Amir Ata Saei

Amir Ata Saei

Assistant Professor
Visiting address: Solnavägen 9, Biomedicum, 17165 Solna
Postal address: C1 Mikrobiologi, tumör- och cellbiologi, C1 CTMR Engstrand Saei Dibavar, 171 77 Stockholm

About me

  • I am an assistant professor at the Department of Microbiology, Tumor and Cell Biology at Karolinska Institutet and a junior group leader (SNF Ambizione Fellow) at the Hall Lab at Biozentrum (University of Basel), Switzerland. Alumnus of the Zubarev Lab at Karolinska Institutet and the Gygi Lab at Harvard Medical School. Read more about our research at

    2014 - 2019: Ph.D. in Medical Science with Prof. Roman A. Zubarev (supervisor) and Prof. Thomas Helleday (co-supervisor) from Department of Medical Biochemistry and Biophysics, Karolinska Institute. Thesis: Molecular Mechanisms and Targets of New Anticancer Treatments

    2015: Research School for Drug Discovery and Development, SciLifeLab, Sweden

    2004 - 2010: Doctorate of Pharmacy from Tabriz University of Medical Sciences

    Academic Appointments

    2024 - present: Assistant Professor at the Department of Microbiology, Cell and Tumor Biology, Karolinska Institutet, Stockholm, Sweden

    2023 - present: Junior Group Leader (Swiss National Science Foundation Ambizione Fellow) at Biozentrum, University of Basel, Switzerland

    2022 - 2023: Postdoctoral fellow at Michael N. Hall's Lab at Biozentrum, University of Basel, Switzerland

    2020 - 2022: Postdoctoral fellow at Steven P. Gygi's Lab at Department of Cell Biology, Harvard Medical School, Boston, USA

    2019 - 2020: Postdoctoral fellow at Roman A. Zubarev's Lab at Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden

    Academic grants, honors and awards


  • 2024: Karolinska Institutet Research Incubator Fellowship

    2024: Magnus Bergvalls Stiftelse

    2023: Jeanssons Stiftelser

    2023: Åke Wibergs Stiftelse

    2023: Swedish Research Council Starting Grant within Medicine and Health (6M SEK)

    2023: Ambizione Fellowship from Swiss National Science Foundation (11.6M SEK)

    2022: Karolinska Institutet Faculty Funded Assistant Professorship (7M SEK)

    2023: Ruth och Richard Julins stiftelse

    2023: Alex och Eva Wallströms stiftelse

    2022-2023: Karolinska Institutet Research Foundation Grant

    2021: SLS Stiftelsen Albert Nilssons Forskningsfond Grant

    2020-2023: Swedish Research Council International Postdoctoral Fellowship (3, 15M SEK)

    2020: Karolinska Institute Research Grant

    2020: Loo and Hans Ostermans Foundation Research Grant

    2019: Thermo Scientific Tandem Mass Tag Gold Award

    2019: CancerFonden Research Grant (co-applicant)


  • We use novel tools in mass spectrometry-based proteomics, biochemistry, systems biology and data-driven approaches to study cancer metabolism. We are mainly focused on colon cancer at the intersection of cancer cell metabolism, dietary nutrients and the microbiome. The ultimate aim is to develop novel drugs and therapeutic modalities against colon cancer and other metabolic disorders.

    Main publications:

    14. Gharibi H, Ashkarran AA, Jafari M, Voke E, Landry MP, Saei AA*, Mahmoudi M*. A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core facilities. Nature Communications [co-corresponding author].

    13. Saei AA*, Lundin A, Lyu H, Gharibi H, Luo H, Teppo j, Zhang X, Gaetani M, Végvári Á, Holmdahl R, Gygi SP, Zubarev RA*. 2023. Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification. BioRxiv [co-corresponding author].

    12. Ashkarran AA, Gharibi H, Abou Zeki D, Radu I, Khalighinejad F, Keyhanian K, Abrahamsson KK, Ionete C, Saei AA*, Morteza Mahmoudi*. 2023. Multi-Omics Analysis of Magnetically Levitated Plasma Biomolecules. Biosensors and Bioelectronics, 114862 [co-corresponding author].

    11. Saei AA, Gharibi H et al. 2023. Massive solubility changes of neuronal proteins upon simulated traumatic brain injury reveal the role of shockwave in irreversible damage. Molecules 28, 6768.

    10. Saei AA*, Lundström SL, Lyu H, Gharibi H, Lu W, Fang P, Zhang X, Meng Z, Wang J, Gaetani M, Végvári Á, Gygi SP, Zubarev RA*. 2022. Mapping the GALNT1 substrate landscape with versatile proteomics tools. BioRxiv [co-corresponding author].

    9. Nickchi P, Mirzaie M, Baumann M, Saei AA*, Jafari M*. 2022. Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2. BioRxiv [co-corresponding author].

    8. Ashkarran AA, Gharibi H, Voke E, Landry MP, Saei AA*, Mahmoudi M*. 2022. Measurements of heterogeneity in proteomics analysis of the nanoparticle protein corona across core facilities. Nature Communications. 6610 [co-corresponding author].

    7. Gharibi H, Chernobrovkin A, Eriksson G, Saei AA et al. 2022. Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass. Journal of the American Chemical Society 144, 6, 2484–2487 (covered in Science journal commentary).

    6. Sabatier P, Beusch CM, Saei AA et al. 2021. An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation. Nature Communications 12: 6558.

    5. Saei AA* at el. 2021. System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). Nature Communications 12, 1296 [co-corresponding author]. featured in Editor’s highlights on structural biology, biochemistry and biophysics]

    4. Saei AA et al. 2020. Comprehensive chemical proteomics in target deconvolution of redox active drug auranofin. Redox Biology 32, 101491.

    3. Saei AA et al. 2019. ProTargetMiner: A proteome signature library of anticancer molecules for functional discovery. Nature Communications 10, 5715.

    2. Gaetani M§, Sabatier P§, Saei AA§, et al. 2019. Proteome Integral Solubility Alteration (PISA): a high-throughput proteomics assay for target deconvolution. Journal of Proteome Research 18, 11, 4027–4037.

    1. Saei AA et al. 2018. Comparative proteomics of dying and surviving cancer cells improves the identification of drug targets and sheds light on cell life/death decisions. Molecular and Cellular Proteomics 17, 6, 1144-1155.


All other publications


  • Junior Group Leader, Biozentrum, University of Basel, 2023-
  • Assistant Professor, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 2024-2029

Degrees and Education

  • Degree Of Doctor Of Philosophy, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 2019

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