Research graph
References from MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions. Local targets link to admitted publications; unresolved targets remain external evidence.
Global burden of 369 diseases, injuries in 204 countries and territories 1990 –2019: a systematic analysis for the Global Burden of Disease Study 2019
10.1016/s0140-6736(20)30925-9 · 2020 · External reference
Measuring underreporting and under-ascertainment in infectious disease datasets: a comparison of methods
10.1186/1471-2458-14-147 · 2014 · External reference
Towards a genomics-informed, real-time, global pathogen surveillance system
10.1038/nrg.2017.88 · 2018 · External reference
Global disparities in SARS-CoV-2 genomic surveillance
10.1038/s41467-022-33713-y · 2022 · External reference
Unifying the epidemiological and evolutionary dynamics of pathogens
10.1126/science.1090727 · 2004 · External reference
Discovering the phylodynamics of RNA viruses
10.1371/journal.pcbi.1000505 · 2009 · External reference
Viral phylodynamics
2013 · External reference
On the generalized “birth-and-death” process
10.1214/aoms/1177730285 · 1948 · External reference
The coalescent
10.1016/0304-4149(82)90011-4 · 1982 · External reference
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
10.1073/pnas.1207965110 · 2013 · External reference
Phylodynamics of infectious disease epidemics
10.1534/genetics.109.106021 · 2009 · External reference
Complex population dynamics and the coalescent under neutrality
10.1534/genetics.111.134627 · 2012 · External reference
Quantifying and mitigating the effect of preferential sampling on phylodynamic inference
10.1371/journal.pcbi.1004789 · 2016 · External reference
Inferring epidemiological dynamics with Bayesian coalescent inference: the merits of deterministic and stochastic models
10.1534/genetics.114.172791 · 2015 · External reference
Exploring the demographic history of DNA sequences using the generalized skyline plot
10.1093/oxfordjournals.molbev.a003776 · 2001 · External reference
Bayesian coalescent inference of past population dynamics from molecular sequences
10.1093/molbev/msi103 · 2005 · External reference
Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics
10.1093/molbev/msn090 · 2008 · External reference
An efficient coalescent epoch model for Bayesian phylogenetic inference
10.1093/sysbio/syac015 · 2022 · External reference
Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci
10.1093/molbev/mss265 · 2013 · External reference
The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach
10.1093/molbev/msg043 · 2003 · External reference
The genomic and epidemiological dynamics of human influenza A virus
10.1038/nature06945 · 2008 · External reference
Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage
10.1038/ng.3195 · 2015 · External reference
HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations
10.1126/science.1256739 · 2014 · External reference
1970s and “Patient 0” HIV-1 genomes illuminate early HIV/AIDS history in North America
10.1038/nature19827 · 2016 · External reference
Global circulation patterns of seasonal influenza viruses vary with antigenic drift
10.1038/nature14460 · 2015 · External reference
MERS-CoV spillover at the camel-human interface
2018 · External reference
Genomic and epidemiological monitoring of yellow fever virus transmission potential
10.1126/science.aat7115 · 2018 · External reference
SCOTTI: efficient reconstruction of transmission within outbreaks with the structured coalescent
10.1371/journal.pcbi.1005130 · 2016 · External reference
Bayesian phylogeography finds its roots
10.1371/journal.pcbi.1000520 · 2009 · External reference
GISAID’s role in pandemic response
10.46234/ccdcw2021.255 · 2021 · External reference
Estimating a binary character’s effect on speciation and extinction
10.1080/10635150701607033 · 2007 · External reference
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods
10.1098/rstb.2012.0198 · 2013 · External reference
Phylodynamics with migration: a computational framework to quantify population structure from genomic data
10.1093/molbev/msw064 · 2016 · External reference
The coalescent in two partially isolated diffusion populations
10.1017/s0016672300027683 · 1988 · External reference
Unresolved reference
1990 · External reference
The coalescent and the genealogical process in geographically structured population
10.1007/bf00173909 · 1990 · External reference
Bayesian phylodynamic inference with complex models
2018 · External reference
New routes to phylogeography: a Bayesian structured coalescent approximation
10.1371/journal.pgen.1005421 · 2015 · External reference
Impact and mitigation of sampling bias to determine viral spread: evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations
10.1093/ve/vead010 · 2023 · External reference
MASCOT: parameter and state inference under the marginal structured coalescent approximation
10.1093/bioinformatics/bty406 · 2018 · External reference
Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance
10.1093/sysbio/syy007 · 2018 · External reference
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST
10.1093/bioinformatics/btx088 · 2017 · External reference
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
10.1371/journal.pcbi.1006650 · 2019 · External reference
A stochastic simulator of birth-death master equations with application to phylodynamics
10.1093/molbev/mst057 · 2013 · External reference
The structured coalescent and its approximations
10.1093/molbev/msx186 · 2017 · External reference
Unresolved reference
External reference
Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations
10.1111/j.1365-294x.2004.02101.x · 2004 · External reference
Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations
10.1111/j.1365-294x.2004.02393.x · 2005 · External reference
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
10.1038/nature22401 · 2017 · External reference
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
10.1038/nature22400 · 2017 · External reference
Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia
10.1186/s12879-019-4566-2 · 2019 · External reference
The confounding effect of population structure on Bayesian skyline plot inferences of demographic history
10.1371/journal.pone.0062992 · 2013 · External reference
Global migration dynamics underlie evolution and persistence of human influenza A (H3N2)
10.1371/journal.ppat.1000918 · 2010 · External reference
Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans
10.1073/pnas.1109314108 · 2011 · External reference
Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2
10.1371/journal.ppat.1003932 · 2014 · External reference
Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations
10.1093/ve/vez030 · 2019 · External reference
Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State
10.1126/scitranslmed.abf0202 · 2021 · External reference
Joint inference of migration and reassortment patterns for viruses with segmented genomes
10.1093/molbev/msab342 · 2022 · External reference
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
10.1093/ve/vey016 · 2018 · External reference
BEAST: Bayesian evolutionary analysis by sampling trees
10.1186/1471-2148-7-214 · 2007 · External reference
10.1007/978-3-319-24277-4_9
10.1007/978-3-319-24277-4_9 · External reference
ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
10.1111/2041-210x.12628 · 2017 · External reference
Unresolved reference
External reference
CODA: convergence diagnosis and output analysis for MCMC
2006 · External reference
