BSRC "Alexander Fleming" Publications

2023 - (45)

Katerina Karkali, Samuel W Vernon, Richard A Baines, George Panayotou, Enrique Martín-Blanco. 2023, "Puckered and JNK signaling in pioneer neurons coordinates the motor activity of the Drosophila embryo", Nat Commun. , 2023 Dec 11; 14(1):8186. doi: 10.1038/s41467-023-43783-1. [PubMed].

Lefa P, Samiotaki M, Farmaki T. 2023, "Proteome Analysis of the ROF-FKBP Mutants Reveals Functional Relations among Heat Stress Responses, Plant Development, and Protein Quality Control during Heat Acclimation in Arabidopsis thaliana. ", ACS Omega., 2023 Dec 26; 9(2):2391-2408. doi: 10.1021/acsomega.3c06773 [PubMed].

Megarioti AH, Esch BM, Athanasopoulos A, Koulouris D, Makridakis M, Lygirou V, Samiotaki M, Zoidakis J, Sophianopoulou V, André B, Fröhlich F, Gournas C. 2023, "Ferroptosis-protective membrane domains in quiescence.", Cell Rep., 2023 Dec 26; 42(12):113561. doi: 10.1016/j.celrep.2023.113561. Epub 2023 Dec 12. [PubMed].

Goutakoli P, Papadaki G, Repa A, Avgoustidis N, Kalogiannaki E, Flouri I, Bertsias A, Zoidakis J, Samiotaki M, Bertsias G, Semitekolou M, Verginis P, Sidiropoulos P. 2023, "A Peripheral Blood Signature of Increased Th1 and Myeloid Cells Combined with Serum Inflammatory Mediators Is Associated with Response to Abatacept in Rheumatoid Arthritis Patients.", Cells., 2023 Dec 9; 12(24):2808. doi: 10.3390/cells12242808. [PubMed].

Karampitsakos T, Galaris A, Chrysikos S, Papaioannou O, Vamvakaris I, Barbayianni I, Kanellopoulou P, Grammenoudi S, Anagnostopoulos N, Stratakos G, Katsaras M, Sampsonas F, Dimakou K, Manali ED, Papiris S, Tourki B, Juan-Guardela BM, Bakakos P, Bouros D, Herazo-Maya JD, Aidinis V, Tzouvelekis A. 2023, "Expression of PD-1/PD-L1 axis in mediastinal lymph nodes and lung tissue of human and experimental lung fibrosis indicates a potential therapeutic target for idiopathic pulmonary fibrosis.", Respir Res., 24(1):279. [PubMed].

Karousi P, Samiotaki M, Makridakis M, Zoidakis J, Sideris DC, Scorilas A, Carell T, Kontos CK. 2023, "3'-tRF-Cys^GCA overexpression in HEK-293 cells alters the global expression profile and modulates cellular processes and pathways.", Funct Integr Genomics., 2023 Nov 21; 23(4):341. doi: 10.1007/s10142-023-01272-0. [PubMed].

Aleksandra Stanojevic, Martina Samiotaki, Vasiliki Lygirou, Mladen Marinkovic, Vladimir Nikolic, Suzana Stojanovic-Rundic, Radmila Jankovic, Antonia Vlahou, George Panayotou, Remond J A Fijneman, Sergi Castellví-Bel, Jerome Zoidakis, Milena Cavic. 2024, "Data-Independent Acquisition Mass Spectrometry Analysis of FFPE Rectal Cancer Samples Offers In-Depth Proteomics Characterization of the Response to Neoadjuvant Chemoradiotherapy", Int J Mol Sci., 2023 Oct 21;24(20) :15412. doi: 10.3390/ijms242015412. [PubMed].

Nikitopoulou I, Vassiliou AG, Athanasiou N, Jahaj E, Akinosoglou K, Dimopoulou I, Orfanos SE, Dimakopoulou V, Schinas G, Tzouvelekis A, Aidinis V, Kotanidou A. 2023, "Increased Levels of Galectin-3 in Critical COVID-19", Int J Mol Sci., 2023 Oct 31; 24(21):15833. [PubMed].

Bekas N, Samiotaki M, Papathanasiou M, Mokos P, Pseftogas A, Xanthopoulos K, Thanos D, Mosialos G, Dafou D. 2023, "Inactivation of Tumor Suppressor CYLD Inhibits Fibroblast Reprogramming to Pluripotency.", Cancers (Basel)., 2023 Oct 15; 15(20):4997. doi: 10.3390/cancers15204997. [PubMed].

Gerokonstantis DT, Mantzourani C, Gkikas D, Wu KC, Hoang HN, Triandafillidi I, Barbayianni I, Kanellopoulou P, Kokotos AC, Moutevelis-Minakakis P, Aidinis V, Politis PK, Fairlie DP, Kokotos G. 2023, "N-(2-Aminophenyl)-benzamide Inhibitors of Class I HDAC Enzymes with Antiproliferative and Antifibrotic Activity.", J Med Chem., 2023 Oct 26; 66(20):14357-14376. [PubMed].

Christos Tzaferis, Evangelos Karatzas, Fotis A Baltoumas, Georgios A Pavlopoulos, George Kollias, Dimitris Konstantopoulos. 2023, "SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data", Comput Struct Biotechnol J., 2023 Oct 20 :21:5382-5393. doi: 10.1016/j.csbj.2023.10.032. eCollection 2023. [PubMed].

Marianthi Kiparaki, Nicholas E Baker. 2023, "Protocol for assessing translation in living Drosophila imaginal discs by O-propargyl-puromycin incorporation", STAR Protoc., 2023 Oct 19; 4(4):102653. doi: 10.1016/j.xpro.2023.102653. Online ahead of print. [PubMed].

Christos Tzaferis, Evangelos Karatzas, Fotis A. Baltoumas, Georgios A. Pavlopoulos, George Kollias, Dimitris Konstantopoulos. 2023, "SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data", Computational and Structural Biotechnology Journal, October 20. ISSN 2001-0370, [doi], [ARTICLE].

Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N. Ivanova, I. Min Chen, David Paez-Espino, Evangelos Karatzas, Novel Metagenome Protein Families Consortium, Ioannis Iliopoulos, Konstantinos Konstantinidis, James M. Tiedje, Jennifer Pett-Ridge, David Baker, Axel Visel, Christos A. Ouzounis, Sergey Ovchinnikov, Aydin Buluç & Nikos C. Kyrpides. 2023, "Unraveling the functional dark matter through global metagenomics", Nature, October 11. doi: 10.1038/s41586-023-06583-7 [Nature], [PubMed].

Fotis A Baltoumas, Evangelos Karatzas, Sirui Liu, Sergey Ovchinnikov, Yorgos Sofianatos, I-Min Chen, Nikos C Kyrpides, Georgios A Pavlopoulos. 2023, "NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes", Nucleic Acids Res., 2023 Oct 9: gkad800. doi: 10.1093/nar/gkad800. Online ahead of print. [PubMed].

Tsopela V, Korakidis E, Lagou D, Kalliampakou KI, Milona RS, Kyriakopoulou E, Mpekoulis G, Gemenetzi I, Stylianaki EA, Sideris CD, Sioli A, Kefallinos D, Sideris DC, Aidinis V, Eliopoulos AG, Kambas K, Vassilacopoulou D, Vassilaki N. 2023, "L-Dopa decarboxylase modulates autophagy in hepatocytes and is implicated in dengue virus-caused inhibition of autophagy completion. ", Biochim Biophys Acta Mol Cell Res., 2024 Jan; 1871(1):119602. [PubMed].

Barbayianni I, Kanellopoulou P, Fanidis D, Nastos D, Ntouskou ED, Galaris A, Harokopos V, Hatzis P, Tsitoura E, Homer R, Kaminski N, Antoniou KM, Crestani B, Tzouvelekis A, Aidinis V, . 2023, "SRC and TKS5 mediated podosome formation in fibroblasts promotes extracellular matrix invasion and pulmonary fibrosis", Nat Commun., 2023 Sep 21; 14(1):5882. [PubMed].

Kaffe E, Tisi A, Magkrioti C, Aidinis V, Mehal WZ, Flavell RA, Maccarrone M. 2023, "Bioactive signaling lipids as drivers of chronic liver diseases. Bioactive signaling lipids as drivers of chronic liver diseases.", J Hepatol., 2023 Sep 21: S0168-8278(23)05099-7. [PubMed].

Galaris A, Fanidis D, Tsitoura E, Kanellopoulou P, Barbayianni I, Ntatsoulis K, Touloumi K, Gramenoudi S, Karampitsakos T, Tzouvelekis A, Antoniou K, Aidinis V. 2023, "Increased lipocalin-2 expression in pulmonary inflammation and fibrosis.", Front Med., 2023 Sep 7; 10:1195501. [PubMed].

Papadaki V, Erpapazoglou Z, Kokkori M, Rogalska ME, Potiri M, Birladeanu A, Tsakiri EN, Ashktorab H, Smoot DT, Papanikolopoulou K, Samiotaki M, Kafasla P. 2023, "IQGAP1 mediates the communication between the nucleus and the mitochondria via NDUFS4 alternative splicing", NAR Cancer., 2023 Aug 24; 5(3):zcad046. [PubMed], [DOI].

Voutyraki C, Choromidis A, Meligkounaki A, Vlachopoulos NA, Theodorou V, Grammenoudi S, Athanasiadis E, Monticelli S, Giangrande A, Delidakis C, Zacharioudaki E. 2023, "Growth deregulation and interaction with host hemocytes contribute to tumor progression in a Drosophila brain tumor model.", Proc Natl Acad Sci U S A., 2023 Aug 15; 120(33). [PubMed].

Karatzas E, Baltoumas FA, Aplakidou E, Kontou PI, Stathopoulos P, Stefanis L, Bagos PG, Pavlopoulos GA. 2023, "Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources.", Bioinformatics., 2023 Aug 4 :btad490. doi: 10.1093/bioinformatics/btad490 [PubMed].

Anastasios Liakos, Anna-Chloe Synacheri, Dimitris Konstantopoulos, Georgios C Stefos, Matthieu D Lavigne, Maria Fousteri. 2023, "Enhanced frequency of transcription pre-initiation complexes assembly after exposure to UV irradiation results in increased repair activity and reduced probabilities for mutagenesis", Nucleic Acids Research, gkad593 [doi].

Marianthi Kiparaki, Nicholas E Baker. 2023, "Ribosomal protein mutations and cell competition: autonomous and nonautonomous effects on a stress response", Genetics., 2023 Jul 6; 224(3):iyad080. doi: 10.1093/genetics/iyad080. [PubMed].

Pantazopoulou M, Lamprokostopoulou A, Karampela DS, Alexaki A, Delis A, Coens A, Samiotaki M, Kriebardis AG, Melki R, Pagakis SN, Stefanis L, Vekrellis K. 2023, "Differential intracellular trafficking of extracellular vesicles in microglia and astrocytes. ", Cell Mol Life Sci., 2023 Jun 30; 80(7):193. doi: 10.1007/s00018-023-04841-5. [PubMed].

Kokoli M., Karatzas E., Baltoumas FA., Schneider R., Pafilis E., Paragkamian S., Doncheva TN., Jensen LJ., Pavlopoulos GA. 2023, "Arena3D^web: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration", NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad053 [doi], [PubMed].

Ioannis Temponeras, Martina Samiotaki, Despoina Koumantou, Martha Nikopaschou, Jonas J W Kuiper, George Panayotou, Efstratios Stratikos. 2024, "Distinct modulation of cellular immunopeptidome by the allosteric regulatory site of ER aminopeptidase 1", Eur J Immunol. , 2023 Aug; 53(8):e2350449. doi: 10.1002/eji.202350449. Epub 2023 May 15. [PubMed].

Magkrioti C, Kaffe E, Aidinis V. 2023, "The Role of Autotaxin and LPA Signaling in Embryonic Development, Pathophysiology and Cancer.", Int J Mol Sci., May 5; 24(9):8325. [PubMed].

Temponeras I, Samiotaki M, Koumantou D, Nikopaschou M, Kuiper JJW, Panayotou G, Stratikos E. 2023, "Distinct modulation of cellular immunopeptidome by the allosteric regulatory site of ER aminopeptidase 1.", Eur J Immunol., 2023 May 3: e2350449. doi: 10.1002/eji.202350449. Online ahead of print. [PubMed].

Ergina Vourkou, Eva D Rouiz Ortega, Sumeet Mahajan, Amrit Mudher, Efthimios M C Skoulakis. 2023, "Human Tau Aggregates Are Permissive to Protein Synthesis-Dependent Memory in Drosophila Tauopathy Models", J Neurosci., 2023 Apr 19; 43(16):2988-3006. doi: 10.1523/JNEUROSCI.1374-22.2023. Epub 2023 Mar 3. [PubMed].

Papadopoulou D, Roumelioti F, Tzaferis C, Chouvardas P, Pedersen AK, Charalampous F, Christodoulou-Vafeiadou E, Ntari L, Karagianni N, Denis MC, Olsen JV, Matralis AN, Kollias G. 2023, "Repurposing antipsychotic drug Amisulpride for targeting synovial fibroblast activation in arthritis", JCI insight, 2023 Apr 4; e165024 [PubMed].

Katsiougiannis S, Stergiopoulos A, Moustaka K, Havaki S, Samiotaki M, Stamatakis G, Tenta R, Skopouli FN. 2023, "Salivary gland epithelial cell in Sjögren's syndrome: Metabolic shift and altered mitochondrial morphology toward an innate immune cell function. ", J Autoimmun. , 2023 Apr ;136:103014. doi: 10.1016/j.jaut.2023.103014. Epub 2023 Mar 8. [PubMed].

Skodra C, Michailidis M, Moysiadis T, Stamatakis G, Ganopoulou M, Adamakis IS, Angelis L, Ganopoulos I, Tanou G, Samiotaki M, Bazakos C, Molassiotis A. 2023, "Disclosing the molecular basis of salinity priming in olive trees using proteogenomic model discovery.", Plant Physiol., 2023 Mar 17; 191(3):1913-1933. doi: 10.1093/plphys/kiac572. [PubMed].

Papadopoulos G, Legaki AI, Georgila K, Vorkas P, Giannousi E, Stamatakis G, Moustakas II, Petrocheilou M, Pyrina I, Gercken B, Kassi E, Chavakis T, Pateras IS, Panayotou G, Gika H, Samiotaki M, Eliopoulos AG, Chatzigeorgiou A. 2023, "Integrated omics analysis for characterization of the contribution of high fructose corn syrup to non-alcoholic fatty liver disease in obesity.", Metabolism., 2023 Mar 28: 155552. doi: 10.1016/j.metabol.2023.155552. Online ahead of print. [PubMed].

Fanidis D, Pezoulas VC, Fotiadis DΙ, Aidinis V. 2023, "n explainable machine learning-driven proposal of pulmonary fibrosis biomarkers.", Comput Struct Biotechnol J., 2023; 21:2305-2315 [PubMed].

T Karampitsakos, A Galaris, I Barbayianni, G DeIuliis, F Ahangari, F Sampsonas, V Sotiropoulou, Aidinis V, AM Bennett, JD Herazo Maya, N Xylourgidis, P Bakakos, D Bouros, N Kaminski, A Tzouvelekis. 2023, "SH2 Domain-Containing Phosphatase-SHP2 Attenuates Fibrotic Responses through Negative Regulation of Mitochondrial Metabolism in Lung Fibroblasts.", Diagnostics 2023, 13 (6), 1166. [PubMed].

Stylianaki EA, Magkrioti C, Ladopoulou EM, Papavasileiou KD, Lagarias P, Melagraki G, Samiotaki M, Panayotou G, Dedos SG, Afantitis A, Aidinis V, Matralis AN. 2023, ""Hit" to lead optimization and chemoinformatic studies for a new series of Autotaxin inhibitors.", Eur J Med Chem., 2023 Mar 5; 249:115130. [PubMed].

Kolokotroni A, Gkikopoulou E, Rinotas V, Douni E. 2023, "Phosphotungstic acid-enhanced microcomputed tomography for quantitative visualization of mouse mammary gland morphology.", Journal of Medical Imaging, 10 (Suppl 2): S22402. doi: 10.1117/1.JMI.10.S2.S22402 [PubMed].

Baltoumas FA., Karatzas E., Paez-Espino D., Venetsianou N., Aplakidou E., Oulas A., Finn RD., Ovchinnikov S., Pafilis E., Kyrpides NC., Pavlopoulos GA. 2023, "Exploring microbial functional biodiversity at the protein family level - from metagenomic sequence reads to annotated protein clusters", Frontiers in Bioinformatics, 03 March 2023, Volume 3 -2023, [doi], [LINK], [PubMed].

Gomes PA, Bodo C, Nogueras-Ortiz C, Samiotaki M, Chen M, Soares-Cunha C, Silva JM, Coimbra B, Stamatakis G, Santos L, Panayotou G, Tzouanou F, Waites CL, Gatsogiannis C, Sousa N, Kapogiannis D, Costa-Silva B, Sotiropoulos I. 2023, "A novel isolation method for spontaneously released extracellular vesicles from brain tissue and its implications for stress-driven brain pathology.", Cell Commun Signal., 2023 Feb 13; 21(1):35. doi: 10.1186/s12964-023-01045-z. [PubMed].

Katerina Karkali, Timothy E Saunders, George Panayotou, Enrique Martín-Blanco. 2023, "JNK signaling in pioneer neurons organizes ventral nerve cord architecture in Drosophila embryos", Nat Commun., 2023 Feb 7; 14(1):675. doi: 10.1038/s41467-023-36388-1. [PubMed].

Grammatikopoulou MG, Skoufas E, Kanellakis S, Sanoudou D, Pavlopoulos GA, Eliopoulos AG, Gkouskou KK. 2023, "Ageotypes revisited: The brain and central nervous system dysfunction as a major nutritional and lifestyle target for healthy aging.", Maturitas., 2023 Feb 6; 170:51-57. doi: 10.1016/j.maturitas.2023.01.013. [PubMed].

Bhattarai S, Subedi U, Manikandan S, Sharma S, Sharma P, Miller C, Bhuiyan MS, Kidambi S, Aidinis V, Sun H, Miriyala S, Panchatcharam M. 2023, "Endothelial Specific Deletion of Autotaxin Improves Stroke Outcomes.", Cells., 2023 Feb 3; 12(3):511. [PubMed].

Boutsika A, Michailidis M, Ganopoulou M, Dalakouras A, Skodra C, Xanthopoulou A, Stamatakis G, Samiotaki M, Tanou G, Moysiadis T, Angelis L, Bazakos C, Molassiotis A, Nianiou-Obeidat I, Mellidou I, Ganopoulos I. 2023, "A wide foodomics approach coupled with metagenomics elucidates the environmental signature of potatoes.", iScience., 2023 Jan 5; 26(1):105917. doi: 10.1016/j.isci.2022.105917. eCollection 2023 Jan 20. [PubMed].

Smaragda Fanourgakis, Anna-Chloe Synacheri, Matthieu D. Lavigne, Dimitris Konstantopoulos, Maria Fousteri. 2023, "Histone H2Bub dynamics in the 5' region of active genes are tightly linked to the UV-induced transcriptional response.", Computational and Structural Biotechnology Journal, 21: 614-629. doi.org/10.1016/j.csbj.2022.12.013 [Link].