R-DeeP-related Publications

R-DeeP Original Publication Citations: link to Google Scholar

R-DeeP Method Publication Citations: link to Google Scholar

 

List of R-DeeP-based publications and similar concepts (proteome-wide approaches)

Below, you will find a list of proteome-wide screens based on our R-DeeP methodology (Caudron-Herger et al., Mol Cell, 2019, first on the list) and similar concepts to identify RNA-dependent proteins by us and others.

 

  1. Caudron-Herger, M. et al. R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation. Molecular Cell (2019). https://doi.org/10.1016/j.molcel.2019.04.018

  2. Mallam, A. L. et al. Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell Reports (2019). https://doi.org/10.1016/j.celrep.2019.09.060

  3. Caudron-Herger, M. et al. Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. Nature Protocols (2020). https://doi.org/10.1038/s41596-019-0261-4

  4. Gerovac, M. et al. Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein. RNA (2020). https://doi.org/10.1261/rna.076992.120

  5. Drew, K et al. A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinary. Developmental Biology (2020). https://doi.org/10.1016/j.ydbio.2020.08.008

  6. Rajagopal, V. et al. Proteome-Wide Identification of RNA-Dependent Proteins in Lung Cancer Cells. Cancers (2022). https://doi.org/10.3390/cancers14246109

  7. Cabrera-Orefice, A. et al. Complexome Profiling - Exploring Mitochondrial Protein Complexes in Health and Disease. Frontiers in Cell and Developmental Biology (2022). https://doi.org/10.3389/fcell.2021.796128

  8. Hollin, T. et al. Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nature Communications (2024). https://doi.org/10.1038/s41467-024-45519-1

  9. Brenes-Álvarez, M. et al. R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning. Nucleic Acids Research (2024). https://doi.org/10.1093/nar/gkae1247

  10. Wäber, N. B. et al. A census of RNA-dependent proteins in yeast. bioRxiv (2024). https://doi.org/10.1101/2024.12.06.627129

  11. Li, P. et al. High-throughput and proteome-wide discovery of endogenous biomolecular condensates. Nature Chemistry (2024). https://doi.org/10.1101/2025.11.19.689340

  12. Hemm, L. et al. RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets. Nature Communications (2025). https://doi.org/10.1016/j.ydbio.2020.08.008

  13. Rajagopal, V. et al. An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions. Nature Communications (2025). https://doi.org/10.1038/s41467-025-57671-3

 

Publications using our R-DeeP methodology

  1. Huppertz, I. et al. Riboregulation of Enolase 1 activity controls glycolysis and embryonic stem cell differentiation. Molecular Cell (2022). https://doi.org/10.1016/j.molcel.2022.05.019

  2. Rass, R. A. et al. Inferring Protein Function in an Emerging Virus: Detection of the Nucleoprotein in Tilapia Lake Virus. J Virol (2022). https://doi.org/10.1128/jvi.01757-21

  3. Wang, B. et al. Nucleotide-induced hyper-oligomarization inactivates transcription termination factor ρ. Nature Communications (2023). https://doi.org/10.1038/s41467-025-56824-8

  4. Gokhale, N. S. et al. Cellular RNA interacts with MAVS to promote antiviral signaling. Science (2024). https://doi.org/10.1126/science.adl0429

  5. Dian, A. L. et al. Hexokinase 2 is an RNA-binding protein that regulates mRNA translation independently of glycolysis and induces melanoma cell proliferation. PLoS Biology (2025). https://doi.org/10.1371/journal.pbio.3003364

  6. Heim, A et al. Translational repression by 4E-T is crutial to maintain the prophase-I arrest in vertebrate oocytes. Nature Communications (2025). https://doi.org/10.1038/s41467-025-62971-9

  7. Good, K. V. et al. MeCP2 NID interaction with RNA: Implication for Rett Syndrome-Relevant Protein Purification. bioRxiv (2025). https://doi.org/10.1101/2025.11.19.689340

 

Publications reproducing graphics from our R-DeeP screens

  1. Adhikari, B et al. PROTAC-mediated degradation reveals a non-catalytic function of AURORA-A kinase. Nature Chemical Biology (2020). https://doi.org/10.3389/fcell.2021.796128

  2. McCarthy, R. L. et al. Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements. Nature Cell Biology (2022). https://doi.org/10.1038/s41556-021-00725-7

  3. Bhuiyan, T. et al. TAF2 condensation in nuclear speckles links basal transcription facord TFIID to RNA splicing factors. Cell Reports (2025). https://doi.org/10.1016/j.celrep.2025.115616

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