Publications

2025

• iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments.
  Olivier-Jimenez D, Derks RJE, Harari O, Cruchaga C, Ali M, Ori A, Di Fraia D, Cabukusta B, Henrie A, Giera M, Mohammed Y
  Anal Chem 2025 (epub ahead of print)
  

2024

• Quantitative mapping of proteasome interactomes and substrates using ProteasomeID.
  Bartolome A, Heiby* JC, Di Fraia* D, Heinze I, Knaudt H, Spaeth E, Omrani O, Minetti A, Hofmann M, Kirkpatrick JM, Dau** T, Ori** A
  Elife 2024, 13, RP93256 * equal contribution, ** co-corresponding authors
  
• NRF2 activation by cysteine as a survival mechanism for triple-negative breast cancer cells.
  Bottoni L, Minetti A, Realini G, Pio E, Giustarini D, Rossi R, Rocchio C, Franci L, Salvini L, Catona O, D'Aurizio R, Rasa M, Giurisato E, Neri F, Orlandini M, Chiariello M, Galvagni F
  Oncogene 2024 (epub ahead of print)
  
• The Aging Synapse: An Integrated Proteomic And Transcriptomic Analysis
  Caterino* C, Ugolini* M, Durso W, Jevdokimenko K, Groth M, Riege K, Görlach M, Fornasiero E, Ori A, Hoffmann S, Cellerino A
  bioRxiv 2024, https://doi.org/10.1101/2024.12. * equal contribution
  
• Optimized Automated Workflow for BioID Improves Reproducibility and Identification of Protein-Protein Interactions.
  Cirri E, Knaudt H, Di Fraia D, Pömpner N, Rahnis N, Heinze I, Ori** A, Dau** T
  J Proteome Res 2024 (epub ahead of print) ** co-corresponding authors
  
• The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases uncovers cholesterol as a regulator of astrocyte reactivity impaired by ApoE4
  Feringa FM, Koppes-den Hertog SJ, Wang L, Derks RJE, Kruijff I, Erlebach L, Heijneman J, Miramontes R, Pömpner N, Blomberg N, Olivier-Jimenez D, Eva Johansen L, Cammack AJ, Giblin A, Toomey CE, Rose IVL, Yuan H, Ward M, Isaacs AM, Kampmann M, Kronenberg-Versteeg D, Lashley T, M.Thompson L, Ori A, Mohammed Y, Giera M, van der Kant R
  bioRxiv 2024, https://doi.org/10.1101/2024.07.
  
• Cell-Type Resolved Protein Atlas of Brain Lysosomes Identifies SLC45A1-Associated Disease as a Lysosomal Disorder.
  Ghoochani A, Heiby JC, Rawat ES, Medoh UN, Di Fraia D, Dong W, Gastou M, Nyame K, Laqtom NN, Gomez-Ospina N, Ori A, Abu-Remaileh M
  bioRxiv 2024, 10.1101/2024.10.14.618295
  
• Impact of inflammatory preconditioning on murine microglial proteome response induced by focal ischemic brain injury.
  Helbing DL, Haas F, Cirri E, Rahnis N, Dau TTD, Kelmer Sacramento E, Oraha N, Böhm L, Lajqi T, Fehringer P, Morrison H, Bauer R
  Front Immunol 2024, 15, 1227355
  
• Denervation alters the secretome of myofibers and thereby affects muscle stem cell lineage progression and functionality.
  Henze H, Hüttner SS, Koch P, Schüler SC, Groth M, von Eyss B, von Maltzahn J
  NPJ Regen Med 2024, 9(1), 10
  
• Role of protein degradation and synthesis in proteostasis loss during the vertebrate brain aging
  Marino A
  Dissertation 2024, Jena, Germany