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Items: 1 to 50 of 86

1.

JUCHMME: A Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis.

Tamposis IA, Tsirigos KD, Theodoropoulou MC, Kontou PI, Tsaousis GN, Sarantopoulou D, Litou ZI, Bagos PG.

Bioinformatics. 2019 Jun 28. pii: btz533. doi: 10.1093/bioinformatics/btz533. [Epub ahead of print]

PMID:
31250907
2.

Susceptibility to leishmaniasis is affected by host SLC11A1 gene polymorphisms: a systematic review and meta-analysis.

Braliou GG, Kontou PI, Boleti H, Bagos PG.

Parasitol Res. 2019 Jun 23. doi: 10.1007/s00436-019-06374-y. [Epub ahead of print] Review.

PMID:
31230160
3.

Ten simple rules for carrying out and writing meta-analyses.

Forero DA, Lopez-Leon S, González-Giraldo Y, Bagos PG.

PLoS Comput Biol. 2019 May 16;15(5):e1006922. doi: 10.1371/journal.pcbi.1006922. eCollection 2019 May. No abstract available.

4.

Season of birth and multiple sclerosis: a systematic review and multivariate meta-analysis.

Pantavou KG, Bagos PG.

J Neurol. 2019 May 4. doi: 10.1007/s00415-019-09346-5. [Epub ahead of print] Review.

PMID:
31055633
5.

Semi-supervised learning of Hidden Markov Models for biological sequence analysis.

Tamposis IA, Tsirigos KD, Theodoropoulou MC, Kontou PI, Bagos PG.

Bioinformatics. 2018 Nov 16. doi: 10.1093/bioinformatics/bty910. [Epub ahead of print]

PMID:
30445435
6.

Extending hidden Markov models to allow conditioning on previous observations.

Tamposis IA, Theodoropoulou MC, Tsirigos KD, Bagos PG.

J Bioinform Comput Biol. 2018 Oct;16(5):1850019. doi: 10.1142/S0219720018500191. Epub 2018 Aug 3.

PMID:
30353782
7.

Methods of Analysis and Meta-Analysis for Identifying Differentially Expressed Genes.

Kontou PI, Pavlopoulou A, Bagos PG.

Methods Mol Biol. 2018;1793:183-210. doi: 10.1007/978-1-4939-7868-7_12.

PMID:
29876898
8.

Multivariate Methods for Meta-Analysis of Genetic Association Studies.

Dimou NL, Pantavou KG, Braliou GG, Bagos PG.

Methods Mol Biol. 2018;1793:157-182. doi: 10.1007/978-1-4939-7868-7_11. Review.

PMID:
29876897
9.

Interleukin gene polymorphisms and susceptibility to HIV-1 infection: a meta-analysis.

Tsiara CG, Nikolopoulos GK, Dimou NL, Pantavou KG, Bagos PG, Mensah B, Talias M, Braliou GG, Paraskeva D, Bonovas S, Hatzakis A.

J Genet. 2018 Mar;97(1):235-251.

10.

Bipartite graphs in systems biology and medicine: a survey of methods and applications.

Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG.

Gigascience. 2018 Apr 1;7(4):1-31. doi: 10.1093/gigascience/giy014. Review.

11.

Bivariate genome-wide association meta-analysis of pediatric musculoskeletal traits reveals pleiotropic effects at the SREBF1/TOM1L2 locus.

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.

Nat Commun. 2017 Jul 25;8(1):121. doi: 10.1038/s41467-017-00108-3.

12.

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.

Theodosiou T, Efstathiou G, Papanikolaou N, Kyrpides NC, Bagos PG, Iliopoulos I, Pavlopoulos GA.

BMC Res Notes. 2017 Jul 14;10(1):278. doi: 10.1186/s13104-017-2607-8.

13.

Apolipoprotein E Polymorphism and Left Ventricular Failure in Beta-Thalassemia: A Multivariate Meta-Analysis.

Dimou NL, Pantavou KG, Bagos PG.

Ann Hum Genet. 2017 Sep;81(5):213-223. doi: 10.1111/ahg.12203. Epub 2017 Jul 2.

PMID:
28670684
14.

Molecular determinants of radiosensitivity in normal and tumor tissue: A bioinformatic approach.

Pavlopoulou A, Bagos PG, Koutsandrea V, Georgakilas AG.

Cancer Lett. 2017 Sep 10;403:37-47. doi: 10.1016/j.canlet.2017.05.023. Epub 2017 Jun 12. Review.

PMID:
28619524
15.

The impact of pneumatic tube system on routine laboratory parameters: a systematic review and meta-analysis.

Kapoula GV, Kontou PI, Bagos PG.

Clin Chem Lab Med. 2017 Oct 26;55(12):1834-1844. doi: 10.1515/cclm-2017-0008. Review.

PMID:
28593926
16.

Predicting Alpha Helical Transmembrane Proteins Using HMMs.

Tsaousis GN, Theodoropoulou MC, Hamodrakas SJ, Bagos PG.

Methods Mol Biol. 2017;1552:63-82. doi: 10.1007/978-1-4939-6753-7_5.

PMID:
28224491
17.

Predicting Beta Barrel Transmembrane Proteins Using HMMs.

Tsaousis GN, Hamodrakas SJ, Bagos PG.

Methods Mol Biol. 2017;1552:43-61. doi: 10.1007/978-1-4939-6753-7_4.

PMID:
28224490
18.

GWAR: robust analysis and meta-analysis of genome-wide association studies.

Dimou NL, Tsirigos KD, Elofsson A, Bagos PG.

Bioinformatics. 2017 May 15;33(10):1521-1527. doi: 10.1093/bioinformatics/btx008.

PMID:
28108451
19.

A meta-analysis of FZD3 gene polymorphisms and their association with schizophrenia.

Pantavou KG, Braliou GG, Kontou PI, Dimou NL, Bagos PG.

Psychiatr Genet. 2016 Dec;26(6):272-280.

PMID:
27755292
20.

PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins.

Tsirigos KD, Elofsson A, Bagos PG.

Bioinformatics. 2016 Sep 1;32(17):i665-i671. doi: 10.1093/bioinformatics/btw444.

PMID:
27587687
21.

Data and programs in support of network analysis of genes and their association with diseases.

Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos GA, Bagos PG.

Data Brief. 2016 Jul 19;8:1036-9. doi: 10.1016/j.dib.2016.07.022. eCollection 2016 Sep.

22.

Network analysis of genes and their association with diseases.

Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos GA, Bagos PG.

Gene. 2016 Sep 15;590(1):68-78. doi: 10.1016/j.gene.2016.05.044. Epub 2016 Jun 2.

23.

Unraveling the mechanisms of extreme radioresistance in prokaryotes: Lessons from nature.

Pavlopoulou A, Savva GD, Louka M, Bagos PG, Vorgias CE, Michalopoulos I, Georgakilas AG.

Mutat Res Rev Mutat Res. 2016 Jan-Mar;767:92-107. doi: 10.1016/j.mrrev.2015.10.001. Epub 2015 Nov 4. Review.

PMID:
27036069
24.

A multivariate method for meta-analysis and comparison of diagnostic tests.

Dimou NL, Adam M, Bagos PG.

Stat Med. 2016 Sep 10;35(20):3509-23. doi: 10.1002/sim.6919. Epub 2016 Mar 4.

PMID:
26940666
25.

Meta-analysis in Stata using gllamm.

Bagos PG.

Res Synth Methods. 2015 Dec;6(4):310-32. doi: 10.1002/jrsm.1157. Epub 2015 Nov 27.

PMID:
26612788
26.

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G.

Database (Oxford). 2015 Jul 11;2015:bav063. doi: 10.1093/database/bav063. eCollection 2015.

27.

Polymorphisms of the CD24 Gene Are Associated with Risk of Multiple Sclerosis: A Meta-Analysis.

Braliou GG, Pantavou KG, Kontou PI, Bagos PG.

Int J Mol Sci. 2015 Jun 1;16(6):12368-81. doi: 10.3390/ijms160612368.

28.

Emerging molecular networks common in ionizing radiation, immune and inflammatory responses by employing bioinformatics approaches.

Georgakilas AG, Pavlopoulou A, Louka M, Nikitaki Z, Vorgias CE, Bagos PG, Michalopoulos I.

Cancer Lett. 2015 Nov 28;368(2):164-72. doi: 10.1016/j.canlet.2015.03.021. Epub 2015 Apr 1. Review.

PMID:
25841996
29.

Key challenges for the creation and maintenance of specialist protein resources.

Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn 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.

Proteins. 2015 Jun;83(6):1005-13. doi: 10.1002/prot.24803. Epub 2015 Apr 22.

30.

The role of genetic polymorphisms of the Renin-Angiotensin System in renal diseases: A meta-analysis.

Braliou GG, Grigoriadou AM, Kontou PI, Bagos PG.

Comput Struct Biotechnol J. 2014 Jun 11;10(16):1-7. doi: 10.1016/j.csbj.2014.05.006. eCollection 2014 Jun.

31.

The association between plasminogen activator inhibitor type 1 (PAI-1) levels, PAI-1 4G/5G polymorphism, and myocardial infarction: a Mendelian randomization meta-analysis.

Nikolopoulos GK, Bagos PG, Tsangaris I, Tsiara CG, Kopterides P, Vaiopoulos A, Kapsimali V, Bonovas S, Tsantes AE.

Clin Chem Lab Med. 2014 Jul;52(7):937-50. doi: 10.1515/cclm-2013-1124.

32.

Multivariate meta-analysis of the association of G-protein beta 3 gene (GNB3) haplotypes with cardiovascular phenotypes.

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.

Mol Biol Rep. 2014 May;41(5):3113-25. doi: 10.1007/s11033-014-3171-0. Epub 2014 Jan 30.

PMID:
24477587
33.

Are sample sizes clear and justified in RCTs published in dental journals?

Koletsi D, Fleming PS, Seehra J, Bagos PG, Pandis N.

PLoS One. 2014 Jan 21;9(1):e85949. doi: 10.1371/journal.pone.0085949. eCollection 2014. Erratum in: PLoS One. 2014;9(3):e85949.

34.

HMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction.

Tsaousis GN, Bagos PG, Hamodrakas SJ.

Biochim Biophys Acta. 2014 Feb;1844(2):316-22. doi: 10.1016/j.bbapap.2013.11.001. Epub 2013 Nov 10.

PMID:
24225132
35.

Effect of hepatitis C virus on immunological and virological responses in HIV-infected patients initiating highly active antiretroviral therapy: a meta-analysis.

Tsiara CG, Nikolopoulos GK, Dimou NL, Bagos PG, Saroglou G, Velonakis E, Hatzakis A.

J Viral Hepat. 2013 Oct;20(10):715-24. doi: 10.1111/jvh.12101. Epub 2013 May 3.

PMID:
24010646
36.

Genetic model selection in genome-wide association studies: robust methods and the use of meta-analysis.

Bagos PG.

Stat Appl Genet Mol Biol. 2013 Jun;12(3):285-308. doi: 10.1515/sagmb-2012-0016. Review.

PMID:
23629457
37.

Percutaneous coronary intervention versus optimal medical therapy for prevention of spontaneous myocardial infarction in subjects with stable ischemic heart disease.

Bangalore S, Pursnani S, Kumar S, Bagos PG.

Circulation. 2013 Feb 19;127(7):769-81. doi: 10.1161/CIRCULATIONAHA.112.131961. Epub 2013 Jan 16.

PMID:
23325526
38.

Meeting report: the seventh conference of the hellenic society for computational biology and bioinformatics.

Hamodrakas SJ, Iliopoulos I, Ouzounis CA, Bagos PG, Promponas VJ.

Comput Struct Biotechnol J. 2013 Jun 16;6:e201303006. doi: 10.5936/csbj.201303006. eCollection 2013. No abstract available.

39.

Use of fibrates and cancer risk: a systematic review and meta-analysis of 17 long-term randomized placebo-controlled trials.

Bonovas S, Nikolopoulos GK, Bagos PG.

PLoS One. 2012;7(9):e45259. doi: 10.1371/journal.pone.0045259. Epub 2012 Sep 19. Review.

40.

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 SJ, Anthopoulos PG, Bagos PG.

J Hum Hypertens. 2013 Apr;27(4):245-55. doi: 10.1038/jhh.2012.37. Epub 2012 Sep 13.

PMID:
22971752
41.

On the covariance of two correlated log-odds ratios.

Bagos PG.

Stat Med. 2012 Jun 30;31(14):1418-31. doi: 10.1002/sim.4474. Epub 2012 Feb 3.

PMID:
22302419
42.

Methylene tetrahydrofolate reductase gene polymorphisms and their association with methotrexate toxicity: a meta-analysis.

Spyridopoulou KP, Dimou NL, Hamodrakas SJ, Bagos PG.

Pharmacogenet Genomics. 2012 Feb;22(2):117-33. doi: 10.1097/FPC.0b013e32834ded2a.

PMID:
22143415
43.

Impact of HIV type 1 DNA levels on spontaneous disease progression: a meta-analysis.

Tsiara CG, Nikolopoulos GK, Bagos PG, Goujard C, Katzenstein TL, Minga AK, Rouzioux C, Hatzakis A.

AIDS Res Hum Retroviruses. 2012 Apr;28(4):366-73. doi: 10.1089/aid.2011.0032. Epub 2011 Aug 30.

PMID:
21877926
44.

Phoenix 100 versus Vitek 2 in the identification of gram-positive and gram-negative bacteria: a comprehensive meta-analysis.

Chatzigeorgiou KS, Sergentanis TN, Tsiodras S, Hamodrakas SJ, Bagos PG.

J Clin Microbiol. 2011 Sep;49(9):3284-91. doi: 10.1128/JCM.00182-11. Epub 2011 Jul 13.

45.

Using graph theory to analyze biological networks.

Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG.

BioData Min. 2011 Apr 28;4:10. doi: 10.1186/1756-0381-4-10.

46.

Cytokine gene polymorphisms in multiple sclerosis: a meta-analysis of 45 studies including 7379 cases and 8131 controls.

Nikolopoulos GK, Masgala A, Tsiara C, Limitsiou OK, Karnaouri AC, Dimou NL, Bagos PG.

Eur J Neurol. 2011 Jul;18(7):944-51. doi: 10.1111/j.1468-1331.2011.03355.x. Epub 2011 Feb 8.

PMID:
21299734
47.
48.

Developing the evidence base for cancer chemoprevention: use of meta-analysis.

Nikolopoulos GK, Bagos PG, Bonovas S.

Curr Drug Targets. 2011 Dec;12(13):1989-97. Review.

PMID:
21158703
49.

OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria.

Tsirigos KD, Bagos PG, Hamodrakas SJ.

Nucleic Acids Res. 2011 Jan;39(Database issue):D324-31. doi: 10.1093/nar/gkq863. Epub 2010 Oct 15.

50.

A multipoint method for meta-analysis of genetic association studies.

Bagos PG, Liakopoulos TD.

Genet Epidemiol. 2010 Nov;34(7):702-15. doi: 10.1002/gepi.20531.

PMID:
20853440

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