Publications are organized as Submitted, Journals, Conferences, Book Chapters and News and Media

Alternatively, all publications along with their citations can be found in Google Scholar and most of them in PubMed


    1. Exploring networks in the STRING & REACTOME database
      Koutrouli M, Sofianatos Y, Hatzis P, Pavlopoulos GA
      Book chapter in Systems Medicine: Integrative, Qualitative and Computational Approaches (submitted)

    2. Diversity, evolution, and classification of virophages uncovered through global metagenomics
      Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, Ivanova NN, Emiley Eloe-Fadrosh E, Tringe S, Kyrpides NC

    3. Large-scale analyses of human microbiomes reveal thousands of small, novel genes and their predicted functions
      Sberro H, Nicholas Greenfield N, Pavlopoulos GA, Kyrpides NC, Bhatt AS
      (submitted) - biorxiv preprint

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    5. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
      Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators, 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.
      Nature Biotechnology. 2018 Mar 19. doi: 10.1038/nbt.4110. PMID:29553575 

    6. Bipartite Graphs in Systems Biology and Medicine: a survey of methods and applications
      Pavlopoulos GA*, Kontou PI*, Pavlopoulou A, Bougioukos C, Markou E, Bagos PG
      GigaScience,Volume 7, Issue 4, 1 April 2018,, *equal first authors PMID:29648623 

    7. HipMCL: A high-performance parallel implementation of the Markov clustering algorithm for large-scale networks.
      Azad A., Pavlopoulos GA, Ouzounis C., Kyrpides NC, Βuluc A.
      Nucleic Acids Research, 5 Jan 2018,, PMID:29315405 

    8. Empirical comparison of visualization tools for larger-scale network analysis
      Pavlopoulos GA, Paez-Espino D, Kyrpides NC, Iliopoulos I.
      Advances in Bioinformatics, vol. 2017, Article ID 1278932, 8 pages, 2017. doi:10.1155/2017/1278932 PMID:28804499 

    9. Non-targeted virus sequence discovery pipeline and virus clustering for metagenomic data
      Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC
      Nature Protocols 2017 Aug;12(8):1673-1682. doi: 10.1038/nprot.2017.063. PMID:28749930 

    10. 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 Research Notes, 2017, 10:278, DOI: 10.1186/s13104-017-2607-8

    11. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
      Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, 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
      Nature Biotechnology, 2017 Jun 12. doi: 10.1038/nbt.3886, PMID:28604660 

    12. ProteoSign: An end-user online differential proteomics statistical analysis platform.
      Efstathiou G, Antonakis AN, Pavlopoulos GA, Theodosiou T, Divanach P, Trudgian DC, Thomas B, Papanikolaou N, Aivaliotis M, Acuto O, Iliopoulos I.
      Nucleic Acids Research, 2017 May 17. doi: 10.1093/nar/gkx444. PMID:28520987 

    13. Protein structure determination using metagenome sequence data
      Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D.
      Science,  20 Jan 2017:Vol. 355, Issue 6322, pp. 294-298, DOI: 10.1126/science.aah4043 PMID:28104891

    14. IMG/VR: A database of cultured and uncultured DNA Viruses and Retroviruses
      Paez-Espino D, Chen AI, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, Reddy TBK, Pavlopoulos GA, 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 W, Rivers AR, Ivanova NN, Kyrpides NC
      Nucleic Acids Research, October 2016, gkw1030v1-gkw1030. PMID:27799466

    15. Uncovering Earth's Virome
      Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC
      Nature, 2016 Aug 17;536(7617):425-430. doi: 10.1038/nature19094. PMID:27533034

    16. DrugQuest: A text-mining workflow for drug association discovery
      Papanikolaou N, Pavlopoulos GA, Theodosiou T, Vizirianakis IS, Iliopoulos I.
      BMC Bioinformatics, June 2016, 17 (Suppl 5):182 DOI 10.1186/s12859-016-1041-6. PMID:27295093

    17. 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 in Brief, 2016 Jul 19;8:1036-9. doi: 10.1016/j.dib.2016.07.022. eCollection 2016. PMID:27508260

    18. Network analysis of genes and their association with diseases
      Kontou PI, Pavlopoulou A., Dimou NL, Pavlopoulos GA, Bagos PG.
      Gene (Elsevier), Volume 590, Issue 1, 15 September 2016, Pages 68-78, doi:10.1016/j.gene.2016.05.044 PMID:27265032

    19. Apolipoprotein A-I inhibits experimental colitis and colitis-propelled carcinogenesis
      Gkouskou KK, Ioannou M, Pavlopoulos GA, Georgila K, Siganou A, Nikolaidis G, Kanellis DC, Moore S, Papadakis KA, Kardassis D, Iliopoulos I, McDyer FA, Drakos E, Eliopoulos AG.
      Oncogene, 2015 Aug 17. doi: 10.1038/onc.2015.307, PMID:26279300

    20. Visualizing Genome and Systems biology: technologies, tools, implementation techniques and trends, past, present and future
      Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright A., Iliopoulos I
      GigaScience, 25 Aug 2015, 4:38 DOI: 10.1186/s13742-015-0077-2 PMID:26309733

    21. Metagenomics: tools and insights for analyzing NGS sequencing data derived from biodiversity studies
      Oulas A, Pavloudi C, Polymenakou P, Papanikolaou N, Pavlopoulos GA , Kotoulas G, Arvanitidis C, Iliopoulos I.
      Bioinformatics and Biology Insights, 25 May 2015, 5;9:75-88. doi: 10.4137/BBI.S12462. eCollection 2015, PMID:25983555

    22. Protein-Protein interaction predictions using text-mining tools
      Papanikolaou N, Pavlopoulos GA, Theodosiou T, Iliopoulos I.
      Methods, 2014, Oct 28. pii: S1046-2023(14) 00352-1. doi: 10.1016/j.ymeth.2014.10.026. PMID:25448298

    23. BioTextQuest+: A knowledge integration platform for literature mining and concept discovery
      Papanikolaou N*, Pavlopoulos GA*, Pafilis E, Theodosiou T, Schneider R, Satagopam V, Ouzounis C, Eliopoulos A, Promponas VJ, Iliopoulos I.
      *equal first authors
      Bioinformatics, 2014,doi: 10.1093/bioinformatics/btu524, PMID:25100685

    24. Unraveling genomic variation from next generation sequencing data
      Pavlopoulos GA, Oulas A, Iacucci E, Sifrim A, Moreau Y, Schneider R, Aerts J, Iliopoulos I.
      BioData Min, 2013 July 6:13, doi:10.1186/1756-0381-6-13 PMID:23885890

    25. Meander: visually exploring the structural variome using space-filling curves
      Pavlopoulos GA, Sifrim A, Sakai R, Kumar PD, Voet T, Moreau Y, Aerts J.
      Nucleic Acids Research, 2013, 1:9 doi:10.1093/nar/gkt254 PMID:23605045

    26. A bioinformatics e-dating story: computational prediction and prioritization of receptor-ligand pairs
      Iacucci E, Tranchevent LC, Popovic D, Pavlopoulos GA,De Moor B, Schneider R, Sifrim A, Moreau Y
      BMC Bioinformatics, 2012, 13(Suppl 18):A7 LINK

    27. Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease
      Sifrim A, Van Houdt JK, Tranchevent LC, Nowakowska B, Sakai R, Pavlopoulos GA, Devriendt K, Vermeesch JR, Moreau Y, Aerts J.
      Genome Medicine, 2012, 4:73 doi:10.1186/gm374. PMID:23013645

    28. ReLiance: A machine learning and literature-based prioritization of Receptor-Ligand pairings
      Iacucci E, Tranchevent LC, Popovic D, Pavlopoulos GA, De Moor B, Schneider R, Moreau Y.
      Bioinformatics (Oxford), 2012 Sep 15;28(18):i569-i574. PMID:22962483

    29. Human Gene Correlation Analysis (HGCA): A tool for the identification of transcriptionally co-expressed genes
      Michalopoulos I, Pavlopoulos GA, Malatras A, Karelas A, Kostadima MA, Schneider R, Kossida S.
      BMC Research Notes, 2012, 5:265. PMID:22672625

    30. Arena3D: Visualizing time-driven phenotypic differences in biological systems
      Secrier M, Pavlopoulos GA, Aerts J, Schneider R.
      BMC Bioinformatics, 2012 Mar 22;13(1):45. PMID:22439608

    31. Caipirini: Using gene sets to search literature
      Soldatos TG, O'Donoghue SI, Satagopam VP, Barbosa-Silva A, Pavlopoulos GA, Wanderley-Nogueira AC, Soares-Cavalcanti NM, Schneider R.
      BioData Min, 2012 Feb 1;5(1):1. PMID:22297131

    32. Which algorithm is better for predicting protein complexes?
      Moschopoulos CN, Pavlopoulos GA, Iacucci E, Aerts J, Likothanassis SD, Schneider R, Kossida S.
      BMC Res Notes, 2011 Dec 20; 4:549. PMID:22185599

    33. Analyzing protein-protein interaction networks with web tools
      Moschopoulos CN, Pavlopoulos GA, Likothanassis SD, Kossida S.
      Current Bioinformatics, 2011 Dec 6;4:389-397(9). LINK

    34. Medusa: A tool for exploring and clustering biological networks
      Pavlopoulos GA, Hooper SD, Sifrim A, Schneider R, Aerts J.
      BMC Res Notes, 2011 Oct 6;4(1):384. PMID:21978489

    35. Using graph theory to analyze biological networks
      Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R.
      BioData Mining, 2011 Apr 28; 4:10. PMID:21527005

    36. GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques
      Satagopam VP, Theodoropoulou MC, Stampolakis CK, Pavlopoulos GA, Papandreou NC, Bagos PG, Schneider R, Hamodrakas SJ.
      Database (Oxford), 2010 Aug 5. PMID:20689020

    37. A reference guide for tree analysis and visualization
      Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R.
      BioData Mining 2010 Feb 22;3(1):1. PMID:20175922

    38. LAITOR-Literature Assistant for Identification of Terms co-Occurrences and Relationships: plant-adaptative responses as a model
      Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM.
      BMC Bioinformatics, 2010 Feb 1;11(1):70. PMID:20122157

    39. jClust: A clustering and visualization toolkit
      Pavlopoulos GA, Moschopoulos CN, Hooper SD, Schneider R, Kossida S.
      Bioinformatics (Oxford), 2009 Aug 1;25(15):1994-6. Epub 2009 May 19. PMID:19454618

    40. OnTheFly: A Tool for automated document-based text annotation, data linking and network generation
      Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R.
      Bioinformatics (Oxford), 2009 Apr 1;25(7):977-8. Epub 2009 Feb 17. PMID:19223449

    41. GIBA:A clustering tool for detecting protein complexes
      Moschopoulos CN, Pavlopoulos GA, Schneider R, Likothanassis SD, Kossida S.
      BMC Bioinformatics, 2009 Jun 16;10 Suppl 6:S11. PMID:19534736

    42. Arena3D: Visualization of Biological Networks in 3D
      Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R.
      BMC Systems Biology, 2008 Nov 28;2:104. PMID:19040715

    43. A survey of visualization tools for biological network analysis
      Pavlopoulos GA, Wegener AL, Schneider R.
      BioData Mining, 2008 Nov 28;1(1):12. PMID:19040716

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    45. OnTheFly 2.0: a tool for automatic annotation of files and biological information extraction
      Pafilis E, Pavlopoulos GA, Satagopam V, Papanikolaou N, Horn H, Arvanitidis C, Jensen L, Schneider R, Iliopoulos I.
      13th IEEE International Conference on Bioinformatics and Bioengineering (BIBE13), 10-13 Nov 2013, Chania, Crete, Greece LINK

    46. A simple genetic algorithm for cancer biomarker mining
      Popovic D, Sifrim A, Pavlopoulos GA, Moreau Y, De Moor B.
      PRIB2012, Lecture Notes in Computer Science, 7632, pp. 222-232, Springer (2012). LINK

    47. Visualizing High Dimensional Datasets Using Parallel Coordinates: Application to Gene Prioritization
      Boogaerts T, Tranchevent LC, Pavlopoulos GA, Aerts J, Vandewalle J.
      12th IEEE International Conference on Bioinformatics and Bioengineering (BIBE12), Nov. 2012, pp. 1-7, Larnaca, Cyprus. LINK

    48. Mining cell cycle-related literature using support vector machines
      Soldatos TG, Pavlopoulos GA
      SETN 2012, Lecture Notes in Computer Science, 7297, pp. 278-284. Springer, Heidelberg (2012) LINK

    49. Towards better prioritization of epigenetically modified DNA regions
      Iacucci E, Popovic D, Pavlopoulos GA, Tranchevent LC, De Moor B, Moreau Y.
      SETN 2012, Lecture Notes in Computer Science, 7297, pp. 270-277. Springer, Heidelberg (2012) LINK

    50. An enhanced Markov clustering method for detecting protein complexes
      Moschopoulos CN, Pavlopoulos GA Likothanassis SD, Kossida S.
      8th IEEE International Conference on Bioinformatics and Bioengineering, 8-10 October 2008, Athens, Greece. LINK

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      Book Chapters

    52. Prediction of miRNA Targets
      Oulas A, Karathanasis N, Louloupi A, Pavlopoulos GA, Iliopoulos I, Poirazi P, Kalantidis K.
      "Biomedical Literature Mining", Methods in Molecular Biology, Humana Press, USA, 2015;1269:207-29. doi: 10.1007/978-1-4939-2291-8_13. PMID:25577381

    53. Biological information extraction and co-occurence analysis
      Pavlopoulos GA, Promponas V. Ouzounis C. Iliopoulos I.
      "Biomedical Literature Mining", Methods in Molecular Biology, Humana Press, USA,
      Volume:1159, Publication Date: May 31, 2014 | ISBN-10: 1493907085 | ISBN-13: 978-1493907083 | Edition: 2014; 1159:77-92. doi: 10.1007/978-1-4939-0709-0_5. PMID:24788262

    54. Interpreting the Omics 'era' data
      Pavlopoulos GA, Iacucci E, Iliopoulos I, Bagos PG.
      Multimedia Services in Intelligent Environments, 17 may, 2013, Chapter 6, Springer-Verlag, Germany, volume 25, 2013, pp79-100, pdoi:10.1007/978-3-319-00375-7_6 LINK

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      News and Media

    • Εμπλουτίζοντας το δέντρο της ζωής αποκωδικοποιώντας το μικροβίωμα
      Γεώργιος Παυλόπουλος, Μιχάλης Χατζηθωμάς, Νίκος Κυρπίδης
      Άρθρο στην Εφημερίδα Αυγή, Ένθετο Πρίσμα, Σελίδες 2-3, 24 Ιουνίου 2017 PNG

    • Ο πλανήτης, εμείς και το μικροβίωμα
      Γεώργιος Παυλόπουλος, Νίκος Κυρπίδης
      Άρθρο κατόπιν πρόσκλησης στην Εφημερίδα Αυγή, Ένθετο Πρίσμα, Σελίδες 2-3, 24 Φεβρουαρίου 2017 PNG

    • Η Βιοπληροφορική και οι εφαρμογές της @ What's Up Doc? @ RadioReboot Station - Listen here (Interview in Greek)
      Credit to Λήδα Αρνέλλου & Δημήτρης Πετάκος

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