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About us Practical matters How to find us D. (Danny) Incarnato, PhD

D. (Danny) Incarnato, PhD

Associate Professor

Faculty of Science and Engineering

Telephone:

+31 50 36 32103

E-mail:

d.incarnato rug.nl

ORCID Research Portal

Publications

Condition-dependent amorphous protein agglomerates control cytoplasmic rheology

Losa, J., Simon, F., Linnik, D., Kaya, S. G., Stuart, M. C. A., Stetsenko, A., de Boer, R., Ho, F. Y., Incarnato, D., Stevens, J., van Eck, J., Fraaije, M. W., Weiss, L. E., van Teeffelen, S., Abeln, S., Guskov, A., Marrink, S.-J., Poolman, B. & Heinemann, M., 10-Apr-2026, (E-pub ahead of print) In: Molecular Cell. 86, 29 p.

Research output: Contribution to journal › Article › Academic › peer-review

RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning

Zhang, C., Borovská, I., Iobashvili, T., Morandi, E., Lionnez, M., Olayinka, O. S., de Boer, R., Clamer, M., Witte, M. D., Pors, K., Schneekloth, J. S. & Incarnato, D., 23-Mar-2026, (E-pub ahead of print) In: Nature Communications. 52 p.

Research output: Contribution to journal › Article › Academic › peer-review

Site-Selective Ligand Selection by Mutational Profiling for Covalent RNA Targeting

Yesley, P., Poulladofonou, G., Incarnato, D. & Velema, W. A., 2-Feb-2026, In: Angewandte Chemie - International Edition. 65, 6, 5 p., e17243.

Research output: Contribution to journal › Article › Academic › peer-review

Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis

Borovská, I., Zhang, C., Dülk, S. L. J., Morandi, E., Cardoso, M. F. S., Bourkia, B. M., van den Homberg, D. A. L., Wolfinger, M. T., Velema, W. A. & Incarnato, D., 25-Jul-2025, (E-pub ahead of print) In: Nature Biotechnology. 21 p.

Research output: Contribution to journal › Article › Academic › peer-review

Low butyrate concentrations exert anti-inflammatory and high concentrations exert pro-inflammatory effects on macrophages

Jiang, M., Incarnato, D., Modderman, R., Lazaro, A. A., Jonkers, I. H., Bianchi, F. & van den Bogaart, G., Oct-2025, In: Journal of Nutritional Biochemistry. 144, 12 p., 109962.

Research output: Contribution to journal › Article › Academic › peer-review

Nucleotide dependency analysis of genomic language models detects functional elements

Tomaz da Silva, P., Karollus, A., Hingerl, J., Galindez, G. S. T., Wagner, N., Hernandez-Alias, X., Incarnato, D. & Gagneur, J., Oct-2025, In: Nature genetics. 57, 10, p. 2589-2602 32 p.

Research output: Contribution to journal › Article › Academic › peer-review

RNA dynamics from experimental and computational approaches

Bussi, G., Bonomi, M., Gkeka, P., Sattler, M., Al-Hashimi, H. M., Auffinger, P., Duca, M., Foricher, Y., Incarnato, D., Jones, A. N., Kirmizialtin, S., Krepl, M., Orozco, M., Palermo, G., Pasquali, S., Salmon, L., Schwalbe, H., Westhof, E. & Zacharias, M., 5-Sept-2024, In: Structure. 32, 9, p. 1281-1287 7 p.

Research output: Contribution to journal › Article › Academic › peer-review

RNA structure probing, dynamics, and folding

Incarnato, D., 5-Jul-2024, RNA as a Drug Target: The Next Frontier for Medicinal Chemistry. Schneekloth, J., Pettersson, M., Mannhold, R., Buschmann, H. & Holenz, J. (eds.). Wiley-VCH Verlag GmbH & Co. KGaA, p. 7-28 22 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

SHAPEwarp-web: Sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data

Scholten, N. R., Haandrikman, D., Tolhuis, J. O., Morandi, E. & Incarnato, D., 5-Jul-2024, In: Nucleic Acids Research. 52, 1, p. 362-367 6 p., gkae348.

Research output: Contribution to journal › Article › Academic › peer-review

Structural and biophysical dissection of RNA conformational ensembles

Bonilla, S. L., Jones, A. N. & Incarnato, D., Oct-2024, In: Current Opinion in Structural Biology. 88, 12 p., 102908.

Research output: Contribution to journal › Review article › peer-review

All (69) publications

Press/media

HMN 2026: How Binding to RNA is not enough - changing its shape is what makes a drug work

Incarnato, D.

06/04/2026

Press/Media: Research › Popular

Researchers Highlights How RNA Shape Changes Drive Drug Function

Incarnato, D.

30/03/2026

Press/Media: Expert Comment › Popular

Binding to RNA is not enough—changing its shape is what makes a drug work, study reveals

Incarnato, D.

29/03/2026

Press/Media: Expert Comment › Popular

Binding to RNA is not enough—changing its shape is what makes a drug work, study reveals

Incarnato, D.

29/03/2026

Press/Media: Expert Comment › Popular

Why Most RNA-Targeting Drugs Fail

Incarnato, D.

27/03/2026

Press/Media: Expert Comment › Popular

Gericht zoeken naar geneesmiddelen die structuur en functie van RNA beïnvloeden

Incarnato, D.

26/03/2026

Press/Media: Public Engagement Activities › Popular

Study shows how to identify drugs altering RNA structure and function

Incarnato, D.

26/03/2026

Press/Media: Public Engagement Activities › Popular

Study maps RNA shape-shifting mechanisms in human and bacterial cells

Incarnato, D. & Borovská, I.

28/07/2025

Press/Media: Expert Comment › Popular

RNA Structural Switches Discovered in Humans and Bacteria

Incarnato, D. & Borovská, I.

28/07/2025

Press/Media: Expert Comment › Popular

L'étude cartographie les mécanismes de changement de forme d'ARN dans les cellules humaines et bactériennes

Incarnato, D. & Borovská, I.

28/07/2025

Press/Media: Expert Comment › Popular

All (52) press/media

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