About: Reassortment Networks and the Evolution of Pandemic H1N1 Swine-Origin Influenza

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Reassortment Networks and the Evolution of Pandemic H1N1 Swine-Origin Influenza
Creator	Janies, Daniel Pomeroy, Laura Bokhari, Shahid
source	PMC
abstract	Prior research developed Reassortment Networks to reconstruct the evolution of segmented viruses under both reassortment and mutation. We report their application to the swine-origin pandemic H1N1 virus (S-OIV). A database of all influenza A viruses, for which complete genome sequences were available in Genbank by October 2009, was created and dynamic programming was used to compute distances between all corresponding segments. A reassortment network was created to obtain the minimum cost evolutionary paths from all viruses to the exemplar S-OIV A/California/04/2009. This analysis took 35 hours on the Cray Extreme Multithreading (XMT) supercomputer, which has special hardware to permit efficient parallelization. Six specific H1N1/H1N2 bottleneck viruses were identified that almost always lie on minimum cost paths to S-OIV. We conjecture that these viruses are crucial to S-OIV evolution and worthy of careful study from a molecular biology viewpoint. In phylogenetics, ancestors are typically medians that have no functional constraints. In our method, ancestors are not inferred, but rather chosen from previously observed viruses along a path of mutation and reassortment leading to the target virus. This specificity and functional constraint render our results actionable for further experiments in vitro and in vivo.
has issue date	2011-06-06(xsd:dateTime)
bibo:doi	10.1109/tcbb.2011.95
bibo:pmid	22076498
has license	cc-by
sha1sum (hex)	df596a3cbca4e5dc29fd6dbe365f1a24b35d1f87
schema:url	https://doi.org/10.1109/tcbb.2011.95
resource representing a document's title	Reassortment Networks and the Evolution of Pandemic H1N1 Swine-Origin Influenza
has PubMed Central identifier	PMC7186031
has PubMed identifier	22076498
schema:publication	IEEE/ACM Trans Comput Biol Bioinform
resource representing a document's body	covid:df596a3cbca4e5dc29fd6dbe365f1a24b35d1f87#body_text
is schema:about of	named entity 'IDENTIFIED' named entity 'METHOD' covid:arg/df596a3cbca4e5dc29fd6dbe365f1a24b35d1f87 named entity 'genome sequences' named entity 'S-OIV' named entity 'viruses' named entity 'database' named entity 'H1N1' named entity 'evolution' named entity 'viruses' named entity 'mutation' named entity 'mutation' named entity 'Influenza' named entity 'H3N2' named entity 'reassortment' named entity 'massive parallelism' named entity 'supercomputer' named entity 'protein' named entity 'Reassortment' named entity 'PNL' named entity 'mutation' named entity 'S-OIV' named entity 'dynamic programming' named entity 'shortest path lengths' named entity 'H1N1' named entity 'evolution' named entity 'hemagglutinin' named entity 'unusually low' named entity 'reassortment' named entity 'polymerase' named entity 'blue box' named entity 'compiler directives' named entity 'phylogenetic' named entity 'dynamic programming' named entity 'National Center for Biotechnology Information' named entity 'reassortment' named entity 'reassortment' named entity 'phylogenetics' named entity 'S-OIV' named entity 'mutation' named entity 'AMD Opteron' named entity 'human origin' named entity 'neuraminidase' named entity 'influenza' named entity 'shortest path' named entity 'epidemic' named entity 'reassortment' named entity 'protein' named entity 'distributed memory' named entity 'reassortment' named entity 'input/output' named entity 'black boxes' named entity 'molecular biology' named entity 'clock cycle' named entity 'evolution' named entity 'layer 2' named entity 'neuraminidase' named entity 'reassortment' named entity 'reassortment' named entity 'polymerase' named entity 'neuraminidase' named entity 'H3N2' named entity 'RNA processing' named entity 'S-OIV' named entity 'shortest path' named entity 'evolutionary history' named entity 'reassortment' named entity 'S-OIV' named entity 'S-OIV' named entity 'spreadsheet' named entity 'reassorted' named entity 'reassortment' named entity 'S-OIV' named entity 'reassortment' named entity 'California' named entity 'influenza' named entity '11.5' named entity 'IEEE' named entity 'S-OIV'

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