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Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/s00438-002-0746-6openalex-snapshot
Ovule-specific MADS-box proteins have conserved protein-protein interactions in monocot and dicot plants
inferredcites →https://doi.org/10.1016/j.biosystems.2010.04.006openalex-snapshot
Comparative protein analysis of the chitin metabolic pathway in extant organisms: A complex network approach
inferredcites →https://doi.org/10.1016/j.copbio.2016.04.007openalex-snapshot
Network-based approaches for analysis of complex biological systems
inferredcites →https://doi.org/10.1038/cr.2008.16openalex-snapshot
Understanding biological functions through molecular networks
inferredcites →https://doi.org/10.1038/nature01741openalex-snapshot
Assessing the redundancy of MADS-box genes during carpel and ovule development
inferredcites →https://doi.org/10.1038/nmeth.2109openalex-snapshot
jModelTest 2: more models, new heuristics and parallel computing
inferredcites →https://doi.org/10.1038/nrg1272openalex-snapshot
Network biology: understanding the cell's functional organization
inferredcites →https://doi.org/10.1046/j.1365-313x.1998.00250.xopenalex-snapshot
Characterization of an AGAMOUS homologue from the conifer black spruce (Picea mariana) that produces floral homeotic conversions when expressed in Arabidopsis
inferredcites →https://doi.org/10.1046/j.1365-313x.2003.01983.xopenalex-snapshot
Conservation of class C function of floral organ development during 300 million years of evolution from gymnosperms to angiosperms
inferredcites →https://doi.org/10.1073/pnas.0404206101openalex-snapshot
Prospects for inferring very large phylogenies by using the neighbor-joining method
inferredcites →https://doi.org/10.1073/pnas.0608218104openalex-snapshot
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
inferredcites →https://doi.org/10.1073/pnas.0610699104openalex-snapshot
Pattern pluralism and the Tree of Life hypothesis
inferredcites →https://doi.org/10.1073/pnas.96.7.3801openalex-snapshot
Horizontal gene transfer among genomes: The complexity hypothesis
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/10.1088/1742-5468/2008/10/p10008openalex-snapshot
Fast unfolding of communities in large networks
inferredcites →https://doi.org/10.1093/bib/bbr040openalex-snapshot
Positional orthology: putting genomic evolutionary relationships into context
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/gbe/evs009openalex-snapshot
Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses
inferredcites →https://doi.org/10.1093/gbe/evt168openalex-snapshot
Parallel Recruitment of Multiple Genes into C4 Photosynthesis
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/icb/icw087openalex-snapshot
Can a Network Approach Resolve How Adaptive vs Nonadaptive Plasticity Impacts Evolutionary Trajectories?
inferredcites →https://doi.org/10.1093/jxb/erq046openalex-snapshot
Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development
inferredcites →https://doi.org/10.1093/molbev/mst197openalex-snapshot
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
inferredcites →https://doi.org/10.1093/molbev/msv191openalex-snapshot
Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize
inferredcites →https://doi.org/10.1093/molbev/msw054openalex-snapshot
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
inferredcites →https://doi.org/10.1093/nar/gkq313openalex-snapshot
A new bioinformatics analysis tools framework at EMBL-EBI
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040023openalex-snapshot
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040205openalex-snapshot
Interior-branch and bootstrap tests of phylogenetic trees.
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1101/gr.8.12.1233openalex-snapshot
Models of Molecular Evolution and Phylogeny: Table 1.
inferredcites →https://doi.org/10.1103/physreve.73.046101openalex-snapshot
Neighborhood properties of complex networks
inferredcites →https://doi.org/10.1104/pp.108.129619openalex-snapshot
Translational Biology: From Arabidopsis Flowers to Grass Inflorescence Architecture
inferredcites →https://doi.org/10.1105/tpc.010082openalex-snapshot
Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops–Triticum) Group
inferredcites →https://doi.org/10.1105/tpc.1.1.37openalex-snapshot
Genes Directing Flower Development in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.105.037200openalex-snapshot
Functional Diversification of the Two C-Class MADS Box GenesOSMADS3andOSMADS58inOryza sativa
inferredcites →https://doi.org/10.1105/tpc.110.081281openalex-snapshot
Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints
inferredcites →https://doi.org/10.1105/tpc.13.8.1735openalex-snapshot
Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops-Triticum) Group
inferredcites →https://doi.org/10.1111/j.1096-0031.1994.tb00179.xopenalex-snapshot
BRANCH SUPPORT AND TREE STABILITY
inferredcites →https://doi.org/10.1111/j.1365-313x.2005.02487.xopenalex-snapshot
Expression of floral MADS‐box genes in basal angiosperms: implications for the evolution of floral regulators
inferredcites →https://doi.org/10.1111/j.1365-313x.2007.03272.xopenalex-snapshot
The D‐lineage MADS‐box gene OsMADS13 controls ovule identity in rice
inferredcites →https://doi.org/10.1111/j.1365-313x.2012.05005.xopenalex-snapshot
Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution
inferredcites →https://doi.org/10.1111/j.1469-8137.2011.03972.xopenalex-snapshot
New grass phylogeny resolves deep evolutionary relationships and discovers C 4 origins
inferredcites →https://doi.org/10.1111/nph.12555openalex-snapshot
MADS reloaded: evolution of the AGAMOUS subfamily genes
inferredcites →https://doi.org/10.1111/tpj.12089openalex-snapshot
Gene family evolution in green plants with emphasis on the origination and evolution of A rabidopsis thaliana genes
inferredcites →https://doi.org/10.1126/science.274.5292.1537openalex-snapshot
Diversification of C-Function Activity in Maize Flower Development
inferredcites →https://doi.org/10.1126/science.278.5338.631openalex-snapshot
A Genomic Perspective on Protein Families
inferredcites →https://doi.org/10.1142/s0218127409024396openalex-snapshot
IDENTIFICATION OF COMMUNITY STRUCTURE IN NETWORKS USING HIGHER ORDER NEIGHBORHOOD CONCEPTS
inferredcites →https://doi.org/10.1146/annurev.genet.39.073003.114725openalex-snapshot
Orthologs, Paralogs, and Evolutionary Genomics
inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot
WGCNA: an R package for weighted correlation network analysis
inferredcites →https://doi.org/10.1186/s12862-015-0418-xopenalex-snapshot
Characterization of an AGAMOUS gene expressed throughout development of the fleshy fruit-like structure produced by Ginkgo biloba around its seeds
inferredcites →https://doi.org/10.1242/dev.112.1.1openalex-snapshot
Genetic interactions among floral homeotic genes of Arabidopsis
inferredcites →https://doi.org/10.1371/journal.pcbi.1001131openalex-snapshot
Detecting Network Communities: An Application to Phylogenetic Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0118731openalex-snapshot
Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0134988openalex-snapshot
What are the Evolutionary Origins of Mitochondria? A Complex Network Approach
inferredcites →https://doi.org/10.1609/icwsm.v3i1.13937openalex-snapshot
Gephi: An Open Source Software for Exploring and Manipulating Networks
inferredcites →https://doi.org/10.3389/fpls.2014.00300openalex-snapshot
Evolution of fruit development genes in flowering plants
inferredcites →https://doi.org/10.48550/arxiv.0812.1770openalex-snapshot
Laplacian Dynamics and Multiscale Modular Structure in Networks
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.7287/peerj.14571v0.1/reviews/1openalex-snapshot
Peer Review #1 of "On the origin of mitochondria: a multilayer network approach (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.14571v0.1/reviews/2openalex-snapshot
Peer Review #2 of "On the origin of mitochondria: a multilayer network approach (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.14571v0.1/reviews/3openalex-snapshot
Peer Review #3 of "On the origin of mitochondria: a multilayer network approach (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.14571v0.2/reviews/3openalex-snapshot
Peer Review #3 of "On the origin of mitochondria: a multilayer network approach (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.14571v0.3/reviews/3openalex-snapshot
Peer Review #3 of "On the origin of mitochondria: a multilayer network approach (v0.3)"
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