On the covariance of two correlated log-odds ratiosPantelis 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...
Using graph theory to analyze biological networksGeorgios 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...
- 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 method is freely available for academic users at http://www.compgen.org/tools/PRED-TAT/...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localizationEvangelia 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/...
- 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/...
- 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...
- 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...
- 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...
- 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...
- 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
..AVAILABILITY: http://bioinformatics.biol.uoa.gr/gpDB CONTACT: shamodr@biol.uoa.gr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...
- 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/...
- 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
..AVAILABILITY: A webserver for academic users is available at http://bioinformatics.biol.uoa.gr/PRED-COUPLE2..
- 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...
- 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...
- 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...
- 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
....
- 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
....
- 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
....
- 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...
- 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.)...
- 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...
- 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...
- 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...
- 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...
- 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
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- 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...
