Author

D. Mathews

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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Biochemistry· 2 Biophysics· 2 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Approach:biophysical modeling· 1 Assay:bulk RNA-seq· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1 Assay:DNA methylation· 1 Organism:E. coli· 1

Frequent Co-Authors

D. Ermolenko· 2 shared M. Zhu· 2 shared A. A. Brandon· 1 shared A. Carmona Baez· 1 shared A. Grossfield· 1 shared A. Spasic· 1 shared C. Bao· 1 shared D. Dutta· 1 shared

Activity by Year

2018-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 10 mutual co-author links

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2 shared papersBiochemistry

D. Ermolenko

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters

T. M. Pham, T. Miffin, H. Sun, K. K. Sharp, X. Wang, M. Zhu, S. Hoshika, R. J. Peterson, S. A. Benner, J. D. Kahn, D. Mathews

This paper improves DNA structure design by introducing a new base pair alphabet with P-Z pairs and thermodynamic parameters, enhancing design accuracy and reducing off-target folding.

bioRxiv · Jun 6, 2023Biophysics

Genetic basis of body shape variation along the benthic-pelagic axis in cichlid fishes

L. DeLorenzo, D. Mathews, A. A. Brandon, M. Joglekar, A. Carmona Baez, E. C. Moore, P. J. Ciccotto, N. B. Roberts, R. B. Roberts, K. E. Powder

The paper identifies 55 QTL associated with body shape variation along the benthic-pelagic axis in Lake Malawi cichlids, showing distinct genetic mechanisms across crosses and species.

bioRxiv · Oct 2, 2021 · PreprintEvolutionary Biology

Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation

C. Bao, M. Zhu, I. Nykonchuk, H. Wakabayashi, D. Mathews, D. Ermolenko

The paper shows that specific length and structure, not high thermodynamic stability, of mRNA stem-loops cause ribosome pauses by inhibiting tRNA binding and slowing translocation.

bioRxiv · Aug 16, 2021Biochemistry

Making ends meet: new functions of mRNA secondary structure

D. Ermolenko, D. Mathews

This paper explores the biological implications of mRNA end proximity caused by secondary structure, suggesting roles in translation initiation and coupling of deadenylation to mRNA decay.

bioRxiv · Apr 29, 2020Biochemistry

Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations

L. G. Smith, Z. Tan, A. Spasic, D. Dutta, L. A. Salas-Estrada, A. Grossfield, D. Mathews

This study compares simulated and experimental free energies of RNA hairpins to assess force field accuracy and proposes methods to improve simulation convergence.

bioRxiv · Jun 22, 2018Biophysics