
@article{Abd03,
  title={{Partial least squares (PLS) regression}},
  author={Abdi, H.},
  journal={Encyclopedia of social sciences research methods (ed. M. Lewis--Beck, A. Bryman and T. Futing)},
  pages={1--7},
  year={2003}
}


@article{Adl07,
  title={rgl: 3{D} visualization device system ({O}pen{GL})},
  author={Adler, Daniel and Murdoch, Duncan},
  journal={R package version 0.75, URL http://CRAN. R-project. org/package= rgl},
  year={2007}
}

@article{Ait82,
  title={The statistical analysis of compositional data},
  author={Aitchison, John},
  journal={Journal of the Royal Statistical Society. Series B (Methodological)},
  pages={139--177},
  year={1982},
  publisher={JSTOR}
}

@article{Amb02,
  author = {Christophe Ambroise and Geoffrey J. McLachlan},
  title = {Selection Bias in Gene Extraction in Tumour Classification on Basis of
  Microarray Gene Expression Data},
  journal = {Proc. Natl. Acad. Sci. USA},
  volume = {99},
  year = {2002},
  number = {1},
  pages = {6562--6566}
}

@article{And14,
  title={Permutational multivariate analysis of variance (PERMANOVA)},
  author={Anderson, Marti J},
  journal={Wiley StatsRef: Statistics Reference Online},
  pages={1--15},
  year={2014},
  publisher={Wiley Online Library}
}

@book{And58,
  title={An Introduction to Multivariate Statistical Analysis},
  author={Anderson, T. W.},
  year={1958},
  publisher={New York : Wiley}
}

@article{Arg18,
  title={Multi-Omics Factor Analysis—a framework for unsupervised integration of multi-omics data sets},
  author={Argelaguet, Ricard and Velten, Britta and Arnol, Damien and Dietrich, Sascha and Zenz, Thorsten and Marioni, John C and Buettner, Florian and Huber, Wolfgang and Stegle, Oliver},
  journal={Molecular systems biology},
  volume={14},
  number={6},
  pages={e8124},
  year={2018}
}

@article{Arg19,
  title={Multi-omics profiling of mouse gastrulation at single-cell resolution},
  author={Argelaguet, Ricard and Clark, Stephen J and Mohammed, Hisham and Stapel, L Carine and Krueger, Christel and Kapourani, Chantriolnt-Andreas and Imaz-Rosshandler, Ivan and Lohoff, Tim and Xiang, Yunlong and Hanna, Courtney W and others},
  journal={Nature},
  volume={576},
  number={7787},
  pages={487--491},
  year={2019},
  publisher={Nature Publishing Group}
}


@article{Aru11,
  title={Enterotypes of the human gut microbiome},
  author={Arumugam, Manimozhiyan and Raes, Jeroen and Pelletier, Eric and Le Paslier, Denis and Yamada, Takuji and Mende, Daniel R and Fernandes, Gabriel R and Tap, Julien and Bruls, Thomas and Batto, Jean-Michel and others},
  journal={nature},
  volume={473},
  number={7346},
  pages={174},
  year={2011},
  publisher={Nature Publishing Group}
}

@article{Bar03,
  title={Partial least squares for discrimination},
  author={Barker, Matthew and Rayens, William},
  journal={Journal of chemometrics},
  volume={17},
  number={3},
  pages={166--173},
  year={2003},
  publisher={Wiley Online Library}
}

@article{Bau15,
  title={R markdown},
  author={Baumer, Benjamin and Udwin, Dana},
  journal={Wiley Interdisciplinary Reviews: Computational Statistics},
  volume={7},
  number={3},
  pages={167--177},
  year={2015},
  publisher={Wiley Online Library}
}

@article{Bec12,
  title={The microbiome of the lung},
  author={Beck, James M and Young, Vincent B and Huffnagle, Gary B},
  journal={Translational Research},
  volume={160},
  number={4},
  pages={258--266},
  year={2012},
  publisher={Elsevier}
}

@article{Ben95,
  title={Controlling the false discovery rate: a practical and powerful approach to multiple testing},
  author={Benjamini, Yoav and Hochberg, Yosef},
  journal={Journal of the royal statistical society. Series B (Methodological)},
  pages={289--300},
  year={1995},
  publisher={JSTOR}
}

@article{Ber08,
  title={The metabonomic signature of celiac disease},
  author={Bertini, Ivano and Calabro, Antonio and De Carli, Valeria and Luchinat, Claudio and Nepi, Stefano   and Porfirio, Berardino and Renzi, Daniela and Saccenti, Edoardo and Tenori, Leonardo},
  journal={Journal of proteome research},
  volume={8},
  number={1},
  pages={170--177},
  year={2008},
  publisher={ACS Publications}
}

@misc{Bla16,
  title={Toward a predictive understanding of {E}arth{'}s microbiomes to address 21st century challenges},
  author={Blaser, Martin J and Cardon, Zoe G and Cho, Mildred K and Dangl, Jeffrey L and Donohue, Timothy J and Green, Jessica L and Knight, Rob and Maxon, Mary E and Northen, Trent R and Pollard, Katherine S and others},
  year={2016},
  publisher={Am Soc Microbiol}
}

@article{Bla19,
  title={What does a zero mean? Understanding false, random and structural zeros in ecology},
  author={Blasco-Moreno, Anabel and P{\'e}rez-Casany, Marta and Puig, Pedro and Morante, Maria and Castells, Eva},
  journal={Methods in Ecology and Evolution},
  volume={10},
  number={7},
  pages={949--959},
  year={2019},
  publisher={Wiley Online Library}
}

@article{Bod19,
  title={A generic multivariate framework for the integration of microbiome longitudinal studies with other data types},
  author={Bodein, Antoine and Chapleur, Olivier and Droit, Arnaud and L{\^e} Cao, Kim-Anh},
  journal={Frontiers in Genetics},
  volume={10},
  year={2019},
  publisher={Frontiers Media SA}
}

@article{Bok13,
  title={Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing},
  author={Bokulich, Nicholas A and Subramanian, Sathish and Faith, Jeremiah J and Gevers, Dirk and Gordon,   Jeffrey I and Knight, Rob and Mills, David A and Caporaso, J Gregory},
  journal={Nature methods},
  volume={10},
  number={1},
  pages={57--59},
  year={2013},
  publisher={Nature Research}
}

@Article{Bou05,
 author = {Boulesteix, AL and Strimmer, K},
 title = {Predicting transcription factor activities from combined analysis of microarray and ChIP data: a  partial least squares approach.},
 journal = {Theor Biol Med Model},
 month = {Sep},
 year = {2005},
 volume = {2},
 number = {23},
}

@article{Bou04,
  title={PLS dimension reduction for classification with microarray data},
  author={Boulesteix, Anne-Laure},
  journal={Statistical applications in genetics and molecular biology},
  volume={3},
  number={1},
  pages={1--30},
  year={2004}
}

@article{Bou07,
  title={{Partial least squares: a versatile tool for the analysis of high-dimensional genomic data}},
  author={Boulesteix, A.L. and Strimmer, K.},
  journal={Briefings in Bioinformatics},
  volume={8},
  number={1},
  pages={32},
  year={2007},
  publisher={Oxford Univ Press}
}

@article{Bre01,
  title={Random forests},
  author={Breiman, Leo},
  journal={Machine learning},
  volume={45},
  number={1},
  pages={5--32},
  year={2001},
  publisher={Springer}
}

@article{Bre14,
  title={Partial least squares discriminant analysis: taking the magic away},
  author={Brereton, Richard G and Lloyd, Gavin R},
  journal={Journal of Chemometrics},
  volume={28},
  number={4},
  pages={213--225},
  year={2014},
  publisher={Wiley Online Library}
}

@article{Bus07,
  title={Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluatio   ns reveals phenotypic prototypes},
  author={Bushel, Pierre R and Wolfinger, Russell D and Gibson, Greg},
  journal={BMC Systems Biology},
  volume={1},
  number={1},
  pages={15},
  year={2007},
  publisher={BioMed Central Ltd}
}

@article{But18,
  title={Integrating single-cell transcriptomic data across different conditions, technologies, and species},
  author={Butler, Andrew and Hoffman, Paul and Smibert, Peter and Papalexi, Efthymia and Satija, Rahul},
  journal={Nature biotechnology},
  volume={36},
  number={5},
  pages={411--420},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{butte00a,
  author  = {Butte, A J and Tamayo, P and Slonim, D and Golub, T R and Kohane, I S},
	title   = {Discovering functional relationships between RNA expression and chemotherapeutic susceptibilit   y using relevance networks},
	journal = {Proceedings of the National Academy of Sciences of the USA},
	year  = {2000},
  volume= {97},
  pages = {12182--12186}
}

@article{Byl06,
  title={OPLS discriminant analysis: combining the strengths of PLS-DA and SIMCA classification},
  author={Bylesj{\"o}, Max and Rantalainen, Mattias and Cloarec, Olivier and Nicholson, Jeremy K and Holmes, Elaine and Trygg, Johan},
  journal={Journal of Chemometrics: A Journal of the Chemometrics Society},
  volume={20},
  number={8-10},
  pages={341--351},
  year={2006},
  publisher={Wiley Online Library}
}


@article{Byl07,
  author = {Bylesj\"{o}, Max   and Eriksson, Daniel   and Kusano, Miyako   and Moritz, Thomas   and Trygg,   Johan  },
	title = {Data integration in plant biology: the O2PLS method for combined modeling of transcript and       metabolite data},
	journal = {The Plant Journal},
	volume = {52},
	pages = {1181--1191},
	year = {2007}
}




@article{Cal17,
  title={The deluge of spurious correlations in big data},
  author={Calude, Cristian S and Longo, Giuseppe},
  journal={Foundations of science},
  volume={22},
  number={3},
  pages={595--612},
  year={2017},
  publisher={Springer}
}

@article{Cam12,
  title={Host genetic and environmental effects on mouse intestinal microbiota},
  author={Campbell, James H and Foster, Carmen M and Vishnivetskaya, Tatiana and Campbell, Alisha G and Yang, Zamin K and Wymore, Ann and Palumbo, Anthony V and Chesler, Elissa J and Podar, Mircea},
  journal={The ISME Journal},
  volume={6},
  number={11},
  pages={2033},
  year={2012},
  publisher={Nature Publishing Group}
}

@article{Cap10,
  title={QIIME allows analysis of high-throughput community sequencing data},
  author={Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse and Bittinger, Kyle and Bushman, Frederic D and Costello, Elizabeth K and Fierer, Noah and Pena, Antonio Gonzalez and Goodrich, Julia K and Gordon, Jeffrey I and others},
  journal={Nature methods},
  volume={7},
  number={5},
  pages={335},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{Cha03,
  title={Calcul des coefficients de r{\'e}gression et du PRESS en r{\'e}gression PLS1},
  author={Chavent, Marie and Patouille, Brigitte},
  journal={Modulad n},
  volume={30},
  pages={1--11},
  year={2003}
}

@article{Cha09,
  title={pwr: Basic functions for power analysis. R package version 1.1. 1},
  author={Champely, Stephane},
  journal={The R Foundation: Vienna},
  year={2009}
}

@misc{Cha12,
  title={pwr: basic functions for power analysis. R package version 1.1-2 [computer program]},
  author={Champely, S},
  year={2012}
}

@article{Che04,
    title = {The ade4 package-{I}- {O}ne-table methods},
    author = {D. Chessel and A.B. Dufour and J. Thioulouse},
    journal = {R News},
    year = {2004},
    volume = {4},
    pages = {5-10},
}

@article{Chi09,
  title={Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures},
  author={Chin, Mark H and Mason, Mike J and Xie, Wei and Volinia, Stefano and Singer, Mike and Peterson, Cory and Ambartsumyan, Gayane and Aimiuwu, Otaren and Richter, Laura and Zhang, Jin and others},
  journal={Cell stem cell},
  volume={5},
  number={1},
  pages={111--123},
  year={2009},
  publisher={Elsevier}
}

@article{Chu10a,
  title={Sparse partial least squares regression for simultaneous dimension reduction and variable selection},
  author={Chun, Hyonho and Kele{\c{s}}, S{\"u}nd{\"u}z},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={72},
  number={1},
  pages={3--25},
  year={2010},
  publisher={Wiley Online Library}
}


@article{Chu10b,
  title={{Sparse Partial Least Squares Classification for High Dimensional Data}},
  author={Chung, D. and Keles, S.},
  journal={Statistical Applications in Genetics and Molecular Biology},
  volume={9},
  number={1},
  pages={17},
  year={2010},
  publisher={bepress}
}

@article{Com94,
  title={Independent component analysis, a new concept?},
  author={Comon, Pierre},
  journal={Signal processing},
  volume={36},
  number={3},
  pages={287--314},
  year={1994},
  publisher={Elsevier}
}


@article{Com08,
  title={{Relationships between sensorial and physicochemical measurements in meat of rabbit from three     different breeding systems using canonical correlation analysis}},
  author={Sylvie Combes and Ignacio Gonz\'{a}lez and  S\'{e}bastien D\'{e}jean and Alain Baccini and         Nathalie Jehl and Herv\'{e} Juin and Laurent Cauquil and BÈatrice Gabinaud, Fran\c{c}ois Lebas, Catherine     Larzul},
  journal={Meat Science, in press},
  year={2008}
}

@article{Dej93,
   author  = "de Jong, S.",
   title   = "SIMPLS: An alternative approach to partial least squares regression",
   journal = "Chemometrics and Intelligent Laboratory Systems",
   volume  = 18,
   pages   = "251--263",
   year    = 1993
}

@article{Dri13,
  title={Pathway-based personalized analysis of cancer},
  author={Drier, Yotam and Sheffer, Michal and Domany, Eytan},
  journal={Proceedings of the National Academy of Sciences},
  volume={110},
  number={16},
  pages={6388--6393},
  year={2013},
  publisher={National Acad Sciences}
}

@Manual{corpcorR,
    title = {corpcor: Efficient Estimation of Covariance and (Partial) Correlation},
    author = {Juliane Schafer and Rainer Opgen-Rhein and Verena Zuber and Miika Ahdesmaki and A. Pedro Duarte Silva and Korbinian Strimmer.},
    year = {2017},
    note = {R package version 1.6.9},
    url = {https://CRAN.R-project.org/package=corpcor},
}

@article{Csa17,
  title={Sparse redundancy analysis of high-dimensional genetic and genomic data},
  author={Csala, Attila and Voorbraak, Frans PJM and Zwinderman, Aeilko H and Hof, Michel H},
  journal={Bioinformatics},
  volume={33},
  number={20},
  pages={3228--3234},
  year={2017},
  publisher={Oxford University Press}
}



@article{csa06,
  title={The igraph software package for complex network research},
  author={Csardi, Gabor and Nepusz, Tamas and others},
  journal={InterJournal, Complex Systems},
  volume={1695},
  number={5},
  pages={1--9},
  year={2006}
}

@article{Day97,
  title={Improved PLS algorithms},
  author={Dayal, Bhupinder S and MacGregor, John F},
  journal={Journal of Chemometrics: A Journal of the Chemometrics Society},
  volume={11},
  number={1},
  pages={73--85},
  year={1997},
  publisher={Wiley Online Library}
}


@article{Dej94,
  title={{Comments on the PLS kernel algorithm}},
  author={De Jong, S. and Ter Braak, CJF},
  journal={Journal of chemometrics},
  volume={8},
  number={2},
  pages={169--174},
  year={1994},
  publisher={Wiley}
}

@article{Dia06,
  title={Gene selection and classification of microarray data using random forest},
  author={D{\'\i}az-Uriarte, Ram{\'o}n and De Andres, Sara Alvarez},
  journal={BMC bioinformatics},
  volume={7},
  number={1},
  pages={3},
  year={2006},
  publisher={BioMed Central}
}
@article{Dra07a,
  title={The ade4 package: implementing the duality diagram for ecologists},
  author={Dray, St{\'e}phane and Dufour, Anne-B{\'e}atrice and others},
  journal={Journal of statistical software},
  volume={22},
  number={4},
  pages={1--20},
  year={2007}
}

@article{Dra07b,
  title={The ade4 package {II}: Two-table and {K}-table methods},
  author={Dray, St{\'e}phane and Dufour, Anne B and Chessel, Daniel and others},
  journal={R news},
  volume={7},
  number={2},
  pages={47--52},
  year={2007}
}

@article{Dud02,
  title={Comparison of discrimination methods for the classification of tumors using gene expression data},
  author={Dudoit, Sandrine and Fridlyand, Jane and Speed, Terence P},
  journal={Journal of the American statistical association},
  volume={97},
  number={457},
  pages={77--87},
  year={2002},
  publisher={Taylor \& Francis}
}

@article{Efr97,
  title={Improvements on cross-validation: the 632+ bootstrap method},
  author={Efron, Bradley and Tibshirani, Robert},
  journal={Journal of the American Statistical Association},
  volume={92},
  number={438},
  pages={548--560},
  year={1997},
  publisher={Taylor \& Francis}
}

@Manual{elasticnetR,
    title = {elasticnet: Elastic-Net for Sparse Estimation and Sparse PCA},
    author = {Hui Zou and Trevor Hastie},
    year = {2018},
    note = {R package version 1.1.1},
    url = {https://CRAN.R-project.org/package=elasticnet},
}

@article{Esc17,
  title={FROGS: find, rapidly, OTUs with galaxy solution},
  author={Escudi{\'e}, Fr{\'e}d{\'e}ric and Auer, Lucas and Bernard, Maria and Mariadassou, Mahendra and Cauquil, Laurent and Vidal, Katia and Maman, Sarah and Hernandez-Raquet, Guillermina and Combes, Sylvie and Pascal, G{\'e}raldine},
  journal={Bioinformatics},
  volume={34},
  number={8},
  pages={1287--1294},
  year={2017},
  publisher={Oxford University Press}
}



@incollection{Esl13,
  title={Multi-group PLS regression: application to epidemiology},
  author={Eslami, Aida and Qannari, El Mostafa and Kohler, Achim and Bougeard, St{\'e}phanie},
  booktitle={New Perspectives in Partial Least Squares and Related Methods},
  pages={243--255},
  year={2013},
  publisher={Springer}
}

@incollection{Esl14b,
  title={Two-block multi-group data analysis. Application to epidemiology},
  author={Eslami, A and Qannari, EM and Kohler, A and Bougeard, S},
  booktitle={New perspectives in Partial Least Squares and Related Methods},
  year={2014},
  publisher={Springer Verlag}
}

@article{Eat73,
  title={The non--singularity of generalized sample covariance matrices},
  author={Eaton, M. L. and Perlman, M. D.},
  journal={Annals of Statistics},
  volume={1},
  pages={470--717},
  year={1973}
}

@article{Eis98,
	author  = {Eisen, M B and Spellman, P T and Brown, P O and Botstein, D},
	title   = {Cluster analysis and display of genome--wide expression patterns},
	journal = {Proceeding of the National Academy of Sciences of the USA},
	year  = {1998},
  volume= {95},
  pages = {14863--14868}
}

@article{Esl14,
  title={Algorithms for multi-group PLS},
  author={Eslami, Aida and Qannari, El Mostafa and Kohler, Achim and Bougeard, St{\'e}phanie},
  journal={Journal of Chemometrics},
  volume={28},
  number={3},
  pages={192-201},
  year={2014},
  publisher={Wiley Online Library}
}

@article{Eyr06,
  title={The HUGO gene nomenclature database, 2006 updates},
  author={Eyre, Tina A and Ducluzeau, Fabrice and Sneddon, Tam P and Povey, Sue and Bruford, Elspeth A and Lush, Michael J},
  journal={Nucleic acids research},
  volume={34},
  number={suppl\_1},
  pages={D319--D321},
  year={2006},
  publisher={Oxford University Press}
}

@article{Fer17,
  title={Combining strong sparsity and competitive predictive power with the L-sOPLS approach for biomarker discovery in metabolomics},
  author={F{\'e}raud, Baptiste and Munaut, Carine and Martin, Manon and Verleysen, Michel and Govaerts, Bernadette},
  journal={Metabolomics},
  volume={13},
  number={11},
  pages={130},
  year={2017},
  publisher={Springer}
}


@article{Fer14,
  title={Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis},
  author={Fernandes, Andrew D and Reid, Jennifer NS and Macklaim, Jean M and McMurrough, Thomas A and        Edgell, David R and Gloor, Gregory B},
  journal={Microbiome},
  volume={2},
  number={1},
  pages={1},
  year={2014},
  publisher={BioMed Central}
}

@article{Fil09,
  title={Principal component analysis for compositional data with outliers},
  author={Filzmoser, Peter and Hron, Karel and Reimann, Clemens},
  journal={Environmetrics},
  volume={20},
  number={6},
  pages={621--632},
  year={2009},
  publisher={Wiley Online Library}
}


@article{For88,
author = {Fornell, Claes and Barclay, Donald W and Rhee, Byong-Duk},
issn = {0027-3171},
journal = {Multivariate Behavioral Research},
month = {jul},
number = {3},
pages = {349--360},
title = {{A Model and Simple Iterative Algorithm For Redundancy Analysis}},
volume = {23},
year = {1988}
}


@book{Fri01,
  title={The elements of statistical learning},
  author={Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert},
  volume={1},
  year={2001},
  publisher={Springer series in statistics New York}
}


@article{Fri06,
  title={Independent component analysis reveals new and biologically significant structures in micro array   data},
  author={Frigyesi, Attila and Veerla, Srinivas and Lindgren, David and H{\"o}glund, Mattias},
  journal={BMC bioinformatics},
  volume={7},
  number={1},
  pages={290},
  year={2006},
  publisher={BioMed Central Ltd}
}

@article{Fri89,
  title={Regularized discriminant analysis},
  author={Friedman, J. H.},
  journal={Journal of the American Statistical Association},
  volume={84},
  pages={165--175},
  year={1989}
}

@article{Fri07,
  title={Pathwise coordinate optimization},
  author={Friedman, Jerome and Hastie, Trevor and H{\"o}fling, Holger and Tibshirani, Robert and others},
  journal={The annals of applied statistics},
  volume={1},
  number={2},
  pages={302--332},
  year={2007},
  publisher={Institute of Mathematical Statistics}
}

@article{Fri10,
  title={Regularization paths for generalized linear models via coordinate descent},
  author={Friedman, Jerome and Hastie, Trevor and Tibshirani, Rob},
  journal={Journal of statistical software},
  volume={33},
  number={1},
  pages={1},
  year={2010},
  publisher={NIH Public Access}
}

@article{Fue04,
  title={Discovery of meaningful associations in genomic data using partial correlation coefficients},
  author={De La Fuente, Alberto and Bing, Nan and Hoeschele, Ina and Mendes, Pedro},
  journal={Bioinformatics},
  volume={20},
  number={18},
  pages={3565--3574},
  year={2004},
  publisher={Oxford University Press}
}



@article{Gag12,
  title={Using control genes to correct for unwanted variation in microarray data},
  author={Gagnon-Bartsch, Johann A and Speed, Terence P},
  journal={Biostatistics},
  volume={13},
  number={3},
  pages={539--552},
  year={2012},
  publisher={Oxford University Press}
}

@article{Ger12,
  title={On the decoding of intracranial data using sparse orthonormalized partial least squares},
  author={van Gerven, Marcel AJ and Chao, Zenas C and Heskes, Tom},
  journal={Journal of neural engineering},
  volume={9},
  number={2},
  pages={026017},
  year={2012},
  publisher={IOP Publishing}
}


@book{Git85,
  title={{Canonical Analysis: A Review with Applications in Ecology}},
  author={Gittins, R.},
  year={1985},
  publisher={Springer-Verlag}
}

@article{Gio14,
    title = {Three-Way Component Analysis Using the {R} Package
      {ThreeWay}},
    author = {Paolo Giordani and Henk A. L. Kiers and Maria Antonietta
      {Del Ferraro}},
    journal = {Journal of Statistical Software},
    year = {2014},
    volume = {57},
    number = {7},
    pages = {1--23},
    url = {http://www.jstatsoft.org/v57/i07/},
  }


@article{Gli15,
  title={Methods for biological data integration: perspectives and challenges},
  author={Gligorijevi{\'c}, Vladimir and Pr{\v{z}}ulj, Nata{\v{s}}a},
  journal={Journal of the Royal Society Interface},
  volume={12},
  number={112},
  pages={20150571},
  year={2015},
  publisher={The Royal Society}
}

@article{Glo17,
  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}
}

@book{Gol96,
  title={{Matrix Computations}},
  author={Golub, G.H. and Van Loan, C.F.},
  year={1996},
  publisher={Johns Hopkins University Press}
}

@incollection{Gol71,
  title={Singular value decomposition and least squares solutions},
  author={Golub, Gene H and Reinsch, Christian},
  booktitle={Linear Algebra},
  pages={134--151},
  year={1971},
  publisher={Springer}
}

@article{Gon08,
  title={{CCA}: An {R} package to extend canonical correlation analysis},
  author={Gonz{\'a}lez, Ignacio and D{\'e}jean, S{\'e}bastien and Martin, Pascal GP and Baccini, Alain},
  journal={Journal of Statistical Software},
  volume={23},
  number={12},
  pages={1--14},
  year={2008},
  publisher={American Statistical Association}
}

@article{Gon09,
  title={Highlighting relationships between heterogeneous biological data through graphical displays based on regularized canonical correlation analysis},
  author={Gonz{\'a}lez, Ignacio and D{\'e}jean, S{\'e}bastien and Martin, PGP and Gon{\c{c}}alves, Olivier and Besse, Philippe and Baccini, Alain},
  journal={Journal of Biological Systems},
  volume={17},
  number={02},
  pages={173--199},
  year={2009},
  publisher={World Scientific}
}

@article{Gon12,
  title={Visualising associations between paired 'omics' data sets},
  author={Gonz{\'a}lez, Ignacio and L{\^e} Cao, Kim-Anh and Davis, Melissa J and D{\'e}jean, S{\'e}bastien   and others},
  journal={BioData mining},
  volume={5},
  number={1},
  pages={19},
  year={2012},
  publisher={BioMed Central Ltd}
}

@article{GTex,
  title={The genotype-tissue expression (GTEx) project},
  author={Lonsdale, John and Thomas, Jeffrey and Salvatore, Mike and Phillips, Rebecca and Lo, Edmund and Shad, Saboor and Hasz, Richard and Walters, Gary and Garcia, Fernando and Young, Nancy and others},
  journal={Nature genetics},
  volume={45},
  number={6},
  pages={580},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{Gui16,
  title={Plankton networks driving carbon export in the oligotrophic ocean},
  author={Guidi, Lionel and Chaffron, Samuel and Bittner, Lucie and Eveillard, Damien and Larhlimi, Abdelhalim and Roux, Simon and Darzi, Youssef and Audic, St{\'e}phane and Berline, L{\'e}o and Brum, Jennifer R and others},
  journal={Nature},
  volume={532},
  number={7600},
  pages={465},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{Gun12,
  title={A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers},
  author={G{\"u}nther, Oliver P and Chen, Virginia and Freue, Gabriela Cohen and Balshaw, Robert F and Tebbutt, Scott J and Hollander, Zsuzsanna and Takhar, Mandeep and McMaster, W Robert and McManus, Bruce M and Keown, Paul A and others},
  journal={BMC bioinformatics},
  volume={13},
  number={1},
  pages={326},
  year={2012},
  publisher={Springer}
}


@article{Gun14,
  title={Novel multivariate methods for integration of genomics and proteomics data: applications in a       kidney transplant rejection study},
  author={G{\"u}nther, Oliver P and Shin, Heesun and Ng, Raymond T and McMaster, W Robert and McManus,       Bruce M and Keown, Paul A and Tebbutt, Scott J and L{\^e} Cao, Kim-Anh},
  journal={Omics: a journal of integrative biology},
  volume={18},
  number={11},
  pages={682--695},
  year={2014},
  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}

@article{Guy02,
  title={Gene selection for cancer classification using support vector machines},
  author={Guyon, Isabelle and Weston, Jason and Barnhill, Stephen and Vapnik, Vladimir},
  journal={Machine learning},
  volume={46},
  number={1-3},
  pages={389--422},
  year={2002},
  publisher={Springer}
}

@article{Hag18,
  title={Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors},
  author={Haghverdi, Laleh and Lun, Aaron TL and Morgan, Michael D and Marioni, John C},
  journal={Nature biotechnology},
  volume={36},
  number={5},
  pages={421--427},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{Ham11,
  title={Potential risk factors associated with human encephalitis: application of canonical correlation     analysis},
  author={Hamid, Jemila S and Meaney, Christopher and Crowcroft, Natasha S and Granerod, Julia and Beyene,   Joseph and others},
  journal={BMC medical research methodology},
  volume={11},
  number={1},
  pages={120},
  year={2011},
  publisher={BioMed Central Ltd}
}

@article{Har11,
  title={Sparse canonical correlation analysis},
  author={Hardoon, David R and Shawe-Taylor, John},
  journal={Machine Learning},
  volume={83},
  number={3},
  pages={331--353},
  year={2011},
  publisher={Springer}
}

@article{Has95,
  title={Penalized discriminant analysis},
  author={Hastie, T. and Buja, A. and Tibshirani, R.},
  journal={Annals of Statistics},
  volume={23},
  pages={73--102},
  year={1995}
}

@article{Has89,
  title={Principal curves},
  author={Hastie, Trevor and Stuetzle, Werner},
  journal={Journal of the American Statistical Association},
  volume={84},
  number={406},
  pages={502--516},
  year={1989},
  publisher={Taylor \& Francis}
}

@article{Haw04,
  title={The problem of overfitting},
  author={Hawkins, Douglas M},
  journal={Journal of chemical information and computer sciences},
  volume={44},
  number={1},
  pages={1--12},
  year={2004},
  publisher={ACS Publications}
}

@article{Her18,
  title={Multivariate analysis of multiple datasets: a practical guide for chemical ecology},
  author={Herv{\'e}, Maxime R and Nicol{\`e}, Florence and L{\^e} Cao, Kim-Anh},
  journal={Journal of chemical ecology},
  volume={44},
  number={3},
  pages={215--234},
  year={2018},
  publisher={Springer}
}

@article{Hie19,
  title={Efficient integration of heterogeneous single-cell transcriptomes using Scanorama},
  author={Hie, Brian and Bryson, Bryan and Berger, Bonnie},
  journal={Nature biotechnology},
  volume={37},
  number={6},
  pages={685--691},
  year={2019},
  publisher={Nature Publishing Group}
}


@inproceedings{Hoe64,
  title={Ridge analysis},
  author={Hoerl, Arthur E},
  booktitle={Chemical engineering progress symposium series},
  volume={60},
  pages={67--77},
  year={1964}
}

@article{Hoe70,
  title={Ridge regression: biased estimation for non-orthogonal problems},
  author={Hoerl, A. E. and Kennard, R. W.},
  journal={Technometrics},
  volume={12},
  pages={55--67},
  year={1970}
}



@article{Hor16,
  title={Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment},
  author={Hornung, Roman and Boulesteix, Anne-Laure and Causeur, David},
  journal={BMC bioinformatics},
  volume={17},
  number={1},
  pages={27},
  year={2016},
  publisher={BioMed Central}
}

@article{Hos98,
  title={{PLS regression methods}},
  author={Hoskuldsson, A.},
  journal={Journal of Chemometrics},
  volume={2},
  number={3},
  pages={211--228},
  year={1988}
}

@article{Hot33,
  title={Analysis of a complex of statistical variables into principal components.},
  author={Hotelling, Harold},
  journal={Journal of educational psychology},
  volume={24},
  number={6},
  pages={417},
  year={1933},
  publisher={Warwick \& York}
}


@article{Hot36,
  title={Relations between two sets of variates},
  author={Hotelling, H.},
  journal={Biometrika},
  volume={28},
  pages={321--377},
  year={1936}
}

@article{Hua06,
  title={Independent component analysis-based penalized discriminant method for tumor classification using   gene expression data},
  author={Huang, De-Shuang and Zheng, Chun-Hou},
  journal={Bioinformatics},
  volume={22},
  number={15},
  pages={1855--1862},
  year={2006},
  publisher={Oxford Univ Press}
}

@article{Hua17,
  title={More is better: recent progress in multi-omics data integration methods},
  author={Huang, Sijia and Chaudhary, Kumardeep and Garmire, Lana X},
  journal={Frontiers in genetics},
  volume={8},
  pages={84},
  year={2017},
  publisher={Frontiers}
}

@article{Hus08,
    title = {{FactoMineR}: A Package for Multivariate Analysis},
    author = {S\'ebastien L\^e and Julie Josse and Fran\c{c}ois
      Husson},
    journal = {Journal of Statistical Software},
    year = {2008},
    volume = {25},
    number = {1},
    pages = {1--18},
    doi = {10.18637/jss.v025.i01},
  }

@article{Hut12,
  title={Structure, function and diversity of the healthy human microbiome},
  author={Huttenhower, Curtis and Gevers, Dirk and Knight, Rob and Abubucker, Sahar and Badger, Jonathan H and Chinwalla, Asif T and Creasy, Heather H and Earl, Ashlee M and FitzGerald, Michael G and Fulton, Robert S and others},
  journal={nature},
  volume={486},
  number={7402},
  pages={207},
  year={2012},
  publisher={Nature Publishing Group}
}

@article{Hyv01,
  title={Independent component analysis: algorithms and applications},
  author={Hyv{\"a}rinen, Aapo and Oja, Erkki},
  journal={Neural networks},
  volume={13},
  number={4},
  pages={411--430},
  year={2001},
  publisher={Elsevier}
}

@article{Ind07,
  title={From dummy regression to prior probabilities in PLS-DA},
  author={Indahl, Ulf G and Martens, Harald and N{\ae}s, Tormod},
  journal={Journal of Chemometrics: A Journal of the Chemometrics Society},
  volume={21},
  number={12},
  pages={529--536},
  year={2007},
  publisher={Wiley Online Library}
}

@article{Ind09,
  title={Canonical partial least squares—a unified PLS approach to classification and regression problems},
  author={Indahl, Ulf G and Liland, Kristian Hovde and N{\ae}s, Tormod},
  journal={Journal of Chemometrics: A Journal of the Chemometrics Society},
  volume={23},
  number={9},
  pages={495--504},
  year={2009},
  publisher={Wiley Online Library}
}


@article{Jia17,
  title={Advances in industrial microbiome based on microbial consortium for biorefinery},
  author={Jiang, Li-Li and Zhou, Jin-Jie and Quan, Chun-Shan and Xiu, Zhi-Long},
  journal={Bioresources and Bioprocessing},
  volume={4},
  number={1},
  pages={11},
  year={2017},
  publisher={SpringerOpen}
}

@book{Jam13,
  title={An introduction to statistical learning},
  author={James, Gareth and Witten, Daniela and Hastie, Trevor and Tibshirani, Robert},
  volume={112},
  year={2013},
  publisher={Springer}
}

@article{Joh07,
  title={Adjusting batch effects in microarray expression data using empirical Bayes methods},
  author={Johnson, W Evan and Li, Cheng and Rabinovic, Ariel},
  journal={Biostatistics},
  volume={8},
  number={1},
  pages={118--127},
  year={2007},
  publisher={Oxford University Press}
}

@book{Jol05,
  title={Principal component analysis},
  author={Jolliffe, Ian},
  year={2005},
  publisher={Wiley Online Library}
}

@article{Jos13,
  title={Robust methods for differential abundance analysis in marker gene surveys},
  author={Joseph, N and Paulson, CS and Corrada Bravo, H and Pop, M},
  journal={Nat. Methods},
  volume={10},
  pages={1200--1202},
  year={2013}
}

@article{Joz10,
  title={Metabolomic and transcriptomic stress response of {E}scherichia coli},
  author={Jozefczuk, Szymon and Klie, Sebastian and Catchpole, Gareth and Szymanski, Jedrzej and Cuadros-Inostroza, Alvaro and Steinhauser, Dirk and Selbig, Joachim and Willmitzer, Lothar},
  journal={Molecular systems biology},
  volume={6},
  number={1},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{Kar03,
  title={A simple rule for the selection of principal components},
  author={Karlis, Dimitris and Saporta, Gilbert and Spinakis, Antonis},
  journal={Communications in Statistics-Theory and Methods},
  volume={32},
  number={3},
  pages={643--666},
  year={2003},
  publisher={Taylor \& Francis}
}

@article{Kha01,
  title={Classification and diagnostic prediction of cancers using gene expression profiling and artificial   neural networks},
  author={Khan, Javed and Wei, Jun S and Ringner, Markus and Saal, Lao H and Ladanyi, Marc and Westermann,   Frank and Berthold, Frank and Schwab, Manfred and Antonescu, Cristina R and Peterson, Carsten and others},
  journal={Nature medicine},
  volume={7},
  number={6},
  pages={673--679},
  year={2001},
  publisher={Nature Publishing Group}
}

@article{Kim12,
  title={Consistent model selection criteria on high dimensions},
  author={Kim, Yongdai and Kwon, Sunghoon and Choi, Hosik},
  journal={Journal of Machine Learning Research},
  volume={13},
  number={Apr},
  pages={1037--1057},
  year={2012}
}


@article{Kim16,
  title={MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis},
  author={Kim, SungHwan and Lin, Chien-Wei and Tseng, George C},
  journal={Bioinformatics},
  volume={32},
  number={13},
  pages={1966--1973},
  year={2016},
  publisher={Oxford University Press}
}

@article{Kje10,
  title={Some common misunderstandings in chemometrics},
  author={Kjeldahl, Karin and Bro, Rasmus},
  journal={Journal of Chemometrics},
  volume={24},
  number={7-8},
  pages={558--564},
  year={2010},
  publisher={Wiley Online Library}
}

@article{Koe11,
  title={Succession of microbial consortia in the developing infant gut microbiome},
  author={Koenig, Jeremy E and Spor, Aym{\'e} and Scalfone, Nicholas and Fricker, Ashwana D and Stombaugh,   Jesse and Knight, Rob and Angenent, Largus T and Ley, Ruth E},
  journal={Proceedings of the National Academy of Sciences},
  volume={108},
  number={Supplement 1},
  pages={4578--4585},
  year={2011},
  publisher={National Acad Sciences}
}

@article{Kon12,
  title={Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis},
  author={Kong, Heidi H and Oh, Julia and Deming, Clay and Conlan, Sean and Grice, Elizabeth A and Beatson, Melony A and Nomicos, Effie and Polley, Eric C and Komarow, Hirsh D and Murray, Patrick R and others},
  journal={Genome research},
  volume={22},
  number={5},
  pages={850--859},
  year={2012},
  publisher={Cold Spring Harbor Lab}
}

@article{Kor11,
  author = {Koren, Omry and Spor, Aymé and Felin, Jenny and Fåk, Frida and Stombaugh, Jesse and Tremaroli,   Valentina and Behre, Carl Johan and Knight, Rob and Fagerberg, Björn and Ley, Ruth E. and Bäckhed,         Fredrik},
  title = {Human oral, gut, and plaque microbiota in patients with atherosclerosis},
  volume = {108},
  number = {Supplement 1},
  pages = {4592-4598},
  year = {2011},
  doi = {10.1073/pnas.1011383107},
  URL = {http://www.pnas.org/content/108/Supplement_1/4592.abstract},
  eprint = {http://www.pnas.org/content/108/Supplement_1/4592.full.pdf},
  journal = {Proceedings of the National Academy of Sciences}
}

@article{Kra08,
    title = {Penalized Partial Least Squares with Applications to
      B-Spline Transformations and Functional Data},
    author = {N. Kraemer and N. Kraemer and A.-L. Boulesteix and G.
      Tutz},
    journal = {Chemometrics and Intelligent Laboratory Systems},
    year = {2008},
    volume = {94},
    number = {60-69},
}

@article{Kun10,
  title={Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates},
  author={Kunin, Victor and Engelbrektson, Anna and Ochman, Howard and Hugenholtz, Philip},
  journal={Environmental microbiology},
  volume={12},
  number={1},
  pages={118--123},
  year={2010},
  publisher={Wiley Online Library}
}


@article{Lazz12,
  title={The cost of large numbers of hypothesis tests on power, effect size and sample size},
  author={Lazzeroni, LC and Ray, A},
  journal={Molecular psychiatry},
  volume={17},
  number={1},
  pages={108},
  year={2012},
  publisher={Nature Publishing Group}
}

@article{Laz12,
  title={Batch effect removal methods for microarray gene expression data integration: a survey},
  author={Lazar, Cosmin and Meganck, Stijn and Taminau, Jonatan and Steenhoff, David and Coletta, Alain and Molter, Colin and Weiss-Sol{\'i}s, David Y and Duque, Robin and Bersini, Hugues and Now{\'e}, Ann},
  journal={Briefings in bioinformatics},
  volume={14},
  number={4},
  pages={469--490},
  year={2012},
  publisher={Oxford University Press}
}

@Article{Le08,
    title = {{FactoMineR}: A Package for Multivariate Analysis},
    author = {S\'ebastien L\^e and Julie Josse and Fran\c{c}ois
      Husson},
    journal = {Journal of Statistical Software},
    year = {2008},
    volume = {25},
    number = {1},
    pages = {1--18},
    doi = {10.18637/jss.v025.i01},
}

@article{Lec08,
  title={A sparse {PLS} for variable selection when integrating omics data.},
  author={L{\^e} Cao, KA and Rossouw, D and Robert-Grani{\'e}, C and Besse, P and others},
  journal={Statistical applications in genetics and molecular biology},
  volume={7},
  number={35},
  year={2008}
}

@article{Lec09b,
  title={integr{O}mics: an {R} package to unravel relationships between two omics datasets},
  author={L{\^e} Cao, Kim-Anh and Gonz{\'a}lez, Ignacio and D{\'e}jean, S{\'e}bastien},
  journal={Bioinformatics},
  volume={25},
  number={21},
  pages={2855--2856},
  year={2009},
  publisher={Oxford Univ Press}
}

@article{Lec09a,
  title={Sparse canonical methods for biological data integration: application to a cross-platform study},
  author={L{\^e} Cao, Kim-Anh and Martin, Pascal GP and Robert-Grani{\'e}, Christ{\`e}le and Besse,          Philippe},
  journal={BMC bioinformatics},
  volume={10},
  number={1},
  pages={34},
  year={2009},
  publisher={BioMed Central Ltd}
}

@article{Lec14,
  title={YuGene: a simple approach to scale gene expression data derived from different platforms for integrated analyses},
  author={L{\^e} Cao, Kim-Anh and Rohart, Florian and McHugh, Leo and Korn, Othmar and Wells, Christine A},
  journal={Genomics},
  volume={103},
  number={4},
  pages={239--251},
  year={2014},
  publisher={Elsevier}
}

@article{Lec11,
  title={Sparse {PLS} {D}iscriminant {A}nalysis: biologically relevant feature selection and graphical       displays for multiclass problems},
  author={L{\^e} Cao, Kim-Anh and Boitard, Simon and Besse, Philippe},
  journal={BMC bioinformatics},
  volume={12},
  number={1},
  pages={253},
  year={2011},
  publisher={BioMed Central Ltd}
}

@article{Lec16,
  title = {MixMC: Multivariate insights into Microbial Communities},
  author = {L{\^e} Cao, Kim-Anh and Costello, Mary-Ellen and Chua, Xin-Yi and Brazeilles, R{\'e}mi and       Rondeau, Pascale},
  journal={PloS one},
  volume={11},
  number={8},
  pages={e0160169},
  year={2016},
  publisher={Public Library of Science}
}

@article{Lee03,
  title={Application of independent component analysis to microarrays},
  author={Lee, Su-In and Batzoglou, Serafim and others},
  journal={Genome biology},
  volume={4},
  number={11},
  pages={76--76},
  year={2003},
  publisher={BioMed Central Ltd}
}

@article{Lee07,
  title={Capturing heterogeneity in gene expression studies by surrogate variable analysis},
  author={Leek, Jeffrey T and Storey, John D},
  journal={PLoS genetics},
  volume={3},
  number={9},
  pages={e161},
  year={2007},
  publisher={Public Library of Science}
}

@article{Lee12,
  title={The sva package for removing batch effects and other unwanted variation in high-throughput experiments},
  author={Leek, Jeffrey T and Johnson, W Evan and Parker, Hilary S and Jaffe, Andrew E and Storey, John D},
  journal={Bioinformatics},
  volume={28},
  number={6},
  pages={882--883},
  year={2012},
  publisher={Oxford University Press}
}

@article{Lee19,
  title={Dynamic molecular changes during the first week of human life follow a robust developmental trajectory},
  author={Lee, Amy H and Shannon, Casey P and Amenyogbe, Nelly and Bennike, Tue B and Diray-Arce, Joann and Idoko, Olubukola T and Gill, Erin E and Ben-Othman, Rym and Pomat, William S and Van Haren, Simon D and others},
  journal={Nature communications},
  volume={10},
  number={1},
  pages={1092},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{Lei98,
    title = {\textup{A Singular Value Decomposition of \textit{k}-Way
      Array for a Principal Component Analysis of Multiway Data,
      \textsc{PTA}-\textit{k}}},
    author = {D. Leibovici and R. Sabatier},
    journal = {Linear Algebra and Its Applications},
    year = {1998},
    volume = {269},
    pages = {307-329},
}

@manual{Lei15,
    title = {\textup{PTAk}: \textup{Principal Tensor Analysis on k
      modes}},
    author = {Leibovici D.G.},
    year = {2015},
    edition = {R package version 1.2-12},
    url = {http://cran.r-project.org/package=PTAk},
}

@article{Lei10,
    title = {\textup{Spatio-Temporal Multiway Decompositions using
      Principal Tensor Analysis on k-modes: the \textsc{R}-package
      \textsc{PTAk}}},
    author = {Didier G. Leibovici},
    journal = {Journal of Statistical Software},
    year = {2010},
    volume = {34},
    number = {10},
    pages = {1--34},
    url = {http://www.jstatsoft.org/v34/i10/},
}

@article{Len01,
  title={Some practical guidelines for effective sample size determination},
  author={Lenth, Russell V},
  journal={The American Statistician},
  volume={55},
  number={3},
  pages={187--193},
  year={2001},
  publisher={Taylor \& Francis}
}

@article{Leu93,
  title={Canonical correlation analysis when the data are curves},
  author={Leurgans, S. E. and Moyeed, R. A. and Silverman, B. W.},
  journal={Journal of the Royal Statistical Society. Series B},
  volume={55},
  pages={725--740},
  year={1993}
}

@article{Li17,
  title={Incorporating biological information in sparse principal component analysis with application to genomic data},
  author={Li, Ziyi and Safo, Sandra E and Long, Qi},
  journal={BMC bioinformatics},
  volume={18},
  number={1},
  pages={332},
  year={2017},
  publisher={BioMed Central}
}


@article{Lia18,
  title={Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities},
  author={Liang, Dachao and Leung, Ross Ka-Kit and Guan, Wenda and Au, William W},
  journal={Gut Pathogens},
  volume={10},
  number={1},
  pages={3},
  year={2018},
  publisher={BioMed Central}
}


@article{Lin19,
  title={scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets},
  author={Lin, Yingxin and Ghazanfar, Shila and Wang, Kevin YX and Gagnon-Bartsch, Johann A and Lo, Kitty K and Su, Xianbin and Han, Ze-Guang and Ormerod, John T and Speed, Terence P and Yang, Pengyi and Yang JYH},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  volume={116},
  number={20},
  pages={9775},
  year={2019},
  publisher={National Academy of Sciences}
}

@article{Liq12,
  title={A novel approach for biomarker selection and the integration of repeated measures experiments from   two assays},
  author={Liquet, Benoit and L\^e Cao, Kim-Anh and Hocini, Hakim and Thi{\'e}baut, Rodolphe},
  journal={BMC bioinformatics},
  volume={13},
  pages={325},
  year={2012}
}

@article{Liq16,
  title={Group and sparse group partial least square approaches applied in genomics context},
  author={Liquet, Benoit and de Micheaux, Pierre Lafaye and Hejblum, Boris P and Thi{\'e}baut, Rodolphe},
  journal={Bioinformatics},
  volume={32},
  number={1},
  pages={35--42},
  year={2016},
  publisher={Oxford University Press}
}

@article{Lis10,
  title={Correction for hidden confounders in the genetic analysis of gene expression},
  author={Listgarten, Jennifer and Kadie, Carl and Schadt, Eric E and Heckerman, David},
  journal={Proceedings of the National Academy of Sciences},
  volume={107},
  number={38},
  pages={16465--16470},
  year={2010},
  publisher={National Acad Sciences}
}

@article{Liu16,
  title={Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer},
  author={Liu, Chao and Srihari, Sriganesh and Lal, Samir and Gautier, Beno{\^i}t and Simpson, Peter T and Khanna, Kum Kum and Ragan, Mark A and L{\^e} Cao, Kim-Anh},
  journal={Molecular oncology},
  volume={10},
  number={1},
  pages={179--193},
  year={2016},
  publisher={Elsevier}
}


@article{Loc13,
  title={Joint and individual variation explained (JIVE) for integrated analysis of multiple data types},
  author={Lock, Eric F and Hoadley, Katherine A and Marron, James Stephen and Nobel, Andrew B},
  journal={The annals of applied statistics},
  volume={7},
  number={1},
  pages={523},
  year={2013},
  publisher={NIH Public Access}
}


@book{Loh13,
  title={Latent variable path modeling with partial least squares},
  author={Lohm{\"o}ller, Jan-Bernd},
  year={2013},
  publisher={Springer Science \& Business Media}
}

@article{Lor87,
  title={{A theoretical foundation for the PLS algorithm}},
  author={Lorber, A. and Wangen, LE and Kowalski, B.R.},
  journal={Journal of Chemometrics},
  volume={1},
  number={19-31},
  pages={13},
  year={1987}
}

@article{Lov15,
  title={Proportionality: a valid alternative to correlation for relative data},
  author={Lovell, David and Pawlowsky-Glahn, Vera and Egozcue, Juan Jos{\'e} and Marguerat, Samuel and B{\"a}hler, J{\"u}rg},
  journal={PLoS computational biology},
  volume={11},
  number={3},
  pages={e1004075},
  year={2015},
  publisher={Public Library of Science}
}

@article{Lue19,
  title={Current best practices in single-cell RNA-seq analysis: a tutorial},
  author={Luecken, Malte D and Theis, Fabian J},
  journal={Molecular systems biology},
  volume={15},
  number={6},
  year={2019},
  publisher={John Wiley \& Sons, Ltd}
}

@article{Mac00,
  title={Scientific method, statistical method and the speed of light},
  author={MacKay, R Jock and Oldford, R Wayne},
  journal={Statistical Science},
  pages={254--278},
  year={2000},
  publisher={JSTOR}
}

@article{Max13,
  title={Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks},
  author={Ma, Xiaotu and Chen, Ting and Sun, Fengzhu},
  journal={Briefings in bioinformatics},
  volume={15},
  number={5},
  pages={685--698},
  year={2013},
  publisher={Oxford University Press}
}

@book {Mar79,
  author = {Kantilal V. Mardia and John T. Kent and John M. Bibby},
  title = {Multivariate Analysis},
  publisher = {Academic Press},
  year = {1979}
}

@article{Mar07,
    title = {Novel aspects of {PPAR}alpha-mediated regulation of lipid and xenobiotic metabolism revealed   through a multrigenomic study},
  author={Martin, P.G.P. and Guillou, H. and Lasserre, F. and D{\'e}jean, S. and Lan, A. and Pascussi, J.-M.  and San Cristobal, M.  and Legrand, P. and Besse, P. and Pineau, T. },
  journal={Hepatology},
  volume={54},
  pages={767--777},
  year={2007}
}

@article{Mar15,
  title={The gut--lung axis in respiratory disease},
  author={Marsland, Benjamin J and Trompette, Aur{\'e}lien and Gollwitzer, Eva S},
  journal={Annals of the American Thoracic Society},
  volume={12},
  number={Supplement 2},
  pages={S150--S156},
  year={2015},
  publisher={American Thoracic Society}
}

@article{Mcm14,
  title={Waste not, want not: why rarefying microbiome data is inadmissible},
  author={McMurdie, Paul J and Holmes, Susan},
  journal={PLoS computational biology},
  volume={10},
  number={4},
  pages={e1003531},
  year={2014},
  publisher={Public Library of Science}
}

@article{Mei10,
  title={Stability selection},
  author={Meinshausen, Nicolai and B{\"u}hlmann, Peter},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={72},
  number={4},
  pages={417--473},
  year={2010},
  publisher={Wiley Online Library}
}


@article{Men16,
  title={Dimension reduction techniques for the integrative analysis of multi-omics data},
  author={Meng, Chen and Zeleznik, Oana A and Thallinger, Gerhard G and Kuster, Bernhard and Gholami, Amin M and Culhane, Aed{\'\i}n C},
  journal={Briefings in bioinformatics},
  volume={17},
  number={4},
  pages={628--641},
  year={2016},
  publisher={Oxford University Press}
}

@article{Mev07,
  author = "Bj¯rn-Helge Mevik and Ron Wehrens",
  title = "The pls Package: Principal Component and Partial Least Squares Regression in R",
  journal = "Journal of Statistical Software",
  volume = "18",
  number = "2",
  day = "10",
  month = "1",
  year = "2007",
  CODEN = "JSSOBK",
  ISSN = "1548-7660",
  bibdate = "2007-01-10",
  URL = "http://www.jstatsoft.org/v18/i02",
  accepted = "2007-01-10",
  submitted = "2006-10-04"
}

@article{mixomics,
  title={mixOmics: an R package for `omics feature selection and multiple data integration},
  author={Florian Rohart and Benoit Gautier and Amrit Singh and Kim-Anh {Le Cao}},
  journal={PLoS Computational Biology},
  pages={},
  year={2017},
  publisher={Cold Spring Harbor Labs Journals}
}

@Manual{mixomicsR,
    title = {mixOmics: Omics Data Integration Project},
    author = {Kim-Anh {Le Cao} and Florian Rohart and Ignacio Gonzalez and Sebastien Dejean with key           contributors Benoit Gautier and Francois Bartolo and contributions from Pierre Monget and Jeff Coquery and FangZou Yao and Benoit Liquet.},
    year = {2017},
    note = {R package version 6.3.0},
    url = {https://CRAN.R-project.org/package=mixOmics},
}

@article{Miz17,
  title={The great importance of normalization of LC--MS data for highly-accurate non-targeted metabolomics},
  author={Mizuno, Hajime and Ueda, Kazuki and Kobayashi, Yuta and Tsuyama, Naohiro and Todoroki, Kenichiro and Min, Jun Zhe and Toyo'oka, Toshimasa},
  journal={Biomedical Chromatography},
  volume={31},
  number={1},
  pages={e3864},
  year={2017},
  publisher={Wiley Online Library}
}


@Manual{MOFAR,
    title = {MOFA: Multi-Omics Factor Analysis},
    author = {Argelaguet R and Velten B and Arnol D and Buettner F and Huber W and Stegle O},
    year = {2020},
    note = {R package version 1.4.0},
    url = {https://bioconductor.org/packages/MOFA/},
  }


@article{Mor10,
  title={Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive   pathways and biomarkers of metabolic syndrome},
  author={Morine, Melissa and McMonagle, Jolene and Toomey, Sinead and Reynolds, Clare and Moloney, Aidan   and Gormley, Isobel and Gaora, Peadar and Roche, Helen},
  journal={BMC bioinformatics},
  volume={11},
  number={1},
  pages={499},
  year={2010},
  publisher={BioMed Central Ltd}
}


@article{MumaR,
  title={muma, An R package for metabolomics univariate and multivariate statistical analysis},
  author={Gaude, Edoardo and Chignola, Francesca and Spiliotopoulos, Dimitrios and Spitaleri, Andrea and Ghitti, Michela and Garc{\`i}a-Manteiga, Jose M and Mari, Silvia and Musco, Giovanna},
  journal={Current Metabolomics},
  volume={1},
  number={2},
  pages={180--189},
  year={2013},
  publisher={Bentham Science Publishers}
}



@article{Mun15,
  title={Sparse and kernel OPLS feature extraction based on eigenvalue problem solving},
  author={Mu{\~n}oz-Romero, Sergio and Arenas-Garc{\'\i}a, Jer{\'o}nimo and G{\'o}mez-Verdejo, Vanessa},
  journal={Pattern Recognition},
  volume={48},
  number={5},
  pages={1797--1811},
  year={2015},
  publisher={Elsevier}
}

@article{Mur96,
  title={A graphical display of large correlation matrices},
  author={Murdoch, DJ and Chow, ED},
  journal={The American Statistician},
  volume={50},
  number={2},
  pages={178--180},
  year={1996},
  publisher={Taylor \& Francis}
}

@article{New10,
  title={Lab-specific gene expression signatures in pluripotent stem cells},
  author={Newman, Aaron M and Cooper, James B},
  journal={Cell stem cell},
  volume={7},
  number={2},
  pages={258--262},
  year={2010},
  publisher={Elsevier}
}

@article{Ngu02a,
  title={{Tumor classification by partial least squares using microarray gene expression data}},
  author={Nguyen, Danh V and Rocke, David M},
  journal={Bioinformatics},
  volume={18},
  number={1},
  pages={39},
  year={2002},
  publisher={Oxford Univ Press}
}

@article{Ngu02b,
  title={Multi-class cancer classification via partial least squares with gene expression profiles},
  author={Nguyen, Danh V and Rocke, David M},
  journal={Bioinformatics},
  volume={18},
  number={9},
  pages={1216--1226},
  year={2002},
  publisher={Oxford University Press}
}

@article {Nic21,
	author = {Nichols, James D. and Oli, Madan K. and Kendall, William. L. and Boomer, G. Scott},
	title = {Opinion: A better approach for dealing with reproducibility and replicability in science},
	volume = {118},
	number = {7},
	elocation-id = {e2100769118},
	year = {2021},
	doi = {10.1073/pnas.2100769118},
	publisher = {National Academy of Sciences},
	issn = {0027-8424},
	URL = {https://www.pnas.org/content/118/7/e2100769118},
	eprint = {https://www.pnas.org/content/118/7/e2100769118.full.pdf},
	journal = {Proceedings of the National Academy of Sciences}
}


@article{Oco16,
  title={R. JIVE for exploration of multi-source molecular data},
  author={O'Connell, Michael J and Lock, Eric F},
  journal={Bioinformatics},
  volume={32},
  number={18},
  pages={2877--2879},
  year={2016},
  publisher={Oxford University Press}
}


@article{Oks10,
  title={Vegan: community ecology package. R package version 1.17-4},
  author={Oksanen, Jari and Blanchet, F Guillaume and Kindt, Roeland and Legendre, Pierre and O’hara, RB and Simpson, Gavin L and Solymos, Peter and Stevens, M Henry H and Wagner, Helene},
  journal={http://cran. r-project. org>. Acesso em},
  volume={23},
  pages={2010},
  year={2010}
}


@article{Pan10,
  title={Incorporating predictor network in penalized regression with application to microarray data},
  author={Pan, Wei and Xie, Benhuai and Shen, Xiaotong},
  journal={Biometrics},
  volume={66},
  number={2},
  pages={474--484},
  year={2010},
  publisher={Wiley Online Library}
}

@article{Par09,
  title={Sparse canonical correlation analysis with application to genomic data integration},
  author={Parkhomenko, Elena and Tritchler, David and Beyene, Joseph},
  journal={Statistical applications in genetics and molecular biology},
  volume={8},
  number={1},
  pages={1--34},
  year={2009},
  publisher={De Gruyter}
}

@article{Pau13,
  title={metagenomeSeq: Statistical analysis for sparse high-throughput sequencing},
  author={Paulson, Joseph Nathaniel and Pop, Mihai and Bravo, Hector Corrada},
  journal={Bioconductor package},
  volume={1},
  number={0},
  pages={63},
  year={2013}
}

@article{Pau16,
  title={Robust methods for differential abundance analysis in marker gene surveys},
  author={Paulson, JN and Stine, OC and Bravo, HC and Pop, M},
  journal={Nat Methods},
  volume={116},
  pages={1477--1490},
  year={2016}
}

@book{Paw15,
  title={Modeling and analysis of compositional data},
  author={Pawlowsky-Glahn, Vera and Egozcue, Juan Jos{\'e} and Tolosana-Delgado, Raimon},
  year={2015},
  publisher={John Wiley \& Sons}
}


@article{Pea01,
  title={LIII. On lines and planes of closest fit to systems of points in space},
  author={Pearson, Karl},
  journal={The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science},
  volume={2},
  number={11},
  pages={559--572},
  year={1901},
  publisher={Taylor \& Francis}
}

@Manual{PMAR,
    title = {PMA: Penalized Multivariate Analysis},
    author = {Daniela Witten and Rob Tibshirani},
    year = {2020},
    note = {R package version 1.2.1},
    url = {https://CRAN.R-project.org/package=PMA},
  }


  @article{Poi20,
  title={Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition},
  author={Poirier, Simon and D{\'e}jean, S{\'e}bastien and Midoux, Cedric and L\^{e} Cao, Kim-Anh and Chapleur, Olivier},
  journal={Bioresour Technol},
  volume={316},
  number={123952},
  year={2020},
  publisher={Cold Spring Harbor Laboratory}
}



@article{Pra12,
  title={A multivariate model of ErbB network composition predicts ovarian cancer cell response to canertinib},
  author={Prasasya, Rexxi D and Vang, Kang Z and Kreeger, Pamela K},
  journal={Biotechnology and bioengineering},
  volume={109},
  number={1},
  pages={213--224},
  year={2012},
  publisher={Wiley Online Library}
}


@manual{RGCCAR,
  title={RGCCA: Regularized and sparse generalized canonical correlation analysis for multiblock data},
  author={Tenenhaus, A and Guillemot, V},
  year={2017},
  url = {https://CRAN.R-project.org/package=RGCCA}
  }


  @article{Ric16,
  title={Statistical Methods in Integrative Genomics},
  author={Richardson, Sylvia and Tseng, George and Sun, Wei},
  journal={Annual Review of Statistics and Its Application},
  volume={3},
  number={1},
  pages={181--209},
  year={2016}
}



@article{Rit15,
  title={The foundation of precision medicine: integration of electronic health records with genomics through basic, clinical, and translational research},
  author={Ritchie, Marylyn D and De Andrade, Mariza and Kuivaniemi, Helena},
  journal={Frontiers in genetics},
  volume={6},
  year={2015},
  publisher={Frontiers Media SA}
}

@article{Rob10,
  title={A scaling normalization method for differential expression analysis of RNA-seq data},
  author={Robinson, Mark D and Oshlack, Alicia},
  journal={Genome biology},
  volume={11},
  number={3},
  pages={R25},
  year={2010},
  publisher={BioMed Central}
}

@article{Roe16,
  title={A tutorial on the use of PLS path modeling in longitudinal studies},
  author={Roemer, Ellen},
  journal={Industrial Management \& Data Systems},
  year={2016},
  publisher={Emerald Group Publishing Limited}
}

@article{Roh16,
  title={MINT: A multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms},
  author={Rohart, Florian and Matigian, Nicholas and Eslami, Aida and Bougeard Stephanie and L\^{e} Cao, Kim-Anh},
  journal={BMC bioinformatics},
  volume={18},
  number={1},
  pages={128},
  year={2017},
  publisher={BioMed Central}
}


@article{Roh17,
  title={mixOmics: An R package for ‘omics feature selection and multiple data integration},
  author={Rohart, Florian and Gautier, Benoit and Singh, Amrit and L{\^e} Cao, Kim-Anh},
  journal={PLoS computational biology},
  volume={13},
  number={11},
  pages={e1005752},
  year={2017},
  publisher={Public Library of Science}
}

@article{Ros11,
  title={Revisiting the role of organic acids in the bicarbonate tolerance of zinc-efficient rice genotypes   },
  author={Rose, Michael T and Rose, Terry J and Pariasca-Tanaka, Juan and Wissuwa, Matthias and others},
  journal={Functional Plant Biology},
  volume={38},
  number={6},
  pages={493--504},
  year={2011},
  publisher={CSIRO}
}

@article{Rou09,
  title={The gut microbiota shapes intestinal immune responses during health and disease},
  author={Round, June L and Mazmanian, Sarkis K},
  journal={Nature reviews immunology},
  volume={9},
  number={5},
  pages={313},
  year={2009},
  publisher={Nature Publishing Group}
}


@article{Rui18,
  title={So you think you can PLS-DA?},
  author={Ruiz-Perez, Daniel and Guan, Haibin and Madhivanan, Purnima and Mathee, Kalai and Narasimhan, Giri},
  journal={BMC Bioinformatics},
  volume={21},
  number={1},
  pages={1--10},
  year={2020},
  publisher={BioMed Central}
}


@manual{Rvaidememoire,
  title={RVAideMemoire: testing and plotting procedures for biostatistics},
  author={Herv{\'e}, Maxime},
  journal={R Package Version 0.9-69. Available online at: https://CRAN. R-project. org/package= RVAideMemoire},
  year={2018}
}


@article{Sac14,
  title={Reflections on univariate and multivariate analysis of metabolomics data},
  author={Saccenti, Edoardo and Hoefsloot, Huub CJ and Smilde, Age K and Westerhuis, Johan A and Hendriks, Margriet MWB},
  journal={Metabolomics},
  volume={10},
  number={3},
  pages={0},
  year={2014},
  publisher={Springer}
}

@article{Sac16,
  title={Approaches to sample size determination for multivariate data: Applications to PCA and PLS-DA of omics data},
  author={Saccenti, Edoardo and Timmerman, Marieke E},
  journal={Journal of Proteome Research},
  volume={15},
  number={8},
  pages={2379--2393},
  year={2016},
  publisher={ACS Publications}
}

@article{Sae18,
  title={A comprehensive evaluation of module detection methods for gene expression data},
  author={Saelens, Wouter and Cannoodt, Robrecht and Saeys, Yvan},
  journal={Nature communications},
  volume={9},
  number={1},
  pages={1--12},
  year={2018},
  publisher={Nature Publishing Group}
}


@article{San12,
  title={HIV-1 vaccine trials: evolving concepts and designs},
  author={Sanou, Missa P and De Groot, Anne S and Murphey-Corb, Michael and Levy, Jay A and Yamamoto, Janet   K},
  journal={The open AIDS journal},
  volume={6},
  pages={274},
  year={2012},
  publisher={Bentham Science Publishers}
}

@book{Sap06,
  author    = {G Saporta},
	title     = {Probabilit\'es analyse des donn\'ees et statistique},
	publisher = {Technip},
	year      = {2006}
}

@article{Sch05,
  title={A shrinkage approach to large-scale covariance matrix estimation and implications for functional   genomics},
  author={Sch{\"a}fer, Juliane and Strimmer, Korbinian},
  journal={Statistical applications in genetics and molecular biology},
  volume={4},
  number={1},
  year={2005}
}

@article{Sch00,
  title={A gene expression database for the molecular pharmacology of cancer},
  author={Scherf, Uwe and Ross, Douglas T and Waltham, Mark and Smith, Lawrence H and Lee, Jae K and Tanabe, Lorraine and Kohn, Kurt W and Reinhold, William C and Myers, Timothy G and Andrews, Darren T and others},
  journal={Nature genetics},
  volume={24},
  number={3},
  pages={236--244},
  year={2000},
  publisher={Nature Publishing Group}
}

@article{Sch13,
  title={The microbiome and cancer},
  author={Schwabe, Robert F and Jobin, Christian},
  journal={Nature Reviews Cancer},
  volume={13},
  number={11},
  pages={800},
  year={2013},
  publisher={Nature Publishing Group}
}


  @Manual{sgPLSR,
    title = {sgPLS: Sparse Group Partial Least Square Methods},
    author = {Liquet, B and Lafaye de Micheaux, P and Broc, C},
    year = {2017},
    note = {R package version 1.7},
    url = {https://CRAN.R-project.org/package=sgPLS},
  }


  @Manual{splsR,
    title = {spls: Sparse Partial Least Squares (SPLS) Regression and Classification},
    author = {Chung, D. and Chun, H. and Keles S.},
    year = {2020},
    note = {R package version 2.2-3},
    url = {https://CRAN.R-project.org/package=spls},
  }


@article{Sha16,
  title={Glyco-centric lectin magnetic bead array (LeMBA)- proteomics dataset of human serum samples from healthy, Barrett\'s esophagus and esophageal adenocarcinoma individuals},
  author={Shah, Alok K and L{\^e} Cao, Kim-Anh and Choi, Eunju and Chen, David and Gautier, Benoit and Nancarrow, Derek and Whiteman, David C and Baker, Peter R and Clauser, Karl R and Chalkley, Robert J and others},
  journal={Data in brief},
  volume={7},
  pages={1058--1062},
  year={2016},
  publisher={Elsevier}
}

@article{She08,
	author = {Shen, Haipeng and Huang, Jianhua Z.},
	title = {Sparse Principal Component Analysis via Regularized Low Rank Matrix Approximation},
	 journal={Journal of multivariate analysis},
  volume={99},
  number={6},
  pages={1015--1034},
  year={2008},
  publisher={Elsevier}
}

@article{Shi06,
  title={The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of      gene expression measurements},
  author={Maqc Consortium and others},
  journal={Nature biotechnology},
  volume={24},
  number={9},
  pages={1151},
  year={2006},
  publisher={NIH Public Access}
}


@article{Shm10,
  author = "Shmueli, Galit",
  doi = "10.1214/10-STS330",
  fjournal = "Statistical Science",
  journal = "Statist. Sci.",
  month = "08",
  number = "3",
  pages = "289--310",
  publisher = "The Institute of Mathematical Statistics",
  title = "To Explain or to Predict?",
  url = "https://doi.org/10.1214/10-STS330",
  volume = "25",
  year = "2010"
  }

@article{Sho06,
  title={The NCI60 human tumour cell line anticancer drug screen},
  author={Shoemaker, Robert H},
  journal={Nature Reviews Cancer},
  volume={6},
  number={10},
  pages={813--823},
  year={2006},
  publisher={Nature Publishing Group}
}

@article{Sil15,
  title={Applying stability selection to consistently estimate sparse principal components in high-dimensional molecular data},
  author={Sill, Martin and Saadati, Maral and Benner, Axel},
  journal={Bioinformatics},
  volume={31},
  number={16},
  pages={2683--2690},
  year={2015},
  publisher={Oxford University Press}
}


@article{Sim08,
  title={The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets--improving meta-analysis and prediction of prognosis},
  author={Sims, Andrew H and Smethurst, Graeme J and Hey, Yvonne and Okoniewski, Michal J and Pepper, Stuart D and Howell, Anthony and Miller, Crispin J and Clarke, Robert B},
  journal={BMC medical genomics},
  volume={1},
  number={1},
  pages={42},
  year={2008},
  publisher={BioMed Central}
}


@article{Sim12,
  title={Standardization and the group lasso penalty},
  author={Simon, Noah and Tibshirani, Robert},
  journal={Statistica Sinica},
  volume={22},
  number={3},
  pages={983},
  year={2012},
  publisher={NIH Public Access}
}

@article{Sim13,
  title={A sparse-group lasso},
  author={Simon, Noah and Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert},
  journal={Journal of computational and graphical statistics},
  volume={22},
  number={2},
  pages={231--245},
  year={2013},
  publisher={Taylor \& Francis Group}
}

@article{Sin19,
  title={DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays},
  author={Singh, Amrit and Shannon, Casey P and Gautier, Beno{\^\i}t and Rohart, Florian and Vacher, Micha{\"e}l and Tebbutt, Scott J and L{\^e} Cao, Kim-Anh},
  journal={Bioinformatics},
  volume={35},
  number={17},
  pages={3055--3062},
  year={2019},
  publisher={Oxford University Press}
}

@article{Smi07,
  title={Assessing the statistical validity of proteomics based biomarkers},
  author={Smit, Suzanne and van Breemen, Mari{\"e}lle J and Hoefsloot, Huub CJ and Smilde, Age K and Aerts, Johannes MFG and De Koster, Chris G},
  journal={Analytica Chimica Acta},
  volume={592},
  number={2},
  pages={210--217},
  year={2007},
  publisher={Elsevier}
}

@incollection{Smy05,
  title={Limma: linear models for microarray data},
  author={Smyth, Gordon K},
  booktitle={Bioinformatics and computational biology solutions using R and Bioconductor},
  pages={397--420},
  year={2005},
  publisher={Springer}
}

@article{Smo11,
  title={Cytoscape 2.8: new features for data integration and network visualization},
  author={Smoot, Michael E and Ono, Keiichiro and Ruscheinski, Johannes and Wang, Peng-Liang and Ideker, Trey},
  journal={Bioinformatics},
  volume={27},
  number={3},
  pages={431--432},
  year={2011},
  publisher={Oxford Univ Press}
}

@article{Som19,
  title={Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets},
  author={Sompairac, Nicolas and Nazarov, Petr V and Czerwinska, Urszula and Cantini, Laura and Biton, Anne and Molkenov, Askhat and Zhumadilov, Zhaxybay and Barillot, Emmanuel and Radvanyi, Francois and Gorban, Alexander and others},
  journal={International journal of molecular sciences},
  volume={20},
  number={18},
  pages={4414},
  year={2019},
  publisher={Multidisciplinary Digital Publishing Institute}
}


@article{Sor01,
  title={Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications},
  author={S{\o}rlie, Therese and Perou, Charles M and Tibshirani, Robert and Aas, Turid and Geisler, Stephanie and Johnsen, Hilde and Hastie, Trevor and Eisen, Michael B and Van De Rijn, Matt and Jeffrey, Stefanie S and others},
  journal={Proceedings of the National Academy of Sciences},
  volume={98},
  number={19},
  pages={10869--10874},
  year={2001},
  publisher={National Acad Sciences}
}

@article{Sow14,
  title={Non-invasive separation of alcoholic and non-alcoholic liver disease with predictive modeling},
  author={Sowa, Jan-Peter and Atmaca, {\"O}zg{\"u}r and Kahraman, Alisan and Schlattjan, Martin and Lindner, Marion and Sydor, Svenja and Scherbaum, Norbert and Lackner, Karoline and Gerken, Guido and Heider, Dominik and others},
  journal={PLoS One},
  volume={9},
  number={7},
  pages={e101444},
  year={2014},
  publisher={Public Library of Science}
}

  @Manual{sRDAR,
    title = {sRDA: Sparse Redundancy Analysis},
    author = {Attila Csala},
    year = {2017},
    note = {R package version 1.0.0},
    url = {https://CRAN.R-project.org/package=sRDA},
  }


@article{Sta87,
  title={Partial least squares analysis with cross-validation for the two-class problem: a Monte Carlo study},
  author={St{\aa}hle, Lars and Wold, Svante},
  journal={Journal of chemometrics},
  volume={1},
  number={3},
  pages={185--196},
  year={1987},
  publisher={Wiley Online Library}
}


@article{Ste18,
  title={Enter the matrix: factorization uncovers knowledge from omics},
  author={Stein-O'Brien, Genevieve L and Arora, Raman and Culhane, Aedin C and Favorov, Alexander V and Garmire, Lana X and Greene, Casey S and Goff, Loyal A and Li, Yifeng and Ngom, Aloune and Ochs, Michael F and others},
  journal={Trends in Genetics},
  year={2018},
  publisher={Elsevier}
}

@article{Sto74,
  title={Cross-validatory choice and assessment of statistical predictions},
  author={Stone, Mervyn},
  journal={Journal of the Royal Statistical Society: Series B (Methodological)},
  volume={36},
  number={2},
  pages={111--133},
  year={1974},
  publisher={Wiley Online Library}
}

@article{Str15,
  title={A linear mixed model spline framework for analysing time course omics data},
  author={Straube, J and Gorse, AD, PROOF and Huang, BE and L\^{e} Cao, K-A. },
  journal={PLoS ONE},
  volume={},
  number={},
  year={2015}
}

@article{Sus20,
  title={Variable selection in microbiome compositional data analysis},
  author={Susin, Antoni and Wang, Yiwen and L{\^e} Cao, Kim-Anh and Calle, M Luz},
  journal={NAR Genomics and Bioinformatics},
  volume={2},
  number={2},
  pages={lqaa029},
  year={2020},
  publisher={Oxford University Press}
}


@article{Sza04,
  title={Predicting drug sensitivity and resistance: profiling ABC transporter genes in cancer cells},
  author={Szak{\'a}cs, Gergely and Annereau, Jean-Philippe and Lababidi, Samir and Shankavaram, Uma and Arciello, Angela and Bussey, Kimberly J and Reinhold, William and Guo, Yanping and Kruh, Gary D and Reimers, Mark and others},
  journal={Cancer cell},
  volume={6},
  number={2},
  pages={129--137},
  year={2004},
  publisher={Elsevier}
}

@article{Szy12,
  title={Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies},
  author={Szyma{\'n}ska, Ewa and Saccenti, Edoardo and Smilde, Age K and Westerhuis, Johan A},
  journal={Metabolomics},
  volume={8},
  number={1},
  pages={3--16},
  year={2012},
  publisher={Springer}
}

@book{Tab07,
  title={Using multivariate statistics},
  author={Tabachnick, Barbara G and Fidell, Linda S and Ullman, Jodie B},
  volume={5},
  year={2007},
  publisher={Pearson Boston, MA}
}

@article{TCGA12,
  title={Comprehensive molecular portraits of human breast tumours},
  author={{Cancer Genome Atlas Network} and others},
  journal={Nature},
  volume={490},
  number={7418},
  pages={61--70},
  year={2012},
  publisher={Nature Publishing Group}
}

@article{Tan04,
  title={{Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models}},
  author={Tan, Y. and Shi, L. and Tong, W. and Gene Hwang, GT and Wang, C.},
  journal={Computational Biology and Chemistry},
  volume={28},
  number={3},
  pages={235--243},
  year={2004},
  publisher={Elsevier}
}


@article{Tap09,
  title={Notes on the practical utility of OPLS},
  author={Tapp, Henri S and Kemsley, E Kate},
  journal={TrAC Trends in Analytical Chemistry},
  volume={28},
  number={11},
  pages={1322--1327},
  year={2009},
  publisher={Elsevier}
}

@article{Tay09,
  title={Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach},
  author={De Tayrac, Marie and L{\^e}, S{\'e}bastien and Aubry, Marc and Mosser, Jean and Husson, Fran{\c{c}}ois},
  journal={BMC genomics},
  volume={10},
  number={1},
  pages={1--17},
  year={2009},
  publisher={BioMed Central}
}

@book{Ten98,
  title={La r{\'e}gression {PLS}: th{\'e}orie et pratique},
  author={Tenenhaus, Michel},
  year={1998},
  publisher={Editions Technip}
}



@article{Ten11,
  title={Regularized generalized canonical correlation analysis},
  author={Tenenhaus, Arthur and Tenenhaus, Michel},
  journal={Psychometrika},
  volume={76},
  number={2},
  pages={257--284},
  year={2011},
  publisher={Springer}
}

@article{Ten14,
  title={Variable selection for generalized canonical correlation analysis},
  author={Tenenhaus, Arthur and Philippe, Cathy and Guillemot, Vincent and L\^{e} Cao, Kim-Anh and Grill,        Jacques and Frouin, Vincent},
  journal={Biostatistics},
  pages={kxu001},
  year={2014},
  publisher={Biometrika Trust}
}


@article{Ten15,
  title={Kernel generalized canonical correlation analysis},
  author={Tenenhaus, Arthur and Philippe, Cathy and Frouin, Vincent},
  journal={Computational Statistics \& Data Analysis},
  volume={90},
  pages={114--131},
  year={2015},
  publisher={Elsevier}
}


@article{Ten16,
  title={A benchmark for RNA-seq quantification pipelines},
  author={Teng, Mingxiang and Love, Michael I and Davis, Carrie A and Djebali, Sarah and Dobin, Alexander    and Graveley, Brenton R and Li, Sheng and Mason, Christopher E and Olson, Sara and Pervouchine, Dmitri     and others},
  journal={Genome biology},
  volume={17},
  number={1},
  pages={74},
  year={2016},
  publisher={BioMed Central}
}

@article{Ten17,
  title={Regularized Generalized Canonical Correlation Analysis: A Framework for Sequential Multiblock       Component Methods},
  author={Tenenhaus, Michel and Tenenhaus, Arthur and Groenen, Patrick JF},
  journal={Psychometrika},
  pages={1--41},
  year={2017},
  publisher={Springer}
}


@article{The15,
  title={Analysis of the human adult urinary metabolome variations with age, body mass index, and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses},
  author={Th{\'e}venot, Etienne A and Roux, Aur{\'e}lie and Xu, Ying and Ezan, Eric and Junot, Christophe},
  journal={Journal of proteome research},
  volume={14},
  number={8},
  pages={3322--3335},
  year={2015},
  publisher={ACS Publications}
}

@article{Tia19,
  title={Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments},
  author={Tian, Luyi and Dong, Xueyi and Freytag, Saskia and L\^{e} Cao, Kim-Anh and Su, Shian and JalalAbadi, Abolfazl and Amann-Zalcenstein, Daniela and Weber, Tom S and Seidi, Azadeh and Jabbari, Jafar S and others},
  journal={Nature methods},
  volume={16},
  number={6},
  pages={479--487},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{Tib96,
  title={Regression shrinkage and selection via the lasso},
  author={Tibshirani, Robert},
  journal={Journal of the Royal Statistical Society. Series B (Methodological)},
  pages={267--288},
  year={1996},
  publisher={JSTOR}
}


@Manual{timeOmicsR,
    title = {timeOmics: Time-Course Multi-Omics data integration},
    author = {Antoine Bodein and Olivier Chapleur and Kim-Anh L{\^e} Cao and Arnaud Droit},
    year = {2020},
    note = {R package version 1.0.0},
    url = {http://bioconductor.org/packages/release/bioc/html/timeOmics.html},
}



@article{Tre17,
  title={The gut microbiome in human neurological disease: a review},
  author={Tremlett, Helen and Bauer, Kylynda C and Appel-Cresswell, Silke and Finlay, Brett B and Waubant, Emmanuelle},
  journal={Annals of neurology},
  volume={81},
  number={3},
  pages={369--382},
  year={2017},
  publisher={Wiley Online Library}
}

@article {Try02,
  author = {Trygg, Johan and Wold, Svante},
  title = {Orthogonal projections to latent structures (O-PLS)},
  journal = {Journal of Chemometrics},
  volume = {16},
  number = {3},
  publisher = {John Wiley & Sons, Ltd.},
  issn = {1099-128X},
  url = {http://dx.doi.org/10.1002/cem.695},
  doi = {10.1002/cem.695},
  pages = {119--128},
  keywords = {orthogonal projections to latent structures (O-PLS), orthogonal signal correction (OSC), NIPALS PLS, multivariate data analysis, calibration, preprocessing},
  year = {2002},
}


@inbook{Try07,
  title={Chemometrics techniques for metabonomics},
  author={Trygg, Johan and Lundstedt, Torbj{\"o}rn},
  booktitle={The Handbook of Metabonomics and Metabolomics},
  pages={171--200},
  year={2007},
  publisher={Elsevier}
  }


@article{Tse12,
  title={Comprehensive literature review and statistical considerations for microarray meta-analysis},
  author={Tseng, George C and Ghosh, Debashis and Feingold, Eleanor},
  journal={Nucleic acids research},
  volume={40},
  number={9},
  pages={3785--3799},
  year={2012},
  publisher={Oxford University Press}
}

@article{Ume96,
  title={{SIMCA-P for windows, Graphical Software for Multivariate Process Modeling}},
  author={Umetri, AB},
  journal={Umea, Sweden},
  year={1996}
}

@article{Val16,
  title={A systematic evaluation of normalization methods in quantitative label-free proteomics},
  author={V{\"a}likangas, Tommi and Suomi, Tomi and Elo, Laura L},
  journal={Briefings in bioinformatics},
  volume={19},
  number={1},
  pages={1--11},
  year={2016},
  publisher={Oxford University Press}
}


@article{Vin76,
  title={Canonical ridge and econometrics of joint production},
  author={Vinod, H. D.},
  journal={Journal of Econometrics},
  volume={6},
  pages={129--137},
  year={1976}
}

@book{Vri15,
  title={R for Dummies},
  author={De Vries, Andrie and Meys, Joris},
  year={2015},
  publisher={John Wiley \& Sons}
}

@article{Vzi13,
  title={Discovering disease-disease associations by fusing systems-level molecular data},
  author={{\v{Z}}itnik, Marinka and Janji{\'c}, Vuk and Larminie, Chris and Zupan, Bla{\v{z}} and Pr{\v{z}}ulj, Nata{\v{s}}a},
  journal={Scientific reports},
  volume={3},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{Waa08,
  title={Quantifying the association between gene expressions and DNA-markers by penalized canonical correlation analysis},
  author={Waaijenborg, Sandra and de Witt Hamer, Philip C Verselewel and Zwinderman, Aeilko H},
  journal={Statistical applications in genetics and molecular biology},
  volume={7},
  number={1},
  year={2008},
  publisher={De Gruyter}
}

@article{Wan15,
  title={A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data},
  author={Wang, Ting and Guan, Weihua and Lin, Jerome and Boutaoui, Nadia and Canino, Glorisa and Luo, Jianhua and Celed{\'o}n, Juan Carlos and Chen, Wei},
  journal={Epigenetics},
  volume={10},
  number={7},
  pages={662--669},
  year={2015},
  publisher={Taylor \& Francis}
}


@article{Wan19,
  title={Managing Batch Effects in Microbiome Data},
  author={Wang, Yiwen and L\^{e} Cao, Kim-Anh},
  journal={Briefings in Bioinformatics},
  volume={21},
  numer={6},
  pages={1477--4054},
  year={2019},
}

@article{Wan20,
  title={A multivariate method to correct for batch effects in microbiome data},
  author={Wang, Yiwen and L{\^e} Cao, Kim-Anh},
  journal={bioRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory}
}

@article{Wan21,
title = {Testing high dimensional covariance matrices via posterior Bayes factor},
journal = {Journal of Multivariate Analysis},
volume = {181},
pages = {104674},
year = {2021},
issn = {0047-259X},
doi = {https://doi.org/10.1016/j.jmva.2020.104674},
url = {https://www.sciencedirect.com/science/article/pii/S0047259X20302554},
author = {Zhendong Wang and Xingzhong Xu}
}



@techreport{Weg00,
  title={A survey of Partial Least Squares (PLS) methods, with emphasis on the two-block case},
  author={Wegelin, Jacob A and others},
  institution={University of Washington, Tech. Rep},
  year={2000}
}


@article{Wei97,
	author  = {Weinstein, J N and Myers, T G and O'Connor, P M and Friend, S H and Fornace Jr, A J and Kohn, K W and Fojo, T and Bates, S E and Rubinstein, L V and Anderson, N L and Buolamwini, J K and van Osdol, W W and Monks, A P and Scudiero, D A and Sausville, E A and Zaharevitz, D W and Bunow, B and Viswanadhan, V N and Johnson, G S and Wittes, R E and Paull, K D},
	title   = {An information--intensive approach to the molecular pharmacology of cancer},
	journal = {Science},
	year  = {1997},
  volume= {275},
  pages = {343--349}
}

@article{Wei94,
  title={Predictive statistics and artificial intelligence in the US National Cancer Institute's drug discovery program for cancer and AIDS},
  author={Weinstein, JN and Myers, T. and Buolamwini, J. and Raghavan, K. and Van Osdol, W. and Licht, J. and Viswanadhan, VN and Kohn, KW and Rubinstein, LV and Koutsoukos, AD and others},
  journal={Stem Cells},
  volume={12},
  number={1},
  pages={13--22},
  year={1994},
  publisher={Wiley Online Library}
}

@article{Wei92,
  title={Neural computing in cancer drug development: predicting mechanism of action},
  author={Weinstein, John N and Kohn, Kurt W and Grever, Michael R and Viswanadhan, Vellarkad N and Rubinstein, Lawrence V and Monks, Anne P and Scudiero, Dominic A and Welch, Lester and Koutsoukos, Antonis D and Chiausa, August J and others},
  journal={Science},
  volume={258},
  number={5081},
  pages={447--451},
  year={1992},
  publisher={American Association for the Advancement of Science}
}

@article{Well13,
  title={Stemformatics: visualisation and sharing of stem cell gene expression},
  author={Wells, Christine A and Mosbergen, Rowland and Korn, Othmar and Choi, Jarny and Seidenman, Nick and Matigian, Nicholas A and Vitale, Alejandra M and Shepherd, Jill},
  journal={Stem Cell Research},
  volume={10},
  number={3},
  pages={387--395},
  year={2013},
  publisher={Elsevier}
}

@article{Wes08,
  title={Assessment of PLSDA cross validation},
  author={Westerhuis, Johan A and Hoefsloot, Huub CJ and Smit, Suzanne and Vis, Daniel J and Smilde, Age K and van Velzen, Ewoud JJ and van Duijnhoven, John PM and van Dorsten, Ferdi A},
  journal={Metabolomics},
  volume={4},
  number={1},
  pages={81--89},
  year={2008},
  publisher={Springer}
}
@article{Wes10,
  title={Multivariate paired data analysis: multilevel PLSDA versus OPLSDA},
  author={Westerhuis, Johan A and van Velzen, Ewoud JJ and Hoefsloot, Huub CJ and Smilde, Age K},
  journal={Metabolomics},
  volume={6},
  number={1},
  pages={119--128},
  year={2010},
  publisher={Springer}
}


@article{Wil15,
  title={Sparse canonical correlation analysis from a predictive point of view},
  author={Wilms, Ines and Croux, Christophe},
  journal={Biometrical Journal},
  volume={57},
  number={5},
  pages={834--851},
  year={2015},
  publisher={Wiley Online Library}
}

@article{Wil16,
  title={Robust sparse canonical correlation analysis},
  author={Wilms, Ines and Croux, Christophe},
  journal={BMC systems biology},
  volume={10},
  number={1},
  pages={72},
  year={2016},
  publisher={BioMed Central}
}

@article{Wit09,
  title={A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis},
  author={Witten, Daniela M and Tibshirani, Robert and Hastie, Trevor},
  journal={Biostatistics},
  volume={10},
  number={3},
  pages={515--534},
  year={2009},
  publisher={Oxford University Press}
}

@article{Wit13,
  title={PMA: Penalized multivariate analysis},
  author={Witten, Daniela and Tibshirani, Rob and Gross, Sam and Narasimhan, Balasubramanian},
  journal={R package version},
  volume={1},
  number={9},
  year={2013}
}

@inbook{Wol66,
  title={Estimation of principal components and related models by iterative least squares},
  author={Wold, Herman},
  booktitle={Multivariate analysis},
  pages={391--420},
  year={1966},
  publisher={New York: Academic Press}
}


@misc{Wol82,
  title={Soft modelling: The basic design and some extensions. Systems under indirect observations (Vol. 2, pp. 1--52)},
  author={Wold, H},
  year={1982},
  publisher={Elsevier Science}
}


@article{Wol87,
  title={Principal component analysis},
  author={Wold, Svante and Esbensen, Kim and Geladi, Paul},
  journal={Chemometrics and intelligent laboratory systems},
  volume={2},
  number={1},
  pages={37--52},
  year={1987},
  publisher={Elsevier}
}
@article{Wol01,
  title={PLS-regression: a basic tool of chemometrics},
  author={Wold, Svante and Sj{\"o}str{\"o}m, Michael and Eriksson, Lennart},
  journal={Chemometrics and intelligent laboratory systems},
  volume={58},
  number={2},
  pages={109--130},
  year={2001},
  publisher={Elsevier}
}


@article{Wol77,
author = {van den Wollenberg, Arnold L.},
doi = {10.1007/BF02294050},
issn = {0033-3123},
journal = {Psychometrika},
month = {jun},
number = {2},
pages = {207--219},
title = {{Redundancy analysis an alternative for canonical correlation analysis}},
url = {http://link.springer.com/10.1007/BF02294050},
volume = {42},
year = {1977}
}

@article{Wor13,
  title={Multivariate analysis in metabolomics},
  author={Worley, Bradley and Powers, Robert},
  journal={Current Metabolomics},
  volume={1},
  number={1},
  pages={92--107},
  year={2013},
  publisher={Bentham Science Publishers}
}

@article{Xia17,
  title={Hypothesis testing and statistical analysis of microbiome},
  author={Xia, Yinglin and Sun, Jun},
  journal={Genes \& diseases},
  volume={4},
  number={3},
  pages={138--148},
  year={2017},
  publisher={Elsevier}
}

@book{Xia18a,
  title={Statistical analysis of microbiome data with R},
  author={Xia, Yinglin and Sun, Jun and Chen, Ding-Geng},
  year={2018},
  publisher={Springer}
}

@incollection{Xia18b,
  title={Introductory Overview of Statistical Analysis of Microbiome Data},
  author={Xia, Yinglin and Sun, Jun and Chen, Ding-Geng},
  booktitle={Statistical Analysis of Microbiome Data with R},
  pages={43--75},
  year={2018},
  publisher={Springer}
}

@article{Yan02,
  title={Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation},
  author={Yang, Yee Hwa and Dudoit, Sandrine and Luu, Percy and Lin, David M and Peng, Vivian and Ngai, John and Speed, Terence P},
  journal={Nucleic acids research},
  volume={30},
  number={4},
  pages={e15--e15},
  year={2002},
  publisher={Oxford University Press}
}

@article{Yao12,
  title={Independent {P}rincipal {C}omponent {A}nalysis for biologically meaningful dimension reduction of large biological data sets},
  author={Yao, Fangzhou and Coquery, Jeff and L{\^e} Cao, Kim-Anh},
  journal={BMC bioinformatics},
  volume={13},
  number={1},
  pages={24},
  year={2012},
  publisher={BioMed Central Ltd}
}


@article{Yua06,
  title={Model selection and estimation in regression with grouped variables},
  author={Yuan, Ming and Lin, Yi},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={68},
  number={1},
  pages={49--67},
  year={2006},
  publisher={Wiley Online Library}
}

@article{Zau09,
  title={Defining the healthy" core microbiome" of oral microbial communities},
  author={Zaura, Egija and Keijser, Bart JF and Huse, Susan M and Crielaard, Wim},
  journal={BMC microbiology},
  volume={9},
  number={1},
  pages={259},
  year={2009},
  publisher={BioMed Central}
}

@article{Zou05,
  title={Regularization and variable selection via the elastic net},
  author={Zou, Hui and Hastie, Trevor},
  journal={Journal of the royal statistical society: series B (statistical methodology)},
  volume={67},
  number={2},
  pages={301--320},
  year={2005},
  publisher={Wiley Online Library}
}

@article{Zou06,
  title={Sparse principal component analysis},
  author={Zou, Hui and Hastie, Trevor and Tibshirani, Robert},
  journal={Journal of computational and graphical statistics},
  volume={15},
  number={2},
  pages={265--286},
  year={2006},
  publisher={Taylor \& Francis}
}





























































































