Thuy N Nguyen, Christine Ingle, Samuel Thompson, and Kimberly A Reynolds. The genetic landscape of a metabolic interaction. May 2023a.
Vanessa Nguyen, Ethan Ahler, Katherine A Sitko, Jason J Stephany, Dustin J Maly, and Douglas M Fowler. Molecular determinants of hsp90 dependence of src kinase revealed by deep mutational scanning. Protein Science, 32(7):e4656, July 2023b.
Erik Nijkamp, Jeffrey A. Ruffolo, Eli N. Weinstein, Nikhil Naik, and Ali Madani. ProGen2: Exploring the boundaries of protein language models. ArXiv, abs/2206.13517, 2022.
Pascal Notin, Mafalda Dias, Jonathan Frazer, Javier Marchena-Hurtado, Aidan N. Gomez, Debora S. Marks, and Yarin Gal. Trancection: protein fitness prediction with autoregressive transformers and inference-time retrieval. In ICML, 2022a.
Pascal Notin, Lood Van Niekerk, Aaron W. Kollasch, Daniel Ritter, Yarin Gal, and Debora Susan Marks. TranceptEVE: Combining Family-specific and Family-agnostic Models of Protein Sequences for Improved Fitness Prediction. December 2022b. URL https://openreview.net/forum?id=170o9DcLmR1.
Pascal Notin, Ruben Weitzman, Debora S. Marks, and Yarin Gal. Proteinnpt: Improving protein property prediction and design with non-parametric transformers. Advances in Neural Information Processing Systems, 37, 2023.
Christina Nutschel, Alexander Fulton, Olav Zimmermann, Ulrich Schwaneberg, Karl-Erich Jaeger, and Holger Gohlke. Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A. Journal of Chemical Information and Modeling, 60(3):1568-1584, March 2020. ISSN 1549-9596, 1549-960X. doi: 10.1021/acs.jcim.9b00954. URL https://pubs.acs.org/doi/10.1021/acs.jcim.9b00954.
C. Anders Olson, Nicholas C. Wu, and Ren Sun. A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain. Current Biology, 24(22):2643-2651, November 2014. ISSN 09609822. doi: 10.1016/j.cub.2014.09.072. URL https://linkinghub.elsevier.com/retrieve/pii/S0960982214012688.
Martin K Ostermaier, Christian Peterhans, Rolf Jaussi, Xavier Deupi, and Jörg Standfuss. Functional map of arrestin-1 at single amino acid resolution. Proceedings of the National Academy of Sciences, 111(5): 1825–1830, February 2014.
Vikas Pejaver, Alicia B Byrne, Bing-Jian Feng, Kymberleigh A Pagel, Sean D Mooney, Rachel Karchin, Anne O'Donnell-Luria, Steven M Harrison, Sean V Tavtigian, Marc S Greenblatt, et al. Calibration of computational tools for missense variant pathogenicity classification and clingen recommendations for pp3/bp4 criteria. The American Journal of Human Genetics, 109(12):2163-2177, 2022.
Victoria O. Pokusaeva, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen S. Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, Dmitry N. Ivanov, Arseniy V. Akopyan, Sergey Ya. Avvakumov, Inna S. Povolotskaya, Guillaume J. Filion, Lucas B. Carey, and Fyodor A. Kondrashov. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLOS Genetics, 15(4):e1008079, April 2019. ISSN 1553-7404. doi: 10.1371/journal.pgen.1008079. URL https://dx.doi.org/10.1371/journal.pgen.1008079.
Hangfei Qi, C. Anders Olson, Nicholas C. Wu, Ruian Ke, Claude Loverdo, Virginia Chu, Shawna Truong, Roland Remenyi, Zugen Chen, Yushen Du, Sheng-Yao Su, Laith Q. Al-Mawsawi, Ting-Ting Wu, Shu-Hua Chen, Chung-Yen Lin, Weidong Zhong, James O. Lloyd-Smith, and Ren Sun. A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity. PLoS Pathogens, 10(4):e1004064, April 2014. ISSN 1553-7374. doi: 10.1371/journal.ppat.1004064. URL https://dx.plos.org/10.1371/journal.ppat.1004064.
Daniel Quang, Yifei Chen, and Xiaohui Xie. DANN: a deep learning approach for annotating the pathogenicity of genetic variants. Bioinformatics, 31(5):761-763, 2015.
Alec Radford, Jeff Wu, Rewon Child, David Luan, Dario Amodei, and Ilya Sutskever. Language models are unsupervised multitask learners. 2019. URL https://api_semanticscholar.org/CorpusID:160025533.
Daniele Raimondi, Ibrahim Tanyalcin, Julien Ferte, Andrea Gazzo, Gabriele Orlando, Tom Lenaerts, Marianne Rooman, and Wim Vranken. DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. Nucleic acids research, 45(W1):W201-W206, 2017.
Roshan Rao, Nicholas Bhattacharya, Neil Thomas, Yan Duan, Xi Chen, John Canny, Pieter Abbeel, and Yun S. Song. Evaluating Protein Transfer Learning with TAPE, June 2019. URL http://arxiv.org/abs/1906.08230. arXiv:1906.08230 [cs, q-bio, stat].