Author

Rodolfo Ciuffa

ETH ZurichORCID 0000-0002-7611-7665Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Systems Biology· 3 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Assay:proteomics· 4 Approach:experimental assay· 2 Organism:human· 2 Research Focus:protein structure prediction· 2 Research Focus:cell-cell communication· 1 Research Focus:deconvolution· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Ruedi H. AebersoldiD· 4 shared Andrea FossatiiD· 3 shared Federico UlianaiD· 3 shared Matthias GstaigeriD· 3 shared Fabian FrommeltiD· 2 shared Martin MehnertiD· 2 shared Alessandro Ori‬‬iD· 1 shared Anthony Wayne PurcelliD· 1 shared

Activity by Year

2021-2023 · peak 2/yr

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10 top collaborators · 31 mutual co-author links

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4 shared papersSystems Biology

Ruedi H. AebersoldORCID

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4 papers

Recent·Most cited

DIP-MS: A novel ultra-deep interaction proteomics for the deconvolution of protein complexes

Fabian Frommelt, Andrea Fossati, Federico Uliana, Fabian Wendt, Peng Xue, Moritz Heusel, Bernd Wollscheid, Ruedi H. Aebersold, Rodolfo Ciuffa, Matthias Gstaiger

DIP-MS resolves protein complex isoforms using deep learning and mass spectrometry, revealing new subunits in human prefoldin complexes.

bioRxiv · Mar 22, 2023 · PreprintSystems Biology

Novel biochemical, structural and systems insights into inflammatory signaling revealed by contextual interaction proteomics

Rodolfo Ciuffa, Federico Uliana, Jonathan Mannion, Martin Mehnert, Tencho Tenev, Cathy Marulli, Ari Satanowski, Lena Maria Leone Keller, Pilar Natalia Rodilla-Ramírez, Alessandro Ori‬‬, Matthias Gstaiger, Pascal Meier, Ruedi H. Aebersold

The paper presents an integrated experimental and computational strategy to model protein-protein interactions in cellular context, applied to the TNF-receptor signaling complex.

Proceedings of the National Academy of Sciences · Sep 30, 2022Peer-reviewedSystems Biology

Systematic dissection of phosphorylation-dependent YAP1 complex formation elucidates a key role for PTPN14 in Hippo signal integration

Federico Uliana, Rodolfo Ciuffa, Ranjan Kumar Mishra, Andrea Fossati, Fabian Frommelt, Martin Mehnert, Eivind Salmorin Birkeland, Matthias Peter, Nicolas Tapon, Ruedi H. Aebersold, Matthias Gstaiger

The paper develops an experimental strategy to link phosphorylation events with protein complex formation, revealing PTPN14's role in regulating YAP1's interaction with LATS1/2 kinases.

bioRxiv · Mar 13, 2022 · PreprintSystems Biology

Towards a systematic characterization of protein complex function: a natural language processing and machine-learning framework

Varun S. Sharma, Andrea Fossati, Rodolfo Ciuffa, Marija Buljan, Evan G. Williams, Zhen Chen, Wenguang Shao, Patrick G. A. Pedrioli, Anthony Wayne Purcell, María Rodríguez Martínez, Jiangning Song, Matteo Manica, Ruedi H. Aebersold, Chen Li

PCfun annotates protein complex function using natural language processing and machine learning, integrating word embeddings from PubMed Central articles with supervised and unsupervised methods.

bioRxiv · Feb 24, 2021 · PreprintBioinformatics