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@article{dobzhansky1973nothing,
title={Nothing in biology makes sense except in the light of evolution},
author={Dobzhansky, Theodosius},
journal={The American Biology Teacher},
volume={35},
number={3},
pages={125--129},
year={1973},
publisher={National Association of Biology Teachers}
}
@article{king1995replication,
title={Replication, replication},
author={King, Gary},
journal={PS: Political Science \& Politics},
volume={28},
number={3},
pages={444--452},
year={1995},
publisher={Cambridge University Press},
doi = {10.2307/420301}
}
@article{ioannidis2005most,
title={Why most published research findings are false},
author={Ioannidis, John PA},
journal={PLoS medicine},
volume={2},
number={8},
pages={e124},
year={2005},
publisher={Public Library of Science},
doi={10.1371/journal.pmed.0020124}
}
@article{prinz2011believe,
title={Believe it or not: how much can we rely on published data on potential drug targets?},
author={Prinz, Florian and Schlange, Thomas and Asadullah, Khusru},
journal={Nature reviews Drug discovery},
volume={10},
number={9},
pages={712--712},
year={2011},
publisher={Nature Publishing Group},
doi={10.1038/nrd3439-c1}
}
@article{peng2011reproducible,
title={Reproducible research in computational science},
author={Peng, Roger D},
journal={Science},
volume={334},
number={6060},
pages={1226--1227},
year={2011},
publisher={American Association for the Advancement of Science},
doi={}
}
@article{sandve2013ten,
title={Ten simple rules for reproducible computational research},
author={Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind},
journal={PLoS computational biology},
volume={9},
number={10},
pages={e1003285},
year={2013},
publisher={Public Library of Science San Francisco, USA},
doi={10.1371/journal.pcbi.1003285}
}
@misc{mcnutt2014reproducibility,
title={Reproducibility},
author={McNutt, Marcia},
year={2014},
publisher={American Association for the Advancement of Science},
doi={10.1126/science.1250475}
}
@article{peng2015reproducibility,
title={The reproducibility crisis in science: A statistical counterattack},
author={Peng, Roger},
journal={Significance},
volume={12},
number={3},
pages={30--32},
year={2015},
publisher={Wiley Online Library},
doi={10.1111/j.1740-9713.2015.00827.x}
}
@article{baker2016reproducibility,
title={Is there a reproducibility crisis?},
author={Baker, Monya},
journal={Nature},
volume={533},
number={26},
pages={353--66},
year={2016},
doi={10.1038/d41586-019-00067-3}
}
@article{michonneau2016rotl,
author = {Michonneau, Fran{\c{c}}ois and Brown, Joseph W. and Winter, David J.},
doi = {10.1111/2041-210X.12593},
issn = {2041210X},
journal = {Methods in Ecology and Evolution},
keywords = {Open Tree of Life,comparative methods,macroevolution,phylogenetics},
number = {12},
pages = {1476--1481},
title = {{rotl: an R package to interact with the Open Tree of Life data}},
volume = {7},
year = {2016}
}
@article{powers2019open,
title={Open science, reproducibility, and transparency in ecology},
author={Powers, Stephen M and Hampton, Stephanie E},
journal={Ecological Applications},
volume={29},
number={1},
pages={e01822},
year={2019},
publisher={Wiley Online Library},
doi={10.1002/eap.1822}
}
@misc{opentreeoflife2019synth,
author = {OpenTreeOfLife and
Benjamin Redelings and
Luna Luisa Sanchez Reyes and
Karen A. Cranston and
Jim Allman and
Mark T. Holder and
Emily Jane McTavish},
title = {Open Tree of Life Synthetic Tree},
month = dec,
year = 2019,
publisher = {Zenodo},
version = {12.3},
doi = {10.5281/zenodo.3937742},
url = {https://doi.org/10.5281/zenodo.3937742}
}
@article{sanchez2019datelife,
title={DateLife: Leveraging databases and analytical tools to reveal the dated Tree of Life},
author={S{\'a}nchez-Reyes, Luna L and O’Meara, Brian C},
journal={bioRxiv},
pages={782094},
year={2019},
publisher={Cold Spring Harbor Laboratory},
doi={10.1101/782094}
}
@article{nguyen2020phylotastic,
title={Phylotastic: improving access to tree-of-life knowledge with flexible, on-the-fly delivery of trees},
author={Nguyen, Van D and Nguyen, Thanh H and Tayeen, Abu Saleh Md and Laughinghouse IV, H Dail and S{\'a}nchez-Reyes, Luna L and Wiggins, Jodie and Pontelli, Enrico and Mozzherin, Dmitry and O’Meara, Brian and Stoltzfus, Arlin},
journal={Evolutionary Bioinformatics},
volume={16},
pages={1176934319899384},
year={2020},
publisher={SAGE Publications Sage UK: London, England},
doi={10.1177/1176934319899384}
}
@article{mctavish2021opentree,
author = {Mctavish, Emily Jane and Sánchez-Reyes, Luna Luisa and Holder, Mark T},
title = "{OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life}",
journal = {Systematic Biology},
year = {2021},
month = {05},
issn = {1063-5157},
doi = {10.1093/sysbio/syab033},
url = {https://doi.org/10.1093/sysbio/syab033}
}
@online{repdef2021,
author = {{Curating for Reproducibility Consortium}},
title = {{Defining "Reproducibility"}},
url = {{https://cure.web.unc.edu/defining-reproducibility/}},
urldate={August 15, 2021}
}
@online{phylotasticedtools,
author = {{Wiggins, Jodie and Phylotastic Team}},
title = {{Scientific data in your classroom}},
url = {{https://jwiggi18.github.io/phyloEd/}},
urldate={August 15, 2021}
}
@online{galacticedtools,
author = {{Wilkins, Matt and Galactic Polymath}},
title = {{support K-16 education and scicomm}},
url = {{https://github.com/galacticpolymath/galacticEdTools}},
urldate={August 15, 2021}
}
@online{opentreeAPIs,
author={OpenTreeOfLife and
Benjamin Redelings and
Karen A. Cranston and
Jim Allman and
Mark T. Holder and
Emily Jane McTavish},
title = {{Open Tree of Life APIs v. 3.0}},
url = {{https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs}},
}