About: Effects of memory on the shapes of simple outbreak trees

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Effects of memory on the shapes of simple outbreak trees Goto Sponge NotDistinct Permalink

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
has title	Effects of memory on the shapes of simple outbreak trees
Creator	Boyd, Michael Colijn, Caroline Kwan, Christopher Plazzotta, Giacomo
Source	PMC
abstract	Genomic tools, including phylogenetic trees derived from sequence data, are increasingly used to understand outbreaks of infectious diseases. One challenge is to link phylogenetic trees to patterns of transmission. Particularly in bacteria that cause chronic infections, this inference is affected by variable infectious periods and infectivity over time. It is known that non-exponential infectious periods can have substantial effects on pathogens’ transmission dynamics. Here we ask how this non-Markovian nature of an outbreak process affects the branching trees describing that process, with particular focus on tree shapes. We simulate Crump-Mode-Jagers branching processes and compare different patterns of infectivity over time. We find that memory (non-Markovian-ness) in the process can have a pronounced effect on the shapes of the outbreak’s branching pattern. However, memory also has a pronounced effect on the sizes of the trees, even when the duration of the simulation is fixed. When the sizes of the trees are constrained to a constant value, memory in our processes has little direct effect on tree shapes, but can bias inference of the birth rate from trees. We compare simulated branching trees to phylogenetic trees from an outbreak of tuberculosis in Canada, and discuss the relevance of memory to this dataset.
has issue date	2016-02-18(xsd:dateTime)
bibo:doi	10.1038/srep21159
bibo:pmid	26888437
has license	cc-by
sha1sum (hex)	77fc830cd32e8b07cd22a11a8d519f9d35f7d7ff
schema:url	https://doi.org/10.1038/srep21159
resource representing a document's title	Effects of memory on the shapes of simple outbreak trees
has PubMed Central identifier	PMC4758066
has PubMed identifier	26888437
schema:publication	Sci Rep
resource representing a document's body	covid:77fc830cd32e8b07cd22a11a8d519f9d35f7d7ff#body_text
is schema:about of	named entity 'However' named entity 'memory' named entity 'non-exponential' named entity 'sizes' named entity 'compare' named entity 'OUTBREAK' covid:arg/77fc830cd32e8b07cd22a11a8d519f9d35f7d7ff named entity 'CAUSE' named entity 'DERIVED' named entity 'FIXED' named entity 'SIMULATION' named entity 'COMPARE' named entity 'EFFECT' named entity 'HOW' named entity 'DESCRIBING' named entity 'ASK' named entity 'MODE' named entity 'HAVE' named entity 'USED' named entity 'FOCUS' named entity 'NESS' named entity 'CHRONIC INFECTIONS' named entity 'UNDERSTAND' named entity 'OUTBREAKS' named entity 'HERE' named entity 'LITTLE' named entity 'INFERENCE' named entity 'CONSTANT VALUE' named entity 'KNOWN' named entity 'SIMULATE' named entity 'CHALLENGE' named entity 'VARIABLE' named entity 'OPEN' named entity 'TREE' named entity 'EXPONENTIAL' named entity 'PATHOGENS' named entity 'SEQUENCE DATA' named entity 'MEMORY' named entity 'INFECTIOUS DISEASES' named entity 'PROCESS' named entity 'PATTERNS' named entity 'TOOLS' named entity 'NON-' named entity 'INCLUDING' named entity 'BRANCHING' named entity 'NATURE' named entity 'MEMORY' named entity 'SIMPLE' named entity 'DIRECT' named entity 'CONSTRAINED' named entity 'PARTICULAR' named entity 'RELEVANCE' named entity 'TREES' named entity 'EFFECTS' named entity 'BACTERIA ' named entity 'CANADA' named entity 'DISCUSS' named entity 'TIME' named entity 'DYNAMICS' named entity 'DURATION' named entity 'OUTBREAK' named entity 'EFFECTS' named entity 'DATASET' named entity 'DIFFERENT' named entity 'TUBERCULOSIS' named entity 'PATTERN' named entity 'SHAPES' named entity 'SHAPES' named entity 'BIAS' named entity 'OUR' named entity '27S' named entity 'TO LINK' named entity 'AFFECTED' named entity 'BUT' named entity 'INFECTIOUS' named entity 'INFECTIVITY' named entity 'BIRTH RATE' named entity 'TRANSMISSION'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software