Literature DB >> 21622662

TimeTree2: species divergence times on the iPhone.

Sudhir Kumar1, S Blair Hedges.   

Abstract

SUMMARY: Scientists, educators and the general public often need to know times of divergence between species. But they rarely can locate that information because it is buried in the scientific literature, usually in a format that is inaccessible to text search engines. We have developed a public knowledgebase that enables data-driven access to the collection of peer-reviewed publications in molecular evolution and phylogenetics that have reported estimates of time of divergence between species. Users can query the TimeTree resource by providing two names of organisms (common or scientific) that can correspond to species or groups of species. The current TimeTree web resource (TimeTree2) contains timetrees reported from molecular clock analyses in 910 published studies and 17 341 species that span the diversity of life. TimeTree2 interprets complex and hierarchical data from these studies for each user query, which can be launched using an iPhone application, in addition to the website. Published time estimates are now readily accessible to the scientific community, K-12 and college educators, and the general public, without requiring knowledge of evolutionary nomenclature. AVAILABILITY: TimeTree2 is accessible from the URL http://www.timetree.org, with an iPhone app available from iTunes (http://itunes.apple.com/us/app/timetree/id372842500?mt=8) and a YouTube tutorial (http://www.youtube.com/watch?v=CxmshZQciwo).

Entities:  

Mesh:

Year:  2011        PMID: 21622662      PMCID: PMC3129528          DOI: 10.1093/bioinformatics/btr315

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  4 in total

Review 1.  Molecular clocks: four decades of evolution.

Authors:  Sudhir Kumar
Journal:  Nat Rev Genet       Date:  2005-08       Impact factor: 53.242

2.  TimeTree: a public knowledge-base of divergence times among organisms.

Authors:  S Blair Hedges; Joel Dudley; Sudhir Kumar
Journal:  Bioinformatics       Date:  2006-10-04       Impact factor: 6.937

3.  Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals.

Authors:  Fabia U Battistuzzi; Alan Filipski; S Blair Hedges; Sudhir Kumar
Journal:  Mol Biol Evol       Date:  2010-01-21       Impact factor: 16.240

4.  Relaxed phylogenetics and dating with confidence.

Authors:  Alexei J Drummond; Simon Y W Ho; Matthew J Phillips; Andrew Rambaut
Journal:  PLoS Biol       Date:  2006-03-14       Impact factor: 8.029

  4 in total
  66 in total

1.  The Hematopoietic Expression Viewer: expanding mobile apps as a scientific tool.

Authors:  Regis A James; Mitchell M Rao; Edward S Chen; Margaret A Goodell; Chad A Shaw
Journal:  Bioinformatics       Date:  2012-05-09       Impact factor: 6.937

2.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Authors:  Koichiro Tamura; Glen Stecher; Daniel Peterson; Alan Filipski; Sudhir Kumar
Journal:  Mol Biol Evol       Date:  2013-10-16       Impact factor: 16.240

3.  Contraction of the type I IFN locus and unusual constitutive expression of IFN-α in bats.

Authors:  Peng Zhou; Mary Tachedjian; James W Wynne; Victoria Boyd; Jie Cui; Ina Smith; Christopher Cowled; Justin H J Ng; Lawrence Mok; Wojtek P Michalski; Ian H Mendenhall; Gilda Tachedjian; Lin-Fa Wang; Michelle L Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-22       Impact factor: 11.205

4.  Relaxing the Molecular Clock to Different Degrees for Different Substitution Types.

Authors:  Hui-Jie Lee; Nicolas Rodrigue; Jeffrey L Thorne
Journal:  Mol Biol Evol       Date:  2015-04-29       Impact factor: 16.240

Review 5.  It's more than stamp collecting: how genome sequencing can unify biological research.

Authors:  Stephen Richards
Journal:  Trends Genet       Date:  2015-05-20       Impact factor: 11.639

6.  Estimating divergence times in large molecular phylogenies.

Authors:  Koichiro Tamura; Fabia Ursula Battistuzzi; Paul Billing-Ross; Oscar Murillo; Alan Filipski; Sudhir Kumar
Journal:  Proc Natl Acad Sci U S A       Date:  2012-11-05       Impact factor: 11.205

7.  Nocturnality in synapsids predates the origin of mammals by over 100 million years.

Authors:  K D Angielczyk; L Schmitz
Journal:  Proc Biol Sci       Date:  2014-10-22       Impact factor: 5.349

8.  Grouping substitution types into different relaxed molecular clocks.

Authors:  Hui-Jie Lee; Hirohisa Kishino; Nicolas Rodrigue; Jeffrey L Thorne
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2016-07-19       Impact factor: 6.237

Review 9.  Inflammasome Activation Can Mediate Tissue-Specific Pathogenesis or Protection in Staphylococcus aureus Infection.

Authors:  Jason H Melehani; Joseph A Duncan
Journal:  Curr Top Microbiol Immunol       Date:  2016       Impact factor: 4.291

10.  Trends in genome dynamics among major orders of insects revealed through variations in protein families.

Authors:  Nadav Rappoport; Michal Linial
Journal:  BMC Genomics       Date:  2015-08-07       Impact factor: 3.969

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.