P G Bagos

Summary

Affiliation: University of Athens
Country: Greece

Publications

  1. 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
  2. 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
  3. ncbi request reprint Chlamydia pneumoniae infection and the risk of multiple sclerosis: a meta-analysis
    P G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, 15701, Greece
    Mult Scler 12:397-411. 2006
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications28

  1. 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...
  2. 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
    ....
  3. ncbi request reprint Chlamydia pneumoniae infection and the risk of multiple sclerosis: a meta-analysis
    P G Bagos
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, 15701, Greece
    Mult Scler 12:397-411. 2006
    ..Even though the presence of Cpn is clearly more likely in MS patients, these findings are insufficient to establish an etiologic relation...
  4. 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...
  5. 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...
  6. 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
    ....
  7. 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...
  8. 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...
  9. 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
    ....
  10. 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...
  11. 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...
  12. 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...
  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. ncbi 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...
  15. doi request reprint Effect of hepatitis C virus on immunological and virological responses in HIV-infected patients initiating highly active antiretroviral therapy: a meta-analysis
    C G Tsiara
    Hellenic Centre for Disease Control and Prevention, Athens, Greece
    J Viral Hepat 20:715-24. 2013
    ..Although this effect diminishes over time, early administration of HAART in the setting of co-infection seems to be justified...
  16. doi request reprint Cytokine gene polymorphisms in multiple sclerosis: a meta-analysis of 45 studies including 7379 cases and 8131 controls
    G K Nikolopoulos
    Hellenic Centre for Diseases Control and Prevention, Athens, Greece
    Eur J Neurol 18:944-51. 2011
    ..Within its limitations, the current literature-based meta-analysis does not indicate that specific polymorphic variations of genes encoding pro-inflammatory and anti-inflammatory cytokines affect susceptibility to multiple sclerosis...
  17. 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...
  18. 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...
  19. 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...
  20. 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/...
  21. 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...
  22. 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/...
  23. ncbi 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
    ....
  24. 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...
  25. 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...
  26. 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...
  27. ncbi request reprint Integrin, alpha 2 gene C807T polymorphism and risk of ischemic stroke: a meta-analysis
    Georgios K Nikolopoulos
    Hellenic Center for Disease Control and Prevention, Athens, Greece
    Thromb Res 119:501-10. 2007
    ..However, the research findings remain controversial...
  28. 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/...