A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Proteomic Analysis of the Soybean Symbiosome Identifies New Symbiotic Proteins

(2015) Victoria C. Clarke et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Phosphoproteomics of the Ataxia Telangiectasia-Mutated (ATM) and Ataxia Telangiectasia-Mutated and Rad3-related (ATR) Dependent DNA Damage Response inArabidopsis thaliana

(2015) Elisabeth Roitinger et al.   MOLECULAR & CELLULAR PROTEOMICS

Transcriptomic Analysis ofSinorhizobium melilotiandMedicago truncatulaSymbiosis Using Nitrogen Fixation–Deficient Nodules

(2015) Claus Lang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Primary transcripts of microRNAs encode regulatory peptides

(2015) Dominique Lauressergues et al.   NATURE

Ubiquitin-Mediated Proteasomal Degradation of Oleosins is Involved in Oil Body Mobilization During Post-Germinative Seedling Growth in Arabidopsis

(2015) Carine Deruyffelaere et al.   PLANT AND CELL PHYSIOLOGY

Phosphorylation of Leghemoglobin at S45 is Most Effective to Disrupt the Molecular Environment of Its Oxygen Binding Pocket

(2015) Kaushik Bhar et al.   PROTEIN JOURNAL

Identification of nodule-specific cysteine-rich plant peptides in endosymbiotic bacteria

(2015) Hajnalka Durgo et al.   PROTEOMICS

Pentatricopeptide Repeat Proteins in Plants

(2014) Alice Barkan et al.   Annual Review of Plant Biology

An improved genome release (version Mt4.0) for the model legume Medicago truncatula

(2014) Haibao Tang et al.   BMC GENOMICS

Fate map of Medicago truncatula root nodules

(2014) T. T. Xiao et al.   DEVELOPMENT

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs

(2014) K. J. van Wijk et al.   PLANT CELL

Medicago truncatula symbiotic peptide NCR247 contributes to bacteroid differentiation through multiple mechanisms

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

Host plant peptides elicit a transcriptional response to control theSinorhizobium meliloticell cycle during symbiosis

(2014) Jon Penterman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

Novel Parallelized Quadrupole/Linear Ion Trap/Orbitrap Tribrid Mass Spectrometer Improving Proteome Coverage and Peptide Identification Rates

(2013) Michael W. Senko et al.   ANALYTICAL CHEMISTRY

Transport and Metabolism in Legume-Rhizobia Symbioses

(2013) Michael Udvardi et al.   Annual Review of Plant Biology

Antimicrobial Nodule-Specific Cysteine-Rich Peptides Induce Membrane Depolarization-Associated Changes in the Transcriptome of Sinorhizobium meliloti

(2013) Hilda Tiricz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MScDB: A Mass Spectrometry-centric Protein Sequence Database for Proteomics

(2013) Harald Marx et al.   JOURNAL OF PROTEOME RESEARCH

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Regulatory Patterns of a Large Family of Defensin-Like Genes Expressed in Nodules of Medicago truncatula

(2013) Sumitha Nallu et al.   PLoS One

Cell- and Tissue-Specific Transcriptome Analyses of Medicago truncatula Root Nodules

(2013) Erik Limpens et al.   PLoS One

Reconstruction of protein networks from an atlas of maize seed proteotypes

(2013) J. W. Walley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

(2013) Sushmita Roy et al.   PLoS Computational Biology

A Proteogenomic Survey of theMedicago truncatulaGenome

(2012) Jeremy D. Volkening et al.   MOLECULAR & CELLULAR PROTEOMICS

Rapid Phosphoproteomic and Transcriptomic Changes in the Rhizobia-legume Symbiosis

(2012) Christopher M. Rose et al.   MOLECULAR & CELLULAR PROTEOMICS

EDS1 Contributes to Nonhost Resistance of Arabidopsis thaliana Against Erwinia amylovora

(2012) Manon Moreau et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

The Rules of Engagement in the Legume-Rhizobial Symbiosis

(2011) Giles E.D. Oldroyd et al.   Annual Review of Genetics

Identification and characterization of plant Haspin kinase as a histone H3 threonine kinase

(2011) Daisuke Kurihara et al.   BMC PLANT BIOLOGY

Cysteine-Rich Peptides (CRPs) mediate diverse aspects of cell-cell communication in plant reproduction and development

(2011) E. Marshall et al.   JOURNAL OF EXPERIMENTAL BOTANY

Large-Scale Label-Free Quantitative Proteomics of the Pea aphid-BuchneraSymbiosis

(2011) Anton Poliakov et al.   MOLECULAR & CELLULAR PROTEOMICS

Dynamo maker ready to roll

(2011) Susan Young   NATURE

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA

(2011) Craig D. Wenger et al.   PROTEOMICS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants

(2010) H. Nakagami et al.   PLANT PHYSIOLOGY

Differentiation of Symbiotic Cells and Endosymbionts in Medicago truncatula Nodulation Are Coupled to Two Transcriptome-Switches

(2010) Nicolas Maunoury et al.   PLoS One

The Medicago truncatula gene expression atlas web server

(2009) Ji He et al.   BMC BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Large-Scale Phosphoprotein Analysis in Medicago truncatula Roots Provides Insight into in Vivo Kinase Activity in Legumes

(2009) P. A. Grimsrud et al.   PLANT PHYSIOLOGY

Molecular Determinants of a Symbiotic Chronic Infection

(2008) Katherine E. Gibson et al.   Annual Review of Genetics

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

A gene expression atlas of the model legumeMedicago truncatula

(2008) Vagner A. Benedito et al.   PLANT JOURNAL

Blue light-induced autophosphorylation of phototropin is a primary step for signaling

(2008) S.-i. Inoue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA