Xiaoming Liu, Xueqiu Jian, and Eric Boerwinkle. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Human mutation, 32(8):894-899, 2011.
Xiaoming Liu, Chang Li, Chengcheng Mou, Yibo Dong, and Yicheng Tu. dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. Genome medicine, 12(1):1-8, 2020.
Benjamin J Livesey and Joseph A Marsh. Updated benchmarking of variant effect predictors using deep mutational scanning. Molecular Systems Biology, page e11474, 2023.
Russell S Lo, Gareth A Cromie, Michelle Tang, Kevin Teng, Katherine Owens, Amy Sirr, J Nathan Kutz, Hiroki Morizono, Ljubica Caldovic, Nicholas Ah Mew, Andrea Gropman, and Aimée M Dudley. The functional impact of 1,570 individual amino acid substitutions in human OTC. American Journal of Human Genetics, 110(5):863-879, May 2023.
Christian B. Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James S. Fraser, and Willow Coyote-Maestas. DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology. Genome Biology, 24(1):36, February 2023. ISSN 1474-760X. doi: 10.1186/s13059-023-02880-6. URL https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02880-6.
Mark R MacRae, Dhenesh Puvanendran, Max A B Haase, Nicolas Coudray, Ljuvica Kolich, Cherry Lam, Minkyung Baek, Gira Bhabha, and Damian C Ekiert. Protein-protein interactions in the mla lipid transport system probed by computational structure prediction and deep mutational scanning. Journal of Biological Chemistry, 299(6):104744, June 2023.
Ali Madani, Bryan McCann, Nikhil Naik, Nitish Shirish Keskar, Namrata Anand, Raphael R. Eguchi, Po-Ssu Huang, and Richard Socher. ProGen: Language modeling for protein generation, 2020.
Nawar Malhis, Matthew Jacobson, Steven JM Jones, and Jörg Gsponer. LIST-S2: taxonomy based sorting of deleterious missense mutations across species. Nucleic acids research, 48(W1):W154-W161, 2020.
Céline Marquet, Michael Heinzinger, Tobias Olenyi, Christian Dallago, Kyra Erckert, Michael Bernhofer, Dmitrii Nechaev, and Burkhard Rost. Embeddings from protein language models predict conservation and variant effects. Human Genetics, 141(10):1629-1647, October 2022. ISSN 1432-1203. doi: 10.1007/s00439-021-02411-y.
Kenneth A. Matreyek, Lea M. Starita, Jason J. Stephany, Beth Martin, Melissa A. Chiasson, Vanessa E. Gray, Martin Kircher, Arineh Khechaduri, Jennifer N. Dines, Ronald J. Hause, Smita Bhatia, William E. Evans, Mary V. Relling, Wenjian Yang, Jay Shendure, and Douglas M. Fowler. Multiplex assessment of protein variant abundance by massively parallel sequencing. Nature Genetics, 50(6):874-882, June 2018. ISSN 1061-4036, 1546-1718. doi: 10.1038/s41588-018-0122-z. URL https://www.nature.com/articles/s41588-018-0122-z.
Kenneth A. Matreyek, Jason J. Stephany, Ethan Ahler, and Douglas M. Fowler. Integrating thousands of PTEN variant activity and abundance measurements reveals variant subgroups and new dominant negatives in cancers. Genome Medicine, 13(1):165, December 2021. ISSN 1756-994X. doi: 10.1186/s13073-021-00984-x. URL https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00984-x.
Florian Mattenberger, Victor Latorre, Omer Tirosh, Adi Stern, and Ron Geller. Globally defining the effects of mutations in a picornavirus capsid. eLife, 10:e64256, January 2021. ISSN 2050-084X. doi: 10.7554/eLife.64256. URL https://elifesciences.org/articles/64256.
David Mavor, Kyle Barlow, Samuel Thompson, Benjamin A Barad, Alain R Bonny, Clinton L Cario, Garrett Gaskins, Zairan Liu, Laura Deming, Seth D Axen, Elena Caceres, Weilin Chen, Adolfo Cuesta, Rachel E Gate, Evan M Green, Kaitlin R Hulce, Weiyue Ji, Lillian R Kenner, Bruk Mensa, Leanna S Morinishi, Steven M Moss, Marco Mravic, Ryan K Muir, Stefan Niekamp, Chimno I Nnadi, Eugene Palovcak, Erin M Poss, Tyler D Ross, Eugenia C Salcedo, Stephanie K See, Meena Subramaniam, Allison W Wong, Jennifer Li, Kurt S Thorn, Shane O ConchuiR, Benjamin P Roscoe, Eric D Chow, Joseph L DeRisi, Tanja Kortemme, Daniel N Bolon, and James S Fraser. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. eLife, 5:e15802, April 2016. ISSN 2050-084X. doi: 10.7554/eLife.15802. URL https://elifesciences.org/articles/15802.
Richard N. McLaughlin, Jr., Frank J. Poelwijk, Arjun Raman, Walraj S. Gosal, and Rama Ranganathan. The spatial architecture of protein function and adaptation. Nature, 491(7422):138-142, November 2012. ISSN 0028-0836, 1476-4687. doi: 10.1038/nature11500. URL https://www.nature.com/articles/nature11500.