Author

S. K. Denny

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 2 Biochemistry· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Approach:experimental assay· 2 Research Focus:benchmarking· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Research Focus:protein folding & dynamics· 1

Frequent Co-Authors

D. Herschlag· 3 shared I. Jarmoskaite· 2 shared K. Kappel· 2 shared P. P. Vaidyanathan· 2 shared R. Das· 2 shared W. J. Greenleaf· 2 shared W. R. Becker· 2 shared C. J. Layton· 1 shared

Activity by Year

2018-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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3 shared papersBiophysics

D. Herschlag

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3 papers

Recent·Most cited

Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements

J. H. Shin, S. L. Bonilla, S. K. Denny, W. Greenleaf, D. Herschlag

This paper uses high-throughput thermodynamic measurements to analyze the energetic architecture of an RNA tertiary motif, revealing non-linear cooperativity and exceptions to established stability-abundance relationships.

Proceedings of the National Academy of Sciences · Mar 10, 2023Peer-reviewedBiophysics

Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding

W. R. Becker, I. Jarmoskaite, K. Kappel, P. P. Vaidyanathan, S. K. Denny, R. Das, W. J. Greenleaf, D. Herschlag

The paper quantitatively tests RNA secondary structure prediction algorithms using RNA-MaP, revealing significant deviations between predictions and experimental stabilities.

bioRxiv · Mar 8, 2019 · PreprintBiophysics

A quantitative and predictive model for RNA binding by human Pumilio proteins

I. Jarmoskaite, S. K. Denny, P. P. Vaidyanathan, W. R. Becker, J. O. L. Andreasson, C. J. Layton, K. Kappel, V. Shivashankar, R. Sreenivasan, R. Das, W. J. Greenleaf, D. Herschlag

The paper develops a predictive model for RNA binding by human PUM1 and PUM2 using RNA-MaP data, showing residue flipping and positional coupling, and validates it against in vivo crosslinking data.

bioRxiv · Aug 29, 2018Biochemistry