Amir Ata Saei

I am an assistant professor at the Department of Microbiology, Tumor and Cell Biology at Karolinska Institutet. Previously junior group leader (SNSF Ambizione Fellow) with Michael N. Hall's Lab at Biozentrum (University of Basel), Switzerland. Alumnus of the Zubarev Lab at Karolinska Institutet and the Gygi Lab at Harvard Medical School.

Understanding the molecular basis of metabolic diseases has become critical for the development of next-generation therapeutic strategies. My research program lies at the intersection of chemical proteomics, metabolomics, and computational strategies to uncover the intricate interplay between metabolites, proteins, diet, and gut microbiota in different metabolic disease states. By developing and leveraging innovative tools—including the Proteome Integral Solubility Alteration (PISA) assay and the multifaceted PISA-REX platform—we provide unprecedented insights into protein expression, stability, and redox regulation, which will revolutionize our understanding of metabolite interactome, key biological processes, and disease mechanisms.
Combining advanced proteomics and classical biochemical approaches, we seek to identify and validate therapeutic targets and biomarkers in metabolic diseases. In our long view of our studies, these findings are meant to be translational in the area of precision therapies and diagnostics, enhancing patient outcomes and quality of life.

As a hobby, we also continue developing proteomics techniques to answer questions of biomedical importance. Read more about our research at SaeiLab.com

Education

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

2025: Novo Nordisk Excellence Emerging Investigator Grant – Endocrinology and Metabolism 2025 (17M SEK)

2025: Ruth och Richard Julins stiftelse

2024: KIRI postdoctoral grant

2024: Cancerfonden Project Grant

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)
2023: Ruth och Richard Julins stiftelse
2023: Alex och Eva Wallströms stiftelse

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

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)

Main publications:

18. Krishnan A, Anahtar MN, Valeri JA, Jin W, Donghia NM, Sieben L, Luttens A, Fromer J, Bandyopadhyay P, Chen JC, Rehman D, Desai R, Edwards P, Lach RS, Aschtgen MS, Gaborieau M, Gaetani M, Palace SG, Omori S, Khonde L, Moroz YS, Blough B, Jin C, Loh E, Grad YH, Saei AA, Coley CW, Wong F, Collins JJ. A generative deep learning approach to de novo antibiotic design. Cell.

17. Sadeghi SA, Fang F, Nimavard RT, Wang Q, Zhu G, Saei AA, Sun L, Mahmoudi M. Mass spectrometry-based top-down proteomics for proteoform profiling of protein coronas. Nature Protocols.

16. Gharibi H, Saei AA, Chernobrovkin AL, Lundstrom SL, Lyu H, Meng Z, Vegvari A, Gaetani M, Zubarev RA. Towards a species search engine: KISSE offers a rigorous statistical framework for bone collagen tandem mass spectrometry data. Advanced Science.

15. Ashkarran AA, Gharibi H, Sadeghi SA, Modaresi SM, Wang Q, Lin TJ, Yerima G, Tamadon A, Sayadi M, Jafari M, Lin Z, Ritz D, Khakhniashvili D, Guha A, Mofrad MRK, Sun L, Landry MP, Saei AA*, Mahmoudi AA*.Small molecule modulation of protein corona for deep plasma proteome profiling. Nature Communications [corresponding author].

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 [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. Advanced Science [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 [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 [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 [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 [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.

Teaching proteomics, biology, metabolism, microbiome-related courses, cell biology and chemistry across four departments at Karolinska Institutet