Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response

Wax biosynthesis in response to danger: its regulation upon abiotic and biotic stress

(2020) Milena Lewandowska et al.   NEW PHYTOLOGIST

Gene expression profiling of tomato roots interacting with Pseudomonas fluorescens unravels the molecular reprogramming that occurs during the early phases of colonization

(2019) Riccardo Scotti et al.   SYMBIOSIS

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

Fulvic acid-induced disease resistance to Botrytis cinerea in table grapes may be mediated by regulating phenylpropanoid metabolism

(2019) Dandan Xu et al.   FOOD CHEMISTRY

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

The genetics of fruit flavour preferences

(2018) Harry J. Klee et al.   NATURE REVIEWS GENETICS

The ‘TranSeq’ 3’ End Sequencing Method for High-Throughput Transcriptomics and Gene Space Refinement in Plant Genomes

(2018) Oren Tzfadia et al.   PLANT JOURNAL

Short-chain dehydrogenase/reductase governs steroidal specialized metabolites structural diversity and toxicity in the genusSolanum

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

Canalization of Tomato Fruit Metabolism

(2017) Saleh Alseekh et al.   PLANT CELL

Dynamic metabolic reprogramming of steroidal glycol-alkaloid and phenylpropanoid biosynthesis may impart early blight resistance in wild tomato (Solanum arcanum Peralta)

(2017) Balkrishna A. Shinde et al.   PLANT MOLECULAR BIOLOGY

A chemical genetic roadmap to improved tomato flavor

(2017) Denise Tieman et al.   SCIENCE

Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

(2016) Elise Albert et al.   JOURNAL OF EXPERIMENTAL BOTANY

Solanum pennelliibackcross inbred lines (BILs) link small genomic bins with tomato traits

(2016) Itai Ofner et al.   PLANT JOURNAL

The WEIZMASS spectral library for high-confidence metabolite identification

(2016) Nir Shahaf et al.   Nature Communications

GAME9 regulates the biosynthesis of steroidal alkaloids and upstream isoprenoids in the plant mevalonate pathway

(2016) Pablo D. Cárdenas et al.   Nature Communications

PGP repository: a plant phenomics and genomics data publication infrastructure

(2016) Daniel Arend et al.   Database-The Journal of Biological Databases and Curation

A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

(2016) D. Fulop et al.   G3-Genes Genomes Genetics

Embedding standards in metabolomics: the Metabolomics Society data standards task group

(2015) Reza M. Salek et al.   Metabolomics

Domestication selected for deceleration of the circadian clock in cultivated tomato

(2015) Niels A Müller et al.   NATURE GENETICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Tomato R2R3-MYB Proteins SlANT1 and SlAN2: Same Protein Activity, Different Roles

(2015) Claudia Kiferle et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence

(2014) Emma L. Schymanski et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Linking Gene Expression and Membrane Lipid Composition ofArabidopsis

(2014) Jedrzej Szymanski et al.   PLANT CELL

Transcriptional Regulation of Fruit Ripening by Tomato FRUITFULL Homologs and Associated MADS Box Proteins

(2014) M. Fujisawa et al.   PLANT CELL

OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants

(2013) Vaibhav Srivastava et al.   BMC GENOMICS

Anthocyanins Double the Shelf Life of Tomatoes by Delaying Overripening and Reducing Susceptibility to Gray Mold

(2013) Yang Zhang et al.   CURRENT BIOLOGY

Dissection of Tomato Lycopene Biosynthesis through Virus-Induced Gene Silencing

(2013) E. Fantini et al.   PLANT PHYSIOLOGY

Regulation of ethylene biosynthesis at the level of 1-aminocyclopropane-1-carboxylate oxidase (ACO) gene

(2012) Izabela Ruduś et al.   ACTA PHYSIOLOGIAE PLANTARUM

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

A fungal elicitor enhances the resistance of tomato fruit to Fusarium oxysporum infection by activating the phenylpropanoid metabolic pathway

(2012) Rosalba Troncoso-Rojas et al.   PHYTOPARASITICA

CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

(2011) Carsten Kuhl et al.   ANALYTICAL CHEMISTRY

Virus-induced gene silencing in detached tomatoes and biochemical effects of phytoene desaturase gene silencing

(2011) Irene Romero et al.   JOURNAL OF PLANT PHYSIOLOGY

GLYCOALKALOID METABOLISM1 Is Required for Steroidal Alkaloid Glycosylation and Prevention of Phytotoxicity in Tomato

(2011) M. Itkin et al.   PLANT CELL

Genetic perspectives on crop domestication

(2010) Briana L. Gross et al.   TRENDS IN PLANT SCIENCE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

C22 Isomerization in α-Tomatine-to-Esculeoside A Conversion during Tomato Ripening Is Driven by C27 Hydroxylation of Triterpenoidal Skeleton

(2009) Takao Yamanaka et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Detection and interpretation of expression quantitative trait loci (eQTL)

(2009) Jacob J. Michaelson et al.   METHODS

Ripening-Regulated Susceptibility of Tomato Fruit to Botrytis cinerea Requires NOR But Not RIN or Ethylene

(2009) D. Cantu et al.   PLANT PHYSIOLOGY

Biochemical and Molecular Analysis of Pink Tomatoes: Deregulated Expression of the Gene Encoding Transcription Factor SlMYB12 Leads to Pink Tomato Fruit Color

(2009) A.-R. Ballester et al.   PLANT PHYSIOLOGY

A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation

(2009) D. Orzaez et al.   PLANT PHYSIOLOGY

Fruit-Surface Flavonoid Accumulation in Tomato Is Controlled by a SlMYB12-Regulated Transcriptional Network

(2009) Avital Adato et al.   PLoS Genetics

Integrated Analysis of Transcript, Protein and Metabolite Data To Study Lignin Biosynthesis in Hybrid Aspen

(2008) Max Bylesjö et al.   JOURNAL OF PROTEOME RESEARCH

Metabolite annotations based on the integration of mass spectral information

(2008) Yoko Iijima et al.   PLANT JOURNAL

Gene Expression and Metabolism in Tomato Fruit Surface Tissues

(2008) S. Mintz-Oron et al.   PLANT PHYSIOLOGY