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@article{barlow2020aqau,
author = {Barlow, Jacob T. and Bogatyrev, Said R. and Ismagilov, Rustem F.},
doi = {10.1038/s41467-020-16224-6},
journal = {Nat. Commun.},
number = {1},
pages = {1--13},
pmid = {32444602},
publisher = {Springer US},
title = {{A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities}},
url = {http://dx.doi.org/10.1038/s41467-020-16224-6},
volume = {11},
year = {2020}
}
@article{brooks2015thet,
author = {Brooks, J Paul and Edwards, David J and Harwich, Michael D and Rivera, Maria C and Fettweis, Jennifer M and Serrano, Myrna G and Reris, Robert A and Sheth, Nihar U and Huang, Bernice and Girerd, Philippe and Strauss, Jerome F and Jefferson, Kimberly K and Buck, Gregory A},
doi = {10.1186/s12866-015-0351-6},
journal = {BMC Microbiol.},
month = {dec},
number = {1},
pages = {66},
publisher = {BioMed Central},
title = {{The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies}},
url = {http://www.biomedcentral.com/1471-2180/15/66},
volume = {15},
year = {2015}
}
@article{callahan2017repl,
author = {Callahan, Benjamin J and DiGiulio, Daniel B and Goltsman, Daniela S Aliaga and Sun, Christine L and Costello, Elizabeth K and Jeganathan, Pratheepa and Biggio, Joseph R and Wong, Ronald J and Druzin, Maurice L and Shaw, Gary M and Stevenson, David K and Holmes, Susan P and Relman, David A},
doi = {10.1073/pnas.1705899114},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
month = {sep},
number = {37},
pages = {9966--9971},
title = {{Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/28847941 http://www.pnas.org/content/114/37/9966.long},
volume = {114},
year = {2017}
}
@article{cartwright2018mult,
author = {Cartwright, Charles P. and Pherson, Amanda J. and Harris, Ayla B. and Clancey, Matthew S. and Nye, Melinda B.},
doi = {10.1016/j.diagmicrobio.2018.05.022},
journal = {Diagn. Microbiol. Infect. Dis.},
number = {3},
pages = {173--178},
pmid = {29937222},
publisher = {Elsevier Inc.},
title = {{Multicenter study establishing the clinical validity of a nucleic-acid amplification–based assay for the diagnosis of bacterial vaginosis}},
url = {https://doi.org/10.1016/j.diagmicrobio.2018.05.022},
volume = {92},
year = {2018}
}
@article{chng2020meta,
author = {Chng, Kern Rei and Ghosh, Tarini Shankar and Tan, Yi Han and Nandi, Tannistha and Lee, Ivor Russel and Ng, Amanda Hui Qi and Li, Chenhao and Ravikrishnan, Aarthi and Lim, Kar Mun and Lye, David and Barkham, Timothy and Raman, Karthik and Chen, Swaine L. and Chai, Louis and Young, Barnaby and Gan, Yunn Hwen and Nagarajan, Niranjan},
doi = {10.1038/s41559-020-1236-0},
journal = {Nat. Ecol. Evol.},
number = {9},
pages = {1256--1267},
title = {{Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut}},
url = {http://dx.doi.org/10.1038/s41559-020-1236-0},
volume = {4},
year = {2020}
}
@article{clausen2022mode,
title = "Modeling complex measurement error in microbiome experiments",
author = "Clausen, David S and Willis, Amy D",
month = apr,
year = 2022,
url = "http://arxiv.org/abs/2204.12733",
archivePrefix = "arXiv",
eprint = "2204.12733",
primaryClass = "stat.ME",
arxivid = "2204.12733"
}
@article{conover2012ther,
title = "The rank transformation-an easy and intuitive way to connect
many nonparametric methods to their parametric counterparts for
seamless teaching introductory statistics courses",
author = "Conover, W Jay",
journal = "Wiley Interdiscip. Rev. Comput. Stat.",
publisher = "Wiley",
volume = 4,
number = 5,
pages = "432--438",
month = sep,
year = 2012,
url = "https://onlinelibrary.wiley.com/doi/10.1002/wics.1216",
copyright = "http://onlinelibrary.wiley.com/termsAndConditions\#vor",
language = "en",
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doi = "10.1002/wics.1216"
}
@article{contijoch2019gutm,
author = {Contijoch, Eduardo J and Britton, Graham J and Yang, Chao and Mogno, Ilaria and Li, Zhihua and Ng, Ruby and Llewellyn, Sean R and Hira, Sheela and Johnson, Crystal and Rabinowitz, Keren M and Barkan, Revital and Dotan, Iris and Hirten, Robert P and Fu, Shih-Chen and Luo, Yuying and Yang, Nancy and Luong, Tramy and Labrias, Philippe R and Lira, Sergio and Peter, Inga and Grinspan, Ari and Clemente, Jose C and Kosoy, Roman and Kim-Schulze, Seunghee and Qin, Xiaochen and Castillo, Anabella and Hurley, Amanda and Atreja, Ashish and Rogers, Jason and Fasihuddin, Farah and Saliaj, Merjona and Nolan, Amy and Reyes-Mercedes, Pamela and Rodriguez, Carina and Aly, Sarah and Santa-Cruz, Kenneth and Peters, Lauren and Su{\'{a}}rez-Fari{\~{n}}as, Mayte and Huang, Ruiqi and Hao, Ke and Zhu, Jun and Zhang, Bin and Losic, Bojan and Irizar, Haritz and Song, Won-Min and {Di Narzo}, Antonio and Wang, Wenhui and Cohen, Benjamin L and DiMaio, Christopher and Greenwald, David and Itzkowitz, Steven and Lucas, Aimee and Marion, James and Maser, Elana and Ungaro, Ryan and Naymagon, Steven and Novak, Joshua and Shah, Brijen and Ullman, Thomas and Rubin, Peter and George, James and Legnani, Peter and Telesco, Shannon E and Friedman, Joshua R and Brodmerkel, Carrie and Plevy, Scott and Cho, Judy H and Colombel, Jean-Frederic and Schadt, Eric E and Argmann, Carmen and Dubinsky, Marla and Kasarskis, Andrew and Sands, Bruce and Faith, Jeremiah J},
doi = {10.7554/eLife.40553},
journal = {Elife},
month = {jan},
title = {{Gut microbiota density influences host physiology and is shaped by host and microbial factors}},
url = {https://elifesciences.org/articles/40553},
volume = {8},
year = {2019}
}
@article{costea2017towa,
author = {Costea, Paul I and Zeller, Georg and Sunagawa, Shinichi and Pelletier, Eric and Alberti, Adriana and Levenez, Florence and Tramontano, Melanie and Driessen, Marja and Hercog, Rajna and Jung, Ferris-Elias and Kultima, Jens Roat and Hayward, Matthew R and Coelho, Luis Pedro and Allen-Vercoe, Emma and Bertrand, Laurie and Blaut, Michael and Brown, Jillian R M and Carton, Thomas and Cools-Portier, St{\'{e}}phanie and Daigneault, Michelle and Derrien, Muriel and Druesne, Anne and de Vos, Willem M and Finlay, B Brett and Flint, Harry J and Guarner, Francisco and Hattori, Masahira and Heilig, Hans and Luna, Ruth Ann and {van Hylckama Vlieg}, Johan and Junick, Jana and Klymiuk, Ingeborg and Langella, Philippe and {Le Chatelier}, Emmanuelle and Mai, Volker and Manichanh, Chaysavanh and Martin, Jennifer C and Mery, Cl{\'{e}}mentine and Morita, Hidetoshi and O'Toole, Paul W and Orvain, C{\'{e}}line and Patil, Kiran Raosaheb and Penders, John and Persson, S{\o}ren and Pons, Nicolas and Popova, Milena and Salonen, Anne and Saulnier, Delphine and Scott, Karen P and Singh, Bhagirath and Slezak, Kathleen and Veiga, Patrick and Versalovic, James and Zhao, Liping and Zoetendal, Erwin G and Ehrlich, S Dusko and Dore, Joel and Bork, Peer},
doi = {10.1038/nbt.3960},
journal = {Nat. Biotechnol.},
month = {oct},
number = {11},
pages = {1069--1076},
publisher = {Nature Research},
title = {{Towards standards for human fecal sample processing in metagenomic studies}},
url = {http://www.nature.com/doifinder/10.1038/nbt.3960},
volume = {35},
year = {2017}
}
@article{cruz2021equi,
author = {Cruz, Giuliano Netto Flores and Christoff, Ana Paula and de Oliveira, Luiz Felipe Valter},
doi = {10.3389/fmicb.2021.638231},
journal = {Front. Microbiol.},
keywords = {Absolute abundances,Bacteria,Compositional,Hospital,Microbiome,NGS,Next-generation sequencing,Total microbial load},
month = {feb},
number = {February},
pages = {1--16},
title = {{Equivolumetric Protocol Generates Library Sizes Proportional to Total Microbial Load in 16S Amplicon Sequencing}},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.638231/full},
volume = {12},
year = {2021}
}
@article{david2014host,
author = {David, Lawrence A and Materna, Arne C and Friedman, Jonathan and Campos-Baptista, Maria I and Blackburn, Matthew C and Perrotta, Allison and Erdman, Susan E and Alm, Eric J},
doi = {10.1186/gb-2014-15-7-r89},
journal = {Genome Biol.},
month = {jul},
number = {7},
pages = {R89},
publisher = {BioMed Central},
title = {{Host lifestyle affects human microbiota on daily timescales}},
url = {http://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-7-r89},
volume = {15},
year = {2014}
}
@article{diener2021nonr,
author = {Diener, Christian and Hoge, Anna C.H. and Kearney, Sean M. and Kusebauch, Ulrike and Patwardhan, Sushmita and Moritz, Robert L. and Erdman, Susan E. and Gibbons, Sean M.},
doi = {10.1038/s42003-021-01841-8},
journal = {Commun. Biol.},
number = {1},
pmid = {33750910},
publisher = {Springer US},
title = {{Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut}},
url = {http://dx.doi.org/10.1038/s42003-021-01841-8},
volume = {4},
year = {2021}
}
@article{dreo2014opti,
author = {Dreo, Tanja and Pirc, Manca and Ram{\v{s}}ak, {\v{Z}}iva and Pav{\v{s}}i{\v{c}}, Jernej and Milavec, Mojca and {\v{Z}}el, Jana and Gruden, Kristina},
doi = {10.1007/s00216-014-8084-1},
journal = {Anal. Bioanal. Chem.},
month = {oct},
number = {26},
pages = {6513--6528},
pmid = {25173868},
title = {{Optimising droplet digital PCR analysis approaches for detection and quantification of bacteria: a case study of fire blight and potato brown rot}},
url = {http://link.springer.com/10.1007/s00216-014-8084-1},
volume = {406},
year = {2014}
}
@article{fernandes2014unif,
author = {Fernandes, Andrew D and Reid, Jennifer NS and Macklaim, Jean M and McMurrough, Thomas A and Edgell, David R and Gloor, Gregory B},
doi = {10.1186/2049-2618-2-15},
journal = {Microbiome},
month = {may},
number = {1},
pages = {15},
publisher = {BioMed Central},
title = {{Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis}},
url = {http://www.microbiomejournal.com/content/2/1/15},
volume = {2},
year = {2014}
}
@article{fettweis2019thev,
author = {Fettweis, Jennifer M. and Serrano, Myrna G. and Brooks, Jamie Paul and Edwards, David J. and Girerd, Philippe H. and Parikh, Hardik I. and Huang, Bernice and Arodz, Tom J. and Edupuganti, Laahirie and Glascock, Abigail L. and Xu, Jie and Jimenez, Nicole R. and Vivadelli, Stephany C. and Fong, Stephen S. and Sheth, Nihar U. and Jean, Sophonie and Lee, Vladimir and Bokhari, Yahya A. and Lara, Ana M. and Mistry, Shreni D. and Duckworth, Robert A. and Bradley, Steven P. and Koparde, Vishal N. and Orenda, X. Valentine and Milton, Sarah H. and Rozycki, Sarah K. and Matveyev, Andrey V. and Wright, Michelle L. and Huzurbazar, Snehalata V. and Jackson, Eugenie M. and Smirnova, Ekaterina and Korlach, Jonas and Tsai, Yu-Chih and Dickinson, Molly R. and Brooks, Jamie L. and Drake, Jennifer I. and Chaffin, Donald O. and Sexton, Amber L. and Gravett, Michael G. and Rubens, Craig E. and Wijesooriya, N. Romesh and Hendricks-Mu{\~{n}}oz, Karen D. and Jefferson, Kimberly K. and Strauss, Jerome F. and Buck, Gregory A.},
doi = {10.1038/s41591-019-0450-2},
journal = {Nat. Med.},
keywords = {Microbiome,Predictive markers,Urogenital reproductive disorders,vaginal microbiome},
month = {jun},
number = {6},
pages = {1012--1021},
publisher = {Nature Publishing Group},
title = {{The vaginal microbiome and preterm birth}},
url = {http://www.nature.com/articles/s41591-019-0450-2},
volume = {25},
year = {2019}
}
@article{finucane2014atax,
author = {Finucane, Mariel M. and Sharpton, Thomas J. and Laurent, Timothy J. and Pollard, Katherine S.},
doi = {10.1371/journal.pone.0084689},
editor = {Heimesaat, Markus M.},
issn = {1932-6203},
journal = {PLoS One},
month = {jan},
number = {1},
pages = {e84689},
title = {{A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter}},
url = {https://dx.plos.org/10.1371/journal.pone.0084689},
volume = {9},
year = {2014}
}
@article{galazzo2020howt,
author = {Galazzo, Gianluca and van Best, Niels and Benedikter, Birke J. and Janssen, Kevin and Bervoets, Liene and Driessen, Christel and Oomen, Melissa and Lucchesi, Mayk and van Eijck, Pascalle H. and Becker, Heike E. F. and Hornef, Mathias W. and Savelkoul, Paul H. and Stassen, Frank R. M. and Wolffs, Petra F. and Penders, John},
doi = {10.3389/fcimb.2020.00403},
journal = {Front. Cell. Infect. Microbiol.},
month = {aug},
number = {August},
title = {{How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches}},
url = {https://www.frontiersin.org/article/10.3389/fcimb.2020.00403/full},
volume = {10},
year = {2020}
}
@book{gelman2020regr,
title = "Regression and Other Stories",
author = "Gelman, Andrew and Hill, Jennifer and Vehtari, Aki",
publisher = "Cambridge University Press",
month = jul,
year = 2020,
language = "en",
isbn = "9781107023987"
}
@article{gill2016eval,
author = {Gill, Christina and van de Wijgert, Janneke H. H. M. and Blow, Frances and Darby, Alistair C.},
doi = {10.1371/journal.pone.0163148},
editor = {Larsen, Peter E.},
journal = {PLoS One},
month = {sep},
number = {9},
pages = {e0163148},
pmid = {27643503},
publisher = {Public Library of Science},
title = {{Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota}},
url = {http://dx.plos.org/10.1371/journal.pone.0163148 https://dx.plos.org/10.1371/journal.pone.0163148 http://www.ncbi.nlm.nih.gov/pubmed/27643503 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5028042},
volume = {11},
year = {2016}
}
@article{gloor2017micr,
author = {Gloor, Gregory B. and Macklaim, Jean M. and Pawlowsky-Glahn, Vera and Egozcue, Juan J.},
doi = {10.3389/fmicb.2017.02224},
journal = {Front. Microbiol.},
month = {nov},
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