Deep mutational scanning: a new style of protein science

Cited by (1,003)

Items 101–200 of 1,003

1. Robust enzyme discovery and engineering with deep learning using CataPro
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2. Thinking too positive? Revisiting current methods of population genetic selection inference
   Claudia Bank, Gregory B. Ewing, Anna Ferrer-Admetlla, Matthieu Foll, Jeffrey D. Jensen · 2014 · Trends in Genetics
3. Massively parallel characterization of CYP2C9 variant enzyme activity and abundance
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4. SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability
   Gen Li, Shailesh Kumar Panday, Emil G Alexov · 2021 · International Journal of Molecular Sciences
5. DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies
   André J. Faure, Jörn M. Schmiedel, Pablo Baeza-Centurión, Ben Lehner · 2020 · Genome biology
6. Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces
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7. Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain
   Joseph M. Taft, Cédric R. Weber, Beichen Gao, Roy A. Ehling, Jiami Han, Lester Frei, Sean W. Metcalfe, Max D. Overath, Alexander Yermanos, William Kelton et al. · 2022 · Cell
8. Updated benchmarking of variant effect predictors using deep mutational scanning
   Benjamin Livesey, Joseph A. Marsh · 2023 · Molecular Systems Biology
9. Mutation and Epistasis in Influenza Virus Evolution
   Daniel M. Lyons, Adam S. Lauring · 2018 · Viruses
10. Epistasis and evolution: recent advances and an outlook for prediction
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11. The complete local genotype–phenotype landscape for the alternative splicing of a human exon
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12. Deciphering protein evolution and fitness landscapes with latent space models
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13. Using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective Michaelases
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14. MPRAnalyze: statistical framework for massively parallel reporter assays
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15. Sort-seq under the hood: implications of design choices on large-scale characterization of sequence-function relations
    Neil Peterman, Erel Levine · 2016 · BMC Genomics
16. The Use of Whole Genome and Exome Sequencing for Newborn Screening: Challenges and Opportunities for Population Health
    Audrey C. Woerner, Renata C. Gallagher, Jerry E. Vockley, Aashish N. Adhikari · 2021 · Frontiers in Pediatrics
17. Viral factors in influenza pandemic risk assessment
    M. Lipsitch, W. Barclay, R. Raman, C. Russell, J. Belser, S. Cobey, P. Kasson, J. Lloyd-Smith, S. Maurer-Stroh, S. Riley et al. · 2016 · eLife
18. Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?
    Cunliang Geng, Li C. Xue, Jorge Roel‐Touris, Alexandre M. J. J. Bonvin · 2019 · Wiley Interdisciplinary Reviews Computational Molecular Science
19. Functional plasticity and evolutionary adaptation of allosteric regulation
    Megan Leander, Yuchen Yuan, Anthony Meger, Qiang Cui, Srivatsan Raman · 2020 · Proceedings of the National Academy of Sciences
20. Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming
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21. Mapping Degradation Signals and Pathways in a Eukaryotic N-terminome
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22. Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics
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23. High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering
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24. Navigating the landscape of protein folding and proteostasis: from molecular chaperones to therapeutic innovations
    Omer F. Kuzu, Lars Jørgen Tvenge Granerud, Fahri Saatcioglu · 2025 · Signal Transduction and Targeted Therapy
25. Evolutionary Landscapes of Host-Virus Arms Races
    Jeannette L. Tenthorey, Michael Emerman, Harmit Singh Malik · 2022 · Annual Review of Immunology
26. Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature
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27. The background puzzle: how identical mutations in the same gene lead to different disease symptoms
    Jan E. Kammenga · 2017 · FEBS Journal
28. High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast
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29. A resource of variant effect predictions of single nucleotide variants in model organisms
    Omar Wagih, Bede P. Busby, Marco Galardini, Danish Memon, Athanasios Typas, Pedro Beltrão · 2018 · Molecular Systems Biology
30. Systematic Mutant Analyses Elucidate General and Client-Specific Aspects of Hsp90 Function
    Parul Mishra, Julia M. Flynn, Tyler N. Starr, Daniel N. A. Bolon · 2016 · Cell Reports
31. T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes
    Amalie Kai Bentzen, Lina Such, Kamilla Kjærgaard Jensen, Andrea Marion Marquard, Leon Eyrich Jessen, Natalie J. Miller, Candice D. Church, Rikke Lyngaa, David M. Koelle, Jürgen Christian Becker et al. · 2018 · Nature Biotechnology
32. The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography
    Daniel M. Weinreich, Yinghong Lan, Jacob Jaffe, Robert B. Heckendorn · 2018 · Journal of Statistical Physics
33. A mechanistic view of enzyme evolution
    Gloria Yang, Charlotte M. Miton, Nobuhiko Tokuriki · 2020 · Protein Science
34. Recent insights into the genotype–phenotype relationship from massively parallel genetic assays
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35. Deep mutational scanning reveals the structural basis for α-synuclein activity
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36. Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture
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37. Understanding activity-stability tradeoffs in biocatalysts by enzyme proximity sequencing
    Rosario Vanella, Christoph Küng, Alexandre A. Schoepfer, Vanni Doffini, Jin Ren, Michael A. Nash · 2024 · Nature Communications
38. Deep sequencing methods for protein engineering and design
    Emily E. Wrenbeck, Matthew S. Faber, Timothy A. Whitehead · 2016 · Current Opinion in Structural Biology
39. Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations
    Liat Rockah-Shmuel, Ágnes Tóth-Petróczy, Dan S. Tawfik · 2015 · PLoS Computational Biology
40. Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity
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41. Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs
    Michael B. Doud, Orr Ashenberg, Jesse D. Bloom · 2015 · Molecular Biology and Evolution
42. Sensing new chemicals with bacterial transcription factors
    Vincent K. Libis, Baudoin Delépine, Jean‐Loup Faulon · 2016 · Current Opinion in Microbiology
43. From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics
    Manrubia, Susanna, Cuesta, José A., Aguirre, Jacobo, Ahnert, Sebastian E., Altenberg, Lee, Cano, Alejandro V., Catalán, Pablo, Diaz-Uriarte, Ramon, Elena, Santiago F., García-Martín, Juan Antonio et al. · 2021 · Physics of Life Reviews
44. On the Potential of Machine Learning to Examine the Relationship Between Sequence, Structure, Dynamics and Function of Intrinsically Disordered Proteins
    Lindorff-Larsen, Kresten, Kragelund, Birthe B. · 2021 · Journal of Molecular Biology
45. Opportunities and challenges for the computational interpretation of rare variation in clinically important genes
    McInnes, Gregory, Sharo, Andrew G., Koleske, Megan L., Brown, Julia E.H., Norstad, Matthew, Adhikari, Aashish N., Wang, Sheng, Brenner, Steven E., Halpern, Jodi, Koenig, Barbara A. et al. · 2021 · The American Journal of Human Genetics
46. Biophysical Inference of Epistasis and the Effects of Mutations on Protein Stability and Function
    Jakub Otwinowski · 2018 · Molecular Biology and Evolution
47. High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis
    Derek M. Mason, Cédric R. Weber, Cristina Parola, Simon M. Meng, Victor Greiff, William Kelton, Sai T. Reddy · 2018 · Nucleic Acids Research
48. Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin
    Nicholas C. Wu, Jia Xie, Tianqing Zheng, Corwin M. Nycholat, Geramie Grande, James C. Paulson, Richard Alan Lerner, Ian A. Wilson · 2017 · Cell Host & Microbe
49. MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect
    Ammar Tareen, Mahdi Kooshkbaghi, Anna Posfai, William T. Ireland, David M. McCandlish, Justin B. Kinney · 2022 · Genome biology
50. Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation
    On behalf of the Brotman Baty Institute Mutational Scanning Working Group, Gelman, Hannah, Dines, Jennifer N., Berg, Jonathan, Berger, Alice H., Brnich, Sarah, Hisama, Fuki M., James, Richard G., Rubin, Alan F., Shendure, Jay et al. · 2019 · Genome Medicine
51. Rapid Fine Conformational Epitope Mapping Using Comprehensive Mutagenesis and Deep Sequencing
    Caitlin A. Kowalsky, Matthew S. Faber, Aritro Nath, Hailey E. Dann, Vince W. Kelly, Li Liu, Purva Shanker, Ellen K. Wagner, Jennifer A. Maynard, Christina Chan et al. · 2015 · Journal of Biological Chemistry
52. Scalable Functional Assays for the Interpretation of Human Genetic Variation
    Daniel R. Tabet, Victoria Nicole Parikh, Prashant Mali, Frederick P. Roth, Melina Claussnitzer · 2022 · Annual Review of Genetics
53. Getting Momentum: From Biocatalysis to Advanced Synthetic Biology
    Christoffel P. S. Badenhorst, Uwe T. Bornscheuer · 2018 · Trends in Biochemical Sciences
54. Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape
    Nicholas C. Wu, Jakub Otwinowski, Andrew J. Thompson, Corwin M. Nycholat, Armita Nourmohammad, Ian A. Wilson · 2020 · Nature Communications
55. Molecular basis of proton sensing by G protein-coupled receptors
    Howard, Matthew K., Hoppe, Nicholas, Huang, Xi-Ping, Mitrovic, Darko, Billesbølle, Christian B., Macdonald, Christian B., Mehrotra, Eshan, Rockefeller Grimes, Patrick, Trinidad, Donovan D., Delemotte, Lucie et al. · 2025 · Cell
56. MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays
    Rubin, Alan F., Stone, Jeremy, Bianchi, Aisha Haley, Capodanno, Benjamin J., Da, Estelle Y., Dias, Mafalda, Esposito, Daniel, Frazer, Jonathan, Fu, Yunfan, Grindstaff, Sally B. et al. · 2025 · Genome Biology
57. A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site
    Nicholas C. Wu, Andrew J. Thompson, Jia Xie, Chih-Wei Lin, Corwin M. Nycholat, Xueyong Zhu, Richard Alan Lerner, James C. Paulson, Ian A. Wilson · 2018 · Nature Communications
58. Recent advances in user-friendly computational tools to engineer protein function
    Carlos Eduardo Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovský · 2020 · Briefings in Bioinformatics
59. High-throughput directed evolution: a golden era for protein science
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60. Emerging strategies to bridge the gap between pharmacogenomic research and its clinical implementation
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61. Cross-protein transfer learning substantially improves disease variant prediction
    2023
62. Zero-shot prediction of mutation effects with multimodal deep representation learning guides protein engineering
    Peng Cheng, Cong Mao, Jin Tang, Sen Yang, Yu Cheng, Wuke Wang, Qiuxi Gu, Wei Han, Hao Chen, Sihan Li et al. · 2024 · Cell Research
63. Mutational scanning reveals the determinants of protein insertion and association energetics in the plasma membrane
    Assaf Elazar, Jonathan J. Weinstein, Ido Biran, Yearit Fridman, Eitan Bibi, Sarel Jacob Fleishman · 2016 · eLife
64. Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library
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65. The genetic architecture of protein stability
    André J. Faure, Aina Martí-Aranda, Cristina Hidalgo-Carcedo, Toni Beltran, Jörn M. Schmiedel, Ben Lehner · 2024 · Nature
66. Genome scale engineering techniques for metabolic engineering
    Rongming Liu, Marcelo C. Bassalo, Ramsey I. Zeitoun, Ryan T. Gill · 2015 · Metabolic Engineering
67. Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space
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68. A Combined Approach Reveals a Regulatory Mechanism Coupling Src’s Kinase Activity, Localization, and Phosphotransferase-Independent Functions
    Ethan Ahler, Ames C. Register, Sujata Chakraborty, Linglan Fang, Emily M. Dieter, Katherine A. Sitko, Rama Subba Rao Vidadala, Bridget M. Trevillian, Martin G. Golkowski, Hannah Gelman et al. · 2019 · Molecular Cell
69. Harnessing generative AI to decode enzyme catalysis and evolution for enhanced engineering
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70. RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq
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71. Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA
    Orr Ashenberg, Jai P. Padmakumar, Michael B. Doud, Jesse D. Bloom · 2017 · PLoS Pathogens
72. A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery
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73. Molecular Evolution of Transition Metal Bioavailability at the Host–Pathogen Interface
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74. A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase
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75. Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning
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76. Exploring amino acid functions in a deep mutational landscape
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77. DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology
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78. High-Resolution Sequence-Function Mapping of Full-Length Proteins
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79. Different genetic barriers for resistance to HA stem antibodies in influenza H3 and H1 viruses
    Nicholas C. Wu, Andrew J. Thompson, Juhye M. Lee, Wen Su, Britni M. Arlian, Jia Xie, Richard Alan Lerner, Hui‐Ling Yen, Jesse D. Bloom, Ian A. Wilson · 2020 · Science
80. From pharmacogenetics to pharmaco-omics: Milestones and future directions
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81. Automated optimisation of solubility and conformational stability of antibodies and proteins
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82. Perturbing proteomes at single residue resolution using base editing
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83. Engineering allostery
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84. An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation
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85. Defining the landscape of ATP-competitive inhibitor resistance residues in protein kinases
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86. Deep mutational scanning: A versatile tool in systematically mapping genotypes to phenotypes
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87. Deep mutational scanning of S. pyogenes Cas9 reveals important functional domains
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88. Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection
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89. Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical
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90. Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance
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91. Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9
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92. A versatile platform for locus-scale genome rewriting and verification
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93. ProtaBank: A repository for protein design and engineering data
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94. Interpreting protein variant effects with computational predictors and deep mutational scanning
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95. Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites
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96. A review of enzyme design in catalytic stability by artificial intelligence
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97. Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires
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98. Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme
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99. Leveraging massively parallel reporter assays for evolutionary questions
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100. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models
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