ArticleScientific reports2013
A daily-updated tree of (sequenced) life as a reference for genome research.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Protein structures unravel the signatures and patterns of deep time evolution.QRB discovery · 2024Review
- 'Why genes in pieces?'-revisited.Nucleic acids research · 2019Article
- The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.Nucleic acids research · 2019Article
- Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm.Computational and mathematical methods in medicine · 2019Article
- Synopsis of theG3 (Bethesda, Md.) · 2018Article
- Article
- A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters.Scientific reports · 2017Article
- ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.Nucleic acids research · 2017Article
- Resurrecting the Dead (Molecules).Computational and structural biotechnology journal · 2017Review
- Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells?Genome biology and evolution · 2016Article
- One step beyond a ribosome: The ancient anaerobic core.Biochimica et biophysica acta · 2016Review
- Evolution of the Calcium-Based Intracellular Signaling System.Genome biology and evolution · 2016Article
- PANTHER version 10: expanded protein families and functions, and analysis tools.Nucleic acids research · 2016Article
- Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.Biochimie · 2015Article
- Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.Genome biology and evolution · 2015Article
- MDAT- Aligning multiple domain arrangements.BMC bioinformatics · 2015Article
- Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology.Computational and structural biotechnology journal · 2015Review
- The SUPERFAMILY 1.75 database in 2014: a doubling of data.Nucleic acids research · 2015Article
- dcGOR: an R package for analysing ontologies and protein domain annotations.PLoS computational biology · 2014Article
- Hierarchical partitioning of metazoan protein conservation profiles provides new functional insights.PloS one · 2014Article
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Authors and funding
10 authors.
Funding
Abstract
We report a daily-updated sequenced/species Tree Of Life (sTOL) as a reference for the increasing number of cellular organisms with their genomes sequenced. The sTOL builds on a likelihood-based weight calibration algorithm to consolidate NCBI taxonomy information in concert with unbiased sampling of molecular characters from whole genomes of all sequenced organisms. Via quantifying the extent of agreement between taxonomic and molecular data, we observe there are many potential improvements that can be made to the status quo classification, particularly in the Fungi kingdom; we also see that the current state of many animal genomes is rather poor. To augment the use of sTOL in providing evolutionary contexts, we integrate an ontology infrastructure and demonstrate its utility for evolutionary understanding on: nuclear receptors, stem cells and eukaryotic genomes. The sTOL (http://supfam.org/SUPERFAMILY/sTOL) provides a binary tree of (sequenced) life, and contributes to an analytical platform linking genome evolution, function and phenotype.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.