Publications are organized as Submitted, Journals, Conferences, Book Chapters and Newspaper Articles

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


      Submitted

    1. The Hungate Collection: a Catalogue of Isolates and Genomes from the Rumen Microbiome
      Seshadri R, Leahy CS, Attwood GT, Teh HK, Lambie CS, Eloe-Fadrosh E, Pavlopoulos GA, Hadjithomas M, Varghese N, Hungate1000 project collaborators, Perry R, Henderson G, Creevey JC, Terrapon N, Lapebie P, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova N, Kelly JW.
      Nature Biotechnology (addressing revisions)


    2. 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 (addressing revisions)

    3. 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 (addressing revisions)


    4. The human GPCR signal transduction network
      Kontou PI, Pavlopoulou A, Dimou N, Theodoropoulou M, Braliou G, Tsaousis G, Pavlopoulos GA, Hamodrakas SJ, Bagos PG
      Journal of Molecular Biology (submitted)


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      Journals

    6. 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

    7. 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 (IF:~10)

    8. 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
      PMID:28705239

    9. 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 (IF:~43.2)

    10. How to cluster protein sequences: Tools, tips and commands
      Pavlopoulos GA
      MOJ Proteomics and Bioinformatics, 2 June 2017, 5(5): 00174. DOI: 10.15406/mojpb.2017.05.00174 LINK

    11. 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


    12. 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 (IF:~34.5)

    13. 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 (IF:~9.5)

    14. 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 (IF:~38.2)

    15. 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 (IF:~3)

    16. 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

    17. 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 (IF:2.5)

    18. 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 (IF:~9)

    19. 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 (IF:~7.5)

    20. 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 (IF:~3)

    21. 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 (IF:~3.5)

    22. 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 (IF:~6)

    23. 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 (IF:~2)

    24. 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 (IF:~9.5)

    25. 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 (IF:~3)

    26. 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 (IF:~6)

    27. 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 (IF:~6)

    28. 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 (IF:~2)

    29. 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 (IF:~3)

    30. 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 (IF:~2)

    31. 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 (IF:~2)

    32. 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 (IF:~2)

    33. 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 (IF:~2)

    34. 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 (IF:~2)

    35. 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 (IF:~3)

    36. 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 (IF:~2)

    37. 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 (IF:~3)

    38. 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 (IF:~6)

    39. 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 (IF:~6)

    40. 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 (IF:~3)

    41. 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 (IF:~3.5)

    42. 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 (IF:~2)

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      Conferences

    44. 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

    45. 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

    46. 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

    47. 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

    48. 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

    49. 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

    51. 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

    52. 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

    53. 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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      Newspaper Articles

    • 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

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