@article{Philtron2018,
  title={Maximum Rank Reproducibility: A Nonparametric Approach to Assessing Reproducibility in Replicate Experiments},
  author={Philtron, Daisy and Lyu, Yafei and Li, Qunhua and Ghosh, Debashis},
  journal={Journal of the American Statistical Association},
  volume={113},
  number={523},
  pages={1028--1039},
  year={2018},
  publisher={Taylor \& Francis}
}

@article{Regan2010,
author = {Elizabeth A. Regan and John E. Hokanson and James R. Murphy and Barry Make and David A. Lynch and Terri H. Beaty and Douglas Curran-Everett and Edwin K. Silverman and James D. Crapo},
title = {Genetic Epidemiology of COPD (COPDGene) Study Design},
journal = {COPD: Journal of Chronic Obstructive Pulmonary Disease},
volume = {7},
number = {1},
pages = {32-43},
year  = {2011},
publisher = {Taylor & Francis},
doi = {10.3109/15412550903499522},

URL = { 
        https://doi.org/10.3109/15412550903499522
    
},
eprint = { 
        https://doi.org/10.3109/15412550903499522
    
}

}

@article{Hughes2013,
  title={MSPrep—Summarization, normalization and diagnostics for processing of mass spectrometry--based metabolomic data},
  author={Hughes, Grant and Cruickshank-Quinn, Charmion and Reisdorph, Richard and Lutz, Sharon and Petrache, Irina and Reisdorph, Nichole and Bowler, Russell and Kechris, Katerina},
  journal={Bioinformatics},
  volume={30},
  number={1},
  pages={133--134},
  year={2013},
  publisher={Oxford University Press}
}



@article{Cruickshank2018,
  title={Metabolomics and transcriptomics pathway approach reveals outcome-specific perturbations in COPD},
  author={Cruickshank-Quinn, Charmion I and Jacobson, Sean and Hughes, Grant and Powell, Roger L and Petrache, Irina and Kechris, Katerina and Bowler, Russell and Reisdorph, Nichole},
  journal={Scientific reports},
  volume={8},
  number={1},
  pages={17132},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{Evans2009,
  title={Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform for the identification and relative quantification of the small-molecule complement of biological systems},
  author={Evans, Anne M and DeHaven, Corey D and Barrett, Tom and Mitchell, Matt and Milgram, Eric},
  journal={Analytical chemistry},
  volume={81},
  number={16},
  pages={6656--6667},
  year={2009},
  publisher={ACS Publications}
}


@article{Dehaven2010,
  title={Organization of GC/MS and LC/MS metabolomics data into chemical libraries},
  author={DeHaven, Corey D and Evans, Anne M and Dai, Hongping and Lawton, Kay A},
  journal={Journal of cheminformatics},
  volume={2},
  number={1},
  pages={9},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{Bijlsma2006,
  title={Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation},
  author={Bijlsma, Sabina and Bobeldijk, Ivana and Verheij, Elwin R and Ramaker, Raymond and Kochhar, Sunil and Macdonald, Ian A and Van Ommen, Ben and Smilde, Age K},
  journal={Analytical chemistry},
  volume={78},
  number={2},
  pages={567--574},
  year={2006},
  publisher={ACS Publications}
}

@article{chong2018metaboanalyst,
  title={MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis},
  author={Chong, Jasmine and Soufan, Othman and Li, Carin and Caraus, Iurie and Li, Shuzhao and Bourque, Guillaume and Wishart, David S and Xia, Jianguo},
  journal={Nucleic acids research},
  volume={46},
  number={W1},
  pages={W486--W494},
  year={2018},
  publisher={Oxford University Press}
}

@article{irizarry2005multiple,
  title={Multiple-laboratory comparison of microarray platforms},
  author={Irizarry, Rafael A and Warren, Daniel and Spencer, Forrest and Kim, Irene F and Biswal, Shyam and Frank, Bryan C and Gabrielson, Edward and Garcia, Joe GN and Geoghegan, Joel and Germino, Gregory and others},
  journal={Nature methods},
  volume={2},
  number={5},
  pages={345--350},
  year={2005},
  publisher={Nature Publishing Group}
}

@article{zhang2018segmented,
  title={Segmented correspondence curve regression model for quantifying reproducibility of high-throughput experiments},
  author={Zhang, Feipeng and Shen, Frank and Yang, Tao and Li, Qunhua},
  journal={arXiv preprint arXiv:1807.00943},
  year={2018}
}

@article{li2011measuring,
  title={Measuring reproducibility of high-throughput experiments},
  author={Li, Qunhua and Brown, James B and Huang, Haiyan and Bickel, Peter J and others},
  journal={The annals of applied statistics},
  volume={5},
  number={3},
  pages={1752--1779},
  year={2011},
  publisher={Institute of Mathematical Statistics}
}

@article{mahieu2017systems,
  title={Systems-level annotation of a metabolomics data set reduces 25 000 features to fewer than 1000 unique metabolites},
  author={Mahieu, Nathaniel G and Patti, Gary J},
  journal={Analytical chemistry},
  volume={89},
  number={19},
  pages={10397--10406},
  year={2017},
  publisher={ACS Publications}
}

@article{want2013global,
  title={Global metabolic profiling of animal and human tissues via UPLC-MS},
  author={Want, Elizabeth J and Masson, Perrine and Michopoulos, Filippos and Wilson, Ian D and Theodoridis, Georgios and Plumb, Robert S and Shockcor, John and Loftus, Neil and Holmes, Elaine and Nicholson, Jeremy K},
  journal={Nature protocols},
  volume={8},
  number={1},
  pages={17},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{spicer2017navigating,
  title={Navigating freely-available software tools for metabolomics analysis},
  author={Spicer, Rachel and Salek, Reza M and Moreno, Pablo and Ca{\~n}ueto, Daniel and Steinbeck, Christoph},
  journal={Metabolomics},
  volume={13},
  number={9},
  pages={106},
  year={2017},
  publisher={Springer}
}

@incollection{maniscalco2019clinical,
  title={Clinical metabolomics of exhaled breath condensate in chronic respiratory diseases},
  author={Maniscalco, Mauro and Fuschillo, Salvatore and Paris, Debora and Cutignano, Adele and Sanduzzi, Alessandro and Motta, Andrea},
  booktitle={Advances in clinical chemistry},
  volume={88},
  pages={121--149},
  year={2019},
  publisher={Elsevier}
}

@article{sarode2019metabolomics,
  title={Metabolomics profiles of patients with Wilson disease reveal a distinct metabolic signature},
  author={Sarode, Gaurav V and Kim, Kyoungmi and Kieffer, Dorothy A and Shibata, Noreene M and Litwin, Tomas and Czlonkowska, Anna and Medici, Valentina},
  journal={Metabolomics},
  volume={15},
  number={3},
  pages={43},
  year={2019},
  publisher={Springer}
}

@article{liu2019metabolite,
  title={Metabolite Profiles of the Cerebrospinal Fluid in Neurosyphilis Patients Determined by Untargeted Metabolomics Analysis},
  author={Liu, Li-Li and Lin, Yong and Chen, Wei and Tong, Man-Li and Luo, Xi and Lin, Li-Rong and ZHANG, HUILIN and Yan, Jiang-Hua and Niu, Jian-Jun and Yang, Tian-Ci},
  journal={Frontiers in neuroscience},
  volume={13},
  pages={150},
  year={2019},
  publisher={Frontiers}
}

@article{sanchez2019metabolomic,
  title={Metabolomic approaches reveal differences in pea aphid host plant chemistry before and after infestation with different pea aphid host races},
  author={Sanchez Arcos, Carlos Fernando and Kai, Marco and Svato{\v{s}}, Ale{\v{s}} and Gershenzon, Jonathan and Kunert, Grit},
  journal={Frontiers in plant science},
  volume={10},
  pages={188},
  year={2019},
  publisher={Frontiers}
}

@article{allwood2019rapid,
  title={Rapid UHPLC-MS metabolite profiling and phenotypic assays reveal genotypic impacts of nitrogen supplementation in oats},
  author={Allwood, J William and Xu, Yun and Martinez-Martin, Pilar and Palau, Raphaёlle and Cowan, Alexander and Goodacre, Royston and Marshall, Athole and Stewart, Derek and Howarth, Catherine},
  journal={Metabolomics},
  volume={15},
  number={3},
  pages={42},
  year={2019},
  publisher={Springer}
}

@article{lohr2019resolving,
  title={Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling},
  author={Lohr, Kathryn E and Camp, Emma F and Kuzhiumparambil, Unnikrishnan and Lutz, Adrian and Leggat, William and Patterson, Joshua T and Suggett, David J},
  journal={Journal of Experimental Biology},
  volume={222},
  number={8},
  pages={jeb195982},
  year={2019},
  publisher={The Company of Biologists Ltd}
}

@article{sugimoto2010prediction,
  title={Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE-TOFMS data},
  author={Sugimoto, Masahiro and Hirayama, Akiyoshi and Robert, Martin and Abe, Shinobu and Soga, Tomoyoshi and Tomita, Masaru},
  journal={Electrophoresis},
  volume={31},
  number={14},
  pages={2311--2318},
  year={2010},
  publisher={Wiley Online Library}
}

@article{lu2008analytical,
  title={Analytical strategies for LC--MS-based targeted metabolomics},
  author={Lu, Wenyun and Bennett, Bryson D and Rabinowitz, Joshua D},
  journal={Journal of chromatography B},
  volume={871},
  number={2},
  pages={236--242},
  year={2008},
  publisher={Elsevier}
}

@article{li2011measuring,
  title={Measuring reproducibility of high-throughput experiments},
  author={Li, Qunhua and Brown, James B and Huang, Haiyan and Bickel, Peter J and others},
  journal={The annals of applied statistics},
  volume={5},
  number={3},
  pages={1752--1779},
  year={2011},
  publisher={Institute of Mathematical Statistics}
}

@article{arvidsson2008quantprime,
  title={QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR},
  author={Arvidsson, Samuel and Kwasniewski, Miroslaw and Ria{\~n}o-Pach{\'o}n, Diego Mauricio and Mueller-Roeber, Bernd},
  journal={BMC bioinformatics},
  volume={9},
  number={1},
  pages={465},
  year={2008},
  publisher={Springer}
}

@article{talloen2010filtering,
  title={Filtering data from high-throughput experiments based on measurement reliability},
  author={Talloen, Willem and Hochreiter, Sepp and Bijnens, Luc and Kasim, Adetayo and Shkedy, Ziv and Amaratunga, Dhammika and G{\"o}hlmann, Hinrich},
  journal={Proceedings of the National Academy of Sciences},
  volume={107},
  number={46},
  pages={E173--E174},
  year={2010},
  publisher={National Acad Sciences}
}

@article{ac2013reproducibility,
  title={Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories},
  author={AC't Hoen, Peter and Friedl{\"a}nder, Marc R and Alml{\"o}f, Jonas and Sammeth, Michael and Pulyakhina, Irina and Anvar, Seyed Yahya and Laros, Jeroen FJ and Buermans, Henk PJ and Karlberg, Olof and Br{\"a}nnvall, Mathias and others},
  journal={Nature biotechnology},
  volume={31},
  number={11},
  pages={1015},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{marioni2008rna,
  title={RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays},
  author={Marioni, John C and Mason, Christopher E and Mane, Shrikant M and Stephens, Matthew and Gilad, Yoav},
  journal={Genome research},
  volume={18},
  number={9},
  pages={1509--1517},
  year={2008},
  publisher={Cold Spring Harbor Lab}
}

@article{porazinska2010reproducibility,
  title={Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure},
  author={Porazinska, Dorota L and Sung, WAY and GIBLIN-DAVIS, ROBIN M and Thomas, W Kelley},
  journal={Molecular Ecology Resources},
  volume={10},
  number={4},
  pages={666--676},
  year={2010},
  publisher={Wiley Online Library}
}

@article{LiZhang17,
  title={A regression framework for assessing covariate effects on the reproducibility of high-throughput experiments},
  author={Li, Qunhua and Zhang, Feipeng},
  journal={Biometrics},
  volume={74},
  number={3},
  pages={803--813},
  year={2018},
  publisher={Wiley Online Library}
}

@article{landt12,
  title={ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia},
  author={Landt, Stephen G and Marinov, Georgi K and Kundaje, Anshul and Kheradpour, Pouya and Pauli, Florencia and Batzoglou, Serafim and Bernstein, Bradley E and Bickel, Peter and Brown, James B and Cayting, Philip and others},
  journal={Genome research},
  volume={22},
  number={9},
  pages={1813--1831},
  year={2012},
  publisher={Cold Spring Harbor Lab}
}

@article{Donoho04,
  title={Higher criticism for detecting sparse heterogeneous mixtures},
  author={Donoho, David and Jin, Jiashun and others},
  journal={The Annals of Statistics},
  volume={32},
  number={3},
  pages={962--994},
  year={2004},
  publisher={Institute of Mathematical Statistics}
}


@article{hastie1999imputing,
  title={Imputing missing data for gene expression arrays},
  author={Hastie, Trevor and Tibshirani, Robert and Sherlock, Gavin and Eisen, Michael and Brown, Patrick and Botstein, David},
  year={1999},
  publisher={Stanford University Statistics Department Technical report}
}

@article{stacklies2007pcamethods,
  title={pcaMethods—a bioconductor package providing PCA methods for incomplete data},
  author={Stacklies, Wolfram and Redestig, Henning and Scholz, Matthias and Walther, Dirk and Selbig, Joachim},
  journal={Bioinformatics},
  volume={23},
  number={9},
  pages={1164--1167},
  year={2007},
  publisher={Oxford University Press}
}

@article{jacob2014ruv,
  title={RUV for normalization of expression array data},
  author={Jacob, Laurent},
  journal={Bioconductor $$\backslash$geq},
  volume={3},
  year={2014}
}

@article{Storey2004,
  title={Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach},
  author={Storey, John D and Taylor, Jonathan E and Siegmund, David},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={66},
  number={1},
  pages={187--205},
  year={2004},
  publisher={Wiley Online Library}
}

@article{Genovese2002,
  title={Operating characteristics and extensions of the false discovery rate procedure},
  author={Genovese, Christopher and Wasserman, Larry},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={64},
  number={3},
  pages={499--517},
  year={2002},
  publisher={Wiley Online Library}
}

@article{Benjamini1995,
  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)},
  volume={57},
  number={1},
  pages={289--300},
  year={1995},
  publisher={Wiley Online Library}
}

@article{Ruth2011,
  title={False discovery rate controlling procedures for discrete tests},
  author={Heller, Ruth and Gur, Hadas},
  journal={arXiv preprint arXiv:1112.4627},
  year={2011},
  publisher={Citeseer}
}

@article{marioni2008rna,
  title={RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays},
  author={Marioni, John C and Mason, Christopher E and Mane, Shrikant M and Stephens, Matthew and Gilad, Yoav},
  journal={Genome research},
  volume={18},
  number={9},
  pages={1509--1517},
  year={2008},
  publisher={Cold Spring Harbor Lab}
}
