literature.bib

@Article{curated_metagenomic_data,
   Author="Pasolli, E.  and Schiffer, L.  and Manghi, P.  and Renson, A.  and Obenchain, V.  and Truong, D. T.  and Beghini, F.  and Malik, F.  and Ramos, M.  and Dowd, J. B.  and Huttenhower, C.  and Morgan, M.  and Segata, N.  and Waldron, L. ",
   Title="{{A}ccessible, curated metagenomic data through {E}xperiment{H}ub}",
   Journal="Nat Methods",
   Year="2017",
   Volume="14",
   Number="11",
   Pages="1023--1024",
   Month="10"
}

@article{gloor2017microbiome,
  title={Microbiome datasets are compositional: and this is not optional},
  author={Gloor, Gregory B and Macklaim, Jean M and Pawlowsky-Glahn, Vera and Egozcue, Juan J},
  journal={Frontiers in microbiology},
  volume={8},
  pages={2224},
  year={2017},
  publisher={Frontiers}
}

@Article{pmid31142858,
   Author="Zhou, W.  and Sailani, M. R.  and Contrepois, K.  and Zhou, Y.  and Ahadi, S.  and Leopold, S. R.  and Zhang, M. J.  and Rao, V.  and Avina, M.  and Mishra, T.  and Johnson, J.  and Lee-McMullen, B.  and Chen, S.  and Metwally, A. A.  and Tran, T. D. B.  and Nguyen, H.  and Zhou, X.  and Albright, B.  and Hong, B. Y.  and Petersen, L.  and Bautista, E.  and Hanson, B.  and Chen, L.  and Spakowicz, D.  and Bahmani, A.  and Salins, D.  and Leopold, B.  and Ashland, M.  and Dagan-Rosenfeld, O.  and Rego, S.  and Limcaoco, P.  and Colbert, E.  and Allister, C.  and Perelman, D.  and Craig, C.  and Wei, E.  and Chaib, H.  and Hornburg, D.  and Dunn, J.  and Liang, L.  and Rose, S. M. S.  and Kukurba, K.  and Piening, B.  and Rost, H.  and Tse, D.  and McLaughlin, T.  and Sodergren, E.  and Weinstock, G. M.  and Snyder, M. ",
   Title="{{L}ongitudinal multi-omics of host-microbe dynamics in prediabetes}",
   Journal="Nature",
   Year="2019",
   Volume="569",
   Number="7758",
   Pages="663--671",
   Month="05"
}

@misc{arcade_data,
    title = {Spurious Correlations},
    url = {http://www.tylervigen.com/spurious-correlations},
}

@misc{dinosaur_stats,
    author = {Khuyen Tran},
    Year = "2020",
    title = {Can Datasets of a Dinosaur and a Circle have Identical Statistics?},
    url = {https://towardsdatascience.com/how-to-turn-a-dinosaur-dataset-into-a-circle-dataset-with-the-same-statistics-64136c2e2ca0},
}

@misc{dinosaur_stats2,
    author = {Autodesk},
    Year = "2017",
    title = {Same Stats, Different Graphs: Generating Datasets with Varied Appearance and Identical Statistics through Simulated Annealing},
    url = {https://www.autodesk.com/research/publications/same-stats-different-graphs},
}

@misc{tests_as_linear,
    author = {Jonas Kristoffer Lindeløv},
    title = {Common statistical tests are linear models (or: how to teach stats)},
    url = {https://lindeloev.github.io/tests-as-linear/},
}

@article{pearson1897mathematical,
  title={Mathematical contributions to the theory of evolution.—on a form of spurious correlation which may arise when indices are used in the measurement of organs},
  author={Pearson, Karl},
  journal={Proceedings of the royal society of london},
  volume={60},
  number={359-367},
  pages={489--498},
  year={1897},
  publisher={The Royal Society London}
}

@article{ruan2006local,
  title={Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors},
  author={Ruan, Quansong and Dutta, Debojyoti and Schwalbach, Michael S and Steele, Joshua A and Fuhrman, Jed A and Sun, Fengzhu},
  journal={Bioinformatics},
  volume={22},
  number={20},
  pages={2532--2538},
  year={2006},
  publisher={Oxford University Press}
}

@article{friedman2012inferring,
  title={Inferring correlation networks from genomic survey data},
  author={Friedman, Jonathan and Alm, Eric J},
  journal={PLoS Comput Biol},
  volume={8},
  number={9},
  pages={e1002687},
  year={2012},
  publisher={Public Library of Science}
}

@article{nielsen2014identification,
  title={Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes},
  author={Nielsen, H Bj{\o}rn and Almeida, Mathieu and Juncker, Agnieszka Sierakowska and Rasmussen, Simon and Li, Junhua and Sunagawa, Shinichi and Plichta, Damian R and Gautier, Laurent and Pedersen, Anders G and Le Chatelier, Emmanuelle and others},
  journal={Nature biotechnology},
  volume={32},
  number={8},
  pages={822--828},
  year={2014},
  publisher={Nature Publishing Group}
}

@article{zeller2014potential,
  title={Potential of fecal microbiota for early-stage detection of colorectal cancer},
  author={Zeller, Georg and Tap, Julien and Voigt, Anita Y and Sunagawa, Shinichi and Kultima, Jens Roat and Costea, Paul I and Amiot, Aur{\'e}lien and B{\"o}hm, J{\"u}rgen and Brunetti, Francesco and Habermann, Nina and others},
  journal={Molecular systems biology},
  volume={10},
  number={11},
  pages={766},
  year={2014}
}

@article{weiss2016correlation,
  title={Correlation detection strategies in microbial data sets vary widely in sensitivity and precision},
  author={Weiss, Sophie and Van Treuren, Will and Lozupone, Catherine and Faust, Karoline and Friedman, Jonathan and Deng, Ye and Xia, Li Charlie and Xu, Zhenjiang Zech and Ursell, Luke and Alm, Eric J and others},
  journal={The ISME journal},
  volume={10},
  number={7},
  pages={1669--1681},
  year={2016},
  publisher={Nature Publishing Group}
}

@incollection{layeghifard2018constructing,
  title={Constructing and analyzing microbiome networks in R},
  author={Layeghifard, Mehdi and Hwang, David M and Guttman, David S},
  booktitle={Microbiome analysis},
  pages={243--266},
  year={2018},
  publisher={Springer}
}

@article{schwager2017bayesian,
  title={A Bayesian method for detecting pairwise associations in compositional data},
  author={Schwager, Emma and Mallick, Himel and Ventz, Steffen and Huttenhower, Curtis},
  journal={PLoS computational biology},
  volume={13},
  number={11},
  pages={e1005852},
  year={2017},
  publisher={Public Library of Science}
}

@article{kurtz2015sparse,
  title={Sparse and compositionally robust inference of microbial ecological networks},
  author={Kurtz, Zachary D and M{\"u}ller, Christian L and Miraldi, Emily R and Littman, Dan R and Blaser, Martin J and Bonneau, Richard A},
  journal={PLoS Comput Biol},
  volume={11},
  number={5},
  pages={e1004226},
  year={2015},
  publisher={Public Library of Science}
}

@article{rao2021multi,
  title={Multi-kingdom ecological drivers of microbiota assembly in preterm infants},
  author={Rao, Chitong and Coyte, Katharine Z and Bainter, Wayne and Geha, Raif S and Martin, Camilia R and Rakoff-Nahoum, Seth},
  journal={Nature},
  pages={1--6},
  year={2021},
  publisher={Nature Publishing Group}
}


@article{carr2019use,
  title={Use and abuse of correlation analyses in microbial ecology},
  author={Carr, Alex and Diener, Christian and Baliga, Nitin S and Gibbons, Sean M},
  journal={The ISME journal},
  volume={13},
  number={11},
  pages={2647--2655},
  year={2019},
  publisher={Nature Publishing Group}
}