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book.bib
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@Manual{rmarkdown2021,
title = {rmarkdown: Dynamic Documents for R},
author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
year = {2021},
note = {R package version 2.10},
url = {https://github.com/rstudio/rmarkdown},
}
@Book{Xie2018,
title = {R Markdown: The Definitive Guide},
author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2018},
note = {ISBN 9781138359338},
url = {https://bookdown.org/yihui/rmarkdown},
}
@Book{Xie2020,
title = {R Markdown Cookbook},
author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
year = {2020},
note = {ISBN 9780367563837},
url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}
@article{bauchner_citation_2016,
author = {Bauchner, Howard and Golub, Robert M. and Fontanarosa, Phil B.},
title = "{Data Sharing: An Ethical and Scientific Imperative}",
journal = {JAMA},
volume = {315},
number = {12},
pages = {1238-1240},
year = {2016},
month = {03},
issn = {0098-7484},
doi = {10.1001/jama.2016.2420},
url = {https://doi.org/10.1001/jama.2016.2420},
eprint = {https://jamanetwork.com/journals/jama/articlepdf/2504790/jed160017.pdf},
}
@article{bonomi_citation_2020,
author = {Bonomi, Luca and Huang, Yingxiang and Ohno-Machado, Lucila},
date = {2020/07/01},
date-added = {2022-10-26 09:20:24 -0400},
date-modified = {2022-10-26 09:20:24 -0400},
doi = {10.1038/s41588-020-0651-0},
id = {Bonomi2020},
isbn = {1546-1718},
journal = {Nature Genetics},
number = {7},
pages = {646--654},
title = {Privacy challenges and research opportunities for genomic data sharing},
url = {https://doi.org/10.1038/s41588-020-0651-0},
volume = {52},
year = {2020},
bdsk-url-1 = {https://doi.org/10.1038/s41588-020-0651-0}
}
@article{colavizza_citation_2020,
title = {The citation advantage of linking publications to research data},
volume = {15},
issn = {1932-6203},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0230416},
doi = {10.1371/journal.pone.0230416},
abstract = {Efforts to make research results open and reproducible are increasingly reflected by journal policies encouraging or mandating authors to provide data availability statements. As a consequence of this, there has been a strong uptake of data availability statements in recent literature. Nevertheless, it is still unclear what proportion of these statements actually contain well-formed links to data, for example via a URL or permanent identifier, and if there is an added value in providing such links. We consider 531, 889 journal articles published by PLOS and BMC, develop an automatic system for labelling their data availability statements according to four categories based on their content and the type of data availability they display, and finally analyze the citation advantage of different statement categories via regression. We find that, following mandated publisher policies, data availability statements become very common. In 2018 93.7\% of 21,793 PLOS articles and 88.2\% of 31,956 BMC articles had data availability statements. Data availability statements containing a link to data in a repository—rather than being available on request or included as supporting information files—are a fraction of the total. In 2017 and 2018, 20.8\% of PLOS publications and 12.2\% of BMC publications provided DAS containing a link to data in a repository. We also find an association between articles that include statements that link to data in a repository and up to 25.36\% (± 1.07\%) higher citation impact on average, using a citation prediction model. We discuss the potential implications of these results for authors (researchers) and journal publishers who make the effort of sharing their data in repositories. All our data and code are made available in order to reproduce and extend our results.},
language = {en},
number = {4},
urldate = {2022-10-19},
journal = {PLOS ONE},
author = {Colavizza, Giovanni and Hrynaszkiewicz, Iain and Staden, Isla and Whitaker, Kirstie and McGillivray, Barbara},
month = apr,
year = {2020},
note = {Publisher: Public Library of Science},
keywords = {Bibliometrics, Citation analysis, Data management, Open access publishing, Reproducibility, Science policy, Scientific publishing, Support vector machines},
pages = {e0230416},
annote = {justified},
}
@article{cosgriff_citation_2020,
title = {Data sharing in the era of {COVID}-19},
volume = {2},
issn = {2589-7500},
url = {https://doi.org/10.1016/S2589-7500(20)30082-0},
doi = {10.1016/S2589-7500(20)30082-0},
number = {5},
urldate = {2022-10-26},
journal = {The Lancet Digital Health},
author = {Cosgriff, Christopher V and Ebner, Daniel K and Celi, Leo Anthony},
month = may,
year = {2020},
note = {Publisher: Elsevier},
pages = {e224},
annote = {doi: 10.1016/S2589-7500(20)30082-0},
}
@article {mckiernan_citation_2016,
article_type = {journal},
title = {Point of View: How open science helps researchers succeed},
author = {McKiernan, Erin C and Bourne, Philip E and Brown, C Titus and Buck, Stuart and Kenall, Amye and Lin, Jennifer and McDougall, Damon and Nosek, Brian A and Ram, Karthik and Soderberg, Courtney K and Spies, Jeffrey R and Thaney, Kaitlin and Updegrove, Andrew and Woo, Kara H and Yarkoni, Tal},
editor = {Rodgers, Peter},
volume = 5,
year = 2016,
month = {jul},
pub_date = {2016-07-07},
pages = {e16800},
citation = {eLife 2016;5:e16800},
doi = {10.7554/eLife.16800},
url = {https://doi.org/10.7554/eLife.16800},
keywords = {open access, open data, open science, open source, research},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}
@article{piwowar_citation_2011,
author = {Piwowar, Heather A. and Vision, Todd J. and Whitlock, Michael C.},
date = {2011/05/01},
date-added = {2022-10-26 13:49:38 -0400},
date-modified = {2022-10-26 13:49:38 -0400},
doi = {10.1038/473285a},
id = {Piwowar2011},
isbn = {1476-4687},
journal = {Nature},
number = {7347},
pages = {285--285},
title = {Data archiving is a good investment},
url = {https://doi.org/10.1038/473285a},
volume = {473},
year = {2011},
bdsk-url-1 = {https://doi.org/10.1038/473285a}}
@article{sansone_citation_2019,
author = {Sansone, Susanna-Assunta and McQuilton, Peter and Rocca-Serra, Philippe and Gonzalez-Beltran, Alejandra and Izzo, Massimiliano and Lister, Allyson L. and Thurston, Milo and the FAIRsharing Community},
date = {2019/04/01},
date-added = {2023-02-01 10:22:01 -0500},
date-modified = {2023-02-01 10:22:01 -0500},
doi = {10.1038/s41587-019-0080-8},
id = {Sansone2019},
isbn = {1546-1696},
journal = {Nature Biotechnology},
number = {4},
pages = {358--367},
title = {FAIRsharing as a community approach to standards, repositories and policies},
url = {https://doi.org/10.1038/s41587-019-0080-8},
volume = {37},
year = {2019},
bdsk-url-1 = {https://doi.org/10.1038/s41587-019-0080-8}}
@article{tenopir_citation_2020,
doi = {10.1371/journal.pone.0229003},
author = {Tenopir, Carol AND Rice, Natalie M. AND Allard, Suzie AND Baird, Lynn AND Borycz, Josh AND Christian, Lisa AND Grant, Bruce AND Olendorf, Robert AND Sandusky, Robert J.},
journal = {PLOS ONE},
publisher = {Public Library of Science},
title = {Data sharing, management, use, and reuse: Practices and perceptions of scientists worldwide},
year = {2020},
month = {03},
volume = {15},
url = {https://doi.org/10.1371/journal.pone.0229003},
pages = {1-26},
number = {3},
}
@article{thessen_citation_2021,
author = {Thessen, Anne E. AND Bogdan, Paul AND Patterson, David J. AND Casey, Theresa M. AND Hinojo-Hinojo, C{\'e}sar AND de Lange, Orlando AND Haendel, Melissa A.},
doi = {10.1371/journal.pbio.3001129},
journal = {PLOS Biology},
month = {03},
number = {3},
pages = {1-12},
publisher = {Public Library of Science},
title = {From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences},
url = {https://doi.org/10.1371/journal.pbio.3001129},
volume = {19},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1371/journal.pbio.3001129}
}
@article{vesteghem_citation_2020,
author = {Vesteghem, Charles and Brøndum, Rasmus Froberg and Sønderkær, Mads and Sommer, Mia and Schmitz, Alexander and Bødker, Julie Støve and Dybkær, Karen and El-Galaly, Tarec Christoffer and Bøgsted, Martin},
title = "{Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives}",
journal = {Briefings in Bioinformatics},
volume = {21},
number = {3},
pages = {936-945},
year = {2020},
month = {05},
issn = {1477-4054},
doi = {10.1093/bib/bbz044},
url = {https://doi.org/10.1093/bib/bbz044},
eprint = {https://academic.oup.com/bib/article-pdf/21/3/936/33398969/bbz044.pdf},
}
@article{wilkinson_citation_2016,
author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Merc{\`e} and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J. G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and 't Hoen, Peter A. C and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and van der Lei, Johan and van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
date = {2016/03/15},
date-added = {2022-10-26 14:14:12 -0400},
date-modified = {2022-10-26 14:14:12 -0400},
doi = {10.1038/sdata.2016.18},
id = {Wilkinson2016},
isbn = {2052-4463},
journal = {Scientific Data},
number = {1},
pages = {160018},
title = {The FAIR Guiding Principles for scientific data management and stewardship},
url = {https://doi.org/10.1038/sdata.2016.18},
volume = {3},
year = {2016},
bdsk-url-1 = {https://doi.org/10.1038/sdata.2016.18}
}
@article{liu_imaging_2017,
title = {The {Current} {Role} of {Image} {Compression} {Standards} in {Medical} {Imaging}},
volume = {8},
copyright = {http://creativecommons.org/licenses/by/3.0/},
url = {https://www.mdpi.com/2078-2489/8/4/131},
doi = {10.3390/info8040131},
abstract = {With the increasing utilization of medical imaging in clinical practice and the growing dimensions of data volumes generated by various medical imaging modalities, the distribution, storage, and management of digital medical image data sets requires data compression. Over the past few decades, several image compression standards have been proposed by international standardization organizations. This paper discusses the current status of these image compression standards in medical imaging applications together with some of the legal and regulatory issues surrounding the use of compression in medical settings.},
language = {en},
number = {4},
urldate = {2022-01-10},
journal = {Information},
author = {Liu, Feng and Hernandez-Cabronero, Miguel and Sanchez, Victor and Marcellin, Michael W. and Bilgin, Ali},
month = dec,
year = {2017},
note = {Number: 4
Publisher: Multidisciplinary Digital Publishing Institute},
keywords = {DICOM, HEVC, image compression, JPEG, JPEG-LS, JPEG-XR, JPEG2000, medical imaging, standards},
pages = {131},
}
@misc{NIS,
title = {{NIS} {Database} {Documentation}},
url = {https://www.hcup-us.ahrq.gov/db/nation/nis/nisdbdocumentation.jsp},
urldate = {2021-12-17},
}