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@article{moler2003nineteen,
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@incollection{Garcia-Portugues:ads,
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@incollection{frellsen2012towards,
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@article{garciap2016diffusions,
	abstract = "We introduce stochastic models for continuous-time evolution of angles and develop their estimation. We focus on studying Langevin diffusions with stationary distributions equal to well-known distributions from directional statistics, since such diffusions can be regarded as toroidal analogues of the Ornstein--Uhlenbeck process. Their likelihood function is a product of transition densities with no analytical expression, but that can be calculated by solving the Fokker--Planck equation numerically through adequate schemes. We propose three approximate likelihoods that are computationally tractable: (i) a likelihood based on the stationary distribution; (ii) toroidal adaptations of the Euler and Shoji--Ozaki pseudo-likelihoods; (iii) a likelihood based on a specific approximation to the transition density of the wrapped normal process. A simulation study compares, in dimensions one and two, the approximate transition densities to the exact ones, and investigates the empirical performance of the approximate likelihoods. Finally, two diffusions are used to model the evolution of the backbone angles of the protein G (PDB identifier 1GB1) during a molecular dynamics simulation. The software package sdetorus implements the estimation methods and applications presented in the paper.",
	author = "Garc{\'i}a-Portugu{\'e}s, Eduardo and S{\o}rensen, Michael and Mardia, Kanti V. and Hamelryck, Thomas",
	day = "21",
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	issn = "1573-1375",
	journal = "Statistics and Computing",
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	title = "{Langevin diffusions on the torus: estimation and applications}",
	url = "https://doi.org/10.1007/s11222-017-9790-2",
	year = "2017"
}

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	author = "Martin, Darren P and Biagini, Philippe and Lefeuvre, Pierre and Golden, Michael and Roumagnac, Philippe and Varsani, Arvind",
	journal = "Viruses",
	number = "9",
	pages = "1699--1738",
	publisher = "Molecular Diversity Preservation International",
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	year = "2011"
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@article{arunapuram2013statalign,
	author = "Arunapuram, Preeti and Edvardsson, Ingolfur and Golden, Michael and Anderson, James WJ and Nov{\'a}k, {\'A}d{\'a}m and S{\"u}k{\"o}sd, Zsuzsanna and Hein, Jotun",
	journal = "Bioinformatics",
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}

@article{anderson2013quantifying,
	author = "Anderson, James WJ and Nov{\'a}k, {\'A}d{\'a}m and S{\"u}k{\"o}sd, Zsuzsanna and Golden, Michael and Arunapuram, Preeti and Edvardsson, Ingolfur and Hein, Jotun",
	journal = "BMC bioinformatics",
	number = "1",
	pages = "149",
	publisher = "BioMed Central",
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	volume = "14",
	year = "2013"
}

@article{bernardo2013identification,
	author = "Bernardo, Pauline and Golden, Michael and Akram, Mohammad and Nadarajan, Nagaswamy and Fernandez, Emmanuel and Granier, Martine and Rebelo, Anthony G and Peterschmitt, Michel and Martin, Darren P and Roumagnac, Philippe and others",
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}

@article{stenzel2014pigeon,
	author = "Stenzel, Tomasz and Piasecki, Tomasz and Chrz{\k{a}}stek, Klaudia and Julian, Laurel and Muhire, Brejnev M and Golden, Michael and Martin, Darren P and Varsani, Arvind",
	journal = "Journal of General Virology",
	number = "6",
	pages = "1338--1351",
	publisher = "Microbiology Society",
	title = "{Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of Beak and feather disease viruses}",
	volume = "95",
	year = "2014"
}

@article{martin2015rdp4,
	author = "Martin, Darren P. and Murrell, Ben and Golden, Michael and Khoosal, Arjun and Muhire, Brejnev",
	journal = "Virus Evolution",
	publisher = "Oxford University Press",
	title = "{RDP4: Detection and analysis of recombination patterns in virus genomes}",
	year = "2015"
}

@article{filloux2015genomes,
	author = "Filloux, Denis and Murrell, Sasha and Koohapitagtam, Maneerat and Golden, Michael and Julian, Charlotte and Galzi, Serge and Uzest, Marilyne and Rodier-Goud, Marguerite and D{\rq}Hont, Ang{\'e}lique and Vernerey, Marie Stephanie and others",
	journal = "Virus evolution",
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	publisher = "Oxford University Press",
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	year = "2015"
}

@article{game2013oxfold,
	author = "Game, Simon and Golden, Michael and Angela, M Yu",
	title = "{Oxfold II: Project Report}",
	year = "2013"
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@article{filloux2013characterization,
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	publisher = "SFP",
	title = "{Characterization of new endogenous geminiviral elements in yam (\# Dioscorea\# spp.) genomes}",
	year = "2013"
}

@article{bernardo2013molecular,
	author = "Bernardo, Pauline and Fernandez, Emmanuel and Granier, Martine and Golden, Michael and Rebelo, T and Peterschmitt, Michel and Martin, Darren Patrick and Roumagnac, Philippe",
	publisher = "SFP",
	title = "{Molecular characterization of\# Euphorbia caput-medusae stunt virus\#: Evidence for the existence of a new genus within the family\# Geminiviridae}",
	year = "2013"
}

@article{bernardo2013new,
	author = "Bernardo, Pauline and Golden, Michael and Mohd, A and Fernandez, Emmanuel and Granier, Martine and Rebelo, AG and Peterschmitt, Michel and Martin, Darren Patrick and Roumagnac, Philippe",
	title = "{New insights into the evolutionary history of geminiviruses derived through the discovery of divergent viruses isolated from wild plants}",
	year = "2013"
}

@article{filloux2016genomes,
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	year = "2016"
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@phdthesis{golden2013identification,
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	year = "2013"
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@Article{bhattacharya2007founder,
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repository: michaelgoldendev/trait-evolution

repo_name: michaelgoldendev/trait-evolution


text:
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