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Increased taxon sampling reveals thousands of hidden orthologs in flatworms
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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/dvg.22872openalex-snapshot
SmedGD 2.0: The Schmidtea mediterranea genome database
inferredcites →https://doi.org/10.1007/978-0-387-98141-3openalex-snapshot
ggplot2: Elegant Graphics for Data Analysis
inferredcites →https://doi.org/10.1007/978-3-642-86659-3openalex-snapshot
Evolution by Gene Duplication
inferredcites →https://doi.org/10.1007/pl00000885openalex-snapshot
Three classes of C2H2 zinc finger proteins
inferredcites →https://doi.org/10.1007/s10709-008-9311-5openalex-snapshot
Preservation of duplicate genes by originalization
inferredcites →https://doi.org/10.1007/s13127-011-0044-4openalex-snapshot
Higher-level metazoan relationships: recent progress and remaining questions
inferredcites →https://doi.org/10.1016/j.cell.2008.01.003openalex-snapshot
Evo-Devo: Variations on Ancestral Themes
inferredcites →https://doi.org/10.1016/j.cub.2003.11.030openalex-snapshot
EST Analysis of the Cnidarian Acropora millepora Reveals Extensive Gene Loss and Rapid Sequence Divergence in the Model Invertebrates
inferredcites →https://doi.org/10.1016/j.cub.2004.05.015openalex-snapshot
Evolutionary Genomics: Yeasts Accelerate beyond BLAST
inferredcites →https://doi.org/10.1016/j.cub.2004.12.010openalex-snapshot
Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica
inferredcites →https://doi.org/10.1016/j.cub.2004.12.071openalex-snapshot
Origin and Neofunctionalization of a Drosophila Paternal Effect Gene Essential for Zygote Viability
inferredcites →https://doi.org/10.1016/j.cub.2015.03.034openalex-snapshot
A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms
inferredcites →https://doi.org/10.1016/j.cub.2015.06.068openalex-snapshot
Spiralian Phylogeny Informs the Evolution of Microscopic Lineages
inferredcites →https://doi.org/10.1016/j.febslet.2012.06.006openalex-snapshot
Pleckstrin homology (PH) like domains – versatile modules in protein–protein interaction platforms
inferredcites →https://doi.org/10.1016/j.tig.2005.09.007openalex-snapshot
Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians
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/j.tig.2009.07.006openalex-snapshot
More than just orphans: are taxonomically-restricted genes important in evolution?
inferredcites →https://doi.org/10.1016/j.ydbio.2011.01.032openalex-snapshot
Evolutionary implications of morphogenesis and molecular patterning of the blind gut in the planarian Schmidtea polychroa
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s0968-0004(98)01298-5openalex-snapshot
Iterated profile searches with PSI-BLAST—a tool for discovery in protein databases
inferredcites →https://doi.org/10.1016/s1672-0229(10)60008-3openalex-snapshot
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
inferredcites →https://doi.org/10.1038/nature08160openalex-snapshot
The genome of the blood fluke Schistosoma mansoni
inferredcites →https://doi.org/10.1038/nature12031openalex-snapshot
The genomes of four tapeworm species reveal adaptations to parasitism
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
inferredcites →https://doi.org/10.1038/nrg1204openalex-snapshot
The origin of new genes: glimpses from the young and old
inferredcites →https://doi.org/10.1038/nrg3053openalex-snapshot
The evolutionary origin of orphan genes
inferredcites →https://doi.org/10.1038/nrg3174openalex-snapshot
A beginner's guide to eukaryotic genome annotation
inferredcites →https://doi.org/10.1038/srep09417openalex-snapshot
Flatworms have lost the right open reading frame kinase 3 gene during evolution
inferredcites →https://doi.org/10.1073/pnas.0709013104openalex-snapshot
Distinguishing protein-coding and noncoding genes in the human genome
inferredcites →https://doi.org/10.1073/pnas.1516718112openalex-snapshot
Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano
inferredcites →https://doi.org/10.1073/pnas.96.6.2896openalex-snapshot
The use of gene clusters to infer functional coupling
inferredcites →https://doi.org/10.1080/10635150701472164openalex-snapshot
Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
inferredcites →https://doi.org/10.1086/302219openalex-snapshot
When Less Is More: Gene Loss as an Engine of Evolutionary Change
inferredcites →https://doi.org/10.1093/bioinformatics/14.9.755openalex-snapshot
Profile hidden Markov models.
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/btm071openalex-snapshot
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/gbe/evr019openalex-snapshot
The Accumulation of Gene Regulation Through Time
inferredcites →https://doi.org/10.1093/gbe/evs100openalex-snapshot
A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes
inferredcites →https://doi.org/10.1093/gbe/evt102openalex-snapshot
A Broad Genomic Survey Reveals Multiple Origins and Frequent Losses in the Evolution of Respiratory Hemerythrins and Hemocyanins
inferredcites →https://doi.org/10.1093/gbe/evt132openalex-snapshot
Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals
inferredcites →https://doi.org/10.1093/molbev/msj006openalex-snapshot
The “Inverse Relationship Between Evolutionary Rate and Age of Mammalian Genes” Is an Artifact of Increased Genetic Distance with Rate of Evolution and Time of Divergence
inferredcites →https://doi.org/10.1093/molbev/mss228openalex-snapshot
Evidence for Compensatory Evolution of Ribosomal Proteins in Response to Rapid Divergence of Mitochondrial rRNA
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msu143openalex-snapshot
Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia
inferredcites →https://doi.org/10.1093/molbev/msu286openalex-snapshot
Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution
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/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/28.1.292openalex-snapshot
Codon usage tabulated from international DNA sequence databases: status for the year 2000
inferredcites →https://doi.org/10.1093/nar/gkl315openalex-snapshot
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
inferredcites →https://doi.org/10.1093/nar/gkn425openalex-snapshot
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
inferredcites →https://doi.org/10.1093/nar/gkn916openalex-snapshot
Assessing the gene space in draft genomes
inferredcites →https://doi.org/10.1093/nar/gks001openalex-snapshot
Summarizing and correcting the GC content bias in high-throughput sequencing
inferredcites →https://doi.org/10.1093/nar/gku1204openalex-snapshot
The BioGRID interaction database: 2015 update
inferredcites →https://doi.org/10.1093/nar/gkv1148openalex-snapshot
PlanMine – a mineable resource of planarian biology and biodiversity
inferredcites →https://doi.org/10.1093/oso/9780195168174.003.0007openalex-snapshot
Detecting Selection at the Molecular Level
inferredcites →https://doi.org/10.1101/021626openalex-snapshot
TransRate: reference free quality assessment of de-novo transcriptome assemblies
inferredcites →https://doi.org/10.1101/gr.095026.109openalex-snapshot
Recent de novo origin of human protein-coding genes
inferredcites →https://doi.org/10.1101/gr.1589103openalex-snapshot
Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution
inferredcites →https://doi.org/10.1111/j.1365-3024.2011.01319.xopenalex-snapshot
Cestode genomics – progress and prospects for advancing basic and applied aspects of flatworm biology
inferredcites →https://doi.org/10.1126/science.1197761openalex-snapshot
The Ecoresponsive Genome of Daphnia pulex
inferredcites →https://doi.org/10.1126/science.1214457openalex-snapshot
Centrosome Loss in the Evolution of Planarians
inferredcites →https://doi.org/10.1126/science.278.5338.631openalex-snapshot
A Genomic Perspective on Protein Families
inferredcites →https://doi.org/10.1128/jvi.02595-13openalex-snapshot
Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently “Orphan” Viral Proteins
inferredcites →https://doi.org/10.1186/1471-2105-7-270openalex-snapshot
Improving the specificity of high-throughput ortholog prediction
inferredcites →https://doi.org/10.1186/1471-2148-7-53openalex-snapshot
On homology searches by protein Blast and the characterization of the age of genes
inferredcites →https://doi.org/10.1186/1471-2164-14-797openalex-snapshot
The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios
inferredcites →https://doi.org/10.1186/1741-7007-10-88openalex-snapshot
Q&A: What is regeneration, and why look to planarians for answers?
inferredcites →https://doi.org/10.1186/1745-6150-3-38openalex-snapshot
CAIcal: A combined set of tools to assess codon usage adaptation
inferredcites →https://doi.org/10.1186/gb-2000-1-5-reviews3002openalex-snapshot
The F-box protein family.
inferredcites →https://doi.org/10.1186/gb-2011-12-10-r107openalex-snapshot
The draft genome of the carcinogenic human liver fluke Clonorchis sinensis
inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-snapshot
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
inferredcites →https://doi.org/10.1371/journal.pcbi.1000734openalex-snapshot
A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions
inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot
Accelerated Profile HMM Searches
inferredcites →https://doi.org/10.1371/journal.pone.0120081openalex-snapshot
Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms
inferredcites →https://doi.org/10.5860/choice.44-2686openalex-snapshot
Evolutionary genetics: concepts and case studies
inferredcites →https://doi.org/10.7554/elife.01311openalex-snapshot
The life cycle of Drosophila orphan genes
inferredcites →https://doi.org/10.7554/elife.05503openalex-snapshot
Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s41598-021-81888-zopenalex-snapshot
Weighted gene co-expression network analysis identifies modules and functionally enriched pathways in the lactation process
inferred← citeshttps://doi.org/10.1038/srep28071openalex-snapshot
Evolution of the EGFR pathway in Metazoa and its diversification in the planarian Schmidtea mediterranea
inferred← citeshttps://doi.org/10.11606/issn.1984-5154.v21p1-13openalex-snapshot
Um panorama atual sobre a filogenia de Metazoa: conflitos e concordâncias
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