2025
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.
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.
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.
Saei AA, Sun L, Mahmoudi M. The role of protein corona in advancing plasma proteomics. Proteomics.
Gaspar M, Sokolova B, Saei AA, Marques JC, Zubarev R. Beyond the known cuts: trypsin specificity in native proteins. Chemical Communications.
Nickchi P, Vadadokhau U, Mirzaie M, Baumann M, Saei AA*, Jafari M*. 2025. Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2. Proteomics [corresponding author].
Sirazum M, Abdelfattah A, Pandey P, Ashkarran A, Tadjiki A, Sharifi S, Gharibi H, Saei AA, Mahmoudi M, Lavasanifar A. Protein corona composition modulates uptake of polymeric micelles by colorectal cancer cells. Nanoscale Advances.
Sokolova B, Gharibi H, Jafari M, H Lyu, Lovera S, Gaetani M, Saei AA*, Zubarev RA. Above-Filter Digestion Proteomics reveals drug targets and localizes ligand binding site. BioRxiv [corresponding author].
Guha A, Sadeghi SA, Kunhiraman HH, Fang F, Wang Q, Rafieioskouei A, Grumelot S, Gharibi H, Saei AA, Sayadi M, Weintraub NL, Horibata S, Chung-Ming Yang P, Bonakdarpour B, Ghassemi M, Sun L, Mahmoudi M. AI-driven prediction of cardio-oncology biomarkers through protein corona analysis. Chemical Engineering Journal.
2024
Modaresi SM, Sugiyama R, Tram NDT, Jakob RP, Phan CS, Saei AA, Morishita Y, Muehlethaler T, Lim J, Ritz D, Long PSY, Lehner PA, Lim ZH, Degen M, Yao Z, Maier T, Hou Y, Lee JY, Xu J, Yeat AYJ, Koh KTS, Goh WY, Ling SYH, Chua PWL, Yamazaki M, Ee PLR, Hiller S, Morinaka BI. 2024. Antibiotics that Kill Gram-negative Bacteria by Restructuring the Outer Membrane Protein BamA. BioRxiv.
Meng Z, Saei AA, Lyu H, Gaetani M, Zubarev RA. 2024. One-Pot Time-Induced Proteome Integral Solubility Alteration Assay for Automated and Sensitive Drug–Target Identification. Analytical Chemistry.
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*. 2024. Small molecule modulation of protein corona for deep plasma proteome profiling. Nature Communications [corresponding author].
Saei AA*, Lundin A, Lyu H, Gharibi H, Luo H, Teppo j, Zhang X, Gaetani M, Végvári Á, Holmdahl R, Gygi SP, Zubarev RA*. 2024. Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification. Advanced Science [corresponding author].
Lyu H, Gharibi H, Sokolova B, Voiland A, Nilsson B, Meng Z, Gaetani M, Saei AA*, Zubarev RA*. 2024. ThermoTargetMiner as a proteome integral solubility alteration target database for prospective drugs against lung cancer. BioRxiv [corresponding author].
Gharibi H, Ashkarran AA, Jafari M, Voke E, Landry MP, Saei AA*, Mahmoudi M*. 2024. A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core facilities. Nature Communications [corresponding author].
Lyutvinskiy Y, Nagornov KO, Kozhinov AN, Gasilova N, Menin L, Meng Z, Zhang X, Saei AA, Tsybin YO, Makarov A, Zubarev RA. 2024. Adding color to mass spectra: Charge Determination Analysis (CHARDA) assigns charge state to every ion peak. Journal of the American Society for Mass Spectrometry. 35, 902–911.
Zhang X, Meng Z, Beusch C, Gharibi H, Cheng Q, Lyu H, Di Stefano L, Wang J, Saei AA, Végvári Á, Gaetani M, Zubarev RA. 2024. Ultralight ultrafast enzymes. Angewandte Chemie. e202316488.
Lobas AA, Saei AA, Lyu h, Zubarev RA, Gorshkov MV. 2023. Chemical proteomics reveals that the anticancer drug everolimus affects ubiquitin-proteasome system. ACS Pharmacology & Translational Science. 7, 787–796.
Ashkarran AA, Gharibi H, Modaresi SM, Saei AA*, Mahmoudi M. 2024. Standardizing Protein Corona Characterization in Nanomedicine: A Multicenter Study to Enhance Reproducibility and Data Homogeneity. Nano Letters [corresponding author].
Meng Z, Saei AA, Zhang X, Lyu H, Gharibi H, Lundstrom SL, Vegvari A, Gaetani M, Zubarev RA. 2024. Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates. Analytical Chemistry.
Zhang X, Gharibi H, Beusch CM, Meng Z, Saei AA, Gaetani M, Zubarev RA. 2024. Do light eaters live shorter lives? The case of ultralight Caenorhabditis elegans. BioRxiv.
2023
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].
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.
Luo H, Urbonaviciute V, Saei AA, Lyu H, Gaetani M, Végvári Á, Li Y, Zubarev RA, Holmdahl R. 2023. NCF1-dependent production of ROS protects against lupus by regulating plasmacytoid dendritic cell development and functions. JCI Insight. 8, e164875.
2022
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].
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].
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).
Gharibi H, AChernobrovkin AL, Saei AA, Zhang X, Gaetani M, Makarov AA, Zubarev RA. 2022. Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides. Analytical Chemistry. 94, 15048–15056.
Wang J, Rodin S, Saei AA, Zhang X, Zubarev RA. 2022. First Experimental Evidence for Reversibility of Ammonia Loss from Asparagine. International Journal of Molecular Sciences. 23, 8371.
James J, Chen Y, Hernandez CM, Forster F, Dagnell M, Cheng Q, Saei AA, Gharibi H, Fernandez Lahore G, Åstrand A, Malhotra R, Malissen B, Zubarev RA, Arnér ESJ, Holmdahl R. 2022. Redox regulation of PTPN22 affects the severity of T-cell-dependent autoimmune inflammation. Elife. 11, e74549.
Sharifi S, Saei AA, Gharibi H, Mahmoud NN, Harkins S, Dararatana N, Lisabeth EM, Serpooshan V, Végvári Á, Moore A, Mahmoudi M. Mass spectrometry, structural analysis, and anti-inflammatory properties of photo-cross-linked human albumin hydrogels. 2022. ACS applied bio materials. 5, 2643-2663.
2021
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.
Saei AA* at el. 2021. System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). Nature Communications 12, 1296 [corresponding author; featured in Editor’s highlights on structural biology, biochemistry and biophysics].
2020
Saei AA et al. 2020. Comprehensive chemical proteomics in target deconvolution of redox active drug auranofin. Redox Biology 32, 101491.
Peuget S, Zhu J, Sanz G, Singh M, Gaetani M, Chen X, Shi Y, Saei AA, Visnes T, Lindström MS, Rihani A, Moyano-Galceran L, Carlson JW, Hjerpe E, Joneborg U, Lehti K, Hartman J, Helleday T, Zubarev RA, Selivanova G. 2020. Thermal proteome profiling identifies oxidative-dependent inhibition of the transcription of major oncogenes as a new therapeutic mechanism for select anticancer compounds. Cancer Research. 80, 1538-1550.
Mehdipour T, Tohidkia MR, Saei AA, Kazemi A, Khajeh S, Rahimi AAR, Nikfarjam S, Farhadi M, Halimi M, Soleimani R, Zubarev RA, Nouri M. 2020. Tailoring subtractive cell biopanning to identify diffuse gastric adenocarcinoma‐associated antigens via human scFv antibodies. Immunology. 159, 96-108.
2019
Saei AA et al. 2019. ProTargetMiner: A proteome signature library of anticancer molecules for functional discovery. Nature Communications 10, 5715.
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.
Zhang X, Selvaraju K, Saei AA, D’Arcy P, Zubarev RA, Arnér ESJ, Linder S. 2019. Repurposing of auranofin: Thioredoxin reductase remains a primary target of the drug. Biochemie. 162, 46-54.
Zhang X, Espinosa B, Saei AA, D’Arcy P, Zubarev RA, Linder S. 2019. Oxidative stress induced by the deubiquitinase inhibitor b-AP15 is associated with mitochondrial impairment. Oxidative Medicine and Cellular Longevity. 1659468.
Hillert EK, Brnjic S, Zhang X, Mazurkiewicz M, Saei AA, Mofers A, Selvaraju K, Zubarev RA, Linder S, D’Arcy P. 2019. Proteasome inhibitor b-AP15 induces enhanced proteotoxicity by inhibiting cytoprotective aggresome formation. Cancer Letters. 448, 70-83.
2018
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.
Zhang X, Pellegrini P, Saei AA, Hillert EK, Mazurkiewicz M, Hägg Olofsson M, Zubarev RA, D’Arcy P, Linder S. 2018. The deubiquitinase inhibitor b-AP15 induces strong proteotoxic stress and mitochondrial damage. The Biochemical Pharmacology. 156, 291-301.
Kharazian B, Lohse SE, Ghasemi F, Raoufi M, Saei AA, Hashemi F, Farvadi F, Alimohamadi R, Jalali SA, Shokrgozar MA, Hadipour NL, Ejtehadi MR, Mahmoudi M. 2018. Bare surface of gold nanoparticle induces inflammation through unfolding of plasma fibrinogen. Scientific Reports. 8, 12557.
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