Author

J. Vreede

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· 1 Biophysics· 1 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:chromatin & epigenetic regulation· 1 Approach:deep learning· 1 Assay:DNA methylation· 1 Research Focus:drug response / drug discovery· 1 Approach:experimental assay· 1 Research Focus:protein folding & dynamics· 1

Frequent Co-Authors

A. N. Volkov· 1 shared A. Perez de Alba Ortiz· 1 shared B. Ensing· 1 shared D. W. H. Swenson· 1 shared F. Ben Bdira· 1 shared F. Hooft· 1 shared G. Giachin· 1 shared L. Qin· 1 shared

Activity by Year

2019-2021 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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1 shared paperBiochemistry

A. N. Volkov

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Author profile →

3 papers

Recent·Most cited

Sequence dependence of transient Hoogsteen base-pairing in DNA

A. Perez de Alba Ortiz, J. Vreede, B. Ensing

The paper uses advanced simulations to study how DNA sequences affect Hoogsteen base-pairing stability and dynamics.

bioRxiv · Aug 4, 2021Biophysics

Path sampling simulations reveal how the Q61L mutation restricts the dynamics of KRas

S. Roet, F. Hooft, P. G. Bolhuis, D. W. H. Swenson, J. Vreede

The paper uses path sampling simulations to show that the Q61L mutation in KRas restricts its dynamic transitions, favoring rigid states over flexible ones, which may inform therapeutic strategies.

bioRxiv · Feb 28, 2020 · PreprintCancer Biology

Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins

L. Qin, F. Ben Bdira, Y. G. J. Sterckx, A. N. Volkov, J. Vreede, G. Giachin, P. van Schaik, M. Ubbink, R. T. Dame

This study identifies the molecular mechanism by which H-NS proteins switch DNA binding states in response to osmotic changes, showing that ionic strength affects electrostatic interactions between domains.

bioRxiv · Sep 5, 2019Biochemistry