References

1000 Genomes Project Consortium. 2012. “An Integrated Map of Genetic Variation from 1,092 Human Genomes.” Nature 491 (7422): 56–65.

Abbott, Edwin A. 1884. Flatland: A Romance of Many Dimensions. OUP Oxford.

Agresti, Alan. 2007. An Introduction to Categorical Data Analysis. John Wiley.

Altman, Naomi, and Martin Krzywinski. 2017. “Points of Significance: Interpreting p Values.” Nature Methods 14 (3): 213–14. https://doi.org/10.1038/nmeth.4210.

Ambroise, Christophe, and Geoffrey J. McLachlan. 2002. “Selection Bias in Gene Extraction on the Basis of Microarray Gene-Expression Data.” PNAS 99 (10): 6562–66.

Anders, Simon, and Wolfgang Huber. 2010. “Differential Expression Analysis for Sequence Count Data.” Genome Biology 11: R106. http://genomebiology.com/2010/11/10/R106.

Anders, Simon, Alejandro Reyes, and Wolfgang Huber. 2012. “Detecting differential usage of exons from RNA-Seq data.” Genome Research 22 (10): 2008–17.

Anscombe, Francis J. 1948. “The Transformation of Poisson, Binomial and Negative-Binomial Data.” Biometrika, 246–54.

Aure, Miriam Ragle, Valeria Vitelli, Sandra Jernström, Surendra Kumar, Marit Krohn, Eldri U Due, Tonje Husby Haukaas, et al. 2017. “Integrative Clustering Reveals a Novel Split in the Luminal A Subtype of Breast Cancer with Impact on Outcome.” Breast Cancer Research 19 (1): 44.

Bacher, Rhonda, and Christina Kendziorski. 2016. “Design and Computational Analysis of Single-Cell RNA-Sequencing Experiments.” Genome Biology 17 (1): 1.

Baddeley, Adrain, Jesper Moller, and Rasmus Waagepetersen. 2000. “Non- and Semiparametric Estimation of Interaction in Inhomogeneous Point Patterns.” Statistica Neerlandica 54: 329–50.

Baddeley, Adrian J. 1998. “Spatial Sampling and Censoring.” In Stochastic Geometry: Likelihood and Computation, edited by O. E. Barndorff-Nielsen, W. S. Kendall, and M. N. M. van Lieshout, 37–78. Chapman; Hall.

Beisser, Daniela, Gunnar W Klau, Thomas Dandekar, Tobias Müller, and Marcus T Dittrich. 2010. “BioNet: An R-Package for the Functional Analysis of Biological Networks.” Bioinformatics 26 (8): 1129–30.

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

Bellman, Richard Ernest. 1961. Adaptive Control Processes: A Guided Tour. Princeton University Press.

Bendall, Sean C, Garry P Nolan, Mario Roederer, and Pratip K Chattopadhyay. 2012. “A Deep Profiler’s Guide to Cytometry.” Trends in Immunology 33 (7): 323–32.

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.

Benjamini, Yoav, and Marina Bogomolov. 2014. “Selective Inference on Multiple Families of Hypotheses.” Journal of the Royal Statistical Society: Series B 76 (1): 297–318.

Benjamini, Yoav, and Yosef Hochberg. 1995. “Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.” Journal of the Royal Statistical Society B 57: 289–300.

Benjamini, Yoav, and Daniel Yekutieli. 2003. “Hierarchical FDR Testing of Trees of Hypotheses.” Technical report, Department of Statistics; Operations Research, Tel Aviv University.

Berg, Stuart, Dominik Kutra, Thorben Kroeger, Christoph N Straehle, Bernhard X Kausler, Carsten Haubold, Martin Schiegg, et al. 2019. “Ilastik: Interactive Machine Learning for (Bio)image Analysis.” Nature Methods 16 (12): 1226–32.

Bhattacharya, Bhaswar B. 2015. “Power of Graph-Based Two-Sample Tests.” arXiv Preprint arXiv:1508.07530.

Bishop, Christopher M. 2006. Pattern Recognition and Machine Learning. Springer.

Boland, Michael V., and Robert F. Murphy. 2001. “A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells.” Bioinformatics 17 (12): 1213–23.

Bouckaert, Remco, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A Suchard, Andrew Rambaut, and Alexei J Drummond. 2014. “BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.” PLoS Computational Biology 10 (4): e1003537.

Box, George EP, Norman Richard Draper, et al. 1987. Empirical Model-Building and Response Surfaces. Vol. 424. Wiley New York.

Box, George EP, William G Hunter, and J Stuart Hunter. 1978. Statistics for Experimenters: An Introduction to Design, Data Analysis, and Model Building. John Wiley & Sons.

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.

Bronštein, Il’ja N., and Konstantin A Semendjajew. 1979. Taschenbuch Der Mathematik. B.G. Teubner Verlagsgesellschaft, Leipzig; Verlag Nauka, Moscow.

Brooks, Angela N, Li Yang, Michael O Duff, Kasper D Hansen, Jung W Park, Sandrine Dudoit, Steven E Brenner, and Brenton R Graveley. 2011. “Conservation of an RNA Regulatory Map Between Drosophila and Mammals.” Genome Research, 193–202. https://doi.org/10.1101/gr.108662.110.

Bulmer, Michael George. 2003. Francis Galton: Pioneer of Heredity and Biometry. JHU Press.

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.

Callahan, Benjamin J, Paul J McMurdie, and Susan P Holmes. 2017. “Exact Sequence Variants Should Replace Operational Taxonomic Units in Marker Gene Data Analysis.” ISME Journal, 1–5.

Callahan, Benjamin J, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy J Johnson, and Susan P Holmes. 2016. “DADA2: High Resolution Sample Inference from Amplicon Data.” Nature Methods, 1–4.

Cannings, Chris, and Anthony WF Edwards. 1968. “Natural Selection and the de Finetti Diagram.” Annals of Human Genetics 31 (4): 421–28.

Caporaso, J. G., J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, et al. 2010. “QIIME Allows Analysis of High-Throughput Community Sequencing Data.” Nature Methods 7 (5): 335–36.

Carpenter, Anne E, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Han Kang, Ola Friman, David A Guertin, Joo Han Chang, Robert A Lindquist, and Jason Moffat. 2006. “CellProfiler: Image Analysis Software for Identifying and Quantifying Cell Phenotypes.” Genome Biology 7: R100.

Carr, Daniel B, Richard J Littlefield, WL Nicholson, and JS Littlefield. 1987. “Scatterplot Matrix Techniques for Large N.” Journal of the American Statistical Association 82 (398): 424–36.

Chakerian, John, and Susan Holmes. 2012. “Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees.” Journal of Computational and Graphical Statistics 21 (3): 581–99.

Chaumont, Fabrice de, Stéphane Dallongeville, Nicolas Chenouard, Nicolas Hervé, Sorin Pop, Thomas Provoost, Vannary Meas-Yedid, et al. 2012. “Icy: an open bioimage informatics platform for extended reproducible research.” Nature Methods 9: 690–96.

Chen, Min, Yang Xie, and Michael Story. 2011. “An Exponential-Gamma Convolution Model for Background Correction of Illumina BeadArray Data.” Communications in Statistics-Theory and Methods 40 (17): 3055–69.

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/.

Chiu, Sung Nok, Dietrich Stoyan, Wilfrid S. Kendall, and Joseph Mecke. 2013. Stochastic Geometry and Its Applications. Springer.

Clemmensen, Line, Trevor Hastie, Daniela Witten, and Bjarne Ersbøll. 2011. “Sparse Discriminant Analysis.” Technometrics 53: 406–13.

Cleveland, William S. 1988. The Collected Works of John w. Tukey: Graphics 1965-1985. Vol. 5. CRC Press.

Cleveland, William S., Marylyn E. McGill, and Robert McGill. 1988. “The Shape Parameter of a Two-Variable Graph.” Journal of the American Statistical Association 83: 289–300.

Cole, J. R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, et al. 2009. “The Ribosomal Database Project: Improved Alignments and New Tools for rRNA Analysis.” Nucleic Acids Research 37 (Supplement 1): D141–45.

Cook, R. Dennis. 1977. “Detection of Influential Observation in Linear Regression.” Technometrics.

Cressie, Noel A. 1991. Statistics for Spatial Data. John Wiley; Sons.

Diaconis, Persi, and David Freedman. 1980. “Finite Exchangeable Sequences.” The Annals of Probability, 745–64.

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.

Diaconis, Persi, and Susan Holmes. 1994. “Gray Codes for Randomization Procedures.” Statistics and Computing 4 (4): 287–302.

Diaconis, Persi, Susan Holmes, and Richard Montgomery. 2007. “Dynamical Bias in the Coin Toss.” SIAM Review 49 (2): 211–35.

Diday, Edwin, and M Paula Brito. 1989. “Symbolic Cluster Analysis.” In Conceptual and Numerical Analysis of Data, 45–84. Springer.

Diggle, Peter J. 2013. Statistical Analysis of Spatial and Spatio-Temporal Point Patterns. Chapman; Hall/CRCs.

DiGiulio, Daniel B., Benjamin J. Callahan, Paul J. McMurdie, Elizabeth K. Costello, Deirdre J. Lyelle, Anna Robaczewska, Christine L. Sun, et al. 2015. “Temporal and Spatial Variation of the Human Microbiota During Pregnancy.” PNAS.

Dundar, Murat, Ferit Akova, Halid Z. Yerebakan, and Bartek Rajwa. 2014. “A Non-Parametric Bayesian Model for Joint Cell Clustering and Cluster Matching: Identification of Anomalous Sample Phenotypes with Random Effects.” BMC Bioinformatics 15 (1): 1–15. https://doi.org/10.1186/1471-2105-15-314.

Durbin, Richard, Sean Eddy, Anders Krogh, and Graeme Mitchison. 1998. Biological Sequence Analysis. Cambridge University Press.

Efron, Bradley. 2010. Large-Scale Inference: Empirical Bayes Methods for Estimation, Testing, and Prediction. Cambridge University Press.

Efron, Bradley, and Robert J Tibshirani. 1994. An Introduction to the Bootstrap. CRC press.

Efron, B., and R. Tibshirani. 1993. An Introduction to the Bootstrap. Chapman & Hall/CRC.

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

Elson, D, and E Chargaff. 1952. “On the Desoxyribonucleic Acid Content of Sea Urchin Gametes.” Experientia 8 (4): 143–45.

Felsenstein, Joseph. 2004. Inferring Phylogenies. Boston: Sinauer.

Finetti, Bruno de. 1926. “Considerazioni Matematiche Sull’ereditarieta Mendeliana.” Metron 6: 3–41.

Fisher, Ronald Aylmer. 1935. The Design of Experiments. Oliver & Boyd.

Flury, Bernard. 1997. A First Course in Multivariate Statistics. Springer.

Freedman, David A. 1991. “Statistical Models and Shoe Leather.” Sociological Methodology 21 (2): 291–313.

Freedman, David, Robert Pisani, and Roger Purves. 1997. Statistics. New York, NY: WW Norton.

Friedman, Jerome H. 1997. “On Bias, Variance, 0/1—Loss, and the Curse-of-Dimensionality.” Data Mining and Knowledge Discovery 1: 55–77.

Friedman, Jerome H, and Lawrence C Rafsky. 1979. “Multivariate Generalizations of the Wald-Wolfowitz and Smirnov Two-Sample Tests.” The Annals of Statistics, 697–717.

Fukuyama, Julia, Paul J McMurdie, Les Dethlefsen, David A Relman, and Susan Holmes. 2012. “Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies.” In Pac Symp Biocomput. World Scientific.

Gentleman, Robert C, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, et al. 2004. “Bioconductor: Open Software Development for Computational Biology and Bioinformatics.” Genome Biology 5 (10): R80. https://doi.org/10.1186/gb-2004-5-10-r80.

Glass, David J. 2007. Experimental Design for Biologists. Cold Spring Harbor Laboratory Press.

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.

Grantham, Richard, Christian Gautier, Manolo Gouy, M Jacobzone, and R Mercier. 1981. “Codon Catalog Usage Is a Genome Strategy Modulated for Gene Expressivity.” Nucleic Acids Research 9 (1): 213–13.

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

Grolemund, Garrett, and Hadley Wickham. 2017. R for Data Science. O’Reilly.

Grün, Bettina, Theresa Scharl, and Friedrich Leisch. 2012. “Modelling Time Course Gene Expression Data with Finite Mixtures of Linear Additive Models.” Bioinformatics 28 (2): 222–28. https://doi.org/10.1093/bioinformatics/btr653.

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

Hallett, Robin M, Anna Dvorkin-Gheva, Anita Bane, and John A Hassell. 2012. “A Gene Signature for Predicting Outcome in Patients with Basal-Like Breast Cancer.” Scientific Reports 2.

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.

Head, Megan L, Luke Holman, Rob Lanfear, Andrew T Kahn, and Michael D Jennions. 2015. “The Extent and Consequences of p-Hacking in Science.” PLoS Biology 13 (3): e1002106.

Held, M., M. H. A. Schmitz, B. Fischer, T. Walter, B. Neumann, M. H. Olma, M. Peter, J. Ellenberg, and D. W. Gerlich. 2010. “CellCognition: Time-Resolved Phenotype Annotation in High-Throughput Live Cell Imaging.” Nature Methods 7: 747.

Helmholtz, H. von. 1867. Handbuch Der Physiologischen Optik. Leipzig: Leopold Voss.

Henderson, Fergus. 2017. “Software Engineering at Google.” ArXiv e-Prints. https://arxiv.org/abs/1702.01715.

Hoeting, Jennifer A, David Madigan, Adrian E Raftery, and Chris T Volinsky. 1999. “Bayesian Model Averaging: A Tutorial.” Statistical Science, 382–401.

Holmes - Junca, Susan. 1985. “Outils Informatiques Pour l’évaluation de La Pertinence d’un résultat En Analyse Des Données.” PhD thesis, Université Montpellier II, France.

Holmes, Susan. 1999. “Phylogenetic Trees: An Overview.” In Statistics and Genetics, 81–118. IMA 112. New York: Springer.

———. 2003a. “Bootstrapping Phylogenetic Trees: Theory and Methods.” Statistical Science 18 (2): 241–55.

———. 2003b. “Statistics for phylogenetic trees.” Theoretical Population Biology 63 (1): 17–32.

———. 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.

———. 2018. “Statistical Proof? The Problem of Irreproducibility.” Bulletin of the AMS 55 (1): 31–55.

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.

Holmes, Susan, Michael He, Tong Xu, and Peter P Lee. 2005. “Memory t Cells Have Gene Expression Patterns Intermediate Between Naive and Effector.” PNAS 102 (15): 5519–23.

Holmes, Susan, Adam Kapelner, and Peter P Lee. 2009. “An Interactive Java Statistical Image Segmentation System: GemIdent.” Journal of Statistical Software 30 (10).

Hornik, Kurt. 2005. “A CLUE for CLUster Ensembles.” Journal of Statistical Software 14 (12).

Hotelling, Harold. 1933. “Analysis of a Complex of Statistical Variables into Principal Components.” Journal of Educational Psychology 24 (6): 417–41.

———. 1944. “Some Improvements in Weighing and Other Experimental Techniques.” The Annals of Mathematical Statistics 15 (3): 297–306.

Huber, Peter J. 1964. “Robust Estimation of a Location Parameter.” The Annals of Mathematical Statistics 35: 73–101.

Huber, Wolfgang, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, et al. 2015. “Orchestrating High-Throughput Genomic Analysis with Bioconductor.” Nature Methods 12 (2): 115–21.

Hulett, Henry R, William A Bonner, Janet Barrett, and Leonard A Herzenberg. 1969. “Cell Sorting: Automated Separation of Mammalian Cells as a Function of Intracellular Fluorescence.” Science 166 (3906): 747–49.

Ideker, Trey, Owen Ozier, Benno Schwikowski, and Andrew F Siegel. 2002. “Discovering Regulatory and Signalling Circuits in Molecular Interaction Networks.” Bioinformatics 18 Suppl 1 (January): S233–40. http://bioinformatics.oxfordjournals.org/cgi/reprint/18/suppl\_1/S233.

Ignatiadis, Nikolaos, and Wolfgang Huber. 2021. “Covariate Powered Cross-Weighted Multiple Testing.” Journal of the Royal Statistical Society: Series B 83: 720–51. https://doi.org/10.1111/rssb.12411.

Ignatiadis, Nikolaos, Bernd Klaus, Judith Zaugg, and Wolfgang Huber. 2016. “Data-Driven Hypothesis Weighting Increases Detection Power in Genome-Scale Multiple Testing.” Nature Methods 13: 577–80.

Ihaka, Ross. 2003. “Color for Presentation Graphics.” In Proceedings of the 3rd International Workshop on Distributed Statistical Computing, edited by Kurt Hornik and Friedrich Leisch. Vienna, Austria: http://www.r-project.org/conferences/DSC-2003/Proceedings/; ISSN 1609-395X.

Ihaka, Ross, and Robert Gentleman. 1996. “R: A Language for Data Analysis and Graphics.” Journal of Computational and Graphical Statistics 5 (3): 299–314.

Irizarry, R. A., B. Hobbs, F. Collin, Y. D. Beazer-Barclay, K. J. Antonellis, U. Scherf, and T. P. Speed. 2003. “Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data.” Biostatistics 4 (2): 249–64.

Irizarry, Rafael A, Hao Wu, and Andrew P Feinberg. 2009. “A Species-Generalized Probabilistic Model-Based Definition of CpG Islands.” Mammalian Genome 20 (9-10): 674–80.

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.

Jacob, Laurent, Guillaume Obozinski, and Jean-Philippe Vert. 2009. “Group Lasso with Overlap and Graph Lasso.” In Proceedings of the 26th Annual International Conference on Machine Learning, 433–40. ACM.

James, Gareth, Daniela Witten, Trevor Hastie, and Robert Tibshirani. 2013. An Introduction to Statistical Learning. Springer.

Jolicoeur, Pierre, and James E Mosimann. 1960. “Size and Shape Variation in the Painted Turtle. A Principal Component Analysis.” Growth 24: 339–54.

Jolliffe, Ian. 2002. Principal Component Analysis. Wiley Online Library.

Jones, T., A. Carpenter, and P. Golland. 2005. “Voronoi-Based Segmentation of Cells on Image Manifolds.” Computer Vision for Biomedical Image Applications, 535.

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

Kahneman, Daniel. 2011. Thinking, Fast and Slow. Macmillan.

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.

Kaufman, Leonard, and Peter J Rousseeuw. 2009. Finding Groups in Data: An Introduction to Cluster Analysis. Vol. 344. John Wiley & Sons.

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

Kéry, Marc, and J Andrew Royle. 2015. Applied Hierarchical Modeling in Ecology: Analysis of Distribution, Abundance and Species Richness in r and BUGS: Volume 1: Prelude and Static Models. Academic Press.

Korthauer, K., P. K. Kimes, C. Duvallet, A. Reyes, A. Subramanian, M. Teng, C. Shukla, E. J. Alm, and S. C. Hicks. 2019. “A practical guide to methods controlling false discoveries in computational biology.” Genome Biology 20 (1): 118.

Kozich, James J, Sarah L Westcott, Nielson T Baxter, Sarah K Highlander, and Patrick D Schloss. 2013. “Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform.” Applied and Environmental Microbiology 79 (17): 5112–20.

Kristiansson, Erik, Michael Thorsen, Markus J Tamás, and Olle Nerman. 2009. “Evolutionary Forces Act on Promoter Length: Identification of Enriched Cis-Regulatory Elements.” Molecular Biology and Evolution 26 (6): 1299–1307.

Kuan, Pei Fen, Dongjun Chung, Guangjin Pan, James A Thomson, Ron Stewart, and Sündüz Keleş. 2011. “A Statistical Framework for the Analysis of ChIP-Seq Data.” Journal of the American Statistical Association 106 (495): 891–903.

Lai, Tze Leung. 2001. Sequential Analysis. Wiley Online Library.

Lange, Kenneth. 2016. MM Optimization Algorithms. SIAM.

Laufer, Christina, Bernd Fischer, Maximilian Billmann, Wolfgang Huber, and Michael Boutros. 2013. “Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping.” Nature Methods 10: 427–31.

Lawrence, Michael S., Petar Stojanov, Paz Polak, Gregory V. Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, et al. 2013. “Mutational Heterogeneity in Cancer and the Search for New Cancer-Associated Genes.” Nature 499 (7457): 214–18. https://doi.org/10.1038/nature12213.

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.

Leek, Jeffrey T., and John D. Storey. 2007. “Capturing heterogeneity in gene expression studies by surrogate variable analysis.” PLoS Genetics 3 (9): 1724–35.

Li, Wen-Hsiung. 1997. Molecular Evolution. Sinauer Associates Incorporated.

Li, Wen-Hsiung, and Dan Graur. 1991. Fundamentals of Molecular Evolution. Vol. 48. Sinauer Associates Sunderland, MA.

Liberzon, Arthur, Aravind Subramanian, Reid Pinchback, Helga Thorvaldsdóttir, Pablo Tamayo, and Jill P Mesirov. 2011. “Molecular Signatures Database (MSigDB) 3.0.” Bioinformatics 27 (12): 1739–40.

Love, Michael I., Simon Anders, Vladislav Kim, and Wolfgang Huber. 2015. “RNA-Seq Workflow: Gene-Level Exploratory Analysis and Differential Expression.” F1000Research 4 (1070). https://doi.org/10.12688/f1000research.7035.1.

Love, Michael I, Wolfgang Huber, and Simon Anders. 2014. “Moderated Estimation of Fold Change and Dispersion for RNA-seq Data with DESeq2.” Gnome Biology 15 (12): 1–21.

Mandal, Rakesh, Sophie St-Hilaire, John G Kie, and DeWayne Derryberry. 2009. “Spatial Trends of Breast and Prostate Cancers in the United States Between 2000 and 2005.” International Journal of Health Geographics 8 (1): 53.

Mardia, Kanti, John T Kent, and John M Bibby. 1979. Multiariate Analysis. New York: Academic Press.

Marin, Jean-Michel, and Christian Robert. 2007. Bayesian Core: A Practical Approach to Computational Bayesian Statistics. Springer Science & Business Media.

McCormick Jr, William T, Paul J Schweitzer, and Thomas W White. 1972. “Problem Decomposition and Data Reorganization by a Clustering Technique.” Operations Research 20 (5): 993–1009.

McElreath, Richard. 2015. Statistical Rethinking: A Bayesian Course with Examples in R and Stan. Chapman; Hall/CRC.

McLachlan, Geoffrey, and Thriyambakam Krishnan. 2007. The EM Algorithm and Extensions. Vol. 382. John Wiley & Sons.

McLachlan, Geoffrey, and David Peel. 2004. Finite Mixture Models. John Wiley & Sons.

McMurdie, Paul J, and Susan Holmes. 2014. “Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible.” PLoS Computational Biology 10 (4): e1003531.

———. 2015. “Shiny-Phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking.” Bioinformatics 31 (2): 282–83.

Mead, Roger. 1990. The Design of Experiments: Statistical Principles for Practical Applications. Cambridge University Press.

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.

Mollon, John. 1995. “Seeing Colour.” In Colour: Art and Science, edited by T. Lamb and J. Bourriau. Cambridge Unversity Press.

Mood, Alexander M. 1946. “On Hotelling’s Weighing Problem.” The Annals of Mathematical Statistics, 432–46.

Mossel, Elchanan. 2003. “On the Impossibility of Reconstructing Ancestral Data and Phylogenies.” Journal of Computational Biology 10 (5): 669–76.

Mourant, AE, Ada Kopec, and K Domaniewska-Sobczak. 1976. “The Distribution of the Human Blood Groups 2nd Edition.” Oxford University Press London.

Müllner, Daniel. 2013. “Fastcluster: Fast Hierarchical, Agglomerative Clustering Routines for r and Python.” Journal of Statistical Software 53 (9): 1–18.

Nacu, Serban, Rebecca Critchley-Thorne, Peter Lee, and Susan Holmes. 2007. “Gene Expression Network Analysis and Applications to Immunology.” Bioinformatics 23 (7, 7): 850–58. https://doi.org/10.1093/bioinformatics/btm019.

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.

Neumann, B., T. Walter, J. K. Heriche, J. Bulkescher, H. Erfle, C. Conrad, P. Rogers, et al. 2010. “Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes.” Nature 464 (7289): 721–27.

Neyman, Jerzy, and Egon S Pearson. 1936. Sufficient Statistics and Uniformly Most Powerful Tests of Statistical Hypotheses. University California Press.

Nolan, Daniel J, Michael Ginsberg, Edo Israely, Brisa Palikuqi, Michael G Poulos, Daylon James, Bi-Sen Ding, et al. 2013. “Molecular Signatures of Tissue-Specific Microvascular Endothelial Cell Heterogeneity in Organ Maintenance and Regeneration.” Developmental Cell 26 (2): 204–19.

O’Neill, Kieran, Nima Aghaeepour, Josef Špidlen, and Ryan Brinkman. 2013. “Flow Cytometry Bioinformatics.” PLoS Computational Biology 9 (12): e1003365.

Ohnishi, Y., W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, et al. 2014. “Cell-to-Cell Expression Variability Followed by Signal Reinforcement Progressively Segregates Early Mouse Lineages.” Nature Cell Biology 16 (1): 27–37.

Ozsolak, Fatih, and Patrice M Milos. 2011. “RNA sequencing: advances, challenges and opportunities.” Nature Reviews Genetics 12: 87–98.

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

Paradis, Emmanuel. 2011. Analysis of Phylogenetics and Evolution with r. Springer Science & Business Media.

Pau, Grégoire, Florian Fuchs, Oleg Sklyar, Michael Boutros, and Wolfgang Huber. 2010. “EBImage R Package for Image Processing with Applications to Cellular Phenotypes.” Bioinformatics 26 (7): 979–81.

Pearson, Karl. 1901. “LIII. On Lines and Planes of Closest Fit to Systems of Points in Space.” The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science 2 (11): 559–72.

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.

Perrière, Guy, and Jean Thioulouse. 2002. “Use and Misuse of Correspondence Analysis in Codon Usage Studies.” Nucleic Acids Research 30 (20): 4548–55.

Pounds, Stan, and Stephan W Morris. 2003. “Estimating the Occurrence of False Positives and False Negatives in Microarray Studies by Approximating and Partitioning the Empirical Distribution of p-Values.” Bioinformatics 19 (10): 1236–42.

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

Purdom, Elizabeth. 2010. “Analysis of a Data Matrix and a Graph: Metagenomic Data and the Phylogenetic Tree.” Annals of Applied Statistics, July.

Purdom, Elizabeth, and Susan P Holmes. 2005. “Error Distribution for Gene Expression Data.” Statistical Applications in Genetics and Molecular Biology 4 (1).

Rajaram, S., B. Pavie, L. F. Wu, and S. J. Altschuler. 2012. “PhenoRipper: software for rapidly profiling microscopy images.” Nature Methods 9: 635–37.

Reaven, GM, and RG Miller. 1979. “An Attempt to Define the Nature of Chemical Diabetes Using a Multidimensional Analysis.” Diabetologia 16 (1): 17–24.

Reyes, Alejandro, Simon Anders, Robert J. Weatheritt, Toby J. Gibson, Lars M. Steinmetz, and Wolfgang Huber. 2013. “Drift and Conservation of Differential Exon Usage Across Tissues in Primate Species.” Proceedings of the National Academy of Sciences 110 (38): 15377–82. https://doi.org/10.1073/pnas.1307202110.

Reyes, Alejandro, and Wolfgang Huber. 2017. “Alternative Start and Termination Sites of Transcription Drive Most Transcript Isoform Differences Across Human Tissues.” Nucleic Acids Research 46 (2): 582–92. https://doi.org/10.1093/nar/gkx1165.

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.

Rice, John. 2006. Mathematical Statistics and Data Analysis. Cengage Learning.

Ripley, B. D. 1988. Statistical Inference for Spatial Processes. Cambridge University Press.

Robert, Christian, and George Casella. 2009. Introducing Monte Carlo Methods with R. Springer Science & Business Media.

Robins, Garry, Tom Snijders, Peng Wang, Mark Handcock, and Philippa Pattison. 2007. “Recent Developments in Exponential Random Graph (p*) Models for Social Networks.” Social Networks 29 (2): 192–215.

Robinson, M. D., D. J. McCarthy, and G. K. Smyth. 2009. “edgeR: A Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data.” Bioinformatics 26 (1): 139–40. https://doi.org/10.1093/bioinformatics/btp616.

Rocke, David M, and Blythe Durbin. 2001. “A Model for Measurement Error for Gene Expression Arrays.” Journal of Computational Biology 8 (6): 557–69.

Ronquist, Fredrik, Maxim Teslenko, Paul van der Mark, Daniel L Ayres, Aaron Darling, Sebastian Höhna, Bret Larget, Liang Liu, Marc A Suchard, and John P Huelsenbeck. 2012. “MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space.” Systematic Biology 61 (3): 539–42.

Rosen, Michael J, Benjamin J Callahan, Daniel S Fisher, and Susan P Holmes. 2012. “Denoising PCR-Amplified Metagenome Data.” BMC Bioinformatics 13 (1): 283.

Rousseeuw, Peter J. 1987. “Silhouettes: A Graphical Aid to the Interpretation and Validation of Cluster Analysis.” Journal of Computational and Applied Mathematics 20: 53–65.

Rousseeuw, Peter J., and Annick M. Leroy. 1987. Robust Regression and Outlier Detection. Wiley. https://doi.org/10.1002/0471725382.

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

Russ, John C., and F. Brent Neal. 2015. The Image Processing Handbook. 7th ed. CRC Press;

Sankaran, Kris, and Susan Holmes. 2014. “structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data.” Journal of Statistical Software 59 (1): 1–21.

Schilling, Mark F. 1986. “Multivariate Two-Sample Tests Based on Nearest Neighbors.” Journal of the American Statistical Association 81 (395): 799–806.

Schindelin, Johannes, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, et al. 2012. “Fiji: an open-source platform for biological-image analysis.” Nature Methods 9: 676–82.

Schloss, P D, S L Westcott, T Ryabin, J R Hall, M Hartmann, E B Hollister, R A Lesniewski, et al. 2009. “Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities.” Applied and Environmental Microbiology 75 (23): 7537–41.

Schloss, P. D., A. M. Schuber, J. P. Zackular, K. D. Iverson, Young V. B., and Petrosino J. F. 2012. “Stabilization of the Murine Gut Microbiome Following Weaning.” Gut Microbes 3 (4): 383–93.

Schölkopf, Bernhard, Koji Tsuda, and Jean-Philippe Vert. 2004. Kernel Methods in Computational Biology. MIT press.

Schweder, T., and E. Spjøtvoll. 1982. “Plots of P-values to Evaluate Many Tests Simultaneously.” Biometrika 69: 493–502. https://doi.org/10.1093/biomet/69.3.493.

Senn, Stephen. 2004. “Controversies Concerning Randomization and Additivity in Clinical Trials.” Statistics in Medicine 23: 3729–53.

Serra, Jean. 1983. Image Analysis and Mathematical Morphology. Academic Press.

Setiadi, A Francesca, Nelson C Ray, Holbrook E Kohrt, Adam Kapelner, Valeria Carcamo-Cavazos, Edina B Levic, Sina Yadegarynia, et al. 2010. “Quantitative, Architectural Analysis of Immune Cell Subsets in Tumor-Draining Lymph Nodes from Breast Cancer Patients and Healthy Lymph Nodes.” PLoS One 5 (8): e12420.

Shalizi, Cosma. 2017. Advanced Data Analysis from an Elementary Point of View. Cambridge University Press. https://www.stat.cmu.edu/~cshalizi/ADAfaEPoV/ADAfaEPoV.pdf.

Slonim, Noam, Gurinder Singh Atwal, Gašper Tkačik, and William Bialek. 2005. “Information-Based Clustering.” PNAS 102 (51): 18297–302.

Stegle, O., L. Parts, R. Durbin, and J. Winn. 2010. “A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies.” PLoS Computational Biology 6 (5): e1000770.

Steijger, T., J. F. Abril, P. G. Engstrom, F. Kokocinski, T. J. Hubbard, R. Guigo, J. Harrow, et al. 2013. “Assessment of transcript reconstruction methods for RNA-seq.” Nature Methods 10 (12): 1177–84.

Stigler, Stephen M. 2016. The Seven Pillars of Statistical Wisdom. Harvard University Press.

Storey, John D. 2003. “The Positive False Discovery Rate: A Bayesian Interpretation and the q-Value.” The Annals of Statistics 31 (6). https://doi.org/10.1214/aos/1074290335.

Strang, Gilbert. 2009. Introduction to Linear Algebra. Fourth. Wellesley-Cambridge Press.

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

Tibshirani, Robert. 1996. “Regression Shrinkage and Selection via the Lasso.” Journal of the Royal Statistical Society. Series B (Methodological), 267–88.

Tibshirani, Robert, Guenther Walther, and Trevor Hastie. 2001. “Estimating the Number of Clusters in a Data Set via the Gap Statistic.” JRSSB 63 (2): 411–23.

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.

Tseng, George C, and Wing H Wong. 2005. “Tight Clustering: A Resampling-Based Approach for Identifying Stable and Tight Patterns in Data.” Biometrics 61 (1): 10–16.

Tukey, John W. 1977. “Exploratory Data Analysis.” Massachusetts: Addison-Wesley.

Tversky, Amos, and Daniel Kahneman. 1974. “Heuristics and Biases: Judgement Under Uncertainty.” Science 185: 1124–30.

———. 1975. “Judgment Under Uncertainty: Heuristics and Biases.” In Utility, Probability, and Human Decision Making, 141–62. Springer.

Verhulst, Pierre-François. 1845. “Recherches mathématiques Sur La Loi d’accroissement de La Population.” Nouveaux Mémoires de l’Académie Royale Des Sciences Et Belles-Lettres de Bruxelles 18: 1–42.

Vetterli, Martin, Jelena Kovačević, and Vivek Goyal. 2014. Foundations of Signal Processing. Cambridge University Press.

Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. “Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy.” Applied and Environmental Microbiology 73 (16): 5261.

Wasserstein, Ronald L, and Nicole A Lazar. 2016. “The ASA’s Statement on p-Values: Context, Process, and Purpose.” The American Statistician.

Wertheim, Joel O, and Michael Worobey. 2009. “Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2.” PLoS Computational Biology 5 (5): e1000377.

Wickham, Hadley. 2010. “A Layered Grammar of Graphics.” Journal of Computational and Graphical Statistics 19 (1): 3–28.

———. 2014. “Tidy Data.” Journal of Statistical Software 59 (10).

———. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer New York. http://had.co.nz/ggplot2/book.

Wiel, Mark A, Tonje G Lien, Wina Verlaat, Wessel N Wieringen, and Saskia M Wilting. 2016. “Better Prediction by Use of Co-Data: Adaptive Group-Regularized Ridge Regression.” Statistics in Medicine 35 (3): 368–81.

Wilkinson, Leland. 1999. “Dot Plots.” The American Statistician 53 (3): 276.

———. 2005. The Grammar of Graphics. Springer.

Wills, Quin F, Kenneth J Livak, Alex J Tipping, Tariq Enver, Andrew J Goldson, Darren W Sexton, and Chris Holmes. 2013. “Single-Cell Gene Expression Analysis Reveals Genetic Associations Masked in Whole-Tissue Experiments.” Nature Biotechnology 31 (8): 748–52.

Wilson, Greg, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, and Tracy K. Teal. 2017. “Good Enough Practices in Scientific Computing.” Edited by Francis Ouellette. PLOS Computational Biology 13 (6): e1005510. https://doi.org/10.1371/journal.pcbi.1005510.

Witten, Daniela M, and Robert Tibshirani. 2011. “Penalized Classification Using Fisher’s Linear Discriminant.” JRSSB 73 (5): 753–72.

Witten, Daniela M, Robert Tibshirani, and Trevor Hastie. 2009. “A Penalized Matrix Decomposition, with Applications to Sparse Principal Components and Canonical Correlation Analysis.” Biostatistics, kxp008.

Wright, Erik S. 2015. “DECIPHER: Harnessing Local Sequence Context to Improve Protein Multiple Sequence Alignment.” BMC Bioinformatics 16 (1): 1.

Wu, CF Jeff, and Michael S Hamada. 2011. Experiments: Planning, Analysis, and Optimization. Vol. 552. John Wiley & Sons.

Yu, Hongxiang, Diana L Simons, Ilana Segall, Valeria Carcamo-Cavazos, Erich J Schwartz, Ning Yan, Neta S Zuckerman, et al. 2012. “PRC2/EED-EZH2 Complex Is up-Regulated in Breast Cancer Lymph Node Metastasis Compared to Primary Tumor and Correlates with Tumor Proliferation in Situ.” PloS One 7 (12): e51239.

Zeileis, Achim, Christian Kleiber, and Simon Jackman. 2008. “Regression Models for Count Data in R.” Journal of Statistical Software 27 (8). http://www.jstatsoft.org/v27/i08/.

Zeller, Georg, Julien Tap, Anita Y Voigt, Shinichi Sunagawa, Jens Roat Kultima, Paul I Costea, Aurélien Amiot, et al. 2014. “Potential of Fecal Microbiota for Early-Stage Detection of Colorectal Cancer.” Molecular Systems Biology 10 (11): 766. https://doi.org/10.15252/msb.20145645.

Zou, Hui, Trevor Hastie, and Robert Tibshirani. 2006. “Sparse Principal Component Analysis.” Journal of Computational and Graphical Statistics 15 (2): 265–86.

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