BSRC "Alexander Fleming" Publications

2021 - (55)

Dimopoulos A, Koukoutegos K, Psomopoulos EF, Moulos P, . 2021, "Combining multiple RNA-Seq data analysis algorithms using Machine Learning improves differential isoform expression analysis", Methods Protoc, 2021, 4(4):68 [PubMed].

Bothos E, Ntoumou E, Kelaidoni K, Roukas D, Drakoulis N, Papasavva M, Karakostis FA, Moulos P, Karakostis K. 2021, "Clinical pharmacogenomics in action: design, assessment and implementation of a novel pharmacogenetic panel supporting drug selection for diseases of the central nervous system (CNS)", J Transl Med., 2021, 19(1):151 [PubMed].

Moulos P. 2021, "recoup: versatile signal visualization from genomic sequencing", BMC Bioinformatics , 2021, 22(1):2 [PubMed].

Fanidis D, Moulos P. 2021, "Integrative, normalization-insusceptible statistical analysis of RNA-Seq data, with improved differential expression and unbiased downstream functional analysis", Briefings in Bioinformatics, 2021 22(3):bbaa156. [PubMed].

Tsitoura E, Trachalaki A, Vasarmidi E, Mastrodemou S, Margaritopoulos GA, Kokosi M, Fanidis D, Galaris A, Aidinis V, Renzoni E, Tzanakis N, Wells AU, Antoniou KM. 2021, "Collagen 1a1 Expression by Airway Macrophages Increases In Fibrotic ILDs and Is Associated With FVC Decline and Increased Mortality", Front Immunol., 2021 Nov 17; 12:645548. [PubMed].

Panagopoulou M, Fanidis D, Aidinis V, Chatzaki E. 2021, "ENPP2 Methylation in Health and Cancer", Int J Mol Sci., 2021 Nov 4; 22(21):11958 [PubMed].

Fanidis D, Moulos P, Aidinis V. 2021, "Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis", Sci Rep., 2021 Nov 5; 11(1):21712 [PubMed].

Michael Röling, Mahsa Mollapour Sisakht, Enrico Ne, Panagiotis Moulos, Raquel Crespo, Mateusz Stoszko, Elisa De Crignis, Helen Bodmer, Tsung Wai Kan, Maryam Akbarzadeh, Vaggelis Harokopos, Pantelis Hatzis ,Robert-Jan Palstra, Tokameh Mahmoudi. 2021, "A Two-Color Haploid Genetic Screen Identifies Novel Host Factors Involved in HIV-1 Latency", mBio. , 2021 Dec 7; e0298021. doi: 10.1128/mBio.02980-21. Online ahead of print. [PubMed].

Voutyraki C, Choromidis A, Theodorou V, Efraimoglou C, Anagnostopoulos G, Magadi SS, Grammenoudi S, Zacharioudaki E, Delidakis C. 2021, "Repression of differentiation genes by Hes transcription factors fuels neural tumour growth in Drosophila", Int J Dev Biol., Nov 22. doi: 10.1387/ijdb.210187cd. Online ahead of print. [PubMed].

George Stamatakis, Martina Samiotaki, Ioannis Temponeras, George Panayotou, Efstratios Stratikos. 2021, "Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 Spike Glycoprotein", J Biol Chem., 2021 Oct 21; 297(5):101329. doi: 10.1016/j.jbc.2021.101329. Online ahead of print. [PubMed].

Vasiliki-Dimitra C Tsolaki, Sofia K Georgiou-Siafis, Athina I Tsamadou, Stefanos A Tsiftsoglou, Martina Samiotaki, George Panayotou, Asterios S Tsiftsoglou. 2021, "Hemin accumulation and identification of a heme-binding protein clan in K562 cells by proteomic and computational analysis", J Cell Physiol., 2021 Oct 7. doi: 10.1002/jcp.30595. Online ahead of print. [PubMed].

Kosmidis S, Denny CA, Dranovsky A, Skoulakis EMC. 2021, "Editorial: Molecular and Cellular Underpinnings of Age-Related Memory Loss.", Front Cell Dev Biol., 2021 Aug 20;, 9:743187. doi: 10.3389/fcell.2021.743187. eCollection 2021. [PubMed].

Kreon Koukoulas, Antonis Giakountis, Angeliki Karagiota, Martina Samiotaki, George Panayotou, George Simos, Ilias Mylonis. 2021, "ERK signaling controls productive HIF-1 binding to chromatin and cancer cell adaptation to hypoxia through HIF-1α interaction with NPM1", Mol Oncol., 2021 Aug 13. doi: 10.1002/1878-0261.13080. Online ahead of print. [PubMed].

Ioanna Maria Gkotinakou, Christina Befani, Martina Samiotaki, George Panayotou, Panagiotis Liakos. 2021, "Novel HIF-2α interaction with Reptin52 impairs HIF-2 transcriptional activity and EPO secretion", Biochem Biophys Res Commun., 2021 Jun 11; 557:143-150. doi: 10.1016/j.bbrc.2021.03.176. Epub 2021 Apr 14. [PubMed].

Ntatsoulis K, Karampitsakos T, Tsitoura E, Stylianaki EA, Matralis AN, Tzouvelekis A, Antoniou K, Aidinis V. 2021, "Commonalities Between ARDS, Pulmonary Fibrosis and COVID-19: The Potential of Autotaxin as a Therapeutic Target.", Front Immunol., 2021 Oct 4; 12:687397 [PubMed].

Nikitopoulou I, Fanidis D, Ntatsoulis K, Moulos P, Mpekoulis G, Evangelidou M, Vassiliou AG, Dimakopoulou V, Jahaj E, Tsipilis S, Orfanos SE, Dimopoulou I, Angelakis E, Akinosoglou K, Vassilaki N, Tzouvelekis A, Kotanidou A, Aidinis V. 2021, "Increased Autotaxin Levels in Severe COVID-19, Correlating with IL-6 Levels, Endothelial Dysfunction Biomarkers, and Impaired Functions of Dendritic Cells.", Int J Mol Sci., 2021 Sep 16; 22(18):10006. [PubMed].

Baltoumas FA., Zafeiropoulou S., Karatzas E., Paragkamian S., Thanati F., Iliopoulos I., Eliopoulos GA., Schneider R., Jensen LJ., Pafilis E., Pavlopoulos GA. 2021, "OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis", NAR Genomics and Bioinformatics, Volume 3 Issue 4, December 2021 [doi], [URL].

Sfikakis PP, Verrou KM, Ampatziadis-Michailidis G, Tsitsilonis O, Paraskevis D, Kastritis E, Lianidou E, Moutsatsou P, Terpos E, Trougakos I, Chini V, Manoloukos M, Moulos P, Pavlopoulos GA, Kollias G, Hatzis P, Dimopoulos MA. 2021, "Blood Transcriptomes of Anti-SARS-CoV-2 Antibody-Positive Healthy Individuals Who Experienced Asymptomatic Versus Clinical Infection", Front. Immunol., 05 October 2021, [doi], [URL].

Papadopoulou D, Drakopoulos A, Lagarias P, Melagraki G, Kollias G, Afantitis A. 2021, "In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes", Int. J. Mol. Sci., 22(19), 10220; [doi].

Papazian Ι, Tsoukala Ε, Boutou Α, Karamita Μ, Kambas Κ, Iliopoulou L, Fischer R, Kontermann RE, Denis MC, Kollias G, Lassmann H & Probert L. 2021, "Fundamentally different roles of neuronal TNF receptors in CNS pathology: TNFR1 and IKKβ promote microglial responses and tissue injury in demyelination while TNFR2 protects against excitotoxicity in mice", J Neuroinflammation, 18(1):222. doi: 10.1186/s12974-021-02200-4 [PubMed].

Pallavi Subramanian, Sofia Gargani, Alessandra Palladini, Margarita Chatzimike, Michal Grzybek, Mirko Peitzsch, Anastasios D Papanastasiou, Iryna Pyrina, Vasileios Ntafis, Bettina Gercken, Mathias Lesche, Andreas Petzold, Anupam Sinha, Marina Nati, Veera Raghavan Thangapandi, Ioannis Kourtzelis, Margarita Andreadou, Anke Witt, Andreas Dahl, Ralph Burkhardt, Robert Haase, António Miguel de Jesus Domingues, Ian Henry, Nicola Zamboni, Peter Mirtschink, Kyoung-Jin Chung, Jochen Hampe, Ünal Coskun, Dimitris L Kontoyiannis, Triantafyllos Chavakis. 2021, "The RNA binding protein HuR is a gatekeeper of liver homeostasis.", Hepatology., 2021 Sep 14. doi: 10.1002/hep.32153. Online ahead of print. [PubMed].

Oikonomou N, Schuijs MJ, Chatzigiagkos A, Androulidaki A, Aidinis V, Hammad H, Lambrecht BN, Pasparakis M. 2021, "Airway epithelial cell necroptosis contributes to asthma exacerbation in a mouse model of house dust mite-induced allergic inflammation.", Mucosal Immunol., 2021 Sep; 14(5):1160-1171 [PubMed].

Birladeanu A-M, Rogalska M, Potiri M, Papadaki V, Andreadou M, Kontoyiannis DL, Lewis JD, Erpapazoglou Z, Kafasla P. 2021, "The scaffold protein IQGAP1 links heat-induced stress signals to alternative splicing regulation in gastric cancer cells.", Oncogene, 1–15 [PubMed].

Baltoumas F.A., Zafeiropoulou S. Karatzas E., Koutrouli, M., Thanati F., Voutsadaki K., Gkonta M., Hotova J., Kasionis, I., Hatzis P., Pavlopoulos G.A. 2021, "Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review", Biomolecules, 2021, 11, 1245 [doi], [PubMed].

Iliopoulou L, Kollias G. 2021, "Harnessing murine models of Crohn's disease ileitis to advance concepts of pathophysiology and treatment", Mucosal Immunol., doi: 10.1038/s41385-021-00433-3 [PubMed].

Thanati F, Karatzas E, Baltoumas FA, Stravopodis DJ, Eliopoulos AG, Pavlopoulos GA. 2021, "FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists", Biology., 2021; 10(7):665 [PubMed].

Elisa De Crignis, Tanvir Hossain, Shahla Romal, Fabrizia Carofiglio, Panagiotis Moulos, Mir Mubashir Khalid, Shringar Rao, Ameneh Bazrafshan, Monique Ma Verstegen, Farzin Pourfarzad, Christina Koutsothanassis, Helmuth Gehart, Tsung Wai Kan, Robert-Jan Palstra, Charles Boucher, Jan Nm IJzermans, Meritxell Huch, Sylvia F Boj, Robert Vries, Hans Clevers, Luc Jw van der Laan, Pantelis Hatzis, Tokameh Mahmoudi. 2021, "Application of human liver organoids as a patient-derived primary model for HBV infection and related hepatocellular carcinoma.", Elife., 2021 Jul 30; 10:e60747. doi: 10.7554/eLife.60747. [PubMed].

Androulla N Miliotou, Dionysia Papagiannopoulou, Efthymia Vlachaki, Martina Samiotaki, Dimitra Laspa, Stamatia Theodoridou, Asterios S Tsiftsoglou, Lefkothea C Papadopoulou. 2021, "PTD-mediated delivery of α-globin chain into Κ-562 erythroleukemia cells and α-thalassemic (HBH) patients' RBCs ex vivo in the frame of Protein Replacement Therapy", J Biol Res (Thessalon), 2021 Jul 20; 28(1):16. doi: 10.1186/s40709-021-00148-3. [PubMed].

Kostaki EG, Pavlopoulos GA, Verrou KM, Ampatziadis-Michailidis G, Harokopos V, Hatzis P, Moulos P, Siafakas N, Pournaras S, Hadjichristodoulou C, Chatzopoulou F, Chatzidimitriou D, Panagopoulos P, Lourida P, Argyraki A, Lytras T, Sapounas S, Gerolymatos G, Panagiotakopoulos G, Prezerakos P, Tsiodras S, Sypsa V, Hatzakis A, Anastassopoulou C, Spanakis N, Tsakris A, Dimopoulos MA, Kotanidou A, Sfikakis P, Kollias G, Magiorkinis G, Paraskevis D. 2021, "Molecular Epidemiology of SARS-CoV-2 in Greece Reveals Low Rates of Onward Virus Transmission after Lifting of Travel Restrictions Based on Risk Assessment during Summer 2020.", mSphere., 2021 Jun 30: e0018021. doi: 10.1128/mSphere.00180-21 [PubMed].

Mpekoulis G, Frakolaki E, Taka S, Ioannidis A, Vassiliou AG, Kalliampakou KI, Patas K, Karakasiliotis I, Aidinis V, Chatzipanagiotou S, Angelakis E, Vassilacopoulou D, Vassilaki N. 2021, "Alteration of L-Dopa decarboxylase expression in SARS-CoV-2 infection and its association with the interferon-inducible ACE2 isoform.", PLoS One., 2021 Jun 29; 16(6):e0253458. [PubMed].

Koutrouli M, Karatzas E, Papanikolopoulou K, Pavlopoulos GA. 2021, "NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization.", Genomics Proteomics and Bioinformatics., 2021 Jun 22: S1672-0229(21)00130-3. doi: 10.1016/j.gpb.2021.02.005 [PubMed].

Georganta EM, Moressis A, Skoulakis EMC. 2021, " Associative Learning Requires Neurofibromin to Modulate GABAergic Inputs to Drosophila Mushroom Bodies", J Neurosci., 2021 Jun 16;41(24):5274-5286. doi: 10.1523/JNEUROSCI.1605-20.2021. Epub 2021 May 10 [PubMed].

Evangelos Karagiannis, Michail Michailidis, Christina Skodra, George Stamatakis, Marilena Dasenaki, Ioannis Ganopoulos, Martina Samiotaki, Nikolaos S Thomaidis, Athanassios Molassiotis, Georgia Tanou. 2021, "Proteo-metabolomic journey across olive drupe development and maturation", Food Chem., 2021 Nov 30; 363:130339. doi: 10.1016/j.foodchem.2021.130339. Epub 2021 Jun 9. [PubMed].

Karatzas E, Gkonta M, Hotova Joana, Baltoumas FA, Kontou PI, Bobotsis CJ, Bagos PG, Pavlopoulos GA. 2021, "VICTOR: A visual analytics web application for comparing cluster sets", Computers in Biology and Medicine., June 8, 104557, ISSN 0010-4825, [doi], [PubMed].

Filippou P, Zarza X, Antoniou C, Obata T, Villarroel CA, Ganopoulos I, Harokopos V, Gohari G, Aidinis V, Madesis P, Christou A, Fernie AR, Tiburcio AF, Fotopoulos V. 2021, "Systems biology reveals key tissue-specific metabolic and transcriptional signatures involved in the response of Medicago truncatula plant genotypes to salt stress.", Comput Struct Biotechnol J., 2021 Apr 8; 19:2133-2147 [PubMed].

Nikitopoulou I, Ninou I, Manitsopoulos N, Dimopoulou I, Orfanos SE, Aidinis V, Kotanidou A. 2021, "A role for bronchial epithelial autotaxin in ventilator-induced lung injury.", Intensive Care Med Exp., 2021 Mar 29; 9(1):12 [PubMed].

Nanou A, Bourbouli M, Vetrano S, Schaeper U, Ley S, Kollias G. 2021, "Endothelial Tpl2 regulates vascular barrier function via JNK-mediated degradation of claudin-5 promoting neuroinflammation or tumor metastasis", Cell Rep., May 25; 35(8):109168. doi: 10.1016/j.celrep.2021.109168. [PubMed].

Koutrouli M, Theodosiou T, Iliopoulos I, Pavlopoulos GA. 2021, "The network analysis profiler (NAP v2.0): A web tool for visual topological comparison between multiple networks", EMBnet.journal, v. 26, p. e943, May 2021. ISSN 2226-6089. [doi], [Article].

Theodorakis V., Antonakis AN., Baltsavia I., Pavlopoulos GA., Samiotaki M., Amoutzias G., Theodosiou T., Acuto O., Efstathiou G., Iliopoulos I. 2021, "ProteoSign v2: A faster and evolved user-friendly online tool for statistical analyses of differential proteomics", Nucleic Acids Res., 2021 May 8: gkab329. doi:10.1093/nar/gkab329 [PubMed].

Davidson S, Coles M, Thomas T, Kollias G, Ludewig B, Turley S, Brenner M & Buckley CD. 2021, "Fibroblasts as immune regulators in infection, inflammation and cancer", Nat Rev Immunol., Apr 28. doi: 10.1038/s41577-021-00540-z. Online ahead of print. [PubMed].

Ntari L, Nikolaou C, Kranidioti K, Papadopoulou D, Christodoulou-Vafeiadou E, Chouvardas P, Meier F, Geka C, Denis MC, Karagianni N, Kollias G. 2021, "Combination of subtherapeutic anti-TNF dose with dasatinib restores clinical and molecular arthritogenic profiles better than standard anti-TNF treatment", J Transl Med., 19: 165 [PubMed].

Karatzas E., Baltoumas FA, Panayiotou NA, Schneider R, Pavlopoulos GA. 2021, "Arena3D^web: interactive 3D visualization of multilayered networks", Nucleic Acids Research, 2021 Apr 22:gkab278, doi: 10.1093/nar/gkab278 [PubMed].

Prados A, Onder L, Cheng HW, Mörbe U, Lütge M, Gil-Cruz C, Perez-Shibayama C, Koliaraki V, Ludewig B, Kollias G. 2021, "Fibroblastic reticular cell lineage convergence in Peyer's patches governs intestinal immunity", Nat Immunol., Mar 11. doi: 10.1038/s41590-021-00894-5. Online ahead of print. [PubMed].

Stefanos Testempasis, Georgia Tanou, Ioannis Minas, Martina Samiotaki, Athanassios Molassiotis, Georgios Karaoglanidis. 2021, "Unraveling Interactions of the Necrotrophic Fungal Species Botrytis cinerea With 1-Methylcyclopropene or Ozone-Treated Apple Fruit Using Proteomic Analysis.", Front Plant Sci., 2021 Mar 10; 12:644255. doi: 10.3389/fpls.2021.644255. eCollection 2021. [PubMed].

Ray R, Sinha S, Aidinis V, Rai V. 2021, "Atx regulates skeletal muscle regeneration via LPAR1 and promotes hypertrophy", Cell Rep., 2021 Mar 2; 34(9):108809. [PubMed].

Georgios C Stefos, Eszter Szantai, Dimitris Konstantopoulos, Martina Samiotaki, Maria Fousteri. 2021, "aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin", Nucleic Acids Research, gkab144 https://doi.org/10.1093/nar/gkab144 [doi].

Komatsu N, Win S, Yan M, Huynh NC, Sawa S, Tsukasaki M, Terashima A, Pluemsakunthai W, Kollias G, Nakashima T, Takayanagi H. 2021, "Plasma cells promote osteoclastogenesis and periarticular bone loss in autoimmune arthritis", J Clin Invest., 131(6):143060. doi: 10.1172/JCI143060. [PubMed].

Hayer S, Vervoordeldonk MJ, Denis MC, Armaka M, Hoffmann M, Bäcklund J, Nandakumar KS, Niederreiter B, Geka C, Fischer A, Woodworth N, Blüml S, Kollias G, Holmdahl R, Apparailly F, Koenders MI. 2021, "'SMASH' recommendations for standardised microscopic arthritis scoring of histological sections from inflammatory arthritis animal models. ", Ann Rheum Dis., Feb 18:annrheumdis-2020-219247. doi: 10.1136/annrheumdis-2020-219247. Online ahead of print. [PubMed].

Mouchlis VD, Afantitis A, Serra A, Fratello M, Papadiamantis AG, Aidinis V, Lynch I, Greco D, Melagraki G. 2021, "Advances in de Novo Drug Design: From Conventional to Machine Learning Methods", Int J Mol Sci, 2021 Feb 7; 22(4):1676. [PubMed].

Antoniou KM, Tsitoura E, Vasarmidi E, Symvoulakis EK, Aidinis V, Tzilas V, Tzouvelekis A, Bouros D. 2021, "Precision medicine in idiopathic pulmonary fibrosis therapy: From translational research to patient-centered care.", Curr Opin Pharmacol., 2021 Feb 5; 57:71-80 [PubMed].

Zannikou M, Barbayianni I, Fanidis D, Grigorakaki T, Vlachopoulou E, Konstantopoulos D, Fousteri M, Nikitopoulou I, Kotanidou A, Kaffe E, Aidinis V. 2021, "MAP3K8 Regulates Cox-2-Mediated Prostaglandin E 2 Production in the Lung and Suppresses Pulmonary Inflammation and Fibrosis.", J Immunol, 2021 Feb 1; 206(3):607-620. [PubMed].

Verrou KM, Vlachogiannis NI, Ampatziadis-Michailidis G, Moulos P, Pavlopoulos GA, Hatzis P, Kollias G, Sfikakis PP. 2021, "Distinct transcriptional profile of blood mononuclear cells in Behcet's disease: insights into the central role of neutrophil chemotaxis", Rheumatology (Oxford), 2021 Jan 25; keab052. doi: 10.1093/rheumatology/keab052. Online ahead of print [PubMed].

Akhmedov A, Crucet M, Simic B, Kraler S, Bonetti NR, Ospelt C, Distler O, Ciurea A, Liberale L, Jauhiainen M, Metso J, Miranda M, Cydecian R, Schwarz L, Fehr V, Zilinyi R, Amrollahi-Sharifabadi M, Ntari L, Karagianni N, Ruschitzka F, Laaksonen R, Vanhoutte PM, Kollias G, Camici GG, Lüscher TF. 2021, "TNFα induces endothelial dysfunction in rheumatoid arthritis via LOX-1 and arginase 2: reversal by monoclonal TNFα antibodies", Cardiovasc Res. , 2021 Jan 23; cvab005. doi: 10.1093/cvr/cvab005. Online ahead of print. [PubMed].

Dudeck J, Kotrba J, Immler R, Hoffmann A, Voss M, Alexaki VI, Morton L, Jahn SR, Katsoulis-Dimitriou K, Winzer S, Kollias G, Fischer T, Nedospasov SA, Dunay IR, Chavakis T, Müller AJ, Schraven B, Sperandio M, Dudeck A. 2021, "Directional mast cell degranulation of tumor necrosis factor into blood vessels primes neutrophil extravasation", Immunity. , 2021 Jan 15: S1074-7613(20)30545-8. doi: 10.1016/j.immuni.2020.12.017. Online ahead of print [PubMed].

Kontou P. Pavlopoulou A, Dimou N, Theodoropoulou M, Braliou G, Tsaousis G, Pavlopoulos GA, Hamodrakas S., Bagos PG. 2021, "The human GPCR signal transduction network", Network Modeling Analysis in Health Informatics and Bioinformatics, (2021) 10:3, [DOI].