P G Bagos

Summary

Publications

  1. doi request reprint Genetic model selection in genome-wide association studies: robust methods and the use of meta-analysis
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2 4, Lamia 35100, Greece
    Stat Appl Genet Mol Biol 12:285-308. 2013
  2. doi request reprint On the covariance of two correlated log-odds ratios
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2 4, Lamia, GR35100, Greece
    Stat Med 31:1418-31. 2012
  3. pmc Using graph theory to analyze biological networks
    Georgios A Pavlopoulos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Lamia, 35100, Greece
    BioData Min 4:10. 2011
  4. doi request reprint Generalized least squares for assessing trends in cumulative meta-analysis with applications in genetic epidemiology
    Pantelis G Bagos
    Department of Informatics with Applications in Biomedicine, University of Central Greece, Papasiopoulou 2 4, Lamia, GR 35100, Greece
    J Clin Epidemiol 62:1037-44. 2009
  5. doi request reprint Apolipoprotein E polymorphisms and type 2 diabetes: a meta-analysis of 30 studies including 5423 cases and 8197 controls
    P G Anthopoulos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
    Mol Genet Metab 100:283-91. 2010
  6. doi request reprint Combined prediction of Tat and Sec signal peptides with hidden Markov models
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2 4, Lamia 35100, Greece
    Bioinformatics 26:2811-7. 2010
  7. doi request reprint A multipoint method for meta-analysis of genetic association studies
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Lamia, Greece
    Genet Epidemiol 34:702-15. 2010
  8. pmc Meta-analysis of haplotype-association studies: comparison of methods and empirical evaluation of the literature
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Lamia, Greece
    BMC Genet 12:8. 2011
  9. doi request reprint Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece
    J Proteome Res 7:5082-93. 2008
  10. doi request reprint A unification of multivariate methods for meta-analysis of genetic association studies
    Pantelis G Bagos
    University of Central Greece
    Stat Appl Genet Mol Biol 7:Article31. 2008

Collaborators

Detail Information

Publications37

  1. doi request reprint Genetic model selection in genome-wide association studies: robust methods and the use of meta-analysis
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2 4, Lamia 35100, Greece
    Stat Appl Genet Mol Biol 12:285-308. 2013
    ..Possible extensions and proposals for future work are also discussed...
  2. doi request reprint On the covariance of two correlated log-odds ratios
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2 4, Lamia, GR35100, Greece
    Stat Med 31:1418-31. 2012
    ..Future applications of the method are discussed...
  3. pmc Using graph theory to analyze biological networks
    Georgios A Pavlopoulos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Lamia, 35100, Greece
    BioData Min 4:10. 2011
    ..This network profiling combined with knowledge extraction will help us to better understand the biological significance of the system...
  4. doi request reprint Generalized least squares for assessing trends in cumulative meta-analysis with applications in genetic epidemiology
    Pantelis G Bagos
    Department of Informatics with Applications in Biomedicine, University of Central Greece, Papasiopoulou 2 4, Lamia, GR 35100, Greece
    J Clin Epidemiol 62:1037-44. 2009
    ..In many research areas, a temporal evolution of the effect size (ES) is present, leading to diminishing effects and would be advantageous to have methods capable of detecting it...
  5. doi request reprint Apolipoprotein E polymorphisms and type 2 diabetes: a meta-analysis of 30 studies including 5423 cases and 8197 controls
    P G Anthopoulos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
    Mol Genet Metab 100:283-91. 2010
    ..Further studies are needed in order to elucidate the metabolic mechanism of this association as well as to study its effects on larger populations...
  6. doi request reprint Combined prediction of Tat and Sec signal peptides with hidden Markov models
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2 4, Lamia 35100, Greece
    Bioinformatics 26:2811-7. 2010
    ..The purpose of this work is to develop a novel method for predicting and discriminating Sec from Tat signal peptides at better accuracy...
  7. doi request reprint A multipoint method for meta-analysis of genetic association studies
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Lamia, Greece
    Genet Epidemiol 34:702-15. 2010
    ..Applications in two already published meta-analyses provide encouraging results concerning the robustness and the usefulness of the method and we expect that it would be widely used in the future...
  8. pmc Meta-analysis of haplotype-association studies: comparison of methods and empirical evaluation of the literature
    Pantelis G Bagos
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Lamia, Greece
    BMC Genet 12:8. 2011
    ..In this work, methods for performing meta-analysis of haplotype association studies are summarized, compared and presented in a unified framework along with an empirical evaluation of the literature...
  9. doi request reprint Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece
    J Proteome Res 7:5082-93. 2008
    ..PRED-LIPO is freely available at http://bioinformatics.biol.uoa.gr/PRED-LIPO/, and we anticipate that it will be a valuable tool for the experimentalists studying secreted proteins and lipoproteins from Gram-positive bacteria...
  10. doi request reprint A unification of multivariate methods for meta-analysis of genetic association studies
    Pantelis G Bagos
    University of Central Greece
    Stat Appl Genet Mol Biol 7:Article31. 2008
    ..Illustrative examples of code in Stata are given in the appendix. It is anticipated that the methods developed in this work will be widely applied in the meta-analysis of genetic association studies...
  11. doi request reprint The association between apolipoprotein E gene polymorphisms and essential hypertension: a meta-analysis of 45 studies including 13,940 cases and 16,364 controls
    S Stoumpos
    Department of Cell Biology and Biophysics, University of Athens, Athens, Greece
    J Hum Hypertens 27:245-55. 2013
    ..Further studies are needed in order to fully address questions about the etiological mechanism of the particular association, as well as to study the effect in populations of African descent...
  12. doi request reprint Prediction of signal peptides in archaea
    P G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece
    Protein Eng Des Sel 22:27-35. 2009
    ..The method, PRED-SIGNAL, and the results are freely available for academic users at http://bioinformatics.biol.uoa.gr/PRED-SIGNAL/ and we anticipate that it will be a valuable tool for the computational analysis of archaeal genomes...
  13. pmc PRED-GPCR: GPCR recognition and family classification server
    P K Papasaikas
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
    Nucleic Acids Res 32:W380-2. 2004
    ..The server returns all single-motif matches along with the combined results for the corresponding families. The service is available online since October 2003 at http://bioinformatics.biol.uoa.gr/PRED-GPCR...
  14. pmc Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15701, Greece
    BMC Bioinformatics 6:7. 2005
    ..Also, we describe, for the first time, an effective way to combine the individual predictors, at will, to a single consensus prediction method...
  15. pmc A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models
    Nikolaos G Sgourakis
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 157 01, Greece
    BMC Bioinformatics 6:104. 2005
    ..The method predicts the coupling preferences of GPCRs to Gs, Gi/o and Gq/11, but not G12/13 subfamilies...
  16. ncbi request reprint PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localization
    Evangelia I Petsalaki
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15701, Greece
    Genomics Proteomics Bioinformatics 4:48-55. 2006
    ..Furthermore, PredSL is the only method capable for the prediction of these subcellular localizations that is available as a stand-alone application through the URL:http://bioinformatics.biol.uoa.gr/PredSL/...
  17. pmc A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15701, Greece
    BMC Bioinformatics 5:29. 2004
    ..The model is trained in a discriminative manner, aiming at maximizing the probability of correct predictions rather than the likelihood of the sequences...
  18. ncbi request reprint Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: application to complete genomes
    Zoi I Litou
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece
    J Bioinform Comput Biol 6:387-401. 2008
    ..The prediction tool, the database with the proteins identified in the genomes, and supplementary material are available online at http://bioinformatics.biol.uoa.gr/CW-PRED/...
  19. doi request reprint How many 3D structures do we need to train a predictor?
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece
    Genomics Proteomics Bioinformatics 7:128-37. 2009
    ..Therefore, we should concentrate our efforts on utilizing new techniques for the development of even better scoring predictors...
  20. doi request reprint Fcgamma receptor polymorphisms and their association with periodontal disease: a meta-analysis
    Niki L Dimou
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, Greece
    J Clin Periodontol 37:255-65. 2010
    ..A systematic review and a meta-analysis were conducted in order to investigate the potential association of Fcgamma receptor (FcgammaR) polymorphisms with susceptibility to aggressive and chronic periodontal disease...
  21. doi request reprint gpDB: a database of GPCRs, G-proteins, effectors and their interactions
    Margarita C Theodoropoulou
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 157 01, Greece
    Bioinformatics 24:1471-2. 2008
    ....
  22. ncbi request reprint A method for meta-analysis of case-control genetic association studies using logistic regression
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
    Stat Appl Genet Mol Biol 6:Article17. 2007
    ..A STATA command performing all the available computations is available at http://bioinformatics.biol.uoa.gr/~pbagos/metagen/...
  23. ncbi request reprint Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks
    Nikolaos G Sgourakis
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
    Bioinformatics 21:4101-6. 2005
    ..To date all published methods that predict the coupling specificity of GPCRs are restricted to three main coupling groups G(i/o), G(q/11) and G(s), not including G(12/13)-coupled or other promiscuous receptors...
  24. pmc Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 157 01, Greece
    BMC Bioinformatics 7:189. 2006
    ..However, no clear and formal explanation of the algorithms that retains the probabilistic interpretation of the models has been presented so far in the literature...
  25. ncbi request reprint The GNB3 C825T polymorphism and essential hypertension: a meta-analysis of 34 studies including 14,094 cases and 17,760 controls
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, Greece
    J Hypertens 25:487-500. 2007
    ..In an effort to clarify earlier inconclusive results, we performed a meta-analysis of population-based case-control genetic association studies...
  26. ncbi request reprint A novel method for GPCR recognition and family classification from sequence alone using signatures derived from profile hidden Markov models
    P K Papasaikas
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
    SAR QSAR Environ Res 14:413-20. 2003
    ..A web-based version of the application is freely available at URL: http:/bioinformatics.biol.uoa.gr/PRED-GPCR...
  27. ncbi request reprint beta-Barrel transmembrane proteins: Geometric modelling, detection of transmembrane region, and structural properties
    Ioannis K Valavanis
    Faculty of Informatics and Telecommunications, University of Athens, Panepistimiopolis, Athens 15784, Greece
    Comput Biol Chem 30:416-24. 2006
    ..In addition, we quantify the abundance of all amino acids and the average hydrophobicity for external and internal beta-stranded residues along the axis of beta-barrel, thus confirming and extending other researchers' results...
  28. pmc PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15701, Greece
    Nucleic Acids Res 32:W400-4. 2004
    ....
  29. pmc A database for G proteins and their interaction with GPCRs
    Antigoni L Elefsinioti
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 157 01, Greece
    BMC Bioinformatics 5:208. 2004
    ....
  30. doi request reprint Plasminogen activator inhibitor-1 4G/5G and 5,10-methylene-tetrahydrofolate reductase C677T polymorphisms in polycystic ovary syndrome
    Pantelis G Bagos
    Department of Informatics with Applications in Biomedicine, University of Central Greece, Lamia 35100, Greece
    Mol Hum Reprod 15:19-26. 2009
    ..Further studies are needed in order to investigate the etiologic mechanism behind this association, as well as the interrelations with other components of the metabolic syndrome (hypertension, diabetes, etc.)...
  31. ncbi request reprint Plasminogen activator inhibitor-1 4G/5G polymorphism and risk of ischemic stroke: a meta-analysis
    Argirios E Tsantes
    Laboratory of Hematology and Blood Bank Unit, Attikon General Hospital, School of Medicine, University of Athens, Athens, Greece
    Blood Coagul Fibrinolysis 18:497-504. 2007
    ..The effect of this genotype on risk of ischemic stroke in acute stressful diseases and the role of cohort studies in genetic epidemiology, however, warrant further investigation...
  32. ncbi request reprint Lack of association between the platelet glycoprotein Ia C807T gene polymorphism and coronary artery disease: a meta-analysis
    Argirios E Tsantes
    Laboratory of Hematology and Blood Bank Unit, Attikon General Hospital, School of Medicine, University of Athens, Athens, Greece
    Int J Cardiol 118:189-96. 2007
    ..The importance of the GPla gene C807T polymorphism as a genetic risk factor for coronary artery disease (CAD) remains controversial. To assess this association, we performed a meta-analysis of published data...
  33. ncbi request reprint Association between the plasminogen activator inhibitor-1 4G/5G polymorphism and venous thrombosis. A meta-analysis
    Argirios E Tsantes
    Laboratory of Hematology and Blood Bank Unit, Attikon General Hospital, School of Medicine, University of Athens, Athens, Greece
    Thromb Haemost 97:907-13. 2007
    ..Recommendation for detection of this polymorphism in evaluating thrombophilia in such patients might be considered...
  34. doi request reprint Polymorphisms of the insulin receptor and the insulin receptor substrates genes in polycystic ovary syndrome: a Mendelian randomization meta-analysis
    Anastasios Ioannidis
    Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2 4, 351 00 Lamia, Greece
    Mol Genet Metab 99:174-83. 2010
    ....
  35. pmc Phoenix 100 versus Vitek 2 in the identification of gram-positive and gram-negative bacteria: a comprehensive meta-analysis
    Kalliopi Stavroula Chatzigeorgiou
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens, Greece
    J Clin Microbiol 49:3284-91. 2011
    ..Future simultaneous assessment of the instruments against molecular comparator procedures may facilitate interpretation of the current observations...
  36. ncbi request reprint TMRPres2D: high quality visual representation of transmembrane protein models
    Ioannis C Spyropoulos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
    Bioinformatics 20:3258-60. 2004
    ..Several important biological and physical sequence attributes can be embedded in the graphical representation...
  37. ncbi request reprint No evidence for association of CTLA-4 gene polymorphisms with the risk of developing multiple sclerosis: a meta-analysis
    Pantelis G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, Greece
    Mult Scler 13:156-68. 2007
    ....