mutation_data.bib

@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}
}
@article{klesmith2015comprehensive,
  title={Comprehensive sequence-flux mapping of a levoglucosan utilization pathway in E. coli},
  author={Klesmith, Justin R and Bacik, John-Paul and Michalczyk, Ryszard and Whitehead, Timothy A},
  journal={ACS synthetic biology},
  volume={4},
  number={11},
  pages={1235--1243},
  year={2015},
  publisher={ACS Publications}
}
@article{haddox2018mapping,
  title={Mapping mutational effects along the evolutionary landscape of HIV envelope},
  author={Haddox, Hugh K and Dingens, Adam S and Hilton, Sarah K and Overbaugh, Julie and Bloom, Jesse D},
  journal={Elife},
  volume={7},
  pages={e34420},
  year={2018},
  publisher={eLife Sciences Publications Limited}
}
@article{romero2015dissecting,
  title={Dissecting enzyme function with microfluidic-based deep mutational scanning},
  author={Romero, Philip A and Tran, Tuan M and Abate, Adam R},
  journal={Proceedings of the National Academy of Sciences},
  volume={112},
  number={23},
  pages={7159--7164},
  year={2015},
  publisher={National Acad Sciences}
}
@article{firnberg2014comprehensive,
  title={A comprehensive, high-resolution map of a gene’s fitness landscape},
  author={Firnberg, Elad and Labonte, Jason W and Gray, Jeffrey J and Ostermeier, Marc},
  journal={Molecular biology and evolution},
  volume={31},
  number={6},
  pages={1581--1592},
  year={2014},
  publisher={Oxford University Press}
}
@article{deng2012deep,
  title={Deep sequencing of systematic combinatorial libraries reveals $\beta$-lactamase sequence constraints at high resolution},
  author={Deng, Zhifeng and Huang, Wanzhi and Bakkalbasi, Erol and Brown, Nicholas G and Adamski, Carolyn J and Rice, Kacie and Muzny, Donna and Gibbs, Richard A and Palzkill, Timothy},
  journal={Journal of molecular biology},
  volume={424},
  number={3-4},
  pages={150--167},
  year={2012},
  publisher={Elsevier}
}
@article{stiffler2015evolvability,
  title={Evolvability as a function of purifying selection in TEM-1 $\beta$-lactamase},
  author={Stiffler, Michael A and Hekstra, Doeke R and Ranganathan, Rama},
  journal={Cell},
  volume={160},
  number={5},
  pages={882--892},
  year={2015},
  publisher={Elsevier}
}
@article{jacquier2013capturing,
  title={Capturing the mutational landscape of the beta-lactamase TEM-1},
  author={Jacquier, Herv{\'e} and Birgy, Andr{\'e} and Le Nagard, Herv{\'e} and Mechulam, Yves and Schmitt, Emmanuelle and Glodt, J{\'e}r{\'e}my and Bercot, Beatrice and Petit, Emmanuelle and Poulain, Julie and Barnaud, Guil{\`e}ne and others},
  journal={Proceedings of the National Academy of Sciences},
  volume={110},
  number={32},
  pages={13067--13072},
  year={2013},
  publisher={National Acad Sciences}
}
@article{findlay2018comprehensive,
  title={Comprehensive characterization of transcript diversity at the human NODAL locus},
  author={Findlay, Scott D and Postovit, Lynne-Marie},
  journal={BioRxiv},
  pages={254409},
  year={2018},
  publisher={Cold Spring Harbor Laboratory}
}
@article{mclaughlin2012spatial,
  title={The spatial architecture of protein function and adaptation},
  author={McLaughlin Jr, Richard N and Poelwijk, Frank J and Raman, Arjun and Gosal, Walraj S and Ranganathan, Rama},
  journal={Nature},
  volume={491},
  number={7422},
  pages={138--142},
  year={2012},
  publisher={Nature Publishing Group}
}
@article{kitzman2015massively,
  title={Massively parallel single-amino-acid mutagenesis},
  author={Kitzman, Jacob O and Starita, Lea M and Lo, Russell S and Fields, Stanley and Shendure, Jay},
  journal={Nature methods},
  volume={12},
  number={3},
  pages={203--206},
  year={2015},
  publisher={Nature Publishing Group}
}
@article{doud2016accurate,
  title={Accurate measurement of the effects of all amino-acid mutations on influenza hemagglutinin},
  author={Doud, Michael B and Bloom, Jesse D},
  journal={Viruses},
  volume={8},
  number={6},
  pages={155},
  year={2016},
  publisher={Multidisciplinary Digital Publishing Institute}
}
@article{pokusaeva2019experimental,
  title={An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape},
  author={Pokusaeva, Victoria O and Usmanova, Dinara R and Putintseva, Ekaterina V and Espinar, Lorena and Sarkisyan, Karen S and Mishin, Alexander S and Bogatyreva, Natalya S and Ivankov, Dmitry N and Akopyan, Arseniy V and Avvakumov, Sergey Ya and others},
  journal={PLoS genetics},
  volume={15},
  number={4},
  pages={e1008079},
  year={2019},
  publisher={Public Library of Science San Francisco, CA USA}
}
@article{mishra2016systematic,
  title={Systematic mutant analyses elucidate general and client-specific aspects of Hsp90 function},
  author={Mishra, Parul and Flynn, Julia M and Starr, Tyler N and Bolon, Daniel NA},
  journal={Cell reports},
  volume={15},
  number={3},
  pages={588--598},
  year={2016},
  publisher={Elsevier}
}
@article{kelsic2016rna,
  title={RNA structural determinants of optimal codons revealed by MAGE-Seq},
  author={Kelsic, Eric D and Chung, Hattie and Cohen, Niv and Park, Jimin and Wang, Harris H and Kishony, Roy},
  journal={Cell systems},
  volume={3},
  number={6},
  pages={563--571},
  year={2016},
  publisher={Elsevier}
}
@article{melnikov2014comprehensive,
  title={Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes},
  author={Melnikov, Alexandre and Rogov, Peter and Wang, Li and Gnirke, Andreas and Mikkelsen, Tarjei S},
  journal={Nucleic acids research},
  volume={42},
  number={14},
  pages={e112--e112},
  year={2014},
  publisher={Oxford University Press}
}
@article{brenan2016phenotypic,
  title={Phenotypic characterization of a comprehensive set of MAPK1/ERK2 missense mutants},
  author={Brenan, Lisa and Andreev, Aleksandr and Cohen, Ofir and Pantel, Sasha and Kamburov, Atanas and Cacchiarelli, Davide and Persky, Nicole S and Zhu, Cong and Bagul, Mukta and Goetz, Eva M and others},
  journal={Cell reports},
  volume={17},
  number={4},
  pages={1171--1183},
  year={2016},
  publisher={Elsevier}
}
@article{rockah2015systematic,
  title={Systematic mapping of protein mutational space by prolonged drift reveals the deleterious effects of seemingly neutral mutations},
  author={Rockah-Shmuel, Liat and T{\'o}th-Petr{\'o}czy, {\'A}gnes and Tawfik, Dan S},
  journal={PLoS computational biology},
  volume={11},
  number={8},
  pages={e1004421},
  year={2015},
  publisher={Public Library of Science San Francisco, CA USA}
}
@article{wu2015functional,
  title={Functional constraint profiling of a viral protein reveals discordance of evolutionary conservation and functionality},
  author={Wu, Nicholas C and Olson, C Anders and Du, Yushen and Le, Shuai and Tran, Kevin and Remenyi, Roland and Gong, Danyang and Al-Mawsawi, Laith Q and Qi, Hangfei and Wu, Ting-Ting and others},
  journal={PLoS genetics},
  volume={11},
  number={7},
  pages={e1005310},
  year={2015},
  publisher={Public Library of Science San Francisco, CA USA}
}
@article{aakre2015evolving,
  title={Evolving new protein-protein interaction specificity through promiscuous intermediates},
  author={Aakre, Christopher D and Herrou, Julien and Phung, Tuyen N and Perchuk, Barrett S and Crosson, Sean and Laub, Michael T},
  journal={Cell},
  volume={163},
  number={3},
  pages={594--606},
  year={2015},
  publisher={Elsevier}
}
@article{qi2014quantitative,
  title={A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity},
  author={Qi, Hangfei and Olson, C Anders and Wu, Nicholas C and Ke, Ruian and Loverdo, Claude and Chu, Virginia and Truong, Shawna and Remenyi, Roland and Chen, Zugen and Du, Yushen and others},
  journal={PLoS pathogens},
  volume={10},
  number={4},
  pages={e1004064},
  year={2014},
  publisher={Public Library of Science San Francisco, USA}
}
@article{matreyek2018multiplex,
  title={Multiplex assessment of protein variant abundance by massively parallel sequencing},
  author={Matreyek, Kenneth A and Starita, Lea M and Stephany, Jason J and Martin, Beth and Chiasson, Melissa A and Gray, Vanessa E and Kircher, Martin and Khechaduri, Arineh and Dines, Jennifer N and Hause, Ronald J and others},
  journal={Nature genetics},
  volume={50},
  number={6},
  pages={874--882},
  year={2018},
  publisher={Nature Publishing Group}
}
@article{bandaru2017deconstruction,
  title={Deconstruction of the Ras switching cycle through saturation mutagenesis},
  author={Bandaru, Pradeep and Shah, Neel H and Bhattacharyya, Moitrayee and Barton, John P and Kondo, Yasushi and Cofsky, Joshua C and Gee, Christine L and Chakraborty, Arup K and Kortemme, Tanja and Ranganathan, Rama and others},
  journal={Elife},
  volume={6},
  pages={e27810},
  year={2017},
  publisher={eLife Sciences Publications Limited}
}
@article{roscoe2013analyses,
  title={Analyses of the effects of all ubiquitin point mutants on yeast growth rate},
  author={Roscoe, Benjamin P and Thayer, Kelly M and Zeldovich, Konstantin B and Fushman, David and Bolon, Daniel NA},
  journal={Journal of molecular biology},
  volume={425},
  number={8},
  pages={1363--1377},
  year={2013},
  publisher={Elsevier}
}
@article{roscoe2014systematic,
  title={Systematic exploration of ubiquitin sequence, E1 activation efficiency, and experimental fitness in yeast},
  author={Roscoe, Benjamin P and Bolon, Daniel NA},
  journal={Journal of molecular biology},
  volume={426},
  number={15},
  pages={2854--2870},
  year={2014},
  publisher={Elsevier}
}
@article{mavor2016determination,
  title={Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting},
  author={Mavor, David and Barlow, Kyle and Thompson, Samuel and Barad, Benjamin A and Bonny, Alain R and Cario, Clinton L and Gaskins, Garrett and Liu, Zairan and Deming, Laura and Axen, Seth D and others},
  journal={Elife},
  volume={5},
  pages={e15802},
  year={2016},
  publisher={eLife Sciences Publications Limited}
}
@article{chan2017correlation,
  title={Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints},
  author={Chan, Yvonne H and Venev, Sergey V and Zeldovich, Konstantin B and Matthews, C Robert},
  journal={Nature communications},
  volume={8},
  number={1},
  pages={1--12},
  year={2017},
  publisher={Nature Publishing Group}
}
@article{melamed2013deep,
  title={Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly (A)-binding protein},
  author={Melamed, Daniel and Young, David L and Gamble, Caitlin E and Miller, Christina R and Fields, Stanley},
  journal={Rna},
  volume={19},
  number={11},
  pages={1537--1551},
  year={2013},
  publisher={Cold Spring Harbor Lab}
}
@article{starita2013activity,
  title={Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis},
  author={Starita, Lea M and Pruneda, Jonathan N and Lo, Russell S and Fowler, Douglas M and Kim, Helen J and Hiatt, Joseph B and Shendure, Jay and Brzovic, Peter S and Fields, Stanley and Klevit, Rachel E},
  journal={Proceedings of the National Academy of Sciences},
  volume={110},
  number={14},
  pages={E1263--E1272},
  year={2013},
  publisher={National Acad Sciences}
}
@article{araya2012fundamental,
  title={A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function},
  author={Araya, Carlos L and Fowler, Douglas M and Chen, Wentao and Muniez, Ike and Kelly, Jeffery W and Fields, Stanley},
  journal={Proceedings of the National Academy of Sciences},
  volume={109},
  number={42},
  pages={16858--16863},
  year={2012},
  publisher={National Acad Sciences}
}