, the diverse chemistry set of the future

(2016) E. T. Wurtzel et al.   SCIENCE

A new cyanogenic metabolite in Arabidopsis required for inducible pathogen defence

(2015) Jakub Rajniak et al.   NATURE

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

The glucosinolate breakdown product indole-3-carbinol acts as an auxin antagonist in roots ofArabidopsis thaliana

(2015) Ella Katz et al.   PLANT JOURNAL

The role of proteomics in progressing insights into plant secondary metabolism

(2015) María J. Martínez-Esteso et al.   Frontiers in Plant Science

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Investigation of triterpene synthesis and regulation in oats reveals a role for  -amyrin in determining root epidermal cell patterning

(2014) A. C. Kemen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Signatures of Specialized Metabolism in Plants

(2014) L. Chae et al.   SCIENCE

Protein Analysis by Shotgun/Bottom-up Proteomics

(2013) Yaoyang Zhang et al.   CHEMICAL REVIEWS

Brassinosteroid signalling

(2013) J.-Y. Zhu et al.   DEVELOPMENT

Diverse Roles of Strigolactones in Plant Development

(2012) Philip B. Brewer et al.   Molecular Plant

Salicylic acid beyond defence: its role in plant growth and development

(2011) M. Rivas-San Vicente et al.   JOURNAL OF EXPERIMENTAL BOTANY

Targeted proteomics for metabolic pathway optimization: Application to terpene production

(2011) Alyssa M. Redding-Johanson et al.   METABOLIC ENGINEERING

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

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

Jasmonate-induced defenses: a tale of intelligence, collaborators and rascals

(2011) Carlos L. Ballaré   TRENDS IN PLANT SCIENCE

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression

(2009) T. Obayashi et al.   DNA RESEARCH

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS