Browsing by Author "Hamodrakas, S. J."
Now showing items 1-17 of 17
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Apolipoprotein E polymorphisms and type 2 diabetes: A meta-analysis of 30 studies including 5423 cases and 8197 controls
Anthopoulos, P. G.; Hamodrakas, S. J.; Bagos, P. G. (2010)Type 2 diabetes mellitus (T2DM) is a highly complicated metabolic disorder for which there is worldwide effort for the identification of susceptibility genes. Polymorphisms of the Apolipoprotein E (ApoE) gene are associated ... -
The association between apolipoprotein E gene polymorphisms and essential hypertension: a meta-analysis of 45 studies including 13 940 cases and 16 364 controls
Stoumpos, S.; Hamodrakas, S. J.; Anthopoulos, P. G.; Bagos, P. G. (2013)The apolipoprotein E single-nucleotide polymorphisms are among the potential candidate genes that may serve as modulators in susceptibility to essential hypertension. In an effort to clarify earlier inconclusive results, ... -
Bacterial β-barrel outer membrane proteins: A common structural theme implicated in a wide variety of functional roles
Bagos, P. G.; Hamodrakas, S. J. (2008)β-barrel outer membrane proteins constitute the second and less well-studied class of transmembrane proteins. They are present exclusively in the outer membrane of Gram-negative bacteria and presumably in the outer membrane ... -
Computational methods for the prediction of GPCRs coupling selectivity
Sgourakis, N. G.; Bagos, P. G.; Hamodrakas, S. J. (2008)GPCRs comprise a wide and diverse class of eukaryotic transmembrane proteins with well-established pharmacological significance. As a consequence of recent genome projects, there is a wealth of information at the sequence ... -
CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria
Fimereli, D. K.; Tsirigos, K. D.; Litou, Z. I.; Liakopoulos, T. D.; Bagos, P. G.; Hamodrakas, S. J. (2012)Gram-positive bacteria have surface proteins that are often implicated in virulence. A group of extracellular proteins attached to the cell wall contains an LPXTG-like motif that is target for cleavage and covalent coupling ... -
Cytokine gene polymorphisms in periodontal disease: a meta-analysis of 53 studies including 4178 cases and 4590 controls
Nikolopoulos, G. K.; Dimou, N. L.; Hamodrakas, S. J.; Bagos, P. G. (2008)Aim: We conducted a systematic review and a meta-analysis, in order to investigate the potential association of cytokine gene polymorphisms with either aggressive or chronic periodontal disease. Material and Methods: A ... -
ExTopoDB: a database of experimentally derived topological models of transmembrane proteins
Tsaousis, G. N.; Tsirigos, K. D.; Andrianou, X. D.; Liakopoulos, T. D.; Bagos, P. G.; Hamodrakas, S. J. (2010)ExTopoDB is a publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains information collected from studies in the literature that report the use of biochemical methods ... -
Fc gamma receptor polymorphisms and their association with periodontal disease: a meta-analysis
Dimou, N. L.; Nikolopoulos, G. K.; Hamodrakas, S. J.; Bagos, P. G. (2010)Aim: A systematic review and a meta-analysis were conducted in order to investigate the potential association of Fc gamma receptor (Fc gamma R) polymorphisms with susceptibility to aggressive and chronic periodontal disease. ... -
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques
Satagopam, V. P.; Theodoropoulou, M. C.; Stampolakis, C. K.; Pavlopoulos, G. A.; Papandreou, N. C.; Bagos, P. G.; Schneider, R.; Hamodrakas, S. J. (2010)G-protein coupled receptors (GPCRs) are a major family of membrane receptors in eukaryotic cells. They play a crucial role in the communication of a cell with the environment. Ligands bind to GPCRs on the outside of the ... -
gpDB: a database of GPCRs, G-proteins, effectors and their interactions
Theodoropoulou, M. C.; Bagos, P. G.; Spyropoulos, I. C.; Hamodrakas, S. J. (2008)gpDB is a publicly accessible, relational database, containing information about G-proteins, G-protein coupled receptors (GPCRs) and effectors, as well as information concerning known interactions between these molecules. ... -
HMMpTM: Improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction
Tsaousis, G. N.; Bagos, P. G.; Hamodrakas, S. J. (2014)During the last two decades a large number of Computational methods have been developed for predicting transmembrane protein topology. Current predictors rely on topogenic signals in the protein sequence, such as the ... -
How Many 3D Structures Do We Need to Train a Predictor?
Bagos, P. G.; Tsaousis, G. N.; Hamodrakas, S. J. (2009)It has been shown that the progress in the determination of membrane protein structure grows exponentially, with approximately the same growth rate as that of the water-soluble proteins. In order to investigate the effect ... -
Methylene tetrahydrofolate reductase gene polymorphisms and their association with methotrexate toxicity: a meta-analysis
Spyridopoulou, K. P.; Dimou, N. L.; Hamodrakas, S. J.; Bagos, P. G. (2012)Objective A systematic review and a meta-analysis were conducted, to investigate the possible association of methylene tetrahydrofolate reductase (MTHFR) gene polymorphisms with adverse effects related to methotrexate ... -
Phoenix 100 versus Vitek 2 in the Identification of Gram-Positive and Gram-Negative Bacteria: a Comprehensive Meta-Analysis
Chatzigeorgiou, K. S.; Sergentanis, T. N.; Tsiodras, S.; Hamodrakas, S. J.; Bagos, P. G. (2011)Phoenix 100 and Vitek 2 (operating with the current colorimetric cards) are commonly used in hospital laboratories for rapid identification of microorganisms. The present meta-analysis aims to evaluate and compare their ... -
Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: Application to complete genomes
Litou, Z. I.; Bagos, P. G.; Tsirigos, K. D.; Liakopoulos, T. D.; Hamodrakas, S. J. (2008)Surface proteins in Gram-positive bacteria are frequently implicated in virulence. We have focused on a group of extracellular cell wall-attached proteins (CWPs), containing an LPXTG motif for cleavage and covalent coupling ... -
Prediction of Lipoprotein Signal Peptides in Gram-Positive Bacteria with a Hidden Markov Model
Bagos, P. G.; Tslrigos, K. D.; Liakopoulos, T. D.; Hamodrakas, S. J. (2008)We present a Hidden Markov Model method for the prediction of lipoprotein signal peptides of Gram-positive bacteria, trained on a set of 67 experimentally verified lipoproteins. The method outperforms LipoP and the methods ... -
Prediction of signal peptides in archaea
Bagos, P. G.; Tsirigos, K. D.; Plessas, S. K.; Liakopoulos, T. D.; Hamodrakas, S. J. (2009)Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, ...