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    Pavlopoulos, Georgios

    TitleBioinformaticist PD Fellow
    SchoolLawrence Berkeley National Lab
    DepartmentJoint Genome Institute
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/296-5628
    vCardDownload vCard

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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. 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 Jun 12. PMID: 28604660.
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      2. 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 May 17. PMID: 28520987.
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      3. 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 Jan 20; 355(6322):294-298. PMID: 28104891.
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      4. 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. 2016 Oct 30. PMID: 27799466.
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      5. 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 Aug 25; 536(7617):425-30. PMID: 27533034.
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      6. 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.
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      7. Papanikolaou N, Pavlopoulos G, Theodosiou T, Vizirianakis IS, Iliopoulos I. DrugQuest - a text mining workflow for drug association discovery. BMC Bioinformatics. 2016; 17 Suppl 5:182. PMID: 27295093.
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      8. 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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      9. 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.
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      10. 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 May 12; 35(19):2496-505. PMID: 26279300.
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      11. 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.
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      12. 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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      13. 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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      14. 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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      15. 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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      16. 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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      17. 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; 6(1):13. PMID: 23885890.
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      18. 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.
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      19. 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.
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      20. 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.
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      21. 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; 5:265. PMID: 22672625.
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      22. Secrier M, Pavlopoulos G, Aerts J, Schneider R. Arena3D: visualizing time-driven phenotypic differences in biological systems. BMC Bioinformatics. 2012; 13:45. PMID: 22439608.
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      23. 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; 5(1):1. PMID: 22297131.
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      24. 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; 4:549. PMID: 22185599.
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      25. Pavlopoulos G, Hooper SD, Sifrim A, Schneider R, Aerts J. Medusa: A tool for exploring and clustering biological networks. BMC Res Notes. 2011; 4:384. PMID: 21978489.
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      26. 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; 4:10. PMID: 21527005.
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      27. 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; 2010:baq019. PMID: 20689020.
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      28. 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; 11:70. PMID: 20122157.
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      29. Moschopoulos CN, Pavlopoulos G, Schneider R, Likothanassis SD, Kossida S. GIBA: a clustering tool for detecting protein complexes. BMC Bioinformatics. 2009; 10 Suppl 6:S11. PMID: 19534736.
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      30. Pavlopoulos G, Moschopoulos CN, Hooper SD, Schneider R, Kossida S. jClust: a clustering and visualization toolbox. Bioinformatics. 2009 Aug 1; 25(15):1994-6. PMID: 19454618.
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      31. 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 1; 25(7):977-8. PMID: 19223449.
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      32. Pavlopoulos G, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R. Arena3D: visualization of biological networks in 3D. BMC Syst Biol. 2008; 2:104. PMID: 19040715.
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      33. Pavlopoulos G, Wegener AL, Schneider R. A survey of visualization tools for biological network analysis. BioData Min. 2008; 1:12. PMID: 19040716.
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