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Resurrected protein interaction networks reveal the innovation potential of ancient whole genome duplication
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/meet.14504201249openalex-snapshot
The angiosperm phylogeny Website ‐ a tool for reference and teaching in a time of change
inferredcites →https://doi.org/10.1002/pmic.200300636openalex-snapshot
Functional and topological characterization of protein interaction networks
inferredcites →https://doi.org/10.1002/pmic.200500228openalex-snapshot
Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large‐scale organization and robustness
inferredcites →https://doi.org/10.1002/pro.580openalex-snapshot
A structure‐based benchmark for protein–protein binding affinity
inferredcites →https://doi.org/10.1007/0-387-33916-7openalex-snapshot
Power Laws, Scale-Free Networks and Genome Biology
inferredcites →https://doi.org/10.1007/978-0-387-84796-2_11openalex-snapshot
Combinatorial Action of Petunia MADS Box Genes and Their Protein Products
inferredcites →https://doi.org/10.1007/978-3-642-86659-3openalex-snapshot
Evolution by Gene Duplication
inferredcites →https://doi.org/10.1007/s10577-009-9055-9openalex-snapshot
Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes
inferredcites →https://doi.org/10.1007/s11103-004-0416-7openalex-snapshot
Defining subdomains of the K domain important for protein?protein interactions of plant MADS proteins
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Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence
inferredcites →https://doi.org/10.1016/j.bpj.2010.12.378openalex-snapshot
Nonspecific Binding Limits the Number of Proteins in a Cell and Shapes their Interaction Networks
inferredcites →https://doi.org/10.1016/j.cell.2014.09.003openalex-snapshot
Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module
inferredcites →https://doi.org/10.1016/j.cub.2005.04.035openalex-snapshot
Gene Complexity and Gene Duplicability
inferredcites →https://doi.org/10.1016/j.devcel.2008.05.002openalex-snapshot
A Repressor Complex Governs the Integration of Flowering Signals in Arabidopsis
inferredcites →https://doi.org/10.1016/j.devcel.2009.03.011openalex-snapshot
Regulation of Floral Patterning by Flowering Time Genes
inferredcites →https://doi.org/10.1016/j.devcel.2013.02.013openalex-snapshot
A Conserved Genetic Pathway Determines Inflorescence Architecture in Arabidopsis and Rice
inferredcites →https://doi.org/10.1016/j.gene.2004.12.014openalex-snapshot
MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants
inferredcites →https://doi.org/10.1016/j.jgg.2012.02.008openalex-snapshot
Gene Duplication and the Evolution of Plant MADS-box Transcription Factors
inferredcites →https://doi.org/10.1016/j.pbi.2005.01.001openalex-snapshot
Polyploidy and genome evolution in plants
inferredcites →https://doi.org/10.1016/j.pbi.2011.09.002openalex-snapshot
The end of innocence: flowering networks explode in complexity
inferredcites →https://doi.org/10.1016/j.pbi.2012.01.003openalex-snapshot
Redundancy and rewiring of genetic networks following genome-wide duplication events
inferredcites →https://doi.org/10.1016/j.pbi.2012.01.015openalex-snapshot
Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants
inferredcites →https://doi.org/10.1016/j.pbi.2012.03.011openalex-snapshot
Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model
inferredcites →https://doi.org/10.1016/j.pbi.2015.12.004openalex-snapshot
Molecular mechanisms of floral organ specification by MADS domain proteins
inferredcites →https://doi.org/10.1016/j.pbi.2016.03.015openalex-snapshot
Ancient WGD events as drivers of key innovations in angiosperms
inferredcites →https://doi.org/10.1016/j.semcdb.2009.10.004openalex-snapshot
The ‘ABC’ of MADS domain protein behaviour and interactions
inferredcites →https://doi.org/10.1016/j.semcdb.2009.10.005openalex-snapshot
Floral organ identity: 20 years of ABCs
inferredcites →https://doi.org/10.1016/j.tibs.2015.03.011openalex-snapshot
Gene dosage imbalances: action, reaction, and models
inferredcites →https://doi.org/10.1016/j.tree.2005.07.008openalex-snapshot
Genome duplication and the origin of angiosperms
inferredcites →https://doi.org/10.1016/s0022-5193(03)00028-6openalex-snapshot
Evolving protein interaction networks through gene duplication
inferredcites →https://doi.org/10.1038/150563a0openalex-snapshot
CANALIZATION OF DEVELOPMENT AND THE INHERITANCE OF ACQUIRED CHARACTERS
inferredcites →https://doi.org/10.1038/30918openalex-snapshot
Collective dynamics of ‘small-world’ networks
inferredcites →https://doi.org/10.1038/35054083openalex-snapshot
Complexes of MADS-box proteins are sufficient to convert leaves into floral organs
inferredcites →https://doi.org/10.1038/msb.2008.48openalex-snapshot
Constraints imposed by non‐functional protein–protein interactions on gene expression and proteome size
inferredcites →https://doi.org/10.1038/nature01521openalex-snapshot
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
inferredcites →https://doi.org/10.1038/nature02178openalex-snapshot
Optimization of specificity in a cellular protein interaction network by negative selection
inferredcites →https://doi.org/10.1038/nature03239openalex-snapshot
Interaction network containing conserved and essential protein complexes in Escherichia coli
inferredcites →https://doi.org/10.1038/nature06148openalex-snapshot
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
inferredcites →https://doi.org/10.1038/nature09916openalex-snapshot
Ancestral polyploidy in seed plants and angiosperms
inferredcites →https://doi.org/10.1038/nature11119openalex-snapshot
The tomato genome sequence provides insights into fleshy fruit evolution
inferredcites →https://doi.org/10.1038/ncomms3280openalex-snapshot
FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes
inferredcites →https://doi.org/10.1038/ng1286openalex-snapshot
Repression of AGAMOUS-LIKE 24 is a crucial step in promoting flower development
inferredcites →https://doi.org/10.1038/ng1530openalex-snapshot
Modularity and evolutionary constraint on proteins
inferredcites →https://doi.org/10.1038/nmeth0910-667openalex-snapshot
Exhaustive benchmarking of the yeast two-hybrid system
inferredcites →https://doi.org/10.1038/nrg1272openalex-snapshot
Network biology: understanding the cell's functional organization
inferredcites →https://doi.org/10.1038/sj.embor.7400090openalex-snapshot
The yeast coexpression network has a small‐world, scale‐free architecture and can be explained by a simple model
inferredcites →https://doi.org/10.1038/srep02920openalex-snapshot
Uncovering the role of elementary processes in network evolution
inferredcites →https://doi.org/10.1038/srep07187openalex-snapshot
Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar
inferredcites →https://doi.org/10.1038/srep44948openalex-snapshot
Protein interaction evolution from promiscuity to specificity with reduced flexibility in an increasingly complex network
inferredcites →https://doi.org/10.1046/j.1365-313x.1997.12050999.xopenalex-snapshot
Specific interactions between the K domains of AG and AGLs, members of the MADS domain family of DNA binding proteins
inferredcites →https://doi.org/10.1073/pnas.0711043105openalex-snapshot
Preferential protection of protein interaction network hubs in yeast: Evolved functionality of genetic redundancy
inferredcites →https://doi.org/10.1073/pnas.1009392108openalex-snapshot
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions
inferredcites →https://doi.org/10.1073/pnas.1209312109openalex-snapshot
Cellular crowding imposes global constraints on the chemistry and evolution of proteomes
inferredcites →https://doi.org/10.1080/10635150390235520openalex-snapshot
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
inferredcites →https://doi.org/10.1080/10635150802429642openalex-snapshot
A Rapid Bootstrap Algorithm for the RAxML Web Servers
inferredcites →https://doi.org/10.1086/509662openalex-snapshot
An Evaluation of A‐Function: Evidence from theAPETALA1andAPETALA2Gene Lineages
inferredcites →https://doi.org/10.1086/658923openalex-snapshot
Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region
inferredcites →https://doi.org/10.1093/aob/mcv151openalex-snapshot
Molecular mechanisms governing differential robustness of development and environmental responses in plants
inferredcites →https://doi.org/10.1093/aob/mcw018openalex-snapshot
The significance of developmental robustness for species diversity
inferredcites →https://doi.org/10.1093/aob/mcw066openalex-snapshot
Robust views on plasticity and biodiversity
inferredcites →https://doi.org/10.1093/bioinformatics/bti263openalex-snapshot
ProtTest: selection of best-fit models of protein evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btl446openalex-snapshot
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btl683openalex-snapshot
Comparison of human protein–protein interaction maps
inferredcites →https://doi.org/10.1093/bioinformatics/btq675openalex-snapshot
Cytoscape 2.8: new features for data integration and network visualization
inferredcites →https://doi.org/10.1093/bioinformatics/bts199openalex-snapshot
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
inferredcites →https://doi.org/10.1093/genetics/165.2.821openalex-snapshot
Duplication and Diversification in the APETALA1/FRUITFULL Floral Homeotic Gene Lineage: Implications for the Evolution of Floral Development
inferredcites →https://doi.org/10.1093/genetics/166.2.1011openalex-snapshot
Patterns of Gene Duplication and Functional Evolution During the Diversification of the AGAMOUS Subfamily of MADS Box Genes in Angiosperms
inferredcites →https://doi.org/10.1093/hesc/9780199292233.001.0001openalex-snapshot
The Evolution of Plants
inferredcites →https://doi.org/10.1093/jxb/ern094openalex-snapshot
Interaction study of MADS-domain proteins in tomato
inferredcites →https://doi.org/10.1093/jxb/ers233openalex-snapshot
MADS-box Genes and Floral Development: the Dark Side
inferredcites →https://doi.org/10.1093/jxb/ert482openalex-snapshot
Sequential action of FRUITFULL as a modulator of the activity of the floral regulators SVP and SOC1
inferredcites →https://doi.org/10.1093/molbev/msl182openalex-snapshot
Functional Diversification of B MADS-Box Homeotic Regulators of Flower Development: Adaptive Evolution in Protein–Protein Interaction Domains after Major Gene Duplication Events
inferredcites →https://doi.org/10.1093/molbev/msl197openalex-snapshot
Evidence of Interaction Network Evolution by Whole-Genome Duplications: A Case Study in MADS-Box Proteins
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msp129openalex-snapshot
Evolution of Plant MADS Box Transcription Factors: Evidence for Shifts in Selection Associated with Early Angiosperm Diversification and Concerted Gene Duplications
inferredcites →https://doi.org/10.1093/molbev/msp160openalex-snapshot
Metabolic Adaptation after Whole Genome Duplication
inferredcites →https://doi.org/10.1093/molbev/msp181openalex-snapshot
Pistillata—Duplications as a Mode for Floral Diversification in (Basal) Asterids
inferredcites →https://doi.org/10.1093/molbev/msq044openalex-snapshot
Interactions among Proteins of Floral MADS-Box Genes in Basal Eudicots: Implications for Evolution of the Regulatory Network for Flower Development
inferredcites →https://doi.org/10.1093/molbev/mss183openalex-snapshot
Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkr944openalex-snapshot
Phytozome: a comparative platform for green plant genomics
inferredcites →https://doi.org/10.1093/nar/gku986openalex-snapshot
PLAZA 3.0: an access point for plant comparative genomics
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003913openalex-snapshot
The Yeast Protein Interaction Network Evolves Rapidly and Contains Few Redundant Duplicate Genes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025957openalex-snapshot
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
inferredcites →https://doi.org/10.1098/rsif.2013.0771openalex-snapshot
The relationship between modularity and robustness in signalling networks
inferredcites →https://doi.org/10.1098/rspb.2001.1711openalex-snapshot
The small world inside large metabolic networks
inferredcites →https://doi.org/10.1098/rspb.2002.2269openalex-snapshot
How the global structure of protein interaction networks evolves
inferredcites →https://doi.org/10.1098/rspb.2012.2863openalex-snapshot
The evolutionary origins of modularity
inferredcites →https://doi.org/10.1101/gr.080978.108openalex-snapshot
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
inferredcites →https://doi.org/10.1101/gr.205301openalex-snapshot
Identification of Potential Interaction Networks Using Sequence-Based Searches for Conserved Protein-Protein Interactions or “Interologs”
inferredcites →https://doi.org/10.1103/physrevlett.91.138701openalex-snapshot
Preferential Attachment in the Protein Network Evolution
inferredcites →https://doi.org/10.1103/revmodphys.74.47openalex-snapshot
Statistical mechanics of complex networks
inferredcites →https://doi.org/10.1104/pp.112.213447openalex-snapshot
Function Relaxation Followed by Diversifying Selection after Whole-Genome Duplication in Flowering Plants
inferredcites →https://doi.org/10.1105/tpc.105.031831openalex-snapshot
Comprehensive Interaction Map of the Arabidopsis MADS Box Transcription Factors
inferredcites →https://doi.org/10.1105/tpc.11.6.1007openalex-snapshot
Interactions among APETALA1, LEAFY, and TERMINAL FLOWER1 Specify Meristem Fate
inferredcites →https://doi.org/10.1105/tpc.114.127910openalex-snapshot
Structural Basis for the Oligomerization of the MADS Domain Transcription Factor SEPALLATA3 in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.16.00366openalex-snapshot
The Origin of Floral Organ Identity Quartets
inferredcites →https://doi.org/10.1111/j.1365-313x.2009.03985.xopenalex-snapshot
The Arabidopsis floral meristem identity genes AP1, AGL24 and SVP directly repress class B and C floral homeotic genes
inferredcites →https://doi.org/10.1126/science.1073374openalex-snapshot
Hierarchical Organization of Modularity in Metabolic Networks
inferredcites →https://doi.org/10.1126/science.1090289openalex-snapshot
A Protein Interaction Map of Drosophila melanogaster
inferredcites →https://doi.org/10.1126/science.1185244openalex-snapshot
Orchestration of Floral Initiation by APETALA1
inferredcites →https://doi.org/10.1126/science.1203877openalex-snapshot
Evidence for Network Evolution in an Arabidopsis Interactome Map
inferredcites →https://doi.org/10.1126/science.1233465openalex-snapshot
Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution
inferredcites →https://doi.org/10.1126/science.286.5439.509openalex-snapshot
Emergence of Scaling in Random Networks
inferredcites →https://doi.org/10.1126/scisignal.124ec226openalex-snapshot
Mapping the Yeast Protein Interaction Network
inferredcites →https://doi.org/10.1126/scisignal.2003350openalex-snapshot
Cross-Species Protein Interactome Mapping Reveals Species-Specific Wiring of Stress Response Pathways
inferredcites →https://doi.org/10.1155/2014/147648openalex-snapshot
Protein-Protein Interaction Detection: Methods and Analysis
inferredcites →https://doi.org/10.1159/000067642openalex-snapshot
Modeling of Protein Interaction Networks
inferredcites →https://doi.org/10.1186/1471-2148-3-1openalex-snapshot
No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly
inferredcites →https://doi.org/10.1186/1471-2148-6-30openalex-snapshot
A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage
inferredcites →https://doi.org/10.1186/1471-2229-10-129openalex-snapshot
Large scale interaction analysis predicts that the Gerbera hybrida floral E function is provided both by general and specialized proteins
inferredcites →https://doi.org/10.1186/1471-2229-10-148openalex-snapshot
Expression divergence of the AGL6 MADS domain transcription factor lineage after a core eudicot duplication suggests functional diversification
inferredcites →https://doi.org/10.1186/2047-217x-3-17openalex-snapshot
Data access for the 1,000 Plants (1KP) project
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r11openalex-snapshot
Predicting specificity in bZIP coiled-coil protein interactions
inferredcites →https://doi.org/10.1186/gb-2009-10-2-r24openalex-snapshot
SEPALLATA3: the 'glue' for MADS box transcription factor complex formation
inferredcites →https://doi.org/10.1186/gb-2012-13-1-r3openalex-snapshot
A genome triplication associated with early diversification of the core eudicots
inferredcites →https://doi.org/10.1186/s13059-015-0597-1openalex-snapshot
Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis
inferredcites →https://doi.org/10.1186/s13059-016-0908-1openalex-snapshot
Evolution of plant genome architecture
inferredcites →https://doi.org/10.1242/dev.003103openalex-snapshot
Specification of Arabidopsis floral meristem identity by repression of flowering time genes
inferredcites →https://doi.org/10.1242/dev.020255openalex-snapshot
Direct interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis
inferredcites →https://doi.org/10.1242/dev.033076openalex-snapshot
Coming into bloom: the specification of floral meristems
inferredcites →https://doi.org/10.1242/dev.074674openalex-snapshot
Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies
inferredcites →https://doi.org/10.1242/dev.129.1.253openalex-snapshot
SEUSS , a member of a novel family of plant regulatory proteins, represses floral homeotic gene expression with LEUNIG
inferredcites →https://doi.org/10.1242/dev.134080openalex-snapshot
MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution
inferredcites →https://doi.org/10.1371/journal.pbio.0040109openalex-snapshot
Functional Partitioning of Yeast Co-Expression Networks after Genome Duplication
inferredcites →https://doi.org/10.1371/journal.pbio.1000090openalex-snapshot
Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower
inferredcites →https://doi.org/10.1371/journal.pbio.1001446openalex-snapshot
Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication
inferredcites →https://doi.org/10.1371/journal.pcbi.0010026openalex-snapshot
Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions
inferredcites →https://doi.org/10.1371/journal.pcbi.0020088openalex-snapshot
Evolutionary and Physiological Importance of Hub Proteins
inferredcites →https://doi.org/10.1371/journal.pcbi.0030107openalex-snapshot
In Search of the Biological Significance of Modular Structures in Protein Networks
inferredcites →https://doi.org/10.1371/journal.pcbi.1000748openalex-snapshot
Efficient Physical Embedding of Topologically Complex Information Processing Networks in Brains and Computer Circuits
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Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases
inferredcites →https://doi.org/10.1371/journal.pcbi.1004829openalex-snapshot
The Evolutionary Origins of Hierarchy
inferredcites →https://doi.org/10.1371/journal.pgen.1003072openalex-snapshot
Evolution of Minimal Specificity and Promiscuity in Steroid Hormone Receptors
inferredcites →https://doi.org/10.1385/1-59259-958-3:107openalex-snapshot
Yeast Transformation by the LiAc/SS Carrier DNA/PEG Method
inferredcites →https://doi.org/10.1515/9781400841356.38openalex-snapshot
On the evolution of random graphs
inferredcites →https://doi.org/10.1534/genetics.115.182964openalex-snapshot
Evolving Ideas on the Origin and Evolution of Flowers: New Perspectives in the Genomic Era
inferredcites →https://doi.org/10.2174/138920210790218016openalex-snapshot
Plant Protein-Protein Interaction Network and Interactome
inferredcites →https://doi.org/10.2307/4451728openalex-snapshot
Cell Biology Visualizing Cell Processes
inferredcites →https://doi.org/10.25080/tcwv9851openalex-snapshot
Exploring Network Structure, Dynamics, and Function using NetworkX
inferredcites →https://doi.org/10.3732/ajb.0800079openalex-snapshot
Polyploidy and angiosperm diversification
inferredcites →https://doi.org/10.3732/ajb.90.3.461openalex-snapshot
Gunnerales are sister to other core eudicots: implications for the evolution of pentamery
inferredcites →https://doi.org/10.5091/plecevo.2013.738openalex-snapshot
Origin and evolution of petals in angiosperms
inferredcites →https://doi.org/10.5860/choice.39-2183openalex-snapshot
MacClade 4.0: analysis of phylogeny and character evolution
inferredcites →https://doi.org/10.7554/elife.10147openalex-snapshot
Evolution of an ancient protein function involved in organized multicellularity in animals
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/srep44948openalex-snapshot
Protein interaction evolution from promiscuity to specificity with reduced flexibility in an increasingly complex network
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