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Capturing Evolutionary Signatures in Transcriptomes with myTAI
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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/(sici)1521-1878(199907)21:7<604::aid-bies9>3.0.co;2-uopenalex-snapshot
Vertebrate evolution: The developmental origins of adult variation
inferredcites →https://doi.org/10.1002/jez.b.21033openalex-snapshot
In search of the vertebrate phylotypic stage: A molecular examination of the developmental hourglass model and von Baer's third law
inferredcites →https://doi.org/10.1002/jez.b.22618openalex-snapshot
What to compare and how: Comparative transcriptomics for Evo‐Devo
inferredcites →https://doi.org/10.1006/dbio.1995.8041openalex-snapshot
Heterochrony and the Phylotypic Period
inferredcites →https://doi.org/10.1007/978-0-387-98141-3openalex-snapshot
ggplot2: Elegant Graphics for Data Analysis
inferredcites →https://doi.org/10.1007/s004290050082openalex-snapshot
There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development
inferredcites →https://doi.org/10.1007/s12052-012-0424-zopenalex-snapshot
The Body Plan Concept and Its Centrality in Evo-Devo
inferredcites →https://doi.org/10.1007/s12064-012-0149-0openalex-snapshot
The phylotypic stage as a boundary of modular memory: non mechanistic perspective
inferredcites →https://doi.org/10.1016/j.devcel.2011.03.015openalex-snapshot
Mapping Gene Expression in Two Xenopus Species: Evolutionary Constraints and Developmental Flexibility
inferredcites →https://doi.org/10.1016/j.devcel.2012.04.004openalex-snapshot
Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo
inferredcites →https://doi.org/10.1016/j.tig.2007.08.014openalex-snapshot
A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/nature09632openalex-snapshot
A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns
inferredcites →https://doi.org/10.1038/nature09634openalex-snapshot
Gene expression divergence recapitulates the developmental hourglass model
inferredcites →https://doi.org/10.1038/nature11394openalex-snapshot
A transcriptomic hourglass in plant embryogenesis
inferredcites →https://doi.org/10.1038/nature13424openalex-snapshot
Comparative analysis of the transcriptome across distant species
inferredcites →https://doi.org/10.1038/nature16994openalex-snapshot
The mid-developmental transition and the evolution of animal body plans
inferredcites →https://doi.org/10.1038/ncomms1248openalex-snapshot
Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis
inferredcites →https://doi.org/10.1038/ng.2615openalex-snapshot
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
inferredcites →https://doi.org/10.1038/nmeth.3252openalex-snapshot
Orchestrating high-throughput genomic analysis with Bioconductor
inferredcites →https://doi.org/10.1038/nrg3053openalex-snapshot
The evolutionary origin of orphan genes
inferredcites →https://doi.org/10.1038/nrg3229openalex-snapshot
Comparative studies of gene expression and the evolution of gene regulation
inferredcites →https://doi.org/10.1038/nrg3802openalex-snapshot
Evolutionary dynamics of coding and non-coding transcriptomes
inferredcites →https://doi.org/10.1038/nrg3950openalex-snapshot
Determinants of the rate of protein sequence evolution
inferredcites →https://doi.org/10.1073/pnas.1311818110openalex-snapshot
Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/gbe/evt093openalex-snapshot
Evolution of the Correlation between Expression Divergence and Protein Divergence in Mammals
inferredcites →https://doi.org/10.1093/icb/ict068openalex-snapshot
Phylogenetic Analysis of Gene Expression
inferredcites →https://doi.org/10.1093/molbev/mss134openalex-snapshot
Molecular Signatures of the Three Stem Cell Lineages in Hydra and the Emergence of Stem Cell Function at the Base of Multicellularity
inferredcites →https://doi.org/10.1093/molbev/mst007openalex-snapshot
Dictyostelium Development Shows a Novel Pattern of Evolutionary Conservation
inferredcites →https://doi.org/10.1093/molbev/msu286openalex-snapshot
Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution
inferredcites →https://doi.org/10.1093/molbev/msv012openalex-snapshot
Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis
inferredcites →https://doi.org/10.1093/molbev/msv047openalex-snapshot
A “Developmental Hourglass” in Fungi
inferredcites →https://doi.org/10.1093/molbev/msw008openalex-snapshot
Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution
inferredcites →https://doi.org/10.1093/molbev/msw039openalex-snapshot
Post-embryonic Hourglass Patterns Mark Ontogenetic Transitions in Plant Development
inferredcites →https://doi.org/10.1093/molbev/msw044openalex-snapshot
Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes
inferredcites →https://doi.org/10.1093/nar/gkr944openalex-snapshot
Phytozome: a comparative platform for green plant genomics
inferredcites →https://doi.org/10.1101/gr.361602openalex-snapshot
The Bioperl Toolkit: Perl Modules for the Life Sciences
inferredcites →https://doi.org/10.1104/pp.110.171702openalex-snapshot
Genome-Wide Analysis Reveals Gene Expression and Metabolic Network Dynamics during Embryo Development in Arabidopsis
inferredcites →https://doi.org/10.1186/1741-7007-5-1openalex-snapshot
The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information
inferredcites →https://doi.org/10.1186/1741-7007-7-42openalex-snapshot
Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila
inferredcites →https://doi.org/10.1186/1741-7007-8-66openalex-snapshot
Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa
inferredcites →https://doi.org/10.1186/1742-9994-10-18openalex-snapshot
Phylostratigraphic profiles reveal a deep evolutionary history of the vertebrate head sensory systems
inferredcites →https://doi.org/10.1242/dev.107318openalex-snapshot
The developmental hourglass model: a predictor of the basic body plan?
inferredcites →https://doi.org/10.1242/dev.1994.supplement.135openalex-snapshot
Temporal colinearity and the phylotypic progression: a basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony
inferredcites →https://doi.org/10.12688/f1000research.2-191.v1openalex-snapshot
taxize: taxonomic search and retrieval in R
inferredcites →https://doi.org/10.1371/journal.pcbi.1002567openalex-snapshot
ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin
inferredcites →https://doi.org/10.1371/journal.pcbi.1003118openalex-snapshot
Software for Computing and Annotating Genomic Ranges
inferredcites →https://doi.org/10.18637/jss.v040.i08openalex-snapshot
Rcpp : Seamless R and C++ Integration
inferredcites →https://doi.org/10.18637/jss.v064.i04openalex-snapshot
fitdistrplus : An R Package for Fitting Distributions
inferredcites →https://doi.org/10.18637/jss.v064.i07openalex-snapshot
PReMiuM : An R Package for Profile Regression Mixture Models Using Dirichlet Processes
inferredcites →https://doi.org/10.32614/cran.package.dplyropenalex-snapshot
dplyr: A Grammar of Data Manipulation
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.5860/choice.34-1536openalex-snapshot
The shape of life: genes, development, and the evolution of animal form
inferredcites →https://doi.org/10.5962/bhl.title.6303openalex-snapshot
Über Entwickelungsgeschichte der Thiere. Beobachtung und Reflexion
inferredcites →https://doi.org/10.7208/chicago/9780226256573.001.0001openalex-snapshot
The Shape of Life
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s42003-025-08502-0openalex-snapshot
Melanocytes and photosensory organs share a common ancestry that illuminates the origins of the neural crest
inferred← citeshttps://doi.org/10.1038/srep34664openalex-snapshot
High expression of new genes in trochophore enlightening the ontogeny and evolution of trochozoans
inferred← citeshttps://doi.org/10.1093/molbev/msw039openalex-snapshot
Post-embryonic Hourglass Patterns Mark Ontogenetic Transitions in Plant Development
inferred← citeshttps://doi.org/10.1101/gr.227462.117openalex-snapshot
A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing
inferred← citeshttps://doi.org/10.1142/s0219720017500056openalex-snapshot
The origins and evolutionary history of human non-coding RNA regulatory networks
inferred← citeshttps://doi.org/10.32614/cran.package.mytaiopenalex-snapshot
myTAI: Evolutionary Transcriptomics
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