FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4280490853> ?p ?o ?g. }

• W4280490853 abstract "Abstract The genomic era has opened up vast opportunities in molecular systematics, one of which is deciphering the evolutionary history in fine detail. Under this mass of data, analysing the point mutations of standard markers is too crude and slow for fine-scale phylogenetics. Nevertheless, genome dynamics events provide far richer information. The synteny index (SI) between a pair of genomes combines gene order and gene content information, allowing the comparison of genomes of unequal gene content, together with order considerations of their common genes. Recently, genome dynamics has been modelled as a continuous-time Markov process, and gene distance in the genome as a birth–death–immigration process. Nevertheless, due to complexities arising in this setting such as overlapping neighbourhoods and other confounding factors, no precise and provably consistent estimators could be derived. Here, we extend this modelling approach by using techniques from birth–death theory to derive explicit expressions of the system’s probabilistic dynamics in the form of rational functions of the model parameters. This, in turn, allows us to infer analytically the expected distances between organisms based on a transformation of their SI. Despite the complexity of the expressions obtained, we establish additivity of this estimated evolutionary distance (a desirable property yielding phylogenetic consistency). Applying the new measure in simulation studies shows that it attains very accurate results in realistic settings and even under model extensions. In the real-data realm, we applied the new formulation to unique data structure that we constructed - the ordered orthology DB - based on a new version of the EggNOG database, to construct a tree with more than 4.5K taxa. The resulted tree was compared it with a NCBI taxonomy for these organisms. To the best of our knowledge, this is the largest gene-order-based tree constructed and it overcomes flaws found in previous approaches." @default.
• W4280490853 created "2022-05-22" @default.
• W4280490853 creator A5016339366 @default.
• W4280490853 creator A5028854139 @default.
• W4280490853 creator A5057169112 @default.
• W4280490853 creator A5058258753 @default.
• W4280490853 creator A5058881306 @default.
• W4280490853 creator A5063493591 @default.
• W4280490853 date "2022-04-22" @default.
• W4280490853 modified "2023-10-15" @default.
• W4280490853 title "Gene Transfer-based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory" @default.
• W4280490853 cites W1519987066 @default.
• W4280490853 cites W1537236879 @default.
• W4280490853 cites W1776424232 @default.
• W4280490853 cites W1958274537 @default.
• W4280490853 cites W1966972227 @default.
• W4280490853 cites W1985484376 @default.
• W4280490853 cites W1989511261 @default.
• W4280490853 cites W2010908637 @default.
• W4280490853 cites W2026290436 @default.
• W4280490853 cites W2029029999 @default.
• W4280490853 cites W2060425093 @default.
• W4280490853 cites W2069016054 @default.
• W4280490853 cites W2082638565 @default.
• W4280490853 cites W2097706568 @default.
• W4280490853 cites W2098558111 @default.
• W4280490853 cites W2102424972 @default.
• W4280490853 cites W2111929782 @default.
• W4280490853 cites W2112755610 @default.
• W4280490853 cites W2114446330 @default.
• W4280490853 cites W2121166240 @default.
• W4280490853 cites W2138952930 @default.
• W4280490853 cites W2140170649 @default.
• W4280490853 cites W2144345157 @default.
• W4280490853 cites W2148560957 @default.
• W4280490853 cites W2149582283 @default.
• W4280490853 cites W2149628296 @default.
• W4280490853 cites W2159545652 @default.
• W4280490853 cites W2169929748 @default.
• W4280490853 cites W2207020174 @default.
• W4280490853 cites W2262138991 @default.
• W4280490853 cites W2799551362 @default.
• W4280490853 cites W2900629010 @default.
• W4280490853 cites W2962876490 @default.
• W4280490853 cites W3048090444 @default.
• W4280490853 doi "https://doi.org/10.1101/2022.04.21.489106" @default.
• W4280490853 hasPublicationYear "2022" @default.
• W4280490853 type Work @default.
• W4280490853 citedByCount "1" @default.
• W4280490853 crossrefType "posted-content" @default.
• W4280490853 hasAuthorship W4280490853A5016339366 @default.
• W4280490853 hasAuthorship W4280490853A5028854139 @default.
• W4280490853 hasAuthorship W4280490853A5057169112 @default.
• W4280490853 hasAuthorship W4280490853A5058258753 @default.
• W4280490853 hasAuthorship W4280490853A5058881306 @default.
• W4280490853 hasAuthorship W4280490853A5063493591 @default.
• W4280490853 hasBestOaLocation W42804908531 @default.
• W4280490853 hasConcept C104317684 @default.
• W4280490853 hasConcept C141231307 @default.
• W4280490853 hasConcept C41008148 @default.
• W4280490853 hasConcept C54355233 @default.
• W4280490853 hasConcept C70721500 @default.
• W4280490853 hasConcept C86803240 @default.
• W4280490853 hasConceptScore W4280490853C104317684 @default.
• W4280490853 hasConceptScore W4280490853C141231307 @default.
• W4280490853 hasConceptScore W4280490853C41008148 @default.
• W4280490853 hasConceptScore W4280490853C54355233 @default.
• W4280490853 hasConceptScore W4280490853C70721500 @default.
• W4280490853 hasConceptScore W4280490853C86803240 @default.
• W4280490853 hasLocation W42804908531 @default.
• W4280490853 hasOpenAccess W4280490853 @default.
• W4280490853 hasPrimaryLocation W42804908531 @default.
• W4280490853 hasRelatedWork W1872127137 @default.
• W4280490853 hasRelatedWork W1989784896 @default.
• W4280490853 hasRelatedWork W2027675659 @default.
• W4280490853 hasRelatedWork W2030640333 @default.
• W4280490853 hasRelatedWork W2137696956 @default.
• W4280490853 hasRelatedWork W2150953285 @default.
• W4280490853 hasRelatedWork W2207772665 @default.
• W4280490853 hasRelatedWork W2599768688 @default.
• W4280490853 hasRelatedWork W3164573509 @default.
• W4280490853 hasRelatedWork W4297192875 @default.
• W4280490853 isParatext "false" @default.
• W4280490853 isRetracted "false" @default.
• W4280490853 workType "article" @default.