Genetic Epidemiology (applications)

• Georgia G Braliou, Panagiota I Kontou, Haralabia Boleti, Pantelis G Bagos. Susceptibility to leishmaniasis is affected by host SLC11A1 gene polymorphisms: a systematic review and meta-analysis. Parasitology Research, 2019 [PDF] [Pubmed] [Google Scholar]
• Chrissa G Tsiara, Georgios K Nikolopoulos, Niki L Dimou, Katerina G Pantavou, Pantelis G Bagos, Benedicta Mensah, Michael Talias, Georgia G Braliou, Dimitra Paraskeva, Stefanos Bonovas, Angelos Hatzakis. Interleukin gene polymorphisms and susceptibility to HIV-1 infection: a meta-analysis. Journal of Genetics, 2018 [PDF] [Pubmed] [Google Scholar]
• Medina-Gomez C, Kemp JP, Dimou NL, Kreiner E, Chesi A, Zemel BS, Bønnelykke K, Boer CG, Ahluwalia TS, Bisgaard H, Evangelou E, Heppe DHM, Bonewald LF, Gorski JP, Ghanbari M, Demissie S, Duque G, Maurano MT, Kiel DP, Hsu YH, C J van der Eerden B, Ackert-Bicknell C, Reppe S, Gautvik KM, Raastad T, Karasik D, van de Peppel J, Jaddoe VWV, Uitterlinden AG, Tobias JH, Grant SFA, Bagos PG, Evans DM, Rivadeneira F.. Bivariate genome-wide association meta-analysis of pediatric musculoskeletal traits reveals pleiotropic effects at the SREBF1/TOM1L2 locus. Nature Communications 8, Article number: 121 (2017 [PDF] [Pubmed] [Google Scholar]) 
• Pantavou KG, Braliou GG, Kontou PI, Dimou NL, Bagos PG. A meta-analysis of FZD3 gene polymorphisms and their association with schizophrenia. Psychiatric Genetics, 2016 [PDF] [Pubmed] [Google Scholar]
• Braliou GG, Pantavou KG, Kontou PI, Bagos PG. Polymorphisms of the CD24 Gene Are Associated with Risk of Multiple Sclerosis: A Meta-Analysis. International Journal of Molecular Sciences. 2015, 16(6): 12368-12381 [PDF] [Pubmed] [Google Scholar]
• Nikolopoulos G, Bagos P, Tsangaris I, Tsiara C, Kopterides P, Vaiopoulos A, Kapsimali V, Bonovas S, Tsantes A. The association between Plasminogen Activator Inhibitor type 1 (PAI-1) levels, PAI-1 4G/5G polymorphism, and myocardial infarction: a Mendelian Randomization meta-analysis Clinical Chemistry and Laboratory Medicine, 2014 [PDF] [Pubmed] [Google Scholar]
• Braliou GG, Grigoriadou AM, Kontou PI, Bagos PG. The role of genetic polymorphisms of the Renin-Angiotensin System in renal diseases: A meta-analysis. Comput Struct Biotechnol J. 2014 Jun 11;10(16):1-7 [PDF] [Pubmed] [Google Scholar]
• Pereira TV, Kimura L, Suwazono Y, Nakagawa H, Daimon M, Oizumi T, Kayama T, Kato T, Li L, Chen S, Gu D, Renner W, März W, Yamada Y, Bagos PG, Mingroni-Netto RC. Multivariate meta-analysis of the association of G-protein beta 3 gene (GNB3) haplotypes with cardiovascular phenotypes. Mol Biol Rep. 2014 [PDF] [Pubmed] [Google Scholar]
• Tsantes AE, Kopterides P, Bonovas S, Bagos P, Antonakos G, Nikolopoulos GK, Gialeraki A, Kapsimali V, Kyriakou E, Kokori S, Dima K, Armaganidis A, Tsangaris I. Effect of angiotensin converting enzyme gene I/D polymorphism and its expression on clinical outcome in acute respiratory distress syndrome. Minerva Anestesiol. 2013;79(8):861-70.[PDF] [Pubmed] [Google Scholar]
• Stoubos S, Anthopoulos PG, Hamodrakas SJ, Bagos PG. The association between apolipoprotein E gene polymorphisms and essential hypertension: a meta-analysis of 45 studies including 13940 cases and 16364 controls. Journal of Human Hypertension,2012 [PDF] [Pubmed] [Google Scholar]
• Spyridopoulou K, Dimou NL, Hamodrakas SJ, Bagos PG. Methylene Tetrahydrofolate Reductase gene polymorphisms and their association with methotrexate toxicity: A meta-analysis. Pharmacogenetics and Genomics, 2012 49(9):3284-91  [PDF] [Pubmed] [Google Scholar]
• Nikolopoulos GK, Masgala A, Tsiara C, Limitsiou OK, Karnaouri AC, Dimou NL, Bagos PG. Cytokine gene polymorphisms in multiple sclerosis: a meta-analysis of 45 studies including 7,379 cases and 8,131 controls. 2011, European Journal of Neurology, [Pubmed] [PDF] [Google Scholar]
• Anthopoulos PG, Hamodrakas SJ, Bagos PG. Apolipoprotein E polymorphisms and type 2 Diabetes: a meta-analysis of 30 studies including 5423 cases and 8197 controls. 2010, Molecular Genetics and Metabolism, 100(3):283-91 [PDF] [Pubmed] [Google Scholar]
• Dimou NL, Nikolopoulos GK, Hamodrakas SJ, Bagos PG. Fcgamma receptor polymorphisms and their association with periodontal disease: A meta-analysis. 2010 Journal of Clinical Periodontology, 37(3):255-65 [PDF] [Pubmed] [Google Scholar]
• Ioannidis A, Ikonomi E, Dimou NL, Douma L, Bagos PG. Polymorphisms of the Insulin Receptor and the Insulin Receptor Substrates genes in Polycystic Ovary Syndrome: a mendelian randomization meta-analysis. 2010, Molecular Genetics and Metabolism, 99(2):174–183  [PDF] [Pubmed] [Google Scholar]
• Bagos PG. Plasminogen Activator Inhibitor-1 4G/5G and 5,10-methylene-tetrahydrofolate reductase C677T polymorphisms in Polycystic Ovary Syndrome. 2009, Molecular Human Reproduction, 15(1):19-26 [PDF] [Pubmed] [Google Scholar]
• Nikolopoulos GK, Dimou NL, Hamodrakas SJ, Bagos PG. Cytokine gene polymorphisms in periodontal disease: A meta-analysis of 53 studies including 4178 cases and 4590 controls. Journal of Clinical Periodontology, 2008, 35(9):754-67 [PDF] [Pubmed] [Google Scholar]
• Tsantes AE, Nikolopoulos GK, Bagos PG, Bonovas S, Kopterides P, Vaiopoulos G. The effect of the plasminogen activator inhibitor-1 4G/5G polymorphism on the thrombotic risk. Thromb Res. 2008;122(6):736-42 [PDF] [Pubmed] [Google Scholar]
• Tsantes AΕ, Nikolopoulos GΚ, Bagos PG, Tsiara C, Travlou A, Vaiopoulos G. Plasminogen Activator Inhibitor-1 4G/5G Polymorphism and Risk of Ischemic Stroke: a Meta-Analysis. 2007, Blood Coagulation & Fibrinolysis, 18 (5):497-504 [PDF] [Pubmed] [Google Scholar]
• Tsantes AΕ, Nikolopoulos GΚ, Bagos PG, Rapti E, Mantzios G, Kapsimali V, Travlou A. Association between the Plasminogen Activator Inhibitor-1 4G/5G Polymorphism and Venous Thrombosis: a Meta-Analysis. 2007, Thrombosis and Haemostasis, 97 (6): 907-13 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Karnaouri AC, Nikolopoulos GK, Hamodrakas SJ. No evidence for association of CTLA-4 gene polymorphisms with the risk of developing Multiple Sclerosis: a meta-analysis. 2007, Multiple Sclerosis, 13(2): 156-168 [PDF] [Pubmed] [Google Scholar]
• Tsantes AΕ, Nikolopoulos GΚ, Bagos PG, Vaiopoulos G, Travlou A. Lack of association between the platelet glycoprotein Ia C807T gene polymorphism and coronary artery disease: a meta-analysis. 2007, International Journal of Cardiology, 118 (2):189-196  [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Elefsinioti AL, Nikolopoulos GK, Hamodrakas SJ. The GNB3 C825T polymorphism and Essential Hypertension: a meta-analysis of 34 studies including 14094 cases and 17760 controls, 2007, Journal of Hypertension, 25(3): 487-500 [PDF] [Pubmed] [Google Scholar]
• Nikolopoulos GΚ, Tsantes AΕ, Bagos PG, Travlou A, Vaiopoulos G. Integrin, alpha 2 gene C807T Polymorphism and Risk of Ischemic Stroke: a Meta-Analysis. 2007, Thrombosis Research; 119 (4): 501-510 [PDF] [Pubmed] [Google Scholar]

Biostatistics (applications)

meta-analyses of clinical and observational studies

• Farsalinos K, Bagos PG, Giannouchos T, Niaura R, Barbouni A, Poulas K. Smoking prevalence among hospitalized COVID-19 patients and its association with disease severity and mortality: an expanded re-analysis of a recent publication. Harm reduction journal. 2021 Dec;18(1):1-9.Improved strategies to counter the COVID-19 pandemic: Lockdowns vs. primary and community healthcare [PDF] [Pubmed] [Google Scholar]
• Kyriazoglou A, Bagos P. Meta-analysis of BCOR rearranged sarcomas: challenging the therapeutic approach. Acta Oncologica. 2021 Feb 17:1-6 [PDF] [Pubmed] [Google Scholar]
• Piovani D, Christodoulou MN, Hadjidemetriou A, Pantavou K, Zaza P, Bagos PG, Bonovas S, Nikolopoulos GK. Effect of early application of social distancing interventions on Covid-19 mortality over the first pandemic wave: an analysis of longitudinal data from 37 countries. Journal of Infection 2021 82 (1), 133-142 [PDF] [Pubmed] [Google Scholar]
• Pappa SA, Kontou PI, Bagos PG, Braliou GG. Urine-Based Molecular Diagnostic Tests for Leishmaniasis Infection in Human and Canine Populations: A Meta-Analysis. Pathogens. 2021 Mar;10(3):269.[PDF] [Pubmed] [Google Scholar]
• Kapoula GV, Kontou PI, Bagos PG. Diagnostic Performance of Biomarkers Urinary KIM-1 and YKL-40 for Early Diabetic Nephropathy, in Patients with Type 2 Diabetes: A Systematic Review and Meta-Analysis. Diagnostics (Basel). 2020 Nov 7;10(11):909. doi: 10.3390/diagnostics10110909. [PDF] [Pubmed] [Google Scholar]
• Kontou PI, Braliou GG, Dimou NL, Nikolopoulos G, Bagos PG. Antibody Tests in Detecting SARS-CoV-2 Infection: A Meta-Analysis. Diagnostics (Basel). 2020 May 19;10(5):319. doi: 10.3390/diagnostics10050319. [PDF] [Pubmed] [Google Scholar]
• Pantavou KG, Bagos PG. Season of birth and multiple sclerosis: a systematic review and multivariate meta-analysis. J Neurol. 2019 May 4. doi: 10.1007/s00415-019-09346-5. [PDF] [Pubmed] [Google Scholar]
• Georgia V. Kapoula, Panagiota I Kontou, Pantelis G Bagos. Diagnostic Accuracy of Neutrophil GelatinaseAssociated Lipocalin for Predicting Early
  Diabetic Nephropathy in Patients with Type 1 and Type 2 Diabetes Mellitus: A Systematic Review and Meta-analysis. The Journal of Applied Laboratory Medicine, 2019  [PDF] [Pubmed] [Google Scholar]
• Kapoula G, Kontou PI, Bagos PG. The impact of pneumatic tube system on routine laboratory parameters: a systematic review and meta-analysis Clinical Chemistry and Laboratory Medicine, 2017  [PDF] [Pubmed] [Google Scholar]
• Polymeropoulos E, Bagos P ,Toumpoulis I, Papadimitriou M, Rizos I, Patsouris E. Vitamin C for the prevention of postoperative atrial fibrillation after cardiac surgery: a meta-analysis. Advanced Pharmaceutical Bulletin. 2016 6(2):243-50 [PDF] [Pubmed] [Google Scholar]
• Koletsi D, Fleming PS, Seehra J, Bagos PG, Pandis N. Are Sample Sizes Clear and Justified in RCTs Published in Dental Journals? PLoS One. 2014 Jan 21;9(1):e85949. [PDF] [Pubmed] [Google Scholar]
• Bonovas S. Nikolopoulos GK, Bagos PG. Bisphosphonate Use and Risk of Colorectal Cancer: A Systematic Review and Meta-analysis. British Journal of Clinical Pharmacology, 2013 76(3):329-337 [PDF] [Pubmed] [Google Scholar]
• Tsiara C, Nikolopoulos GK, Dimou N, Bagos P, Saroglou G, Velonakis E, Hatzakis A. Effect of Hepatitis C Virus on Immunologic and Virologic Response in HIV Infected Patients Initiating Highly Active Antiretroviral Therapy: An Updated Meta-Analysis Journal of Viral Hepatitis 2013 20(10): 715-724 [PDF] [Pubmed] [Google Scholar]
• Bangalore S, Pursnani S, Kumar S, Bagos PG. Percutaneous Coronary Intervention versus Optimal Medical Therapy for Prevention of Spontaneous Myocardial Infarction in Subjects with Stable Ischemic Heart Disease. Circulation. Circulation. 2013 127(7): 769-781  [PDF] [Pubmed] [Google Scholar]
• Bonovas S, Nikolopoulos GK, Bagos PG. Use of fibrates and cancer risk: a systematic review and meta-analysis of 17 long-term randomized placebo-controlled trials. PLoS One. 2012;7(9):e45259.  [PDF] [Pubmed] [Google Scholar]
• Rabe GL, Wellmann J, Bagos P, Busch MA, Hense HW, Spies C, Weiss-Gerlach E, McCarthy W, Gareca Arizaga MJ, Neuner B. Efficacy of Emergency Department-Initiated Tobacco Control--Systematic Review and Meta-analysis of Randomized Controlled Trials. Nicotine Tob Res. 2012 2013 15 (3), 643-655 [PDF] [Pubmed] [Google Scholar]
• Tsiara CG, Nikolopoulos GK, Bagos PG, Goujard C, Katzenstein TL, Minga AK, Rouzioux C, Hatzakis A. Impact of HIV Type 1 DNA Levels on Spontaneous Disease Progression: A Meta-Analysis.AIDS Res Hum Retroviruses.  2012 ;28(4):366-73.[PDF] [Pubmed] [Google Scholar]
• Chatzigeorgiou KS, Sergentanis TN, Tsiodras S, Hamodrakas SJ, Bagos PG. Phoenix 100 versus Vitek 2 in the identification of Gram positive and Gram negative bacteria: a comprehensive meta-analysis. J Clin Microbiol. 2011 [PDF] [Pubmed] [Google Scholar]
• Nikolopoulos GK, Bagos PG, Bonovas S. Developing the Evidence Base for Cancer Chemoprevention: Use of Meta-Analysis. Curr Drug Targets. 2011, 12: 1989-1997[Pubmed] [PDF] [Google Scholar]
• Bonovas S, Nikolopoulos GK, Filioussi K, Peponi E, Bagos PG, Sitaras NM. Can statin therapy reduce the risk of melanoma? A meta-analysis of randomized controlled trials. European Journal of Epidemiology, 2010;25(1):29-35 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Nikolopoulos G, Ioannidis A. Chlamydia pneumoniae infection and the risk of multiple sclerosis: a meta-analysis. Multiple Sclerosis 2006, 12(4), 397-411 [PDF] [Pubmed] [Google Scholar]

observational, cross-sectional and longitudinal studies

• Stergianou D, Tzanetakou V, Argyropoulou M, Kanni T, Bagos PG, Giamarellos-Bourboulis EJ. Staphylococcus aureus Carriage in Hidradenitis Suppurativa: Impact on Response to Adalimumab. Dermatology.:1-6.[PDF] [Pubmed] [Google Scholar]
• Vassiliki Tsata, Aristea Velegraki, Anastasios Ioannidis, Cornelia Poulopoulou, Pantelis Bagos, Maria Magana, Stylianos Chatzipanagiotou. Effects of Yeast and Bacterial Commensals and Pathogens of the Female Genital Tract on the Transepithelial Electrical Resistance of HeLa Cells. The Open Microbiology Journal, 2016, 10: 90-96 [PDF] [Pubmed] [Google Scholar]
• Ioannidou V, Ioannidis A, Magiorkinis E, Bagos P, Nicolaou C, Legakis N, Chatzipanagiotou S Multilocus sequence typing (and phylogenetic analysis) of Campylobacter jejuni and Campylobacter coli strains isolated from clinical cases in Greece 2013 BMC research notes 6 (1), 359 [PDF] [Pubmed] [Google Scholar]
• Nikolopoulos G, Bagos P, Lytras T, Bonovas S. An Ecological Study of the Determinants of Differences in 2009 Pandemic Influenza Mortality Rates between Countries in Europe. PLoS One. 2011;6(5):e19432 [PDF] [Pubmed] [Google Scholar]
• Tsantes A, Tsangaris I, Nikolopoulos G, Bagos P, Kopterides P, Antonakos G, Dimopoulou I, Vrioni G, Kapsimali V, Dima K, Armaganidis A, Travlou A. The effect of homocysteine on the clinical outcomes of ventilated patients with severe sepsis. Minerva Anesthesiologia, 2010, 76(10):787-94 [PDF] [Pubmed] [Google Scholar]
• Tsangaris I, Tsantes A, Bagos P, Nikolopoulos G, Kroupis C, Kopterides P, Dimopoulou I, Orfanos S, Kardoulaki A, Chideriotis S, Travlou A, Armaganidis A. The effect of plasma homocysteine levels on clinical outcomes of patients with Acute Lung Injury/Acute Respiratory Distress syndrome. The American Journal of the Medical Sciences. 2009, 338(6):474-477 [PDF] [Pubmed] [Google Scholar]
• Liappas IA, Nicolaou C, Chatzipanagiotou S, Tzavellas EO, Piperi C, Papageorgiou C, Boufidou F, Bagos P, Soldatos CR. Vitamin B12 and hepatic enzyme serum levels correlate with interleukin-6 in alcohol-dependent individuals without liver disease. Clin Biochem. 2007, 40 (11): 781-786 [PDF] [Pubmed] [Google Scholar]
• Liappas I, Chatzipanagiotou S, Nicolaou C, Tzavellas E, Bagos P, Soldatos CR. Interrelationship of hepatic function, thyroid activity and mood status in alcohol-dependent individuals. In Vivo. 2006; 20(2): 293-300  [Pubmed] [Google Scholar]
• Liappas I, Piperi C, Malitas PN, Tzavellas E, Liappas AI, Boufidou F, Kalofoutis CA, Bagos P, Rabavilas A, Kalofoutis Α. Correlation of liver dysfunction biological markers to the mood status of alcohol -dependent individuals. 2006, The International Journal of Psychiatry in Clinical Practice, 10 (3): 166-173 [PDF] [Google Scholar]
• Tsirpanlis G, Bagos P, Ioannou D, Bleta A, Marinou I, Lagouranis A, Chatzipanagiotou S, Nicolaou C. Serum albumin: a late reacting negative acute phase protein in clinically evident inflammation in dialysis patients. Nephrol Dial Transplant. 2005, 20:658-659 [PDF] [Pubmed] [Google Scholar]
• Tsirpanlis G, Bagos P, Ioannou D, Bleta A, Marinou I, Lagouranis A, Chatzipanagiotou S, Nicolaou C. The variability and accurate assessment of microinflammation in haemodialysis patients. Nephrol Dial Transplant. 2004, 19(1): 150-157 [PDF] [Pubmed] [Google Scholar]
• Tsirpanlis G, Bagos P, Ioannou D, Bleta A, Marinou I, Lagouranis A, Chatzipanagiotou S, Nicolaou C. Exploring Inflammation in Hemodialysis patients: Persistent and Superimposed Inflammation - a longitudinal study. Kidney Blood Press Res, 2004, 27:63-70 [PDF] [Pubmed] [Google Scholar]
• Tsirpanlis G, Chatzipanagiotou S, Ioannidis A, Ifanti K, Bagos P, Lagouranis A, Poulopoulou C, Nicolaou C. The effect of viable Chlamydia pneumoniae on serum cytokines and adhesion molecules in hemodialysis patients. Kidney Int Suppl. 2003, 84: S72-5 [PDF] [Pubmed] [Google Scholar]
  

Biological sequence analysis and prediction methods

• Ahmed Roumia,Margarita Theodoropoulou,Konstantinos Tsirigos, Henrik Nielsen, Pantelis Bagos.The landscape of eukaryotic transmembrane beta barrel proteins. Journal of Proteome Research. 2020 [PDF] [Pubmed] [Google Scholar]
• amposis IA, Tsirigos KD, Theodoropoulou MC, Kontou PI, Tsaousis GN, Sarantopoulou D, Litou ZI and Bagos PG. JUCHMME: A Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis. Bioinformatics, 2019 [PDF] [Pubmed] [Google Scholar]
  
• Tamposis IA, Tsirigos KD, Theodoropoulou MC, Kontou PI and Bagos PG. Semi-supervised learning of Hidden Markov Models for biological sequence analysis. Bioinformatics, 2018, [PDF] [Pubmed] [Google Scholar]
• Tamposis IA, Theodoropoulou MC, Tsirigos KD, Bagos PG. Extending Hidden Markov Models to allow conditioning on previous observations. Journal of Bioinformatics and Computational Biology. 2018 [PDF] [Pubmed] [Google Scholar]
• Tsirigos KD, Elofsson A, Bagos PG. PRED-TMBB2: Improved topology prediction and detection of beta-barrel outer membrane proteins. Bioinformatics, 2016, 32 (17), i665-i671 [PDF] [Pubmed] [Google Scholar]
• Tsaousis GN, Bagos PG, Hamodrakas SJ HMMpTM: Improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 2014 1844(2):316-22 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Nikolaou EP, Liakopoulos TD, Tsirigos KD. Combined prediction of Tat and Sec signal peptides with Hidden Markov Models. 2010, Bioinformatics, 26: 2811-2817 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Tsirigos KD, Plessas SK, Liakopoulos TD, Hamodrakas SJ. Prediction of signal peptides in Archaea, 2009, Protein Engineering Design and Selection, 22(1): 27-35 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Tsaousis GN, Hamodrakas SJ. How many 3D structures do we need to train a predictor? 2009, Genomics Proteomics and Bioinformatics, 7(3): 128-137 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ. Prediction of lipoprotein signal peptides in Gram-positive bacteria with Hidden a Markov Model, 2008, J Proteome Research, 7(12):5082-93 [PDF] [Pubmed] [Google Scholar]
• Litou ZI, Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ. Prediction of Cell Wall sorting signals in Gram-positive bacteria with a Hidden Markov Model: application to complete genomes. 2008, Journal of Bioinformatics and Computational Biology, 6(2):387-401 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Liakopoulos TD, Hamodrakas SJ. Algorithms for incorporating prior topological information in HMMs: Application to transmembrane proteins. 2006, BMC Bioinformatics; 7:189 [PDF] [Pubmed] [Google Scholar]
• Petsalaki ΕΙ, Bagos PG, Litou ΖΙ, Hamodrakas SJ. PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localization. 2006, Genomics Proteomics and Bioinformatics, 4(1): 48-55 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Liakopoulos TD, Hamodrakas SJ. Evaluation of methods for predicting the topology of ß-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics, 2005, 6:7 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Liakopoulos TD, Promponas VJ, Hamodrakas SJ. Topology prediction of β-barrel outer membrane proteins. PINSA-B, 2005, Β71 (1): 19-41 [PDF] [Pubmed] [Google Scholar]
• Sgourakis NG, Bagos PG, Hamodrakas SJ. Prediction of the coupling specificity of GPCRs to four families of G-proteins using Hidden Markov Models and Artificial Neural Networks. Bioinformatics, 2005, 21(22): 4101-6 [PDF] [Pubmed] [Google Scholar]
• Sgourakis NG, Bagos PG, Papasaikas PK, Hamodrakas SJ. A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile hidden Markov models. BMC Bioinformatics, 2005, 6:104 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Liakopoulos TD, Hamodrakas SJ. Finding beta-barrel outer membrane proteins with a Markov chain model. WSEAS Transactions on Biology and Biomedicine, 2004, 2(1) 186-189 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ. PRED-TMBB: A web server for predicting the topology of β-barrel outer membrane proteins. Nucleic Acids Res, 2004, 32(Web Server Issue). W400-404 [PDF] [Pubmed] [Google Scholar]
• Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ. A Hidden Markov Model capable of predicting and discriminating β-barrel outer membrane proteins. BMC Bioinformatics, 2004, 5:29 [PDF] [Pubmed] [Google Scholar]
• Papasaikas PK, Bagos PG, Litou ZI, Promponas VJ, and Hamodrakas SJ. PRED-GPCR: GPCR recognition and family classification server. Nucleic Acids Res, 2004, 32(Web Server Issue):W380-382 [PDF] [Pubmed] [Google Scholar]
• Papasaikas PK, Bagos PG, Litou ZI and Hamodrakas SJ. A novel method for GPCR recognition and family classification, using fingerprints derived from profile Hidden Markov Models. SAR QSAR Environ Res, 2003, 14(5-6): 413-420 [PDF] [Pubmed] [Google Scholar]

Structural Bioinformatics

• Valavanis IK, Bagos PG, Emiris IZ. Beta-barrel Transmembrane Proteins: Geometric Modelling, Detection of Transmembrane Region, and Structural Properties. Computational Biology and Chemistry, 2006, 30(6):416-24 [PDF] [Pubmed] [Google Scholar]
• Spyropoulos IC, Liakopoulos TD, Bagos PG, and Hamodrakas SJ. TMRPres2D: high quality visual representation of transmembrane protein models. Bioinformatics, 2004, 20(17) 3258-3260 [PDF] [Pubmed] [Google Scholar]

Biological databases

• Ahmed F Roumia, Konstantinos D. Tsirigos, Margarita C. Theodoropoulou, Ioannis A. Tamposis, Stavros J. Hamodrakas, Pantelis G. Bagos. OMPdb: A global hub of beta-barrel outer membrane proteins. Frontiers in Bioinformatics, 2021 [PDF] [Pubmed] [Google Scholar]
• Babbitt PC, Bagos PG,, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Flinn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier M, Sharman JL,Spedding M, ,Tsirigos KD, Vastermark A, Vriend G. Creating a Specialist Protein Resource Network: A meeting report for the Protein Bioinformatics and Community Resources Retreat. Database, 2015 [PDF] [Pubmed] [Google Scholar]
• Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Flinn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 2015 [PDF] [Pubmed] [Google Scholar]
• Tsirigos KD, Bagos PG, Hamodrakas SJ. OMPdb: A database of beta-barrel outer membrane proteins from Gram-negative bacteria, Nucleic Acids Research, 2011, 39(Database issue):D324-31. [PDF] [Pubmed] [Google Scholar]
• Satagopam VP, Theodoropoulou MC, Stampolakis CK, Pavlopoulos GA, Papandreou NC, Bagos PG, Schneider R and Hamodrakas SJ. GPCRs, G-proteins, Effectors and their interactions: Human-gpDB, a database employing advanced visualization tools and data integration techniques. Database, 2010, in press [PDF] [Pubmed] [Google Scholar]
• Tsaousis GN, Tsirigos KD, Andrianou XD, Liakopoulos TD, Bagos PG, Hamodrakas SJ. ExTopoDB: A database of experimentally derived topological models of transmembrane proteins. 2010, Bioinformatics, 26(19):2490-2 [PDF] [Pubmed] [Google Scholar]
• Theodoropoulou MC, Bagos PG, Spyropoulos IC, Hamodrakas SJ. gpDB: a database of GPCRs, G-proteins, effectors and their interactions. Bioinformatics. 2008, 24(12):1471-2. [PDF] [Pubmed] [Google Scholar]
• Elefsinioti AL, Bagos PG, Spyropoulos IC, Hamodrakas SJ. A database for G Proteins and their interaction with GPCRs. BMC Bioinformatics, 2004, 5:208 [PDF] [Pubmed] [Google Scholar] [Highly Accessed]