Belkin, Mikhail, and Partha Niyogi. 2003. “Laplacian Eigenmaps for Dimensionality Reduction and Data Representation.” *Neural Computation* 15 (6): 1373–96.

Bengio, Yoshua, Jean-François Paiement, Pascal Vincent, Olivier Delalleau, Nicolas Le Roux, and Marie Ouimet. 2004. “Out-of-Sample Extensions for LLE, Isomap, MDS, Eigenmaps, and Spectral Clustering.” *Advances in Neural Information Processing Systems* 16: 177–84.

Braak, Cajo ter. 1985. “Correspondence Analysis of Incidence and Abundance Data: Properties in Terms of a Unimodal Respose.” *Biometrics* 41 (January).

Brodie, Eoin L, Todd Z DeSantis, Dominique C Joyner, Seung M Baek, Joern T Larsen, Gary L Andersen, Terry C Hazen, et al. 2006. “Application of a High-Density Oligonucleotide Microarray Approach to Study Bacterial Population Dynamics During Uranium Reduction and Reoxidation.” *Applied and Environmental Microbiology* 72 (9): 6288–98.

Callahan, Ben J, Kris Sankaran, Julia A Fukuyama, Paul J McMurdie, and Susan P Holmes. 2016. “Bioconductor Workflow for Microbiome Data Analysis: From Raw Reads to Community Analyses.” *F1000Research* 5.

Chessel, Daniel, Anne Dufour, and Jean Thioulouse. 2004.

“The ade4 Package - i: One-Table Methods.” *R News* 4 (1): 5–10.

http://CRAN.R-project.org/doc/Rnews/.

Diaconis, Persi, Sharad Goel, and Susan Holmes. 2008.

“Horseshoes in Multidimensional Scaling and Kernel Methods.” *Annals of Applied Statistics* 2: 777.

https://doi.org/DOI:10.1214/08-AOAS165.

Ekman, Gosta. 1954. “Dimensions of Color Vision.” *The Journal of Psychology* 38 (2): 467–74.

Goslee, Sarah C, Dean L Urban, et al. 2007. “The Ecodist Package for Dissimilarity-Based Analysis of Ecological Data.” *Journal of Statistical Software* 22 (7): 1–19.

Greenacre, Michael J. 2007. *Correspondence Analysis in Practice*. Chapman & Hall.

Guillot, Gilles, and François Rousset. 2013. “Dismantling the Mantel Tests.” *Methods in Ecology and Evolution* 4 (4): 336–44.

Hastie, Trevor, and Werner Stuetzle. 1989. “Principal Curves.” *Journal of the American Statistical Association* 84 (406): 502–16.

Hastie, Trevor, Robert Tibshirani, and Jerome Friedman. 2008. *The Elements of Statistical Learning*. 2^{\text{nd}} ed. Springer.

Holmes, Susan. 2006.

“Multivariate Analysis: The French way.” In

*Probability and Statistics: Essays in Honor of David a. Freedman*, edited by D. Nolan and T. P. Speed. Vol. 56. IMS Lecture Notes–Monograph Series. Beachwood, OH: IMS.

http://www.imstat.org/publications/lecnotes.htm.

Holmes, Susan, Alexander V Alekseyenko, Alden Timme, Tyrrell Nelson, Pankaj Jay Pasricha, and Alfred Spormann. 2011. “Visualization and Statistical Comparisons of Microbial Communities Using r Packages on Phylochip Data.” In *Pacific Symposium on Biocomputing*, 142–53. World Scientific.

Izenman, Alan Julian. 2008. “Nonlinear Dimensionality Reduction and Manifold Learning.” In *Modern Multivariate Statistical Techniques: Regression, Classification, and Manifold Learning*, 597–632. New York, NY: Springer New York.

Josse, Julie, and Susan Holmes. 2016. “Measuring Multivariate Association and Beyond.” *Statistics Surveys* 10: 132–67.

Kashyap, Purna C, Angela Marcobal, Luke K Ursell, Samuel A Smits, Erica D Sonnenburg, Elizabeth K Costello, Steven K Higginbottom, et al. 2013. “Genetically Dictated Change in Host Mucus Carbohydrate Landscape Exerts a Diet-Dependent Effect on the Gut Microbiota.” *PNAS* 110 (42): 17059–64.

Kendall, David. 1969. “Incidence Matrices, Interval Graphs and Seriation in Archeology.” *Pacific Journal of Mathematics* 28 (3): 565–70.

Leek, Jeffrey T, Robert B Scharpf, Héctor Corrada Bravo, David Simcha, Benjamin Langmead, W Evan Johnson, Donald Geman, Keith Baggerly, and Rafael A Irizarry. 2010. “Tackling the Widespread and Critical Impact of Batch Effects in High-Throughput Data.” *Nature Reviews Genetics* 11 (10): 733–39.

Moignard, Victoria, Steven Woodhouse, Laleh Haghverdi, Andrew J Lilly, Yosuke Tanaka, Adam C Wilkinson, Florian Buettner, et al. 2015. “Decoding the Regulatory Network of Early Blood Development from Single-Cell Gene Expression Measurements.” *Nature Biotechnology*.

Nelson, Tyrell A, Susan Holmes, Alexander Alekseyenko, Masha Shenoy, Todd DeSantis, Cindy Wu, Gary Andersen, et al. 2010. “PhyloChip Microarray Analysis Reveals Altered Gastrointestinal Microbial Communities in a Rat Model of Colonic Hypersensitivity.” *Neurogastroenterology & Motility*.

Pagès, Jérôme. 2016. *Multiple Factor Analysis by Example Using R*. CRC Press.

Perraudeau, Fanny, Davide Risso, Kelly Street, Elizabeth Purdom, and Sandrine Dudoit. 2017. “Bioconductor Workflow for Single-Cell RNA Sequencing: Normalization, Dimensionality Reduction, Clustering, and Lineage Inference.” *F1000Research* 6.

Prentice, IC. 1977. “Non-Metric Ordination Methods in Ecology.” *The Journal of Ecology*, 85–94.

Rhee, Soo-Yon, Matthew J Gonzales, Rami Kantor, Bradley J Betts, Jaideep Ravela, and Robert W Shafer. 2003. “Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database.” *Nucleic Acids Research* 31 (1): 298–303.

Roweis, Sam T, and Lawrence K Saul. 2000. “Nonlinear Dimensionality Reduction by Locally Linear Embedding.” *Science* 290 (5500): 2323–26.

Tenenbaum, Joshua B, Vin De Silva, and John C Langford. 2000. “A Global Geometric Framework for Nonlinear Dimensionality Reduction.” *Science* 290 (5500): 2319–23.

Trosset, Michael W, and Carey E Priebe. 2008. “The Out-of-Sample Problem for Classical Multidimensional Scaling.” *Computational Statistics & Data Analysis* 52 (10): 4635–42.