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N. Tokuriki · SciRah

Researcher profile · Semantic Scholar

N. Tokuriki

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N. Tokuriki — researcher profile on SciRah

h-index: 40
Works: 145
Citations: 7,606

Most-cited papers

The role of protein dynamics in the evolution of new enzyme function.
E. Campbell, M. Kaltenbach, G. Correy, P. Carr +8 more
2016Nature Chemical Biology296 citations
Semantic Scholar
How mutational epistasis impairs predictability in protein evolution and design
C. Miton, N. Tokuriki
2016Protein Science196 citations Open access
Semantic Scholar
Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily
E. Akiva, J. Copp, N. Tokuriki, P. Babbitt
2017Proceedings of the National Academy of Sciences of the United States of America130 citations Open access
Semantic Scholar
Faculty Opinions recommendation of Multiplexed gene synthesis in emulsions for exploring protein functional landscapes.
N. Tokuriki
2019Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature118 citations Open access
Semantic Scholar
Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme
Gloria Yang, Dave W. Anderson, F. Baier, Elias Dohmen +6 more
2019Nature Chemical Biology102 citations
Semantic Scholar
Laboratory evolution of protein conformational dynamics.
E. Campbell, G. Correy, P. D. Mabbitt, A. Buckle +2 more
2018Current Opinion in Structural Biology97 citations
Semantic Scholar
Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein
B. Clifton, J. Kaczmarski, P. Carr, M. Gerth +2 more
2018Nature Chemical Biology95 citations
Semantic Scholar
Epistasis and intramolecular networks in protein evolution.
C. Miton, Karol Buda, N. Tokuriki
2021Current Opinion in Structural Biology90 citations
Semantic Scholar
Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks.
J. Copp, E. Akiva, P. Babbitt, N. Tokuriki
2018Biochemistry78 citations Open access
Semantic Scholar
A mechanistic view of enzyme evolution
Gloria Yang, C. Miton, N. Tokuriki
2020Protein Science76 citations Open access
Semantic Scholar
Reverse evolution leads to genotypic incompatibility despite functional and active site convergence
M. Kaltenbach, C. Jackson, E. Campbell, F. Hollfelder +1 more
2015eLife76 citations Open access
Semantic Scholar
A revised biosynthetic pathway for the cofactor F420 in prokaryotes
G. Bashiri, J. Antoney, E.N.M. Jirgis, M. V. Shah +11 more
2019Nature Communications70 citations Open access
Semantic Scholar
Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence-Function Relationships.
F. Baier, J. Copp, N. Tokuriki
2016Biochemistry70 citations
Semantic Scholar
Epistasis arises from shifting the rate-limiting step during enzyme evolution of a β-lactamase
C. Fröhlich, H. Bunzel, Karol Buda, A. Mulholland +4 more
2024Nature Catalysis58 citations Open access
Semantic Scholar
Evolution of β-lactamase-mediated cefiderocol resistance
C. Fröhlich, V. Sørum, N. Tokuriki, P. Johnsen +1 more
2022bioRxiv58 citations Open access
Semantic Scholar
Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis
S. Emond, Maya Petek, Emily Kay, Brennen Heames +3 more
2020Nature Communications50 citations Open access
Semantic Scholar
Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects.
Gloria Yang, N. Hong, F. Baier, C. Jackson +1 more
2016Biochemistry50 citations
Semantic Scholar
Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes
F. Baier, N. Hong, Gloria Yang, A. Pabis +6 more
2019eLife46 citations Open access
Semantic Scholar
Pervasive epistasis exposes intramolecular networks in adaptive enzyme evolution
Karol Buda, C. Miton, N. Tokuriki
2023Nature Communications44 citations Open access
Semantic Scholar
Evolution of β-lactamases and enzyme promiscuity.
C. Fröhlich, Johnson Chen, S. Gholipour, Aysenur Erdogan +1 more
2021Protein engineering, design & selection : PEDS42 citations Open access
Semantic Scholar
Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase
Johnson Chen, D. Fowler, N. Tokuriki
2020bioRxiv41 citations Open access
Semantic Scholar
Mechanistic Understanding Enables the Rational Design of Salicylanilide Combination Therapies for Gram-Negative Infections
J. Copp, D. Pletzer, Alistair S Brown, J. J. van der Heijden +8 more
2020mBio41 citations Open access
Semantic Scholar
The adaptive landscape of a metallo-enzyme is shaped by environment-dependent epistasis
Dave W. Anderson, F. Baier, Gloria Yang, N. Tokuriki
2021Nature Communications40 citations Open access
Semantic Scholar
Molecular determinants of protein evolvability.
Karol Buda, C. Miton, Xing-Yu Fan, N. Tokuriki
2023TIBS -Trends in Biochemical Sciences. Regular ed36 citations
Semantic Scholar
Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset
C. Miton, S. Jonas, G. Fischer, Fernanda Duarte +7 more
2018Proceedings of the National Academy of Sciences of the United States of America35 citations Open access
Semantic Scholar
Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity
M. Kaltenbach, S. Emond, F. Hollfelder, N. Tokuriki
2016PLoS Genetics34 citations Open access
Semantic Scholar
Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw.
C. Miton, N. Tokuriki
2022Biochemistry32 citations
Semantic Scholar
The molecular mechanisms underlying hidden phenotypic variation among metallo-ß-lactamases
Raymond D. Socha, Johnson Chen, N. Tokuriki
2018bioRxiv24 citations Open access
Semantic Scholar
Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase
Miha Purg, A. Pabis, F. Baier, N. Tokuriki +2 more
2016Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences24 citations Open access
Semantic Scholar
Environmental selection and epistasis in an empirical phenotype–environment–fitness landscape
J.-Z. Chen, D. Fowler, N. Tokuriki
2022Nature Ecology & Evolution23 citations Open access
Semantic Scholar
Statistical analysis of mutational epistasis to reveal intramolecular interaction networks in proteins.
C. Miton, Johnson Chen, Kalum J. Ost, Dave W. Anderson +1 more
2020Methods in Enzymology23 citations
Semantic Scholar
Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions.
J. Copp, Dave W. Anderson, E. Akiva, P. Babbitt +1 more
2019Methods in Enzymology22 citations
Semantic Scholar
Faculty Opinions recommendation of Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.
N. Tokuriki
2020Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature18 citations
Semantic Scholar
Computational and Experimental Exploration of Protein Fitness Landscapes: Navigating Smooth and Rugged Terrains.
M. Sandhu, John Z. Chen, Dana S. Matthews, M. Spence +6 more
2024Biochemistry16 citations Open access
Semantic Scholar
Leveraging ancestral sequence reconstruction for protein representation learning
D. S. Matthews, M. Spence, A. C. Mater, J. Nichols +6 more
2023bioRxiv16 citations Open access
Semantic Scholar
Understanding epistatic networks in the B1 β-lactamases through coevolutionary statistical modeling and deep mutational scanning
J.-Z. Chen, M. Bisardi, D. Lee, S. Cotogno +3 more
2023bioRxiv13 citations Open access
Semantic Scholar
Neutral drift upon threshold-like selection promotes variation in antibiotic resistance phenotype
A. N. Erdoğan, P. Dasmeh, Raymond D. Socha, Johnson Chen +6 more
2024Nature Communications12 citations Open access
Semantic Scholar
Genetic Perturbation Alters Functional Substates in Alkaline Phosphatase
Morito Sakuma, Shingo Honda, H. Ueno, K. Tabata +3 more
2023Journal of the American Chemical Society12 citations Open access
Semantic Scholar
Increasing the Soluble Expression and Whole-Cell Activity of the Plastic-Degrading Enzyme MHETase through Consensus Design.
Jake W. Saunders, A. Damry, Vanessa Vongsouthi, M. Spence +7 more
2024Biochemistry11 citations Open access
Semantic Scholar
Access to unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis
S. Emond, Maya Petek, Emily Kay, Brennen Heames +3 more
2019bioRxiv8 citations Open access
Semantic Scholar
Exploring Large Protein Sequence Space through Homology- and Representation-based Hierarchical Clustering
John Z. Chen, B. Gall, S. B. Pulsford, N. Tokuriki +1 more
2025Molecular biology and evolution7 citations Open access
Semantic Scholar
Molecular Evolution and Origins of Antibiotic Resistance Genes.
S. Gholipour, Dongkyu Lee, N. Tokuriki
2025Biochemistry6 citations
Semantic Scholar
Stability of multi-species consortia during microbial metabolic evolution
Dan Kehila, Alireza G. Tafreshi, N. Tokuriki
2025bioRxiv6 citations Open access
Semantic Scholar
Evolution of New Metabolic Pathways and Microbial Communities
Dan Kehila, Kimberly Tsz Ching Wong, N. Tokuriki
2023Current Opinion in Systems Biology6 citations
Semantic Scholar
Exploring large protein sequence space through homology- and representation-based hierarchical clustering
J.-Z. Chen, B. Gall, N. Tokuriki, CJ Jackson
2024bioRxiv5 citations Open access
Semantic Scholar
Origin of evolutionary bifurcation in an enzyme
C. Miton, E. Campbell, J. Kaczmarski, Ferran Feixas +7 more
2023bioRxiv5 citations Open access
Semantic Scholar
Widespread promiscuous alkaline phosphatases underscore ancient microbial phosphite utilization
Morito Sakuma, Naoki Konno, S. Gholipour, John Z. Chen +1 more
2025Proceedings of the National Academy of Sciences of the United States of America4 citations Open access
Semantic Scholar
Understanding epistatic networks in the B1 β-lactamases through coevolutionary statistical modeling and deep mutational scanning
J.-Z. Chen, M. Bisardi, D. Lee, S. Cotogno +3 more
2024Nature Communications4 citations Open access
Semantic Scholar
The global β-lactam resistome revealed by comprehensive sequence analysis
S. Gholipour, Johnson Chen, Dongkyu Lee, N. Tokuriki
2024bioRxiv4 citations Open access
Semantic Scholar
Neutral Drift and Threshold Selection Promote Phenotypic Variation
A. N. Erdoğan, P. Dasmeh, Raymond D. Socha, Johnson Chen +6 more
2023bioRxiv4 citations Open access
Semantic Scholar

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Johnson Chen×7
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F. Hollfelder×6
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J. Copp — researcher profile on SciRah

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