BSRC "Alexander Fleming" Publications

2025 - (36)

Iliopoulou L, Tzaferis C, Prados A, Roumelioti F, Koliaraki V, Kollias G. 2025, "Different fibroblast subtypes propel spatially defined ileal inflammation through TNFR1 signalling in murine ileitis.", Nat Commun., 28; 16(1):3023 [PubMed].

Detsika MG, Sakkou M, Triantafyllidou V, Konstantopoulos D, Grigoriou E, Psarra K, Jahaj E, Dimopoulou I, Orfanos SE, Tsirogianni A, Kollias G, Kotanidou A. 2025, "CD55 upregulation in T cells of COVID-19 patients suppresses type-I interferon responses.", Commun Biol., 8(1) :690. [PubMed].

Xu W, Golovchenko NB, Martínez-Vargas IU, Fong A, Rout P, Achi S, Bucar EB, Hsieh JJ, Vidmar KJ, Zhang L, Polydorides AD, Prinz I, Kollias G, Frey MR, Pizarro TT, Verzi MP, Edelblum KL. 2025, "Dysregulation of γδ intraepithelial lymphocytes precedes Crohn's disease-like ileitis.", Sci Immunol., 10(105) :eadk7429. [PubMed].

Roa-Varón, A., Moulos P., Harter, S., David, A., Quattrini, A., Herrera, S. 2025, "Chromosome-level genome assembly of the Vermillion Snapper (Rhomboplites aurorubens)", Scientific Data,

Kalafati, I.P., Tsifintaris, M., Dimitriou, M., Grigoriou, E., Moulos P., Dedoussis, G.V. 2025, "Development and validation of a polygenic risk score for height in a Greek cohort: Association with blood pressure measurements.", Frontiers in Genetics, , 2025, 16:1538975 [PubMed].

Kafyra, M., Kalafati, I.P., Varlamis, I., Kaliora, A.C., Moulos P., Dedoussis, G.V. 2025, "A randomized clinical trial of a dietary intervention and mental health associations in adults with increased genetic risk for obesity", Scientific Reports, 2025, 15(1):14188 [PubMed].

Chalkidi N, Stavropoulou C, Arvaniti VZ, Paraskeva C, Sakkou M, Nikolaou C, Koliaraki V. 2025, "Notch3 regulates pericyte phenotypic plasticity in colorectal cancer.", bioRxiv, PPR1032195, DOI: 10.1101/2025.06.04.657823. [doi].

Iliopoulou L, Tzaferis C, Prados A, Roumelioti F, Koliaraki V, Kollias G. 2025, "Cellular complexity in murine ileitis: Different fibroblasts propel spatially defined ileal inflammation through TNFR1 signalling.", Nat Commun, 16(1): 3023. doi:10.1038/s41467-025-57570-7. [PubMed].

Ntafis V. 2025, "A communication pipeline for in vivo imaging core facilities.", Laboratory Animals Ltd, [doi].

Gkikopoulou E, Syrigos C-C, Mantogiannakou I, Petraki C-E, Stathopoulou M, Dragolia M, Rinotas V, Ntafis V, Rauner M, Douni E. 2025, "RANKL Drives Bone Metastasis in Mammary Cancer: Protective Effects of Anti-Resorptive Treatments.", International Journal of Molecular Sciences, 26(11), 4990; doi.org/10.3390/ijms26114990. [Link].

Ioannou P, Odiatis C, Hadjisavva R, Antoniadou K, Pieri M, Malatras A, Papagregoriou G, Aristotelous A, Skourides P, Samiotaki M, Horaček M, Ljubanović DG, Stylianou K, Deltas C. 2025, "Chemical chaperone 4-phenylbutyrate treatment alleviates the kidney phenotype in a mouse model of Alport syndrome with a pathogenic variant in Col4a3.", Kidney Int., 2025 Jun 6: S0085-2538(25)00426-0. doi: 10.1016/j.kint.2025.05.016. Epub ahead of print. [PubMed].

Charlotte Guffick, Argyris Politis. 2025, "HDX-MS in micelles and membranes for small molecule and biopharmaceutical development", Current Opinion in Structural Biology, Volume 94, October 2025, 103077 [doi].

Vanessa Duerr, Damon Griffiths, Argyris Politis. 2025, "MultiPassMerger: Automated data processing for multipass cyclic ion mobility HDX-MS", Protein Science, 24 May 2025 [doi].

Karatzas P, Brotzakis ZF, Sarimveis H. 2025, "Small Molecules Targeting the Structural Dynamics of AR-V7 Partially Disordered Proteins Using Deep Ensemble Docking.", Journal of Chemical Theory and Computation., 2025 May 13; 21(9):4898-4909. doi: 10.1021/acs.jctc.5c00171 [Link].

Filis G, Bezantakou D, Rigkos K, Noti D, Saridis P, Zarafeta D, Skretas G. 2025, "ProteoSeeker: A Feature-Rich Metagenomic Analysis Tool for Accessible and Comprehensive Metagenomic Exploration. ", Advanced Science., 2025 May; 12(19):e2414877. doi: 10.1002/advs.202414877. [PubMed].

Delivoria DC, Konia E, Matis I, Skretas G. 2025, "Optimization of a High-Throughput Screen for Monitoring Disease-Associated Protein Misfolding and Aggregation in Bacteria.", ACS Synthetic Biology., 2025 May 12. doi: 10.1021/acssynbio.5c00166. [PubMed].

Klonizakis A, Alcoverro-Bertran M, Massó P, Thomas J, de Andrés-Aguayo L, Wei X, Varamogianni-Mamatsi V, Nikolaou C, Graf T. 2025, "Synergistic and antagonistic activities of IRF8 and FOS enhancer pairs during an immune-cell fate switch.", EMBO J., 2025 Apr; 44(7):2025-2055. [doi].

Kimonas Provatas, Nikol Chantzi, Nafsika Amptazi, Michail Patsakis, Akshatha Nayak, Ioannis Mouratidis, Apostolos Zaravinos, Georgios A Pavlopoulos, Ilias Georgakopoulos-Soares. 2025, "invertiaDB: a database of inverted repeats across organismal genomes.", Nucleic Acids Res., 2025 Apr 22; 53(8):gkaf329. doi: 10.1093/nar/gkaf329. [PubMed].

Jingjing Zhao, Fotis A Baltoumas, Maxwell A Konnaris, Ioannis Mouratidis, Zhe Liu, Jasmine Sims, Vikram Agarwal, Georgios A Pavlopoulos, Ilias Georgakopoulos-Soares, Nadav Ahituv. 2025, "MPRAbase a Massively Parallel Reporter Assay database", Genome Res., 2025 Apr 22: gr.280387.124. doi: 10.1101/gr.280387.124. [PubMed].

Nikopaschou M, Samiotaki M, Stylianaki EA, Król K, Gragera P, Raja A, Aidinis V, Chroni A, Fruci D, Panayotou G, Stratikos E. 2025, "ERAP1 activity modulates the immunopeptidome but also affects the proteome, metabolism and stress responses in cancer cells.", Mol Cell Proteomics. , 2025 Apr 4 :100964. [PubMed].

Stylianaki EA, Magkrioti C, Kaffe E, Matralis AN, Aidinis V. 2025, "Amplex red assay, a standardized in vitro protocol to quantify the efficacy of autotaxin inhibitors.", STAR Protoc. , 2025 Apr 1; 6(2):103721. [PubMed].

Chatzidaki MD, Mitsou E. 2025, "Advancements in Nanoemulsion-Based Drug Delivery Across Different Administration Routes.", Pharmaceutics., 2025 Mar 5; 17(3):337. doi: 10.3390/pharmaceutics17030337. [PubMed].

Guillaume Dugied, Estelle Mn Laurent, Mikaël Attia, Jean-Pascal Gimeno, Kamel Bachiri, Payman Samavarchi-Tehrani, Flora Donati, Yannis Rahou, Sandie Munier, Faustine Amara, Mélanie Dos Santos, Nicolas Soler, Stevenn Volant, Natalia Pietrosemoli, Anne-Claude Gingras, Georgios A Pavlopoulos, Sylvie van der Werf, Pascal Falter-Braun, Patrick Aloy, Yves Jacob, Anastassia Komarova, Yorgos Sofianatos, Etienne Coyaud, Caroline Demeret. 2025, "Multimodal SARS-CoV-2 interactome sketches the virus-host spatial organization.", Commun Biol., 2025 Mar 26; 8(1):501. doi: 10.1038/s42003-025-07933-z. [PubMed].

Smyrniotis S, Kanellopoulou P, Magkrioti C, Aidinis V. 2025, "An optimized protocol for generating fibrotic murine precision-cut lung slices.", STAR Protoc., 2025 Mar 24; 6(2):103711. [PubMed].

Antonopoulou G, Magkrioti C, Chatzidaki I, Nastos D, Grammenoudi S, Bozonelos K, Aidinis V. 2025, "Generation of New Knock-Out Mouse Strains of Lysophosphatidic Acid Receptor 1.", Int J Mol Sci., 2025 Mar 20; 26(6):2811. [PubMed].

Michail Patsakis, Kimonas Provatas, Fotis A Baltoumas, Nikol Chantzi, Ioannis Mouratidis, Georgios A Pavlopoulos, Ilias Georgakopoulos-Soares. 2025, "MAFin: Motif Detection in Multiple Alignment Files", Bioinformatics., 2025 Mar 19: btaf125. doi: 10.1093/bioinformatics/btaf125. [PubMed].

Brotzakis ZF, Zhang S, Murtada MH, Vendruscolo M. 2025, "AlphaFold prediction of structural ensembles of disordered proteins.", Nature Communications., 2025 Feb 14; 16(1):1632. doi: 10.1038/s41467-025-56572-9. [PubMed].

Kanoura A, Giakountis A, Filippopoulou C, Karagiota A, Stamatakis G, Samiotaki M, Panayotou G, Simos G, Chachami G. 2025, "Interaction of TFAP2A with the Ku70/80 complex is crucial for HIF-dependent activation of hypoxia-inducible genes.", FEBS J. , 2025 Feb 24. doi: 10.1111/febs.70025. Online ahead of print. [PubMed].

Tomos I, Kanellopoulou P, Nastos D, Aidinis V. 2025, "Pharmacological targeting of ECM homeostasis, fibroblast activation, and invasion for the treatment of pulmonary fibrosis.", Expert Opin Ther Targets., 2025 Feb 22. [PubMed].

George I Gavriilidis, Vasileios Vasileiou, Stella Dimitsaki, Georgios Karakatsoulis, Antonis Giannakakis, Georgios A Pavlopoulos, Fotis Psomopoulos. 2025, "APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19", Bioinformatics. , 2025 Feb 8:btaf063. doi: 10.1093/bioinformatics/btaf063. Online ahead of print. [PubMed].

Karakosta C, Samiotaki M, Bisoukis A, Bougioukas KI, Panayotou G, Papaconstantinou D, Moschos MM. 2025, "Differential Signaling Pathways Identified in Aqueous Humor, Anterior Capsule, and Crystalline Lens of Age-Related, Diabetic, and Post-Vitrectomy Cataract.", Proteomes. , 2025 Feb 3; 13(1):7. doi: 10.3390/proteomes13010007. [PubMed].

Milanesi M, Brotzakis ZF, Vendruscolo M. 2025, "Transient interactions between the fuzzy coat and the cross-β core of brain-derived Aβ42 filaments.", Science Advances., 2025 Jan 17; 11(3):eadr7008. doi: 10.1126/sciadv.adr7008. [PubMed].

Spanou S, Makatounakis T, Filippopoulou C, Dougalis G, Stamatakis G, Nikolaou C, Samiotaki M, Chachami G, Papamatheakis J, Kretsovali A. 2025, "Promyelocytic Leukemia Protein (PML) Regulates Stem Cell Pluripotency Through Novel Sumoylation Targets.", Int J Mol Sci., 2025 Jan 28; 26(3):1145. doi: 10.3390/ijms26031145. [PubMed].

Ioannis Mouratidis, Maxwell A Konnaris, Nikol Chantzi, Candace S Y Chan, Michail Patsakis, Kimonas Provatas, Austin Montgomery, Fotis A Baltoumas, Congzhou M Sha, Manvita Mareboina, Georgios A Pavlopoulos, Dionysios V Chartoumpekis, Ilias Georgakopoulos-Soares. 2024, "Identification of the shortest species-specific oligonucleotide sequences", Genome Res., 2025 Jan 31. doi: 10.1101/gr.280070.124. Online ahead of print. [PubMed].

Mathijs P Scholtes, Maryam Akbarzadeh, Alexandros Galaras, J Alberto Nakauma-Gonzáles, Ameneh Bazrafshan, Vandana Solanki, Bram Torenvliet, Leila Beikmohammadi, Valeria Lozovanu, Shahla Romal, Panagiotis Moulos, Nikoleta Vavouraki, Tsung Wai Kan, Mahesh Algoe, Martin E van Royen, Andrea Sacchetti, Thierry P P van den Bosch, Bert Eussen, Annelies de Klein, Geert J L H van Leenders, Joost L Boormans, Pantelis Hatzis, Robert-Jan Palstra, Tahlita C M Zuiverloon, Tokameh Mahmoudi. 2025, "Integrative analysis of patient-derived tumoroids and ex vivo organoid modeling of ARID1A loss in bladder cancer reveals therapeutic molecular targets", Cancer Lett., 2025 Jan 29:217506. doi: 10.1016/j.canlet.2025.217506. Online ahead of print. [PubMed].

Mouratidis I, Konnaris M, Chantzi N, Chan CSY, Patsakis M, Provatas K, Montgomery A, Baltoumas FA, Sha CM, Mareboina M, Pavlopoulos GA, Chartoumpekis DV, Georgakopoulos-Soares I. 2025, "Identification of the shortest species-specific oligonucleotide sequences.", Genome Res., 2025 Jan 2: gr.280070.124. doi: 10.1101/gr.280070.124. Epub ahead of print. [PubMed].