Publications

Updated publication lists can be also found in: Google Scholar or http://pavlopouloslab.info .

 

1. Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes.

Sberro H, Fremin BJ, Zlitni S, Edfors F, Greenfield N, Snyder MP, Pavlopoulos GA, Kyrpides NC, Bhatt AS.

Cell, 2019 Aug 22;178(5):1245-1259.e14. doi: 10.1016/j.cell.2019.07.016. Epub 2019 Aug 8. PMID:31402174

2. 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

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, 18 Feb 2018, giy014, https://doi.org/10.1093/gigascience/giy014 *equal first authors

4. 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, https://doi.org/10.1093/nar/gkx1313, PMID:29315405

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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  

24. 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

25. 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

26. 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

27. 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

28. 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

29. 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

30. 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).  

31. 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 

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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

38. 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

39. 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

40. 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

41. 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

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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

49. 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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