Plant Protein Interactomes

Automatic selection of reference taxa for protein–protein interaction prediction with phylogenetic profiling

(2012) Martin Simonsen et al.   BIOINFORMATICS

Integrative systems biology: an attempt to describe a simple weed

(2012) Louisa M Liberman et al.   CURRENT OPINION IN PLANT BIOLOGY

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

(2012) Jonathan D. Ellis et al.   MOLECULAR CELL

Effector-Triggered Immunity Signaling: From Gene-for-Gene Pathways to Protein-Protein Interaction Networks

(2012) Walter Gassmann et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

(2012) Sandra Orchard et al.   NATURE METHODS

CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations

(2012) Stefanie De Bodt et al.   NEW PHYTOLOGIST

Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development

(2012) C. Smaczniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IDDI: integrated domain-domain interaction and protein interaction analysis system

(2012) Yul Kim et al.   Proteome Science

Interactome mapping for analysis of complex phenotypes: Insights from benchmarking binary interaction assays

(2012) Pascal Braun   PROTEOMICS

History of protein-protein interactions: From egg-white to complex networks

(2012) Pascal Braun et al.   PROTEOMICS

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

(2012) Alexey I. Nesvizhskii   PROTEOMICS

Uncovering Arabidopsis Membrane Protein Interactome Enriched in Transporters Using Mating-Based Split Ubiquitin Assays and Classification Models

(2012) Jin Chen et al.   Frontiers in Plant Science

Prediction of protein–protein interactions between Ralstonia solanacearum and Arabidopsis thaliana

(2011) Zhi-Gang Li et al.   AMINO ACIDS

PRIN: a predicted rice interactome network

(2011) Haibin Gu et al.   BMC BIOINFORMATICS

Construction of high quality Gateway™ entry libraries and their application to yeast two-hybrid for the monocot model plant Brachypodium distachyon

(2011) Shuanghe Cao et al.   BMC BIOTECHNOLOGY

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Split-protein systems: beyond binary protein–protein interactions

(2011) Sujan S Shekhawat et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

The 14-3-3 Isoforms Chi and Epsilon Differentially Bind Client Proteins from DevelopingArabidopsisSeed

(2011) Kirby N. Swatek et al.   JOURNAL OF PROTEOME RESEARCH

Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction Data Sets

(2011) Xueping Yu et al.   MOLECULAR & CELLULAR PROTEOMICS

Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis

(2011) K. Klopffleisch et al.   Molecular Systems Biology

Next-generation sequencing to generate interactome datasets

(2011) Haiyuan Yu et al.   NATURE METHODS

PDBe: Protein Data Bank in Europe

(2011) S. Velankar et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

The Predicted Arabidopsis Interactome Resource and Network Topology-Based Systems Biology Analyses

(2011) M. Lin et al.   PLANT CELL

TheArabidopsisLeucine-Rich Repeat Receptor–Like Kinases BAK1/SERK3 and BKK1/SERK4 Are Required for Innate Immunity to Hemibiotrophic and Biotrophic Pathogens

(2011) Milena Roux et al.   PLANT CELL

Identification of kinase substrates by bimolecular complementation assays

(2011) Stefan Pusch et al.   PLANT JOURNAL

The TOPLESS Interactome: A Framework for Gene Repression in Arabidopsis

(2011) B. Causier et al.   PLANT PHYSIOLOGY

Large-Scale Protein-Protein Interaction Analysis in Arabidopsis Mesophyll Protoplasts by Split Firefly Luciferase Complementation

(2011) Jian-Feng Li et al.   PLoS One

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

(2011) M. S. Mukhtar et al.   SCIENCE

A kaleidoscopic view of the Arabidopsis core cell cycle interactome

(2011) Jelle Van Leene et al.   TRENDS IN PLANT SCIENCE

Towards Establishment of a Rice Stress Response Interactome

(2011) Young-Su Seo et al.   PLoS Genetics

Protein–Protein Interaction Network and Subcellular Localization of the Arabidopsis Thaliana ESCRT Machinery

(2011) Lynn G. L. Richardson et al.   Frontiers in Plant Science

Computational Identification of Protein-Protein Interactions in Rice Based on the Predicted Rice Interactome Network

(2011) Pengcheng Zhu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

AtPIN: Arabidopsis thaliana Protein Interaction Network

(2010) Marcelo M Brandão et al.   BMC BIOINFORMATICS

Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana

(2010) Feng Xu et al.   BMC GENOMICS

Large scale interaction analysis predicts that the Gerbera hybrida floral E function is provided both by general and specialized proteins

(2010) Satu Ruokolainen et al.   BMC PLANT BIOLOGY

Large-scale protein interactome mapping: strategies and opportunities

(2010) Sam Lievens et al.   Expert Review of Proteomics

Global approaches to study protein–protein interactions among viruses and hosts

(2010) Jorge Mendez-Rios et al.   Future Microbiology

Affinity Purification of theArabidopsis26 S Proteasome Reveals a Diverse Array of Plant Proteolytic Complexes

(2010) Adam J. Book et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Interactions among Proteins of Floral MADS-Box Genes in Basal Eudicots: Implications for Evolution of the Regulatory Network for Flower Development

(2010) C. Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

(2010) Jelle Van Leene et al.   Molecular Systems Biology

NINJA connects the co-repressor TOPLESS to jasmonate signalling

(2010) Laurens Pauwels et al.   NATURE

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

Exhaustive benchmarking of the yeast two-hybrid system

(2010) Yu-Chi Chen et al.   NATURE METHODS

AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis

(2010) P. Li et al.   NUCLEIC ACIDS RESEARCH

PAIR: the predicted Arabidopsis interactome resource

(2010) Mingzhi Lin et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Mapping Plant Interactomes Using Literature Curated and Predicted Protein–Protein Interaction Data Sets

(2010) KiYoung Lee et al.   PLANT CELL

Identification and Characterization of Nuclear Pore Complex Components inArabidopsis thaliana

(2010) Kentaro Tamura et al.   PLANT CELL

Functional Modules in theArabidopsisCore Cell Cycle Binary Protein–Protein Interaction Network

(2010) Joanna Boruc et al.   PLANT CELL

Arabidopsis and the plant immune system

(2010) Marc T. Nishimura et al.   PLANT JOURNAL

Deciphering the Arabidopsis Floral Transition Process by Integrating a Protein-Protein Interaction Network and Gene Expression Data

(2010) F. He et al.   PLANT PHYSIOLOGY

Blind predictions of protein interfaces by docking calculations in CAPRI

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2

(2010) Sylvie Lalonde   Frontiers in Physiology

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

(2009) Stefanie De Bodt et al.   BMC GENOMICS

A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

(2009) Christian A. Grove et al.   CELL

Yeast Two-Hybrid, a Powerful Tool for Systems Biology

(2009) Anna Brückner et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

New GATEWAY vectors for High Throughput Analyses of Protein–Protein Interactions by Bimolecular Fluorescence Complementation

(2009) Christian Gehl et al.   Molecular Plant

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

Transient expression inNicotiana benthamianafluorescent marker lines provides enhanced definition of protein localization, movement and interactionsin planta

(2009) Kathleen Martin et al.   PLANT JOURNAL

VirtualPlant: A Software Platform to Support Systems Biology Research

(2009) M. S. Katari et al.   PLANT PHYSIOLOGY

Protein-Protein Interactions of Tandem Affinity Purified Protein Kinases from Rice

(2009) Jai S. Rohila et al.   PLoS One

Proteomic profiling of tandem affinity purified 14-3-3 protein complexes inArabidopsis thaliana

(2009) Ing-Feng Chang et al.   PROTEOMICS

Bimolecular Fluorescence Complementation (BiFC) Analysis as a Probe of Protein Interactions in Living Cells

(2008) Tom K. Kerppola   Annual Review of Biophysics

Precision and recall estimates for two-hybrid screens

(2008) Hailiang Huang et al.   BIOINFORMATICS

The FF domains of yeast U1 snRNP protein Prp40 mediate interactions with Luc7 and Snu71

(2008) Claudia Ester et al.   BMC BIOCHEMISTRY

Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service

(2008) Jeong-Gu Kim et al.   BMC BIOINFORMATICS

Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling

(2008) Arthur G Hunt et al.   BMC GENOMICS

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

(2008) Mike Boxem et al.   CELL

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays

(2008) S. C. Popescu et al.   GENES & DEVELOPMENT

Interaction study of MADS-domain proteins in tomato

(2008) Charles H. Leseberg et al.   JOURNAL OF EXPERIMENTAL BOTANY

Localizing protein–protein interactions by bimolecular fluorescence complementation in planta

(2008) Vitaly Citovsky et al.   METHODS

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

Literature-curated protein interaction datasets

(2008) Michael E Cusick et al.   NATURE METHODS

Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology

(2008) N. Tsesmetzis et al.   PLANT CELL

Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexesin planta

(2008) Rainer Waadt et al.   PLANT JOURNAL

Vectors for multi-color bimolecular fluorescence complementation to investigate protein-protein interactions in living plant cells

(2008) Lan-Ying Lee et al.   Plant Methods

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

BIOCHEMISTRY: Not Comparable, But Complementary

(2008) L. J. Jensen et al.   SCIENCE

Charting plant interactomes: possibilities and challenges

(2008) Mustafa Morsy et al.   TRENDS IN PLANT SCIENCE

Boosting tandem affinity purification of plant protein complexes

(2008) Jelle Van Leene et al.   TRENDS IN PLANT SCIENCE

Study and selection of in vivo protein interactions by coupling bimolecular fluorescence complementation and flow cytometry

(2007) Montse Morell et al.   Nature Protocols