Biostatistics and Genetic Epidemiology (methodology)- Konstantina E. Vennou, Daniele Piovani, Panagiota I. Kontou, Stefanos Bonovas, Pantelis G. Bagos, Methods for multiple outcome meta-analysis of gene-expression data, MethodsX, 2020, [PDF] [Pubmed] [Google Scholar]
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- Dimou NL, Tsirigos KD, Elofsson A and Bagos PG GWAR: Tools for Robust Analysis and Meta-Analysis of Genome-Wide Association Studies. Bioinformatics, 2017 [PDF] [Pubmed] [Google Scholar]
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- Dimou NL, Adam M, Bagos PG, A Multivariate Method for Meta-Analysis and Comparison of Diagnostic Tests. Statistics in Medicine
2016 [PDF] [Pubmed] [Google Scholar] - Bagos PG, Adam M. On the Covariance of Regression Coefficients. Open Journal of Statistics. 2015 5, 680-701 [HTML] [PDF]
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- Bagos PG, Dimou NL, Liakopoulos TD, Nikolopoulos GK. Meta-Analysis of Family-Based and Case-Control Genetic Association Studies that Use the Same Cases. Statistical Applications in Genetics and Molecular Biology. 2011, 10(1):Article19 [PDF] [Pubmed] [Google Scholar]
- Bagos PG. Meta-analysis of haplotype-association studies: Comparison of methods and empirical evaluation of the literature, 2011, BMC Genetics, 12:8 [PDF] [Pubmed] [Google Scholar] [Highly Accessed]
- Bagos
PG, Liakopoulos TD. A multipoint method for meta-analysis of genetic
association studies. 2010, Genetic Epidemiology, 34(7):702-15 [PDF] [Pubmed] [Google Scholar]
- Bagos PG, Nikolopoulos GK. Mixed-effects
Poisson regression models for meta-analysis of follow-up studies with
constant or varying durations. 2009, The International Journal of
Biostatistics, 5(1), Article 21 [PDF] [Pubmed] [Google Scholar]
- Bagos PG, Nikolopoulos GK.
Generalized least squares for assessing trends in cumulative
meta-analysis with applications in genetic epidemiology. 2009, Journal of
Clinical Epidemiology, 62 (10): 1037-1044 [PDF] [Pubmed] [Google Scholar]
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unification of multivariate methods for meta-analysis of genetic
association studies. 2008, Statistical Applications in Genetics and
Molecular Biology, 7(1), Article 13 [PDF] [Pubmed] [Google Scholar]
- Bagos PG, Nikolopoulos
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studies using logistic regression. 2007, Statistical Applications in
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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]
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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
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- 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
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- 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,
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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
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- 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
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TD, Hamodrakas SJ. Evaluation of methods for predicting the topology of
ß-barrel outer membrane proteins and a consensus prediction method. BMC
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PG, Liakopoulos TD, Promponas VJ, Hamodrakas SJ. Topology
prediction of
β-barrel outer membrane proteins. PINSA-B, 2005, Β71 (1):
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NG, Bagos PG, Hamodrakas SJ. Prediction of the coupling specificity of
GPCRs to four families of G-proteins using Hidden Markov Models and
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NG, Bagos PG, Papasaikas PK, Hamodrakas SJ. A method for the prediction of GPCRs
coupling specificity to G-proteins using refined profile hidden Markov
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PG, Liakopoulos TD, Hamodrakas SJ. Finding beta-barrel outer membrane
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Spyropoulos IC, Hamodrakas SJ. PRED-TMBB: A web server for predicting
the topology of β-barrel outer membrane proteins. Nucleic Acids Res,
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Spyropoulos IC, Hamodrakas SJ. A Hidden Markov Model capable of
predicting and discriminating β-barrel outer membrane proteins. BMC
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PK, Bagos PG, Litou ZI, Promponas VJ, and Hamodrakas SJ. PRED-GPCR:
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and Hamodrakas SJ. A novel method for GPCR recognition and family
classification, using fingerprints derived from profile Hidden Markov
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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]
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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]
- Kontou P, Pavlopoulou A, Dimou N, Theodoropoulou M, Braliou G, Tsaousis G, Pavlopoulos G, Hamodrakas S, Bagos P. The human GPCR signal transduction network. Network Modeling Analysis in Health Informatics and Bioinformatics. 2021 Dec;10(1):1-2. [PDF] [Pubmed] [Google Scholar]
- Vennou KE, Kontou PI, Braliou GG,
Bagos PG. Meta-analysis of gene expression profiles in preeclampsia.
Pregnancy Hypertension. 2020 Jan 1;19:52-60.[PDF] [Pubmed] [Google Scholar]
- Vennou KE, Piovani D, Kontou PI,
Bonovas S, Bagos PG. Multiple outcome meta-analysis of gene-expression
data in inflammatory bowel disease. Genomics. 2020, Pages 1761-1767. [PDF] [Pubmed] [Google Scholar]
- Panagiota I Kontou, Athanasia Pavlopoulou, Georgia G Braliou,
Spyridoula Bogiatzi, Niki L Dimou, Sripal Bangalore, Pantelis G Bagos. Identification of Gene Expression Profiles in Myocardial Infarction: a Systematic Review and Meta-analysis. BMC Medical Genomics, 2018 [PDF] [Pubmed] [Google Scholar]
- Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG. Bipartite Graphs in Systems Biology and Medicine: a survey of methods and applications. GigaScience, 2018 [PDF] [Pubmed] [Google Scholar]
- Theodosiou T, Efstathiou G, Papanikolaou N, Kyrpides NC, Bagos PG, Iliopoulos I, Pavlopoulos GA. NAP: The Network Analysis Profiler, a web tool for easier topological
analysis and comparison of medium-scale biological networks. BMC Research Notes. 2017 [PDF] [Pubmed] [Google Scholar]
- Pavlopoulou A, Bagos PG, Koutsandrea V, Georgakilas AG. Molecular determinants of radiosensitivity in normal and tumor tissue: a bioinformatic approach. Cancer Letters 403 (2017) 37-47 [PDF] [Pubmed] [Google Scholar]
- Kontou P, Pavlopoulou A, Dimou NL,Pavlopoulos G, Bagos PG. Data and programs in support of network analysis of genes and their association with diseases. Data in Brief, 8, 1036-139, 2016, [PDF] [Pubmed] [Google Scholar]
- Kontou P, Pavlopoulou A, Dimou NL,Pavlopoulos G, Bagos PG. Network analysis of genes and their association with diseases. Gene, 2016, 15;590(1):68-78 [PDF] [Pubmed] [Google Scholar]
- Pavlopoulou A, Savva I, Louka M, Bagos PG, Vorgias CE,
Michalopoulos I, Georgakilas AG. Unraveling the mechanisms of extreme radioresistance in prokaryotes: Lessons from nature. Mutation Reviews 2016; 767:92-107 [PDF][Pubmed] [Google Scholar]
- Georgakilas AG, Pavlopoulou A, Louka M, Nikitaki Z, Vorgias CE, Bagos PG, Michalopoulos I. Emerging
molecular networks common in ionizing radiation, immune and
inflammatory responses by employing bioinformatics approaches. Cancer Lett. 2015368(2):164-72 [PDF] [Pubmed] [Google Scholar]
- Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG. Using graph theory to analyze biological networks. BioData Mining. 2011, 4: 10 [PDF] [Pubmed] [Google Scholar] [Highly Accessed]
Editorials and Education Papers
- Konstantinos Farsalinos, Konstantinos Poulas, Dimitrios Kouretas, Apostolos Vantarakis, Michalis Leotsinidis, Dimitrios Kouvelas, Anca Oana Docea, Ronald Kostoff, Grigorios T Gerotziafas, Michael N Antoniou, Riccardo Polosa, Anastastia Barbouni, Vassiliki Yiakoumaki, Theodoros V Giannouchos, Pantelis G Bagos, George Lazopoulos, Boris N Izotov, Victor A Tutelyan, Michael Aschner, Thomas Hartung, Heather M Wallace, Félix Carvalho, Jose L Domingo, Aristides Tsatsakis. Improved strategies to counter the COVID-19 pandemic: Lockdowns vs. primary and community healthcare. Toxicology reports. 2021 Jan 1;8:1-9.[PDF] [Pubmed] [Google Scholar]
- Hatzigeorgiou AG, Bagos P, Benos PV, Nikolaou C, Moreau Y, Kavakiotis I (ECCB 2018 Steering Committee).
ECCB 2018: The 17th European Conference on Computational Biology.
Bioinformatics. 2018 Sep 1;34(17):i595-8. [PDF] [Pubmed] [Google Scholar]
- Paraskevopoulou-Kollia EA, Bagos PG. Bioinformatics Education in Greece: a Survey. Biosaintifika: Journal of Biology & Biology Education. 2017, 9(1):1-10 [HTML] [PDF]
- Hamodrakas SJ, Iliopoulos I, Ouzounis CA, Bagos PG,
Promponas VJ. Meeting report: the seventh conference of the hellenic society
for computational biology and bioinformatics. Comput Struct Biotechnol J. 2013
Jun 16;6:e201303006. doi: 10.5936/csbj.201303006. eCollection 2013. [PDF] [Pubmed] [Google Scholar]
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