Mass-spectrometry-based draft of the Arabidopsis proteome

Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS

(2020) Yangyang Bian et al.   Nature Communications

Complex‐centric proteome profiling by SEC‐SWATH‐MS

(2019) Moritz Heusel et al.   Molecular Systems Biology

The global mass and average rate of rubisco

(2019) Yinon M. Bar-On et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters

(2019) Sanjukta Das et al.   PLoS One

Quantification and discovery of sequence determinants of protein‐per‐mRNA amount in 29 human tissues

(2019) Basak Eraslan et al.   Molecular Systems Biology

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life

(2019) Daniel Gebert et al.   Open Biology

Seed stored mRNAs that are specifically associated to monosome are translationally regulated during germination

(2019) Bing Bai et al.   PLANT PHYSIOLOGY

Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function

(2018) Jie Luo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling

(2017) Zachary McBride et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative analysis of protein interaction network dynamics in yeast

(2017) Albi Celaj et al.   Molecular Systems Biology

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ProteomicsDB

(2017) Tobias Schmidt et al.   NUCLEIC ACIDS RESEARCH

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

Combinatorial interaction network of abscisic acid receptors and coreceptors fromArabidopsis thaliana

(2017) Stefanie V. Tischer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

(2016) Yi Zheng et al.   Molecular Plant

Transcriptomics resources of human tissues and organs

(2016) M. Uhlen et al.   Molecular Systems Biology

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

(2016) Stefka Tyanova et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

KeyPathwayMinerWeb: online multi-omics network enrichment

(2016) Markus List et al.   NUCLEIC ACIDS RESEARCH

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

New insights into the interplay between codon bias determinants in plants

(2015) S. Camiolo et al.   DNA RESEARCH

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry

(2015) Holger Franken et al.   Nature Protocols

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

An autophosphorylation site database for leucine-rich repeat receptor-like kinases inArabidopsis thaliana

(2015) Srijeet K. Mitra et al.   PLANT JOURNAL

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

(2015) Adriaan van der Graaf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Planting molecular functions in an ecological context with Arabidopsis thaliana

(2015) Ute Krämer   eLife

Regularization Paths for Generalized Linear Models via Coordinate Descent

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The C2-domain protein QUIRKY and the receptor-like kinase STRUBBELIG localize to plasmodesmata and mediate tissue morphogenesis in Arabidopsis thaliana

(2014) P. Vaddepalli et al.   DEVELOPMENT

Conserved Peptide Fragmentation as a Benchmarking Tool for Mass Spectrometers and a Discriminating Feature for Targeted Proteomics

(2014) Umut H. Toprak et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch

(2014) Alaji Bah et al.   NATURE

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

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

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

(2014) Kirti Sharma et al.   Cell Reports

Different patterns of gene structure divergence following gene duplication in Arabidopsis

(2013) Yupeng Wang et al.   BMC GENOMICS

A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics

(2013) Harald Marx et al.   NATURE BIOTECHNOLOGY

DMSO enhances electrospray response, boosting sensitivity of proteomic experiments

(2013) Hannes Hahne et al.   NATURE METHODS

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

(2012) Juergen Cox et al.   BMC BIOINFORMATICS

Comparative Large Scale Characterization of PlantversusMammal Proteins Reveals Similar and IdiosyncraticN-α-Acetylation Features

(2012) Willy V. Bienvenut et al.   MOLECULAR & CELLULAR PROTEOMICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

(2012) J. Lloyd et al.   PLANT PHYSIOLOGY

Regulation of planar growth by the Arabidopsis AGC protein kinase UNICORN

(2012) B. Enugutti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Egg Cell-Secreted EC1 Triggers Sperm Cell Activation During Double Fertilization

(2012) S. Sprunck et al.   SCIENCE

Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis

(2011) Renu Goel et al.   Molecular BioSystems

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Protocol: A simple phenol-based method for 96-well extraction of high quality RNA from Arabidopsis

(2011) Mathew S Box et al.   Plant Methods

AtPIN: Arabidopsis thaliana Protein Interaction Network

(2010) Marcelo M Brandão et al.   BMC BIOINFORMATICS

The ubiquitin-proteasome system regulates plant hormone signaling

(2010) Aaron Santner et al.   PLANT JOURNAL

A comprehensive analysis of protein phosphatases in rice and Arabidopsis

(2010) Meng Yang et al.   PLANT SYSTEMATICS AND EVOLUTION

sORF finder: a program package to identify small open reading frames with high coding potential

(2009) Kousuke Hanada et al.   BIOINFORMATICS

The polarly localized D6 PROTEIN KINASE is required for efficient auxin transport in Arabidopsis thaliana

(2009) M. Zourelidou et al.   DEVELOPMENT

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

(2009) Pawel Durek et al.   NUCLEIC ACIDS RESEARCH

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

Two Arabidopsis AGC kinases are critical for the polarized growth of pollen tubes

(2009) Yan Zhang et al.   PLANT JOURNAL

Structural Mechanism of Abscisic Acid Binding and Signaling by Dimeric PYR1

(2009) N. Nishimura et al.   SCIENCE

Variations on a theme: Changes in the floral ABCs in angiosperms

(2009) Anneke S. Rijpkema et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The ABC model and the diversification of floral organ identity

(2009) Amy Litt et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Weak functional constraints on phosphoproteomes

(2009) Christian R. Landry et al.   TRENDS IN GENETICS

DETORQUEO, QUIRKY, and ZERZAUST Represent Novel Components Involved in Organ Development Mediated by the Receptor-Like Kinase STRUBBELIG in Arabidopsis thaliana

(2009) Lynette Fulton et al.   PLoS Genetics

Nuclear localization of the mutant protein phosphatase abi1 is required for insensitivity towards ABA responses in Arabidopsis

(2008) Danièle Moes et al.   PLANT JOURNAL

The Enigmatic LEA Proteins and Other Hydrophilins

(2008) M. Battaglia et al.   PLANT PHYSIOLOGY

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE