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paper.bib
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@article{chambers2015identification,
title={Identification of hemagglutinin residues responsible for {H3N2} antigenic drift during the 2014--2015 influenza season},
author={Chambers, Benjamin S and Parkhouse, Kaela and Ross, Ted M and Alby, Kevin and Hensley, Scott E},
journal={Cell Reports},
volume={12},
number={1},
pages={1--6},
year={2015},
publisher={Elsevier},
doi = {10.1016/j.celrep.2015.06.005},
}
@article{fowler2014deep,
author = {Fowler, Douglas M and Fields, Stanley},
title = {Deep mutational scanning: a new style of protein science.},
journal = {Nature Methods},
year = {2014},
volume = {11},
number = {8},
pages = {801--807},
month = aug,
doi = {10.1038/nmeth.3027},
}
@article{esposito2019mavedb,
title={MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect},
author={Esposito, Daniel and Weile, Jochen and Shendure, Jay and Starita, Lea M and Papenfuss, Anthony T and Roth, Frederick P and Fowler, Douglas M and Rubin, Alan F},
journal={Genome Biology},
volume={20},
number={1},
pages={1--11},
year={2019},
publisher={BioMed Central},
doi={10.1186/s13059-019-1845-6}
}
@article{lee2019mapping,
title={Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin},
author={Lee, Juhye M and Eguia, Rachel and Zost, Seth J and Choudhary, Saket and Wilson, Patrick C and Bedford, Trevor and Stevens-Ayers, Terry and Boeckh, Michael and Hurt, Aeron C and Lakdawala, Seema S and others},
journal={Elife},
volume={8},
year={2019},
publisher={eLife Sciences Publications, Ltd},
doi={10.7554/eLife.49324}
}
@article{starita2017variant,
title={Variant interpretation: functional assays to the rescue},
author={Starita, Lea M and Ahituv, Nadav and Dunham, Maitreya J and Kitzman, Jacob O and Roth, Frederick P and Seelig, Georg and Shendure, Jay and Fowler, Douglas M},
journal={The American Journal of Human Genetics},
volume={101},
number={3},
pages={315--325},
year={2017},
publisher={Elsevier},
doi={10.1016/j.ajhg.2017.07.014}
}
@article{wrenbeck2017deep,
title={Deep sequencing methods for protein engineering and design},
author={Wrenbeck, Emily E and Faber, Matthew S and Whitehead, Timothy A},
journal={Current Opinion in Structural Biology},
volume={45},
pages={36--44},
year={2017},
publisher={Elsevier},
doi={10.1016/j.sbi.2016.11.001}
}
@article{gelman2019recommendations,
title={Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation},
author={Gelman, Hannah and Dines, Jennifer N and Berg, Jonathan and Berger, Alice H and Brnich, Sarah and Hisama, Fuki M and James, Richard G and Rubin, Alan F and Shendure, Jay and Shirts, Brian and others},
journal={Genome Medicine},
volume={11},
number={1},
pages={85},
year={2019},
publisher={Springer},
doi={10.1186/s13073-019-0698-7}
}
@article{rubin2017statistical,
title={A statistical framework for analyzing deep mutational scanning data},
author={Rubin, Alan F and Gelman, Hannah and Lucas, Nathan and Bajjalieh, Sandra M and Papenfuss, Anthony T and Speed, Terence P and Fowler, Douglas M},
journal={Genome Biology},
volume={18},
number={1},
pages={150},
year={2017},
publisher={Springer},
doi={10.1186/s13059-017-1272-5}
}
@Article{ bloom2015software,
title = {Software for the analysis and visualization of deep
mutational scanning data},
author = {Bloom, Jesse D},
journal = {BMC Bioinformatics},
volume = {16},
number = {1},
pages = {1},
year = {2015},
publisher = {BioMed Central},
doi = {10.1186/s12859-015-0590-4}
}
@Article{ echave2016causes,
title = {Causes of evolutionary rate variation among protein
sites},
author = {Echave, Julian and Spielman, Stephanie J and Wilke, Claus
O},
journal = {Nature Reviews Genetics},
year = {2016},
publisher = {Nature Publishing Group},
doi = {10.1038/nrg.2015.18}
}
@software{weile,
author = {Jochen Weile},
title = {{VariantEffect/mavevis: v0.1.2.1: Minor release for
Zenodo DOI minting}},
month = sep,
year = 2019,
publisher = {Zenodo},
version = {v0.1.2.1},
doi = {10.5281/zenodo.3432882},
url = {https://doi.org/10.5281/zenodo.3432882}
}
@unpublished{PyMOL,
annote = {PyMOL
The PyMOL Molecular Graphics System, Version 1.8, Schr{\"o}dinger, LLC.},
author = {{Schr\"odinger, LLC}},
date-added = {2010-08-19 17:29:55 -0400},
date-modified = {2015-12-22 18:04:08 -0400},
month = {November},
title = {The {PyMOL} Molecular Graphics System, Version~1.8},
year = {2015}
}