Pavlopoulos, Georgios

TitleBioinformaticist PD Fellow
InstitutionLawrence Berkeley National Lab
DepartmentJoint Genome Institute
Address1 Cyclotron Road
Berkeley CA 94720
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Azad A, Pavlopoulos G, Ouzounis CA, Kyrpides NC, Buluç A. HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks. Nucleic Acids Res. 2018 Apr 06; 46(6):e33. PMID: 29315405.
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    2. Pavlopoulos G, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG. Bipartite graphs in systems biology and medicine: a survey of methods and applications. Gigascience. 2018 Apr 01; 7(4):1-31. PMID: 29648623.
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    3. Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos G, Hadjithomas M, Varghese NJ, Paez-Espino D, Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat Biotechnol. 2018 Apr; 36(4):359-367. PMID: 29553575.
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    4. Paez-Espino D, Pavlopoulos G, Ivanova NN, Kyrpides NC. Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nat Protoc. 2017 Aug; 12(8):1673-1682. PMID: 28749930.
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    5. Pavlopoulos G, Paez-Espino D, Kyrpides NC, Iliopoulos I. Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. Adv Bioinformatics. 2017; 2017:1278932. PMID: 28804499.
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    6. Theodosiou T, Efstathiou G, Papanikolaou N, Kyrpides NC, Bagos PG, Iliopoulos I, Pavlopoulos G. NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks. BMC Res Notes. 2017 Jul 14; 10(1):278. PMID: 28705239.
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    7. Efstathiou G, Antonakis AN, Pavlopoulos G, Theodosiou T, Divanach P, Trudgian DC, Thomas B, Papanikolaou N, Aivaliotis M, Acuto O, Iliopoulos I. ProteoSign: an end-user online differential proteomics statistical analysis platform. Nucleic Acids Res. 2017 Jul 03; 45(W1):W300-W306. PMID: 28520987.
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    8. Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos G, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat Biotechnol. 2017 Jul; 35(7):676-683. PMID: 28604660.
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    9. Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos G, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Protein structure determination using metagenome sequence data. Science. 2017 01 20; 355(6322):294-298. PMID: 28104891.
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    10. Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos G, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 2017 Jan 04; 45(D1):D457-D465. PMID: 27799466.
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    11. Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos G, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC. Uncovering Earth's virome. Nature. 2016 08 25; 536(7617):425-30. PMID: 27533034.
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    12. Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos G, Bagos PG. Data and programs in support of network analysis of genes and their association with diseases. Data Brief. 2016 Sep; 8:1036-9. PMID: 27508260; PMCID: PMC4969244.
    13. Papanikolaou N, Pavlopoulos G, Theodosiou T, Vizirianakis IS, Iliopoulos I. DrugQuest - a text mining workflow for drug association discovery. BMC Bioinformatics. 2016 Jun 06; 17 Suppl 5:182. PMID: 27295093; PMCID: PMC4905607.
    14. Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos G, Bagos PG. Network analysis of genes and their association with diseases. Gene. 2016 Sep 15; 590(1):68-78. PMID: 27265032.
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    15. Pavlopoulos G, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I. Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience. 2015; 4:38. PMID: 26309733; PMCID: PMC4548842.
    16. Gkouskou KK, Ioannou M, Pavlopoulos G, Georgila K, Siganou A, Nikolaidis G, Kanellis DC, Moore S, Papadakis KA, Kardassis D, Iliopoulos I, McDyer FA, Drakos E, Eliopoulos AG. Apolipoprotein A-I inhibits experimental colitis and colitis-propelled carcinogenesis. Oncogene. 2016 05 12; 35(19):2496-505. PMID: 26279300.
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    17. Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos G, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I. Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights. 2015; 9:75-88. PMID: 25983555; PMCID: PMC4426941.
    18. Papanikolaou N, Pavlopoulos G, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. Bioinformatics. 2015 Mar 15; 31(6):979. PMID: 25673338.
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    19. Oulas A, Karathanasis N, Louloupi A, Pavlopoulos G, Poirazi P, Kalantidis K, Iliopoulos I. Prediction of miRNA targets. Methods Mol Biol. 2015; 1269:207-29. PMID: 25577381.
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    20. Papanikolaou N, Pavlopoulos G, Theodosiou T, Iliopoulos I. Protein-protein interaction predictions using text mining methods. Methods. 2015 Mar; 74:47-53. PMID: 25448298.
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    21. Papanikolaou N, Pavlopoulos G, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery. Bioinformatics. 2014 Nov 15; 30(22):3249-56. PMID: 25100685.
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    22. Pavlopoulos G, Promponas VJ, Ouzounis CA, Iliopoulos I. Biological information extraction and co-occurrence analysis. Methods Mol Biol. 2014; 1159:77-92. PMID: 24788262.
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    23. Pavlopoulos G, Oulas A, Iacucci E, Sifrim A, Moreau Y, Schneider R, Aerts J, Iliopoulos I. Unraveling genomic variation from next generation sequencing data. BioData Min. 2013 Jul 25; 6(1):13. PMID: 23885890; PMCID: PMC3726446.
    24. Pavlopoulos G, Kumar P, Sifrim A, Sakai R, Lin ML, Voet T, Moreau Y, Aerts J. Meander: visually exploring the structural variome using space-filling curves. Nucleic Acids Res. 2013 Jun; 41(11):e118. PMID: 23605045; PMCID: PMC3675473.
    25. Sifrim A, Van Houdt JK, Tranchevent LC, Nowakowska B, Sakai R, Pavlopoulos G, Devriendt K, Vermeesch JR, Moreau Y, Aerts J. Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. Genome Med. 2012; 4(9):73. PMID: 23013645; PMCID: PMC3580443.
    26. Iacucci E, Tranchevent LC, Popovic D, Pavlopoulos G, De Moor B, Schneider R, Moreau Y. ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. Bioinformatics. 2012 Sep 15; 28(18):i569-i574. PMID: 22962483; PMCID: PMC3436818.
    27. Michalopoulos I, Pavlopoulos G, Malatras A, Karelas A, Kostadima MA, Schneider R, Kossida S. Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes. BMC Res Notes. 2012 Jun 06; 5:265. PMID: 22672625; PMCID: PMC3441226.
    28. Secrier M, Pavlopoulos G, Aerts J, Schneider R. Arena3D: visualizing time-driven phenotypic differences in biological systems. BMC Bioinformatics. 2012 Mar 22; 13:45. PMID: 22439608; PMCID: PMC3368716.
    29. Soldatos TG, O'Donoghue SI, Satagopam VP, Barbosa-Silva A, Pavlopoulos G, Wanderley-Nogueira AC, Soares-Cavalcanti NM, Schneider R. Caipirini: using gene sets to rank literature. BioData Min. 2012 Feb 01; 5(1):1. PMID: 22297131; PMCID: PMC3307494.
    30. Moschopoulos CN, Pavlopoulos G, Iacucci E, Aerts J, Likothanassis S, Schneider R, Kossida S. Which clustering algorithm is better for predicting protein complexes? BMC Res Notes. 2011 Dec 20; 4:549. PMID: 22185599; PMCID: PMC3267700.
    31. Pavlopoulos G, Hooper SD, Sifrim A, Schneider R, Aerts J. Medusa: A tool for exploring and clustering biological networks. BMC Res Notes. 2011 Oct 06; 4:384. PMID: 21978489; PMCID: PMC3197509.
    32. Pavlopoulos G, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG. Using graph theory to analyze biological networks. BioData Min. 2011 Apr 28; 4:10. PMID: 21527005; PMCID: PMC3101653.
    33. Satagopam VP, Theodoropoulou MC, Stampolakis CK, Pavlopoulos G, Papandreou NC, Bagos PG, Schneider R, Hamodrakas SJ. GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. Database (Oxford). 2010 Aug 05; 2010:baq019. PMID: 20689020; PMCID: PMC2931634.
    34. Pavlopoulos G, Soldatos TG, Barbosa-Silva A, Schneider R. A reference guide for tree analysis and visualization. BioData Min. 2010 Feb 22; 3(1):1. PMID: 20175922; PMCID: PMC2844399.
    35. Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos G, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM. LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships. BMC Bioinformatics. 2010 Feb 01; 11:70. PMID: 20122157; PMCID: PMC3098111.
    36. Moschopoulos CN, Pavlopoulos G, Schneider R, Likothanassis SD, Kossida S. GIBA: a clustering tool for detecting protein complexes. BMC Bioinformatics. 2009 Jun 16; 10 Suppl 6:S11. PMID: 19534736; PMCID: PMC2697634.
    37. Pavlopoulos G, Moschopoulos CN, Hooper SD, Schneider R, Kossida S. jClust: a clustering and visualization toolbox. Bioinformatics. 2009 Aug 01; 25(15):1994-6. PMID: 19454618; PMCID: PMC2712340.
    38. Pavlopoulos G, Pafilis E, Kuhn M, Hooper SD, Schneider R. OnTheFly: a tool for automated document-based text annotation, data linking and network generation. Bioinformatics. 2009 Apr 01; 25(7):977-8. PMID: 19223449; PMCID: PMC2660876.
    39. Pavlopoulos G, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R. Arena3D: visualization of biological networks in 3D. BMC Syst Biol. 2008 Nov 28; 2:104. PMID: 19040715; PMCID: PMC2637860.
    40. Pavlopoulos G, Wegener AL, Schneider R. A survey of visualization tools for biological network analysis. BioData Min. 2008 Nov 28; 1:12. PMID: 19040716.
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