Protein expression, stability, and redox regulation – Saei Lab

Publications

All publications from group members

• Journal article: JOURNAL OF ORAL MICROBIOLOGY. 2026;18(1):2638646

  Macrophage activation and invasion by P. gingivalis is modulated by PPAD and accessory fimbriae subunits

  Wielento A; Drapala DM; Terekhova M; Jacula A; Artyomov MN; Kochan J; Hasegawa Y; Mizgalska D; Bagaitkar J; Grabiec AM; Potempa J
• Journal article: JOURNAL OF ANTIBIOTICS. 2026;:1-8

  Four new hydroxyl fatty acids, gambaoic acids A-C and gambaoic B methyl ester, from Shrimp Jeotgal-derived Bacillus sp. SNB-066

  Hillman PF; Lee C; Varli M; Zhou R; Han S-A; Yoo M; Lee JY; Kim J-H; Lee S; Lee H; Kim GJ; Choi H; Kim H; Nam S-J
• Journal article: PHYTOTHERAPY RESEARCH. 2026;40(1):159-175

  Atranorin Impedes Glioma Invasiveness and Progression by Inhibiting the Epithelial-Mesenchymal Transition and Stemness in Monotherapy and in Combination Therapy With Temozolomide

  Zhou R; Ahn E-J; Bhosle SR; Yu JY; Yang Y; Park S-Y; Tas I; Gamage C; Pulat S; Varli M; Hur J-S; Kim KK; Lee K-H; Ha H-H; Kim SK; Moon K-S; Kim H
• Journal article: PHYTOMEDICINE. 2025;148:157270

  Physciosporin targeting of cellular myelocytomatosis oncogene in gastric cancer suppresses energy metabolism and metastasis via lysosomal degradation

  Pulat S; Ji M; Oh S; Choi B; Varli M; Park S-Y; Zhou R; Gamage CDB; Hur J-S; Paik M-J; Kim H
• Journal article: MEDCOMM. 2025;6(11):e70446

  Synthesized Depside Molecules Suppress the Progression of Colorectal Cancer by Binding VDAC1/PHB/MMP9 Being at the Crossroads of Stemness, Motility, Apoptosis, and Metabolism

  Varli M; Yu YH; Yu J; Bhosle SR; Kim SK; Kim YG; Ha H-H; Kim H
• Journal article: MOLECULAR BIOMEDICINE. 2025;6(1):81

  Targeting heat shock protein 90 with usnic acid relieves immune suppression via aryl hydrocarbon receptor-mediated mechanisms in lung cancer

  Varli M; Ahn E-J; Bhosle SR; Moon K-S; Ha H-H; Kim H
• Journal article: BIOMOLECULES & THERAPEUTICS. 2025;33(5):842-851

  An Endolichenic Fungi-Derived Fatty Acid, cis-10-Nonadecenoic acid, Suppresses Colorectal Cancer Stemness

  Varli M; Lee E-Y; Park S-Y; Yang Y; Hillman PF; Zhou R; Hur J-S; Nam S-J; Kim H
• Journal article: PHYTOMEDICINE. 2025;145:156973

  4-O-Demethylbarbatic acid has a novel therapeutic impact on the progression of EGFR-driven lung adenocarcinoma

  Varli M; Zhou R; Liu R; Rho JK; Ha H-H; Hur J-S; Kim H
• Article: CHEMICAL COMMUNICATIONS. 2025;61(68):12753-12756

  Beyond the known cuts: trypsin specificity in native proteins

  Gaspar M; Sokolova B; Saei AA; Marques JC; Zubarev RA
• Journal article: CANCER RESEARCH. 2025;85(15):P43

  Chrysophanol Hinders Colorectal Cancer Cell Invasion and Metabolic Functions by Targeting KITENIN/ErbB4 Signaling

  Varli M; Kim E; Zhou R; Pulat S; Gamage CDB; Kim KK; Paik M-J; Kim H
• Journal article: MARINE DRUGS. 2025;23(7):292

  A Marine-Derived Steroid from Rhodococcus sp., 3,12-Dioxochola-4,6-dien-24-oic Acid, Enhances Skin Re-Epithelialization and Tissue Repair

  Varli M; Tan H; Lee C; Lee J; Lee JY; Kim J-H; Lee S; Kim H; Nam S-J
• Journal article: SCIENTIFIC REPORTS. 2025;15(1):22807

  Strictosamide and mitraphylline inhibit cancer cell motility by suppressing epithelial-mesenchymal transition via integrin α4-mediated signaling

  Varli M; Lee K; Bach TT; Binh TD; Kim H; Kang KB
• Journal article: ADVANCED THERAPEUTICS. 2025;8(7)

  Disintegration of the KITENIN/ErbB4 Functional Complex by the Flavonoid Hispidulin Suppresses Colorectal Cancer Progression

  Varli M; Oh S; Kim E; Gokalsin B; Sesal NC; Kim KK; Paik MJ; Kim H
• Article: MOLECULAR PHARMACEUTICS. 2025;22(5):2723-2730

  Beyond Correlation: Establishing Causality in Protein Corona Formation for Nanomedicine

  Rafieioskouei A; Rogale K; Saei AA; Mahmoudi M; Bonakdarpour B
• Article: CHEMICAL ENGINEERING JOURNAL. 2025;509:161134

  AI-driven prediction of cardio-oncology biomarkers through protein corona analysis

  Guha A; Sadeghi SA; Kunhiraman HH; Fang F; Wang Q; Rafieioskouei A; Grumelot S; Gharibi H; Saei AA; Sayadi M; Weintraub NL; Horibata S; Yang PC-M; Bonakdarpour B; Ghassemi M; Sun L; Mahmoudi M
• Article: PROTEOMICS. 2025;25(8):e202400238

  Monitoring Functional Posttranslational Modifications Using a Data-Driven Proteome Informatic Pipeline

  Nickchi P; Vadadokhau U; Mirzaie M; Baumann M; Saei AA; Jafari M
• Journal article: SCIENTIFIC REPORTS. 2025;15(1):6695

  Development and synthesis of diffractaic acid analogs as potent inhibitors of colorectal cancer stem cell traits

  Varli M; Bhosle SR; Jo E; Yu YH; Yang Y; Ha H-H; Kim H
• Journal article: BIOFACTORS. 2025;51(1):e70002

  Lobaric acid suppresses the stemness potential of colorectal cancer cells through mTOR/AKT

  Pulat S; Paguiri JAG; Gamage CDB; Varli M; Zhou R; Park S-Y; Hur J-S; Kim H
• Journal article: BIOFACTORS. 2025;51(1):e2120

  Plectalibertellenone A suppresses colorectal cancer cell motility and glucose metabolism by targeting TGF-β/Smad and Wnt pathways

  Gamage CDB; Kim J-H; Zhou R; Park S-Y; Pulat S; Varli M; Nam S-J; Kim H
• Journal article: STEM CELL REVIEWS AND REPORTS. 2025;21(1):283-286

  Atraric Acid Induces Hair Growth through the Stimulation of Sonic Hedgehog/GLI1 in Human Dermal Papilla Cells

  Pulat S; Kim W; Hwang J-H; Zhou R; Gamage CDB; Varli M; Tas I; Yang Y; Park S-Y; Lim K-M; Hur J-S; Kim H
• Journal article: PHYTOMEDICINE. 2025;136:156247

  Emodin disrupts the KITENIN oncogenic complex by binding ErbB4 and suppresses colorectal cancer progression in dual blockade with KSRP-binding compound

  Varli M; Ji M; Kim E; Kim SJ; Choi B; Ha H-H; Kim KK; Paik M-J; Kim H
• Article: PROTEOMICS. 2025;25(1-2):e2400028

  The role of protein corona in advancing plasma proteomics

  Saei AA; Sun L; Mahmoudi M
• Preprint: BIORXIV. 2024

  Antibiotics that Kill Gram-negative Bacteria by Restructuring the Outer Membrane Protein BamA

  Modaresi SM; Sugiyama R; Tram NDT; Jakob R; Phan C-S; Saei AA; Morishita Y; Mühlethaler T; Lim J; Ritz D; Long PSY; Lehner P; Lim ZH; Degen M; Yao Z; Maier T; Hou Y; Lee JY; Xu J; Yeat AYJ; Koh KTS; Goh WY; Ling S; Chua P; Yamazaki M; Ee PLR; Hiller S; Morinaka B
• Article: ANALYTICAL CHEMISTRY. 2024;96(48):18917-18921

  One-Pot Time-Induced Proteome Integral Solubility Alteration Assay for Automated and Sensitive Drug-Target Identification

  Meng Z; Saei AA; Lyu H; Gaetani M; Zubarev RA
• Journal article: MOLECULES AND CELLS. 2024;47(12):100143

  Unveiling the antimetastatic activity of monoterpene indole alkaloids targeting MMP9 in cancer cells, with a focus on pharmacokinetic and cellular insights

  Varli M; Lee K; Bin Kang K; Kim H
• Journal article: CANCER & METABOLISM. 2024;12(1):36

  TDO2 inhibition counters Benzo[a]pyrene-induced immune evasion and suppresses tumorigenesis in lung adenocarcinoma

  Tas I; Varli M; Pulat S; Sim HB; Kim J-J; Kim H
• Preprint: BIORXIV. 2024

  Shifting Beyond Classical Drug Synergy in Combinatorial Therapy through Solubility Alterations

  Gholizadeh E; Zangene E; Vadadokhau U; Ritz D; Miettinen J; Soliymani R; Baumann M; Wilhelm M; Kankuri E; Kankuri E; Haynes P; Haynes P; Heckman C; Saei A; Jafari M
• Article: NATURE COMMUNICATIONS. 2024;15(1):9638

  Small molecule modulation of protein corona for deep plasma proteome profiling

  Ashkarran AA; Gharibi H; Sadeghi SA; Modaresi SM; Wang Q; Lin T-J; Yerima G; Tamadon A; Sayadi M; Jafari M; Lin Z; Ritz D; Kakhniashvili D; Guha A; Mofrad MRK; Sun L; Landry MP; Saei AA; Mahmoudi M
• Article: ADVANCED SCIENCE. 2024;11(38):e2401502

  Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification

  Saei AA; Lundin A; Lyu H; Gharibi H; Luo H; Teppo J; Zhang X; Gaetani M; Vegvari A; Holmdahl R; Gygi SP; Zubarev RA
• Preprint: BIORXIV. 2024

  Causality Analysis of Protein Corona Composition: Phosphatidylcholine-Enhances Plasma Proteome Profiling by Proteomics

  Rafieioskouei A; Rogale K; Saei AA; Mahmoudi M; Bonakdarpour B
• Journal article: BIORXIV. 2024;:2024.03.06.582595

  Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules.

  Ashkarran AA; Gharibi H; Sadeghi SA; Modaresi SM; Wang Q; Lin T-J; Yerima G; Tamadon A; Sayadi M; Jafari M; Lin Z; Ritz D; Kakhniashvili D; Guha A; Mofrad MRK; Sun L; Landry MP; Saei AA; Mahmoudi M
• Article: ANALYTICAL CHEMISTRY. 2024;96(33):13533-13541

  Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates

  Meng Z; Saei AA; Gharibi H; Zhang X; Lyu H; Lundstrom SL; Vegvari A; Gaetani M; Zubarev RA
• Article: NANO LETTERS. 2024;24(32):9874-9881

  Standardizing Protein Corona Characterization in Nanomedicine: A Multicenter Study to Enhance Reproducibility and Data Homogeneity

  Ashkarran AA; Gharibi H; Modaresi SM; Saei AA; Mahmoudi M
• Preprint: BIORXIV. 2024

  One-Pot Time-Induced Proteome Integral Solubility Alteration (OPTI-PISA) assay for automated and sensitive drug target identification

  Meng Z; Saei AA; Lyu H; Gaetani M; Zubarev R
• Preprint: BIORXIV. 2024

  ThermoTargetMiner as a proteome integral solubility alteration target database for prospective drugs against lung cancer

  Lyu H; Gharibi H; Sokolova B; Voiland A; Nilsson B; Meng Z; Gaetani M; Saei AA; Zubarev R
• Journal article: CANCER CELL INTERNATIONAL. 2024;24(1):253

  Chrysophanol inhibits of colorectal cancer cell motility and energy metabolism by targeting the KITENIN/ErbB4 oncogenic complex

  Varli M; Kim E; Oh S; Pulat S; Zhou R; Gamage CDB; Gokalsin B; Sesal NC; Kim KK; Paik M-J; Kim H
• Editorial: NANOMEDICINE. 2024;19(14):1223-1226

  Multi-omics exploration of biomolecular corona in nanomedicine therapeutics and diagnostics

  Saei AA; Mahmoudi M
• Article: JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY. 2024;35(5):902-911

  Adding Color to Mass Spectra of Biopolymers: Charge Determination Analysis (CHARDA) Assigns Charge State to Every Ion Peak

  Lyutvinskiy Y; Nagornov KO; Kozhinov AN; Gasilova N; Menin L; Meng Z; Zhang X; Saei AA; Fu T; Chamot-Rooke J; Tsybin YO; Makarov A; Zubarev RA
• Preprint: BIORXIV. 2024

  Standardizing protein corona characterization in nanomedicine: a multi-center study to enhance reproducibility and data homogeneity

  Ashkarran AA; Gharibi H; Modaresi SM; Saei AA; Mahmoudi M
• Journal article: JACS AU. 2024;4(4):1521-1537

  Usnic Acid Targets 14-3-3 Proteins and Suppresses Cancer Progression by Blocking Substrate Interaction

  Varli M; Bhosle SR; Kim E; Yang Y; Tas I; Zhou R; Pulat S; Gamage CDB; Park S-Y; Ha H-H; Kim H
• Article: ACS PHARMACOLOGY AND TRANSLATIONAL SCIENCE. 2024;7(3):787-796

  Chemical Proteomics Reveals that the Anticancer Drug Everolimus Affects the Ubiquitin-Proteasome System

  Lobas AA; Saei AA; Lyu H; Zubarev RA; Gorshkov MV
• Preprint: BIORXIV. 2024

  Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates

  Meng Z; Saei AA; Zhang X; Lyu H; Gharibi H; Lundström S; Végvári Á; Gaetani M; Zubarev R
• Journal article: MARINE DRUGS. 2024;22(2):88

  Anithiactin D, a Phenylthiazole Natural Product from Mudflat-Derived Streptomyces sp., Suppresses Motility of Cancer Cells

  Pulat S; Yang I; Lee J; Hwang S; Zhou R; Gamage CDB; Varli M; Tas I; Yang Y; Park S-Y; Hong A; Kim J-H; Oh D-C; Kim H; Nam S-J; Kang H
• Preprint: BIORXIV. 2024

  Do light eaters live shorter lives? The case of ultralightCaenorhabditis elegans

  Zhang X; Gharibi H; Beusch C; Meng Z; Saei A; Gaetani M; Zubarev R
• Article: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 2024;63(3):e202316488

  Ultralight Ultrafast Enzymes

  Zhang X; Meng Z; Beusch CM; Gharibi H; Cheng Q; Lyu H; Di Stefano L; Wang J; Saei AA; Vegvari A; Gaetani M; Zubarev RA
• Article: NATURE COMMUNICATIONS. 2024;15(1):342

  A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core facilities

  Gharibi H; Ashkarran AA; Jafari M; Voke E; Landry MP; Saei AA; Mahmoudi M
• Article: MOLECULES. 2023;28(19):6768

  Massive Solubility Changes in Neuronal Proteins upon Simulated Traumatic Brain Injury Reveal the Role of Shockwaves in Irreversible Damage

  Saei AA; Gharibi H; Lyu H; Nilsson B; Jafari M; Von Holst H; Zubarev RA
• Journal article: HELIYON. 2023;9(9):e19185

  A fatty acid-rich fraction of an endolichenic fungus Phoma sp. suppresses immune checkpoint markers via AhR/ARNT and ESR1

  Varli M; Ngo MT; Kim S-M; Tas I; Zhou R; Gamage CDB; Pulat S; Park S-Y; Sesal NC; Hur J-S; Bin Kang K; Kim H
• Preprint: BIORXIV. 2023

  Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification

  Saei AA; Lundin A; Lyu H; Gharibi H; Luo H; Teppo J; Zhang X; Gaetani M; Végvári Á; Holmdahl R; Gygi S; Zubarev R
• Journal article: CELL AND BIOSCIENCE. 2023;13(1):146

  KITENIN promotes aerobic glycolysis through PKM2 induction by upregulating the c-Myc/hnRNPs axis in colorectal cancer

  Varli M; Kim SJ; Noh M-G; Kim YG; Ha H-H; Kim KK; Kim H
• Journal article: MOLECULAR ORAL MICROBIOLOGY. 2023;38(4):334-346

  Accessory fimbrial subunits and PPAD are necessary for TLR2 activation by Porphyromonas gingivalis.

  Wielento A; Bereta GP; Szczęśniak K; Jacuła A; Terekhova M; Artyomov MN; Hasegawa Y; Grabiec AM; Potempa J
• Journal article: JOURNAL OF DENTAL RESEARCH. 2023;102(5):489-496

  The Role of Gingival Fibroblasts in the Pathogenesis of Periodontitis.

  Wielento A; Lagosz-Cwik KB; Potempa J; Grabiec AM
• Article: JCI INSIGHT. 2023;8(7):e164875

  NCF1-dependent production of ROS protects against lupus by regulating plasmacytoid dendritic cell development and functions

  Luo H; Urbonaviciute V; Saei AA; Lyu H; Gaetani M; Vegvari A; Li Y; Zubarev RA; Holmdahl R
• Journal article: ACS OMEGA. 2023;8(13):12548-12557

  Phthalides Isolated from the Endolichenic Arthrinium sp. EL000127 Exhibits Antiangiogenic Activity

  Gamage CDB; Lee K; Park S-Y; Varli M; Lee CW; Kim S-M; Zhou R; Pulat S; Yang Y; Tas I; Hur J-S; Kang KB; Kim H
• Journal article: CANCER RESEARCH. 2023;83(7):3793

  Regulation of miR-124 expression by promoter methylation in CRC and its relationship with KITENIN expression

  Park S-Y; Zhou R; Gamage CDB; Pulat S; Varli M; Kim H
• Journal article: MARINE DRUGS. 2023;21(3):153

  Marinobazzanan, a Bazzanane-Type Sesquiterpenoid, Suppresses the Cell Motility and Tumorigenesis in Cancer Cells

  Pulat S; Hillman PF; Kim S; Asolkar RN; Kim H; Zhou R; Tas I; Gamage CDB; Varli M; Park S-Y; Park SC; Yang I; Shin J; Oh D-C; Kim H; Nam S-J; Fenical W
• Journal article: SCIENTIFIC REPORTS. 2023;13(1):2811

  1′-O-methyl-averantin isolated from the endolichenic fungus Jackrogersella sp. EL001672 suppresses colorectal cancer stemness via sonic Hedgehog and Notch signaling

  Varli M; Lee E-Y; Yang Y; Zhou R; Tas I; Pulat S; Gamage CDB; Park S-Y; Hur J-S; Nam S-J; Kim H
• Article: ACS BIO & MED CHEM AU. 2023;3(1):62-73

  Sex-Specific Silica Nanoparticle Protein Corona Compositions Exposed to Male and Female BALB/c Mice Plasmas

  Ashkarran AA; Gharibi H; Grunberger JW; Saei AA; Khurana N; Mohammadpour R; Ghandehari H; Mahmoudi M
• Article: BIOSENSORS & BIOELECTRONICS. 2023;220:114862

  Multi-omics analysis of magnetically levitated plasma biomolecules

  Ashkarran AA; Gharibi H; Abou Zeki D; Radu I; Khalighinejad F; Keyhanian K; Abrahamsson CK; Ionete C; Saei AA; Mahmoudi M
• Journal article: CANCERS. 2023;15(2):489

  Libertellenone T, a Novel Compound Isolated from Endolichenic Fungus, Induces G2/M Phase Arrest, Apoptosis, and Autophagy by Activating the ROS/JNK Pathway in Colorectal Cancer Cells

  Gamage CDB; Kim J-H; Yang Y; Tas I; Park S-Y; Zhou R; Pulat S; Varli M; Hur J-S; Nam S-J; Kim H
• Preprint: BIORXIV. 2023

  Massive solubility changes of neuronal proteins upon simulated traumatic brain injury reveal the role of shockwave in irreversible damage

  Saei AA; Gharibi H; Lyu H; Nilsson B; Jafari M; von Holst H; Zubarev R
• Preprint: BIORXIV. 2022

  Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline

  Nickchi P; Vadadokhau U; Mirzaie M; Baumann M; Baumann M; Saei A; Jafari M
• Article: NATURE COMMUNICATIONS. 2022;13(1):6610

  Measurements of heterogeneity in proteomics analysis of the nanoparticle protein corona across core facilities

  Ashkarran AA; Gharibi H; Voke E; Landry MP; Saei AA; Mahmoudi M
• Article: ANALYTICAL CHEMISTRY. 2022;94(43):15048-15056

  Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides

  Gharibi H; Chernobrovkin AL; Saei AA; Zhang X; Gaetani M; Makarov AA; Zubarev RA
• Review: CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY. 2022;52(7):1461-1487

  Breathomics: Review of Sample Collection and Analysis, Data Modeling and Clinical Applications

  Khoubnasabjafari M; Mogaddam MRA; Rahimpour E; Soleymani J; Saei AA; Jouyban A
• Preprint: BIORXIV. 2022

  Multi-Omics Analysis of Magnetically Levitated Plasma Biomolecules

  Ashkarran AA; Gharibi H; Abou Zeki D; Radu I; Khalighinejad F; Keyhanian K; Abrahamsson C; Ionete C; Saei AA; Mahmoudi M
• Journal article: FRONTIERS IN PHARMACOLOGY. 2022;13:986946

  An acetonic extract and secondary metabolites from the endolichenic fungus Nemania sp. EL006872 exhibit immune checkpoint inhibitory activity in lung cancer cell

  Varli M; Pham HT; Kim S-M; Tas I; Gamage CDB; Zhou R; Pulat S; Park S-Y; Sesal NC; Hur J-S; Bin Kang K; Kim H
• Preprint: BIORXIV. 2022

  Mapping the GALNT1 substrate landscape with versatile proteomics tools

  Saei AA; Lundström S; Lyu H; Gharibi H; Lu W; Fang P; Zhang X; Meng Z; Wang J; Gaetani M; Végvári Á; Gygi S; Zubarev R
• Article: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 2022;23(15):8371

  First Experimental Evidence for Reversibility of Ammonia Loss from Asparagine

  Wang J; Rodin S; Saei AA; Zhang X; Zubarev RA
• Article: ACS APPLIED BIO MATERIALS. 2022;5(6):2643-2663

  Mass Spectrometry, Structural Analysis, and Anti-Inflammatory Properties of Photo-Cross-Linked Human Albumin Hydrogels

  Sharifi S; Saei AA; Gharibi H; Mahmoud NN; Harkins S; Dararatana N; Lisabeth EM; Serpooshan V; Vegvari A; Moore A; Mahmoudi M
• Article: ELIFE. 2022;11:e74549

  Redox regulation of PTPN22 affects the severity of T-cell-dependent autoimmune inflammation

  James J; Chen Y; Hernandez CM; Forster F; Dagnell M; Cheng Q; Saei AA; Gharibi H; Lahore GF; astrand A; Malhotra R; Malissen B; Zubarev RA; Arner ESJ; Holmdahl R
• Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2022;144(6):2484-2487

  Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass

  Gharibi H; Chernobrovkin AL; Eriksson G; Saei AA; Timmons Z; Kitchener AC; Kalthoff DC; Liden K; Makarov AA; Zubarev RA
• Journal article: FRONTIERS IN IMMUNOLOGY. 2022;13:823685

  TLR2 Activation by Porphyromonas gingivalis Requires Both PPAD Activity and Fimbriae.

  Wielento A; Bereta GP; Łagosz-Ćwik KB; Eick S; Lamont RJ; Grabiec AM; Potempa J
• Preprint: RESEARCH SQUARE. 2021

  Ultralight ultrafast enzymes

  Zhang X; Meng Z; Beusch C; Gharibi H; Cheng Q; Stefano L; Wang J; Saei A; Vegvari A; Gaetani M; Zubarev R
• Preprint: BIORXIV. 2021

  Redox regulation of PTPN22 affects the severity of T cell dependent autoimmune inflammation

  James J; Chen Y; Hernandez C; Forster F; Dagnell M; Cheng Q; Saei A; Gharibi H; Lahore GF; Åstrand A; Malhotra R; Malissen B; Zubarev R; Arnér ESJ; Holmdahl R
• Preprint: BIORXIV. 2021

  Abnormal (hydroxy)prolines deuterium content redefines hydrogen chemical mass

  Gharibi H; Chernobrovkin A; Eriksson G; Saei AA; Timmons Z; Kitchener A; Kalthoff D; Lidén K; Makarov A; Zubarev R
• Article: NATURE COMMUNICATIONS. 2021;12(1):6558

  An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation

  Sabatier P; Beusch CM; Saei AA; Aoun M; Moruzzi N; Coelho A; Leijten N; Nordenskjold M; Micke P; Maltseva D; Tonevitsky AG; Millischer V; Villaescusa JC; Kadekar S; Gaetani M; Altynbekova K; Kel A; Berggren P-O; Simonson O; Grinnemo K-H; Holmdahl R; Rodin S; Zubarev RA
• Review: ADVANCED SCIENCE. 2021;8(21):e2100556

  Nanotechnology for Targeted Detection and Removal of Bacteria: Opportunities and Challenges

  Hajipour MJ; Saei AA; Walker ED; Conley B; Omidi Y; Lee K-B; Mahmoudi M
• Journal article: PHYTOMEDICINE. 2021;91:153674

  Physciosporin suppresses mitochondrial respiration, aerobic glycolysis, and tumorigenesis in breast cancer

  Tas I; Varli M; Son Y; Han J; Kwak D; Yang Y; Zhou R; Gamage CDB; Pulat S; Park S-Y; Yu YH; Moon K-S; Lee K-H; Ha H-H; Hur J-S; Kim H
• Journal article: JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION. 2021;15(4):3207-3215

  Physical characteristics of black cumin oil emulsions compared to sunflower and corn oils emulsions

  Varli M; Solak R; Turan S; Ramadan MF
• Journal article: SCIENTIFIC REPORTS. 2021;11(1):10770

  hTERT-immortalized gingival fibroblasts respond to cytokines but fail to mimic primary cell responses to Porphyromonas gingivalis.

  Lagosz-Cwik KB; Wielento A; Lipska W; Kantorowicz M; Darczuk D; Kaczmarzyk T; Gibbs S; Potempa J; Grabiec AM
• Article: IRANIAN JOURNAL OF KIDNEY DISEASES. 2021;15(2):121-133

  Predictive Biomarker Panel in Proliferative Lupus Nephritis, Two-Dimensional Shotgun

  Ghasemi M; Kalantari S; Zubarev RA; Nafar M; Saei AA; Heidari S-S; Baghestani AR; Samavat S
• Preprint: RESEARCH SQUARE. 2021

  SIESTA as a universal unbiased proteomics approach for identification and prioritization of enzyme substrates 

  Saei AA; Beusch C; Sabatier P; Wells JA; Gharibi H; Meng Z; Chernobrovkin A; Rodin S; Näreoja K; Thorsell A-G; Karlberg T; Cheng Q; Lundström S; Gaetani M; Végvári Á; Arnér ESJ; Schüler H; Zubarev R
• Article: NATURE COMMUNICATIONS. 2021;12(1):1296

  System-wide identification and prioritization of enzyme substrates by thermal analysis

  Saei AA; Beusch CM; Sabatier P; Wells JA; Gharibi H; Meng Z; Chernobrovkin A; Rodin S; Nareoja K; Thorsell A-G; Karlberg T; Cheng Q; Lundstrom SL; Gaetani M; Vegvari A; Arner ESJ; Schuler H; Zubarev RA
• Article: BIOINTERPHASES. 2021;16(1):011008

  Can the biomolecular corona induce an allergic reaction?-A proof-of-concept study

  Muehe A; Nejadnik H; Muehe H; Rosenberg J; Gharibi H; Saei AA; Lyu S-C; Nadeau KC; Mahmoudi M; Daldrup-Link HE
• Review: JOURNAL OF DRUG TARGETING. 2020;28(10):1018-1033

  Immunotargeting and therapy of cancer by advanced multivalence antibody scaffolds

  Kafil V; Saei AA; Tohidkia MR; Barar J; Omidi Y
• Article: JOURNAL OF PROTEOME RESEARCH. 2020;19(11):4364-4373

  COVID-19: Nanomedicine Uncovers Blood-Clot Mystery

  Saei AA; Sharifi S; Mahmoudi M
• Journal article: ACTA BIOCHIMICA POLONICA. 2020;67(3):303-308

  Influence of the reporter vector backbone on 2-deoxyglucose dependent promoter activation

  Solecka A; Wielento A; Jurczak J; Sowinska W; Wawro M; Kasza A
• Journal article: ANALECTA. 2020;14(1):89-99

  Intensification of cellulose enzymatic hydrolysis by microwave pretreatment

  Varlı M; Ertuğral EG; Jákói Z; Hodúr C; Beszédes S
• Article: REDOX BIOLOGY. 2020;32:101491

  Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin

  Saei AA; Gullberg H; Sabatier P; Beusch CM; Johansson K; Lundgren B; Arvidsson PI; Arner ESJ; Zubarev RA
• Article: CANCER RESEARCH. 2020;80(7):1538-1550

  Thermal Proteome Profiling Identifies Oxidative-Dependent Inhibition of the Transcription of Major Oncogenes as a New Therapeutic Mechanism for Select Anticancer Compounds

  Peuget S; Zhu J; Sanz G; Singh M; Gaetani M; Chen X; Shi Y; Saei AA; Visnes T; Lindstrom MS; Rihani A; Moyano-Galceran L; Carlson JW; Hjerpe E; Joneborg U; Lehti K; Hartman J; Helleday T; Zubarev R; Selivanova G
• Article: IMMUNOLOGY. 2020;159(1):96-108

  Tailoring subtractive cell biopanning to identify diffuse gastric adenocarcinoma-associated antigens via human scFv antibodies

  Mehdipour T; Tohidkia MR; Saei AA; Kazemi A; Khajeh S; Rahimi AAR; Nikfarjam S; Farhadi M; Halimi M; Soleimani R; Zubarev RA; Nouri M
• Article: NATURE COMMUNICATIONS. 2019;10(1):5715

  ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery

  Saei AA; Beusch CM; Chernobrovkin A; Sabatier P; Zhang B; Tokat UG; Stergiou E; Gaetani M; Vegvari A; Zubarev RA
• Article: JOURNAL OF PROTEOME RESEARCH. 2019;18(11):4027-4037

  Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution

  Gaetani M; Sabatier P; Saei AA; Beusch CM; Yang Z; Lundstrom SL; Zubarev RA
• Review: DNA REPAIR. 2019;80:8-15

  Crosstalk between P53 and DNA damage response in ageing

  Mohammadzadeh A; Mirza-Aghazadeh-Attari M; Hallaj S; Saei AA; Alivand MR; Valizadeh A; Yousefi B; Majidinia M
• Review: DNA REPAIR. 2019;80:59-84

  DNA damage response and repair in ovarian cancer: Potential targets for therapeutic strategies

  Mirza-Aghazadeh-Attari M; Ostadian C; Saei AA; Mihanfar A; Darband SG; Sadighparvar S; Kaviani M; Kafil HS; Yousefi B; Majidinia M
• Article: BIOCHIMIE. 2019;162:46-54

  Repurposing of auranofin: Thioredoxin reductase remains a primary target of the drug

  Zhang X; Selvaraju K; Saei AA; D'Arcy P; Zubarev RA; Arner ESJ; Linder S
• Article: OXIDATIVE MEDICINE AND CELLULAR LONGEVITY. 2019;2019:1659468-11

  Oxidative Stress Induced by the Deubiquitinase Inhibitor b-AP15 Is Associated with Mitochondrial Impairment

  Zhang X; Espinosa B; Saei AA; D'Arcy P; Zubarev RA; Linder S
• Article: CANCER LETTERS. 2019;448:70-83

  Proteasome inhibitor b-AP15 induces enhanced proteotoxicity by inhibiting cytoprotective aggresome formation

  Hillert E-K; Brnjic S; Zhang X; Mazurkiewicz M; Saei AA; Mofers A; Selvaraj K; Zubarev R; Linder S; D'Arcy P
• Doctoral thesis: 2019

  Molecular mechanisms and targets of new anticancer treatments

  Saei Dibavar A
• Preprint: BIORXIV. 2018

  Proteome Integral Stability Alteration assay dramatically increases throughput and sensitivity in profiling factor-induced proteome changes

  Gaetani M; Sabatier P; Saei AA; Beusch C; Yang Z; Lundstrom S; Zubarev R
• Article: PROTEOMICS. 2018;18(24):e1800118

  Dynamic Proteomics Reveals High Plasticity of Cellular Proteome: Growth-Related and Drug-Induced Changes in Cancer Cells are Comparable

  Sabatier P; Saei AA; Wang S; Zubarev RA
• Article: BIOCHEMICAL PHARMACOLOGY. 2018;156:291-301

  The deubiquitinase inhibitor b-AP15 induces strong proteotoxic stress and Check for mitochondrial damage

  Zhang X; Pellegrini P; Saei AA; Hillert E-K; Mazurkiewicz M; Olofsson MH; Zubarev RA; D'Arcy P; Linder S
• Preprint: BIORXIV. 2018

  System-wide identification and prioritization of enzyme substrates by thermal analysis (SIESTA)

  Saei AA; Beusch C; Sabatier P; Wells JA; Chernobrovkin A; Rodin S; Näreoja K; Thorsell A-G; Karlberg T; Cheng Q; Lundström S; Gaetani M; Végvári Á; Arnér ESJ; Schüler H; Zubarev R
• Preprint: BIORXIV. 2018

  ProTargetMiner: A proteome signature library of anticancer molecules for functional discovery

  Saei AA; Chernobrovkin A; Sabatier P; Zhang B; Beusch C; Tokat ÜG; Gaetani M; Végvári Á; Zubarev R
• Article: SCIENTIFIC REPORTS. 2018;8(1):12557

  Bare surface of gold nanoparticle induces inflammation through unfolding of plasma fibrinogen

  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
• Article: JOURNAL OF DRUG DELIVERY SCIENCE AND TECHNOLOGY. 2018;46:268-273

  Formulation, characterization and cytotoxicity evaluation of ketotifen-loaded nanostructured lipid carriers

  Dolatabadi JEN; Azami A; Mohammadi A; Hamishehkar H; Panahi-Azar V; Saadat YR; Saei AA
• Article: MOLECULAR & CELLULAR PROTEOMICS. 2018;17(6):1144-1155

  Comparative Proteomics of Dying and Surviving Cancer Cells Improves the Identification of Drug Targets and Sheds Light on Cell Life/Death Decisions

  Saei AA; Sabatier P; Tokat UG; Chernobrovkin A; Pirmoradian M; Zubarev RA
• Review: CHEMISTRY OF MATERIALS. 2017;29(16):6578-6595

  Nanoparticle Surface Functionality Dictates Cellular and Systemic Toxicity

  Saei AA; Yazdani M; Lohse SE; Bakhtiary Z; Serpooshan V; Ghavami M; Asadian M; Mashaghi S; Dreaden EC; Mashaghi A; Mahmoudi M
• Article: DRUG DEVELOPMENT AND INDUSTRIAL PHARMACY. 2017;43(8):1244-1253

  Microparticles containing erlotinib-loaded solid lipid nanoparticles for treatment of non-small cell lung cancer

  Bakhtiary Z; Barar J; Aghanejad A; Saei AA; Nemati E; Dolatabadi JEN; Omidi Y
• Article: COLLOIDS AND SURFACES B-BIOINTERFACES. 2016;143:224-232

  Theranostic MUC-1 aptamer targeted gold coated superparamagnetic iron oxide nanoparticles for magnetic resonance imaging and photothermal therapy of colon cancer

  Azhdarzadeh M; Atyabi F; Saei AA; Varnamkhasti BS; Omidi Y; Fateh M; Ghavami M; Shanehsazzadeh S; Dinarvand R
• Review: NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE. 2016;12(2):287-307

  Targeted superparamagnetic iron oxide nanoparticles for early detection of cancer: Possibilities and challenges

  Bakhtiary Z; Saei AA; Hajipour MJ; Raoufi M; Vermesh O; Mahmoudi M
• Review: TRENDS IN BIOTECHNOLOGY. 2015;33(12):735-746

  Possibilities in Germ Cell Research: An Engineering Insight

  Esfandiari F; Mashinchian O; Ashtiani MK; Ghanian MH; Hayashi K; Saei AA; Mahmoudi M; Baharvand H
• Review: CONTRAST MEDIA & MOLECULAR IMAGING. 2015;10(5):329-355

  Superparamagnetic iron oxide nanoparticles for in vivo molecular and cellular imaging

  Sharifi S; Seyednejad H; Laurent S; Atyabi F; Saei AA; Mahmoudi M
• Article: CURRENT ORGANIC CHEMISTRY. 2015;19(11):982-990

  Biomedical Applications of Superparamagnetic Nanoparticles in Molecular Scale

  Rahman M; Saei AA; Amiri H; Mahmoudi M
• Review: NANOMEDICINE. 2015;10(18):2931-2952

  Nanotoxicology: advances and pitfalls in research methodology

  Azhdarzadeh M; Saei AA; Sharifi S; Hajipour MJ; Alkilany AM; Sharifzadeh M; Ramazani F; Laurent S; Mashaghi A; Mahmoudi M
• Article: APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY. 2014;174(2):667-681

  Inhibition of Survivin Restores the Sensitivity of Breast Cancer Cells to Docetaxel and Vinblastine

  Ghanbari P; Mohseni M; Tabasinezhad M; Yousefi B; Saei AA; Sharifi S; Rashidi MR; Samadi N
• Review: EXPERT OPINION ON DRUG DELIVERY. 2014;11(9):1449-1470

  Superparamagnetic iron oxide nanoparticles for delivery of therapeutic agents: opportunities and challenges

  Laurent S; Saei AA; Behzadi S; Panahifar A; Mahmoudi M
• Article: JOURNAL OF NANOPARTICLE RESEARCH. 2014;16(8):2521

  Fe₃O₄ nanoparticles engineered for plasmid DNA delivery to Escherichia coli

  Saei AA; Barzegari A; Majd MH; Asgari D; Omidi Y
• Review: FUTURE MICROBIOLOGY. 2014;9(5):639-656

  Shrinkage of the human core microbiome and a proposal for launching microbiome biobanks

  Barzegari A; Saeedi N; Saei AA
• Article: FEMS MICROBIOLOGY LETTERS. 2013;348(1):74-78

  Vibration and glycerol-mediated plasmid DNA transformation for Escherichia coli

  Shanehbandi D; Saei AA; Zarredar H; Barzegari A
• Review: JOURNAL OF CANCER RESEARCH AND THERAPEUTICS. 2013;9(4):556-563

  Sphingosin 1-phosphate contributes in tumor progression

  Tabasinezhad M; Samadi N; Ghanbari P; Mohseni M; Saei AA; Sharifi S; Saeedi N; Pourhassan A
• Article: JOURNAL OF MEDICINAL FOOD. 2013;16(2):147-154

  Soy Protein, Genistein, and Daidzein Improve Serum Paraoxonase Activity and Lipid Profiles in Rheumatoid Arthritis in Rats

  Mohammadshahi M; Haidari F; Saei AA; Rashidi B; Mahboob S; Rashidi M-R
• Article: TRAC-TRENDS IN ANALYTICAL CHEMISTRY. 2013;42:216-227

  Electrochemical biosensors for glucose based on metal nanoparticles

  Saei AA; Najafi-Marandi P; Abhari A; de la Guardia M; Dolatabadi JEN
• Article: MOLECULAR BIOLOGY REPORTS. 2012;39(11):9931-9939

  Haematococcus as a promising cell factory to produce recombinant pharmaceutical proteins

  Saei AA; Ghanbari P; Barzegari A
• Article: FUTURE MICROBIOLOGY. 2012;7(9):1037-1046

  The microbiome: the forgotten organ of the astronaut's body - probiotics beyond terrestrial limits

  Saei AA; Barzegari A
• Article: BIOLOGICAL TRACE ELEMENT RESEARCH. 2012;147(1-3):217-225

  Aldehyde and Xanthine Oxidase Activities in Tissues of Streptozotocin-Induced Diabetic Rats: Effects of Vitamin E and Selenium Supplementation

  Ghaffari T; Nouri M; Saei AA; Rashidi M-R
• Article: FUTURE MICROBIOLOGY. 2012;7(5):571-575

  Designing probiotics with respect to the native microbiome

  Barzegari A; Saei AA
• Article: BIOIMPACTS. 2011;1(3):161-170

  Comparison of the Effects of Genistein and Daidzein with Dexamethasone and Soy Protein on Rheumatoid Arthritis in Rats

  Mohammad-Shahi M; Haidari F; Rashidi B; Saei AA; Mahboob S; Rashidi M-R
• Article: JOVE-JOURNAL OF VISUALIZED EXPERIMENTS. 2009;(26):1191

  Cellular toxicity of nanogenomedicine in MCF-7 cell line: MTT assay.

  Ahmadian S; Barar J; Saei AA; Fakhree MAA; Omidi Y
• Article: PHARMAZIE. 2008;63(2):113-121

  Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model - effect of solute structure

  Jouyban A; Fakhree MAA; Ghafourian T; Saei AA; Acree WEJ
• Article: JOURNAL OF DRUG DELIVERY SCIENCE AND TECHNOLOGY. 2008;18(2):149-151

  Solubility of sodium diclofenac in binary water plus alcohol solvent mixtures at 25°C

  Saei AA; Jabbaribar F; Fakhree MAA; Acree WEJ; Jouyban A
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Staff and contact

Group leader

• 

  Amir Ata Saei

  Assistant Professor

  E-mail amir.saei@ki.se

All members of the group

• Arthur Champain

  Research Assistant

  E-mail arthur.champain@ki.se
• Luan Gardenalli

  Other

  E-mail luan.gardenalli@ki.se
• 

  Liuchenxin Han

  Research Assistant

  E-mail liuchenxin.han@ki.se
• 

  Hanna Hjärpsgård

  Phd Student

  E-mail hanna.hjarpsgard@ki.se
• Lorenzo Mancuso

  Other

  E-mail lorenzo.mancuso@ki.se
• Anirudh Nair

  Other

  E-mail anirudh.nair@ki.se
• 

  Mücahit Varlı

  Postdoctoral Studies

  E-mail mucahit.varli@ki.se
• 

  Xueyao Wang

  Phd Student

  E-mail xueyao.wang@ki.se
• 

  Aleksandra Wielento

  Postdoctoral Studies

  E-mail aleksandra.wielento@ki.se