OU_StanCon.bib

@article{hmp_huttenhower,
	title = {Structure, function and diversity of the healthy human microbiome.},
	author = {Huttenhower C, Gevers D, Knight R et al.},
	year = {2012},
	publisher = {Nature},
	volume = {486:},
	pages = {207-214}
}


@article{Qin2009,
	title = {A human gut microbial gene catalogue established by metagenomic sequencing.},
	author = {Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T et al.},
	year = {2009},
	publisher = {Nature},
	volume = {464:},
	pages = {59-65}
}

@article{david_host_2014,
	title = {Host lifestyle affects human microbiota on daily timescales},
	author = {David A, Materna A, Friedman J, Campos-Baptista M,  Blackburn M et al.},
	year = {2014},
	publisher = {Genome Biology}
}

@article{faust_metagenomics_2015,
	title = {Metagenomics meets time series analysis: unraveling microbial community dynamics},
	author = {Faust K, Lahti L, Gonze D, de Vos W M, Raes J},
	year = {2015},
	publisher = {Current Opinion in Microbiology}
}

@book{Iacus_SDE,
	author={Iacus, Stefano M.},
	title={Simulation and Inference for Stochastic Differential Equations with R examples},
	year = {2008},
	publisher = {Springer}
}

@article{solin_sarkka,
	title = {State Space Methods for Efficient Inference in Student-t Process Regression},
	author = {Solin A, S{\"a}rkka S},
	year = {2015},
	publisher = {Artificial Intelligence and Statistics}
}

@article{shah_student-t,
	title = {Student-t Processes as Alternatives to Gaussian Processes},
	author = {Shah A, Wilson A.G, Ghahramani Z},
	year = {2014},
	publisher = {Proc. Int. Conf. Artif. Intell. Stat.},
	pages = {877-885}
}


@article{stan_manual,
	author = {Stan Development Team},
	title = {Modeling Language User's Guide and Reference Manual, Version 2.17.0},
	year = {2017},
	url = { http://mc-stan.org}
}

@article{Goodman2018,
	author= {Goodman A},
	title = {Fitting Ornstein-Uhlenbeck-type Student's t-processes in Stan},
	url = {https://github.com/stan-dev/stancon_talks/tree/master/2018/Contributed-Talks},
	year = {2018}
}

@article{TippingElements,
	title = {Tipping elements in the human intestinal ecosystem},
	publisher = {Nature Communications},
	url = {https://www.nature.com/articles/ncomms5344},
	author = {Lahti L, Saloj{\"a}rvi, J, Salonen A, Scheffer M and de Vos W. M.},
	year = {2014}
}

@article{dennis_2014,
	title = {Density denpendent state space model for population abundance data with unequal time intervals},
	author = {Dennis B, Ponciano J M}, 
	year = {2014},
	publisher = {Ecology},
	volume = {95},
	pages = {2069-75}
}