master-refs.bib

---
---

% This file was created with JabRef 2.9.2.
% Encoding: MacRoman

@STRING{AHG = {Annals of Human Genetics}}

@STRING{AJHG = {American Journal of Human Genetics}}

@STRING{ARB = {Annual Review of Biochemistry}}

@STRING{ARCB = {Annual Review of Cell Biology}}

@STRING{BI = {Bioinformatics}}

@STRING{BIOGEN = {Biochemical Genetics}}

@STRING{BJLS = {Biological Journal of the Linnean Society}}

@STRING{BMB = {Bulletin of Mathematical Biology}}

@STRING{BMCBI = {BMC Bioinformatics}}

@STRING{CABIOS = {Computer Applications in the Biosciences}}

@STRING{CACM = {Communications of the ACM}}

@STRING{CELL = {Cell}}

@STRING{COCB = {Current Opinion in Cell Biology}}

@STRING{COGD = {Current Opinion in Genetics and Development}}

@STRING{ComputChem = {Computers and Chemistry}}

@STRING{COSB = {Current Opinion in Structural Biology}}

@STRING{CSHSQB = {Cold Spring Harbor Symposia Quantitative Biology}}

@STRING{EMBO = {EMBO Journal}}

@STRING{EVO = {Evolution}}

@STRING{GB = {Genome Biology}}

@STRING{GEN = {Genetics}}

@STRING{GR = {Genome Research}}

@STRING{JBSD = {Journal of Biomolecular Structure and Dynamics}}

@STRING{JCB = {Journal of Computational Biology}}

@STRING{JMB = {Journal of Molecular Biology}}

@STRING{JME = {Journal of Molecular Evolution}}

@STRING{JRSS = {Journal of the Royal Statistical Society, B}}

@STRING{JTB = {Journal of Theoretical Biology}}

@STRING{MBE = {Molecular Biology and Evolution}}

@STRING{MBIO = {Mathematical Biosciences}}

@STRING{MCB = {Molecular Cell Biology}}

@STRING{ME = {Methods in Enzymology}}

@STRING{MPE = {Molecular Phylogenetics and Evolution}}

@STRING{NAR = {Nucleic Acids Research}}

@STRING{Nature = {Nature}}

@STRING{NB = {Nature Biotechnology}}

@STRING{NC = {Neural Computation}}

@STRING{NG = {Nature Genetics}}

@STRING{NNB = {Nature New Biology}}

@STRING{PE = {Protein Engineering}}

@STRING{PHTRANSRB = {Philosophical Transactions of the Royal Society B}}

@STRING{PLOSCOMPBIO = {PLoS Computational Biology}}

@STRING{PNAS = {Proceedings of the National Academy of Sciences, USA}}

@STRING{PROCROYB = {Proceedings of the Royal Society B}}

@STRING{PROT = {Proteins}}

@STRING{PROTSCI = {Protein Science}}

@STRING{Science = {Science}}

@STRING{S = Science}

@STRING{SIAM = {SIAM Journal of Applied Mathematics}}

@STRING{SYSB = {Systematic Biology}}

@STRING{SZ = {Systematic Zoology}}

@STRING{TIBTECH = {Trends in Biotechnology}}

@STRING{TIGS = {Trends in Genetics}}

@article{Bouckaert2014,
abstract = {We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.},
author = {Bouckaert, Remco and Heled, Joseph and K{\"{u}}hnert, Denise and Vaughan, Tim and Wu, Chieh-Hsi and Xie, Dong and Suchard, Marc A and Rambaut, Andrew and Drummond, Alexei J},
doi = {10.1371/journal.pcbi.1003537},
file = {:Users/nicmuell/Library/Application Support/Mendeley Desktop/Downloaded/Bouckaert et al. - 2014 - BEAST 2 a software platform for Bayesian evolutionary analysis.pdf:pdf},
issn = {1553-7358},
journal = {PLoS computational biology},
mendeley-groups = {Methods,SkylineTutorial},
month = {apr},
number = {4},
pages = {e1003537},
pmid = {24722319},
publisher = {Public Library of Science},
title = {BEAST 2: a software platform for Bayesian evolutionary analysis.},
url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003537},
volume = {10},
year = {2014}
}

@BOOK{BEAST2book2014,
  title = {Bayesian evolutionary analysis with {BEAST} 2},
  publisher = {Cambridge University Press},
  year = {2014},
  author = {Alexei J. Drummond and Remco R. Bouckaert}
}

@article{Cottam2008ProcRSocB,
	title = {Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus},
	volume = {275},
	issn = {0962-8452, 1471-2954},
	doi = {10.1098/rspb.2007.1442},
	language = {en},
	number = {1637},
	journal = {Proceedings of the Royal Society of London B: Biological Sciences},
	author = {Cottam, Eleanor M. and Thébaud, Gaël and Wadsworth, Jemma and Gloster, John and Mansley, Leonard and Paton, David J. and King, Donald P. and Haydon, Daniel T.},
	month = apr,
	year = {2008},
	pmid = {18230598},
	pages = {887--895},
}

@article{Cottam2008PlosPath,
	title = {Transmission {Pathways} of {Foot}-and-{Mouth} {Disease} {Virus} in the {United} {Kingdom} in 2007},
	volume = {4},
	issn = {1553-7374},
	doi = {10.1371/journal.ppat.1000050},
	number = {4},
	journal = {PLOS Pathogens},
	author = {Cottam, Eleanor M. and Wadsworth, Jemma and Shaw, Andrew E. and Rowlands, Rebecca J. and Goatley, Lynnette and Maan, Sushila and Maan, Narender S. and Mertens, Peter P. C. and Ebert, Katja and Li, Yanmin and Ryan, Eoin D. and Juleff, Nicholas and Ferris, Nigel P. and Wilesmith, John W. and Haydon, Daniel T. and King, Donald P. and Paton, David J. and Knowles, Nick J.},
	month = apr,
	year = {2008},
	keywords = {Cattle, DNA sequence analysis, Foot and mouth disease, Genomics, Nucleotide sequencing, Sequence analysis, Veterinary diseases, Viral genomics},
	pages = {e1000050},
}

@article{deMaio2015,
	title = {New {Routes} to {Phylogeography}: {A} {Bayesian} {Structured} {Coalescent} {Approximation}},
	volume = {11},
	issn = {1553-7404},
	shorttitle = {New {Routes} to {Phylogeography}},
	doi = {10.1371/journal.pgen.1005421},
	number = {8},
	journal = {PLOS Genetics},
	author = {De Maio, Nicola and Wu, Chieh-Hsi and O’Reilly, Kathleen M. and Wilson, Daniel},
	month = aug,
	year = {2015},
	keywords = {Animal phylogenetics, Ebola Virus, effective population size, Phylogenetic analysis, phylogenetics, Phylogeography, Probability density, Zoonoses},
	pages = {e1005421},
}

@article{deMaio2016,
	title = { {SCOTTI}: {Efficient} {Reconstruction} of {Transmission} within {Outbreaks} with the {Structured} {Coalescent}},
	volume = {12},
	issn = {1553-7358},
	doi = {10.1371/journal.pcbi.1005130},
	number = {9},
	journal = {PLOS Computational Biology},
	author = {De Maio, Nicola and Wu, Chieh-Hsi and Wilson, Daniel J.},
	month = sep,
	year = {2016},
	keywords = {epidemiology, Genetic epidemiology, Klebsiella pneumoniae, Pathogens, Phylogenetic analysis, phylogenetics, Simulation and modeling, Viral evolution},
	pages = {e1005130},
}