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| @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} | |
| } | |