1. Arena3Dweb: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration
    Kokoli M., Karatzas E., Baltoumas FA., Schneider R., Pafilis E., Paragkamian S., Doncheva TN., Jensen LJ., Pavlopoulos GA.
    NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad053, PMID:37260509 
  2. Exploring microbial functional biodiversity at the protein family level - from metagenomic sequence reads to annotated protein clusters
    Baltoumas FA., Karatzas E., Paez-Espino D., Venetsianou N., Aplakidou E., Oulas A., Finn RD., Ovchinnikov S., Pafilis E., Kyrpides NC., Pavlopoulos GA.
    Frontiers in Bioinformatics, 03 March 2023, Volume 3 -2023, PMID:36959975
  3. Ageotypes revisited: The brain and central nervous system dysfunction as a major nutritional and lifestyle target for healthy aging
    Skoufas E., Kanellakis S., Sanoudou D., Eliopoulos AG., Pavlopoulos GA., Gkouskou KK.
    Maturitas, 06 Feb 2023, PMID:36773500
  4. Drug genetic associations with COVID-19 manifestations: a data mining and network biology approach
    Charitou T., Kontou PI., Ioannis A Tamposis IA, Pavlopoulos GA., Braliou GG., Bagos PG.
    The Pharmacogenomics Journal, 28 Sept. 2022., PMID:36171417
  5. IL-6 signaling attenuates TNF-α production by plasmacytoid DCs in rheumatoid arthritis
    Papadaki G.,Goutakoli P., Tiniakou I., Grün JR., Grützkau A.,  Pavlopoulos GA., Iliopoulos I., Bertsias G., Boumpas D., Ospelt C., Reizis B., Sidiropoulos P., Verginis  P.
    J Immunol. 2022 Sep 23:ji2100882. doi: 10.4049/jimmunol.2100882. Online ahead of print. PMID: 36426957
  6. Prediction and validation of Biomarkers using multiple UniReD
    Baltsavia I., Theodosiou T., Papanikolaou N., Pavlopoulos GA., Amoutzias GD., Panagopoulou M., Chatzaki E., Andreakos E., Iliopoulos I.
    International Journal of Molecular Sciences, 2022; 23(19):11112., PMID:36232413
  7. Consolidated variant calling from Whole Exome Sequencing data using three variant callers
    Verrou KM., Pavlopoulos GA., Moulos P.
    STAR Protocols (Cell Press),  04 June 2022, Volume 3, Issue 2,  PMID:35669050
  8. The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
    Karatzas E., Koutrouli M., Baltoumas F., Papanikolopoulou K., Bouyioukos C., Pavlopoulos GA.
    Bioinformatics Advances, 13 May 2022;, vbac036,  PMID:36699373
  9. Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey
    Galanis A., Vardakas P., Reczko M., Harokopos V., Hatzis P., Skoulakis E., Pavlopoulos GA., Patalano S.
    Molecular Ecology Resources, 2022 May 20. doi: 10.1111/1755-0998.13626. PMID:35593171 - bioRxiv
  10. DARLING: A web application for detecting disease-related biomedical entity associations using literature mining  
    Karatzas E., Baltoumas FA., Kasionis I., Sanoudou D., Eliopoulos GA., Theodosiou T., Iliopoulos I., Pavlopoulos GA
    Biomolecules, 2022 Mar 30 , 12(4), 520; PMID:35454109
  11. PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types
    Zafeiropoulos H., Paragkamian S., Ninidakis S., Pavlopoulos GA., Jensen LJ., Pafilis E.
    Microorganisms, 2022, 10, 293. PMID:35208748
  12. OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis
    Baltoumas FA., Zafeiropoulou S., Karatzas E., Paragkamian S., Thanati F., Iliopoulos I., Eliopoulos GA., Schneider R., Jensen LJ., Pafilis E., Pavlopoulos GA.
    NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab090,  PMID: 34632381
  13. Blood transcriptomes of anti-SARS-CoV2 antibody positive asymptomatic versus symptomatic individuals
    Sfikakis PP., Verrou KM., Ampatziadis-Michailidis G., Tsitsilonis O., Paraskevis D., Kastritis E., Lianidou E., Moutsatsou P., Terpos E., Trougakos I., Chini V., Manoloukos M., Moulos P., Pavlopoulos GA., Kollias G., Hatzis P., Dimopoulos MA
    Front. Immunol., 05 October 2021 |  PMID:34675930
  14. Biomolecule and bioentity interaction databases in Systems Biology: a comprehensive review
    Baltoumas FA., Zafeiropoulou S., Karatzas E., Koutrouli M., Thanati F., Voutsadaki K., Gkonta M., Hotova J., Kasionis I., Hatzis P., Pavlopoulos GA
    Biomolecules, 2021, 11, 1245.  PMID:34439912 
  15. Flame: A web tool for functional and literature enrichment analysis using multiple gene lists
    Thanati F., Karatzas E., Baltoumas F., Stravopodis DJ., Eliopoulos AG., Pavlopoulos GA
    Biology,14 Jul 2021, 10(7), 665;  PMID:34356520 
  16. Molecular epidemiology of SARS-CoV-2 in Greece demonstrates low rates of onward virus transmission despite the lift in summer travel restrictions
    Kostaki EG, Pavlopoulos GA, Verrou KM, Michailidis GA, Harokopos V, Hatzis P, Moulos P, Siafakas N, Pournaras S, Hadjichristodoulou C, Chatzopoulou F, Chatzidimitriou D, Panagopoulos P, Lourida P, Argyraki A, Lytras T, Sapounas S, Gerolymatos G, Panagiotakopoulos G, Prezerakos P, Tsiodras S, Sypsa V, Hatzakis A, Anastassopoulou C, Spanakis N, Tsakris A, Dimopoulos MA, Kotanidou A, Sfikakis P, Kollias G, Magiorkinis G, Paraskevis D.
    mSphere, 2021 Jun 30:e0018021. doi: 10.1128/mSphere.00180-21. PMID:34190583 
  17. NORMA-The network makeup artist: a web tool for network annotation visualization
    Koutrouli M., Karatzas E, Papanikolopoulou K, Pavlopoulos GA.
    Genomics Proteomics and Bioinformatics, 2021 Jun 22:S1672-0229(21)00130-3. doi: 10.1016/j.gpb.2021.02.005PMID:34171457
  18. VICTOR: A visual analytics web application for comparing cluster sets
    Karatzas E., Gkonta M., Hotova J., Baltoumas FA., Kontou PI., Bobotsis CJ., Bagos PG., Pavlopoulos GA.
    Computers in Biology and Medicine, 8 June 2021, 104557, ISSN 0010-4825, PMID:34139436
  19. The network analysis profiler (NAP v2.0): A web tool for visual topological comparison between multiple networks
    Koutrouli M, Theodosiou T, Iliopoulos I, Pavlopoulos GA.
    EMBnet.journal, v. 26, p. e943, May 2021. ISSN 2226-6089. doi:  LINK
  20. ProteoSign v2: A faster and evolved user-friendly online tool for statistical analyses of differential proteomics 
    Theodorakis V., Antonakis AN., Baltsavia I., Pavlopoulos GA., Samiotaki M., Amoutzias G., Theodosiou T., Acuto O., Efstathiou G., Iliopoulos I.
    Nucleic Acids Res. 2021 May 8:gkab329. doi: 10.1093/nar/gkab329. PMID:33963869
  21. Arena3Dweb: Interactive 3D visualization of multilayered networks
    Karatzas E, Baltoumas FA, Panayiotou NA,Schneider R, Pavlopoulos GA.
    Nucleic Acids Res., 2021 Apr 22:gkab278. doi: 10.1093/nar/gkab278. PMID:33885790
  22. Distinct transcriptional profile of blood mononuclear cells in Behcet's disease: insights into the central role of neutrophil chemotaxis
    Verrou KM, Vlachogiannis NI, Ampatziadis-Michailidis G, Moulos P, Pavlopoulos GA, Hatzis P, Kollias G, Sfikakis PP.
    Rheumatology (Oxford), 2021 Jan 25;keab052. doi: 10.1093/rheumatology/keab052. PMID:33493315
  23. The human GPCR signal transduction network
    Kontou P. Pavlopoulou A, Dimou N, Theodoropoulou M, Braliou G, Tsaousis G, Pavlopoulos GA, Hamodrakas S., Bagos PG
    Network Modeling Analysis in Health Informatics and Bioinformatics, 14 January 2021, 10:3, doi:10.1007/s13721-020-00278-z  LINK  View-Only PDF
  24. Structure Determination of the HgcAB Complex Using Metagenome Sequence Data: Insights into Microbial Mercury Methylation
    Cooper CJ, Zheng K, Rush WK, Johs A, Sanders BC, Pavlopoulos GA, Kyrpides NC, Podar M, Ovchinnikov S, Ragsdale SW, Parks JM
    Communications Biology, 2020 Jun 19;3(1):320. doi:10.1038/s42003-020-1047-5. PMID:32561885
  25. UniProt Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network.
    Theodosiou T, Papanikolaou N, Savvaki M, Bonetto G, Maxouri S, Fakoureli E, Eliopoulos GA, Tavernarakis N, Amoutzias GD, Pavlopoulos GA, Aivaliotis M, Nikoletopoulou V, Tzamarias D, Karagogeos D, Iliopoulos I
    NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa005, PMID:33575553
  26. A guide to conquer the biological network era using graph theory
    Koutrouli M, Karatzas E, Paez-Espino D, Pavlopoulos GA.
    Front. Bioeng. Biotechnol., 31 January 2020 | PMID:32083072
  27. Diversity, evolution, and classification of virophages uncovered through global metagenomics
    Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC.
    Microbiome, 2019 Dec 10;7(1):157. doi: 10.1186/s40168-019-0768-5. PMID:31823797
  28. Large-scale analyses of human microbiomes reveal thousands of small, novel genes and their predicted functions
    Sberro H, Fremin JB, Zlitni S, Edfors F, Greenfield N, Snyder MP,  Pavlopoulos GA, Kyrpides NC, Bhatt AS
    Cell, 2019 Aug 8. pii: S0092-8674(19)30781-0. doi: 10.1016/j.cell.2019.07.016 - biorxiv preprint, PMID:31402174
  29. 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 
  30. 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 
  31. 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 
  32. 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 
  33. 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 
  34. 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 
  35. 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 
  36. 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 
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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