FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2057118148> ?p ?o ?g. }

• W2057118148 endingPage "e77033" @default.
• W2057118148 startingPage "e77033" @default.
• W2057118148 abstract "With the astonishing rate that genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as “marker” genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities (e.g., construction of species trees, phylogenetic based assignment of metagenomic sequence reads to taxonomic groups, phylogeny-based assessment of alpha- and beta-diversity of microbial communities from metagenomic data). We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for “all bacteria and archaea”, 114 for “all bacteria (greatly expanding on the ∼30 commonly used), and 100 s to 1000 s for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously." @default.
• W2057118148 created "2016-06-24" @default.
• W2057118148 creator A5043047513 @default.
• W2057118148 creator A5059066311 @default.
• W2057118148 creator A5086222406 @default.
• W2057118148 date "2013-10-17" @default.
• W2057118148 modified "2023-10-18" @default.
• W2057118148 title "Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups" @default.
• W2057118148 cites W113427216 @default.
• W2057118148 cites W1557572225 @default.
• W2057118148 cites W1583773155 @default.
• W2057118148 cites W1936630560 @default.
• W2057118148 cites W1963946970 @default.
• W2057118148 cites W1975466458 @default.
• W2057118148 cites W1988925586 @default.
• W2057118148 cites W1998377233 @default.
• W2057118148 cites W2000024082 @default.
• W2057118148 cites W2013759002 @default.
• W2057118148 cites W2014097763 @default.
• W2057118148 cites W2027041239 @default.
• W2057118148 cites W2031611770 @default.
• W2057118148 cites W2040163542 @default.
• W2057118148 cites W2052359965 @default.
• W2057118148 cites W2053096433 @default.
• W2057118148 cites W2055043387 @default.
• W2057118148 cites W2062354928 @default.
• W2057118148 cites W2068687524 @default.
• W2057118148 cites W2072812562 @default.
• W2057118148 cites W2077191430 @default.
• W2057118148 cites W2077648335 @default.
• W2057118148 cites W2078969200 @default.
• W2057118148 cites W2084443943 @default.
• W2057118148 cites W2084703535 @default.
• W2057118148 cites W2091232725 @default.
• W2057118148 cites W2091922579 @default.
• W2057118148 cites W2094278068 @default.
• W2057118148 cites W2096859635 @default.
• W2057118148 cites W2097107919 @default.
• W2057118148 cites W2098386120 @default.
• W2057118148 cites W2100733246 @default.
• W2057118148 cites W2102555068 @default.
• W2057118148 cites W2105201042 @default.
• W2057118148 cites W2113601822 @default.
• W2057118148 cites W2115542536 @default.
• W2057118148 cites W2117500540 @default.
• W2057118148 cites W2121152355 @default.
• W2057118148 cites W2121918723 @default.
• W2057118148 cites W2124166542 @default.
• W2057118148 cites W2131026689 @default.
• W2057118148 cites W2132926880 @default.
• W2057118148 cites W2134650310 @default.
• W2057118148 cites W2135947999 @default.
• W2057118148 cites W2139436782 @default.
• W2057118148 cites W2142735254 @default.
• W2057118148 cites W2147694156 @default.
• W2057118148 cites W2149021569 @default.
• W2057118148 cites W2154401636 @default.
• W2057118148 cites W2155066423 @default.
• W2057118148 cites W2166327480 @default.
• W2057118148 cites W2171532415 @default.
• W2057118148 doi "https://doi.org/10.1371/journal.pone.0077033" @default.
• W2057118148 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3798382" @default.
• W2057118148 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24146954" @default.
• W2057118148 hasPublicationYear "2013" @default.
• W2057118148 type Work @default.
• W2057118148 sameAs 2057118148 @default.
• W2057118148 citedByCount "159" @default.
• W2057118148 countsByYear W20571181482013 @default.
• W2057118148 countsByYear W20571181482014 @default.
• W2057118148 countsByYear W20571181482015 @default.
• W2057118148 countsByYear W20571181482016 @default.
• W2057118148 countsByYear W20571181482017 @default.
• W2057118148 countsByYear W20571181482018 @default.
• W2057118148 countsByYear W20571181482019 @default.
• W2057118148 countsByYear W20571181482020 @default.
• W2057118148 countsByYear W20571181482021 @default.
• W2057118148 countsByYear W20571181482022 @default.
• W2057118148 countsByYear W20571181482023 @default.
• W2057118148 crossrefType "journal-article" @default.
• W2057118148 hasAuthorship W2057118148A5043047513 @default.
• W2057118148 hasAuthorship W2057118148A5059066311 @default.
• W2057118148 hasAuthorship W2057118148A5086222406 @default.
• W2057118148 hasBestOaLocation W20571181481 @default.
• W2057118148 hasConcept C104317684 @default.
• W2057118148 hasConcept C116834253 @default.
• W2057118148 hasConcept C15151743 @default.
• W2057118148 hasConcept C18903297 @default.
• W2057118148 hasConcept C189592816 @default.
• W2057118148 hasConcept C193252679 @default.
• W2057118148 hasConcept C198260499 @default.
• W2057118148 hasConcept C44465124 @default.
• W2057118148 hasConcept C54355233 @default.
• W2057118148 hasConcept C71640776 @default.
• W2057118148 hasConcept C78458016 @default.
• W2057118148 hasConcept C86803240 @default.
• W2057118148 hasConcept C90132467 @default.
• W2057118148 hasConcept C98722961 @default.
• W2057118148 hasConceptScore W2057118148C104317684 @default.

• next