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Items: 47

1.

Bipartite graphs in systems biology and medicine: a survey of methods and applications.

Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG.

Gigascience. 2018 Apr 1;7(4):1-31. doi: 10.1093/gigascience/giy014. Review.

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.

Nat Biotechnol. 2018 Apr;36(4):359-367. doi: 10.1038/nbt.4110. Epub 2018 Mar 19.

3.

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks.

Azad A, Pavlopoulos GA, Ouzounis CA, Kyrpides NC, Buluç A.

Nucleic Acids Res. 2018 Apr 6;46(6):e33. doi: 10.1093/nar/gkx1313.

4.

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis.

Pavlopoulos GA, Paez-Espino D, Kyrpides NC, Iliopoulos I.

Adv Bioinformatics. 2017;2017:1278932. doi: 10.1155/2017/1278932. Epub 2017 Jul 18. Review.

5.

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data.

Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC.

Nat Protoc. 2017 Aug;12(8):1673-1682. doi: 10.1038/nprot.2017.063. Epub 2017 Jul 27.

6.

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 Res Notes. 2017 Jul 14;10(1):278. doi: 10.1186/s13104-017-2607-8.

7.

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.

Nat Biotechnol. 2017 Jul;35(7):676-683. doi: 10.1038/nbt.3886. Epub 2017 Jun 12.

8.

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 Res. 2017 Jul 3;45(W1):W300-W306. doi: 10.1093/nar/gkx444.

9.

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. 2017 Jan 20;355(6322):294-298. doi: 10.1126/science.aah4043.

10.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

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 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 WT, Rivers AR, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.

11.

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 25;536(7617):425-30. Epub 2016 Aug 17.

12.

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 Brief. 2016 Jul 19;8:1036-9. doi: 10.1016/j.dib.2016.07.022. eCollection 2016 Sep.

13.

DrugQuest - a text mining workflow for drug association discovery.

Papanikolaou N, Pavlopoulos GA, Theodosiou T, Vizirianakis IS, Iliopoulos I.

BMC Bioinformatics. 2016 Jun 6;17 Suppl 5:182. doi: 10.1186/s12859-016-1041-6.

14.

Network analysis of genes and their association with diseases.

Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos GA, Bagos PG.

Gene. 2016 Sep 15;590(1):68-78. doi: 10.1016/j.gene.2016.05.044. Epub 2016 Jun 2.

15.

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I.

Gigascience. 2015 Aug 25;4:38. doi: 10.1186/s13742-015-0077-2. eCollection 2015. Review.

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. 2016 May 12;35(19):2496-505. doi: 10.1038/onc.2015.307. Epub 2015 Aug 17.

PMID:
26279300
17.

Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.

Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I.

Bioinform Biol Insights. 2015 May 5;9:75-88. doi: 10.4137/BBI.S12462. eCollection 2015. Review.

18.

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery.

Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I.

Bioinformatics. 2015 Mar 15;31(6):979. doi: 10.1093/bioinformatics/btv029. Epub 2015 Feb 11. No abstract available.

PMID:
25673338
19.

Prediction of miRNA targets.

Oulas A, Karathanasis N, Louloupi A, Pavlopoulos GA, Poirazi P, Kalantidis K, Iliopoulos I.

Methods Mol Biol. 2015;1269:207-29. doi: 10.1007/978-1-4939-2291-8_13. Review.

PMID:
25577381
20.

Protein-protein interaction predictions using text mining methods.

Papanikolaou N, Pavlopoulos GA, Theodosiou T, Iliopoulos I.

Methods. 2015 Mar;74:47-53. doi: 10.1016/j.ymeth.2014.10.026. Epub 2014 Oct 28. Review.

PMID:
25448298
21.

BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery.

Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I.

Bioinformatics. 2014 Nov 15;30(22):3249-56. doi: 10.1093/bioinformatics/btu524. Epub 2014 Aug 6. Erratum in: Bioinformatics. 2015 Mar 15;31(6):979.

PMID:
25100685
22.

Biological information extraction and co-occurrence analysis.

Pavlopoulos GA, Promponas VJ, Ouzounis CA, Iliopoulos I.

Methods Mol Biol. 2014;1159:77-92. doi: 10.1007/978-1-4939-0709-0_5. Review.

PMID:
24788262
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 Jul 25;6(1):13. doi: 10.1186/1756-0381-6-13.

24.

Meander: visually exploring the structural variome using space-filling curves.

Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, Lin ML, Voet T, Moreau Y, Aerts J.

Nucleic Acids Res. 2013 Jun;41(11):e118. doi: 10.1093/nar/gkt254. Epub 2013 Apr 19.

25.

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 Med. 2012 Sep 26;4(9):73. doi: 10.1186/gm374. eCollection 2012.

26.

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. 2012 Sep 15;28(18):i569-i574. doi: 10.1093/bioinformatics/bts391.

27.

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 Res Notes. 2012 Jun 6;5:265. doi: 10.1186/1756-0500-5-265.

28.

Arena3D: visualizing time-driven phenotypic differences in biological systems.

Secrier M, Pavlopoulos GA, Aerts J, Schneider R.

BMC Bioinformatics. 2012 Mar 22;13:45. doi: 10.1186/1471-2105-13-45.

29.

Caipirini: using gene sets to rank 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. doi: 10.1186/1756-0381-5-1.

30.

Which clustering algorithm is better for predicting protein complexes?

Moschopoulos CN, Pavlopoulos GA, Iacucci E, Aerts J, Likothanassis S, Schneider R, Kossida S.

BMC Res Notes. 2011 Dec 20;4:549. doi: 10.1186/1756-0500-4-549.

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;4:384. doi: 10.1186/1756-0500-4-384.

32.

Using graph theory to analyze biological networks.

Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG.

BioData Min. 2011 Apr 28;4:10. doi: 10.1186/1756-0381-4-10.

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;2010:baq019. doi: 10.1093/database/baq019.

34.

A reference guide for tree analysis and visualization.

Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R.

BioData Min. 2010 Feb 22;3(1):1. doi: 10.1186/1756-0381-3-1.

35.

LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships.

Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM.

BMC Bioinformatics. 2010 Feb 1;11:70. doi: 10.1186/1471-2105-11-70.

36.

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. doi: 10.1186/1471-2105-10-S6-S11.

37.

jClust: a clustering and visualization toolbox.

Pavlopoulos GA, Moschopoulos CN, Hooper SD, Schneider R, Kossida S.

Bioinformatics. 2009 Aug 1;25(15):1994-6. doi: 10.1093/bioinformatics/btp330. Epub 2009 May 19.

38.

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. 2009 Apr 1;25(7):977-8. doi: 10.1093/bioinformatics/btp081. Epub 2009 Feb 17.

39.

A survey of visualization tools for biological network analysis.

Pavlopoulos GA, Wegener AL, Schneider R.

BioData Min. 2008 Nov 28;1:12. doi: 10.1186/1756-0381-1-12.

40.

Arena3D: visualization of biological networks in 3D.

Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R.

BMC Syst Biol. 2008 Nov 28;2:104. doi: 10.1186/1752-0509-2-104.

41.

Rubeola keratitis: a photographic study of corneal lesions.

Pavlopoulos GP, Giannakos GI, Theodosiadis PG, Moschos MM, Iliakis EK, Theodosiadis GP.

Cornea. 2008 May;27(4):411-6. doi: 10.1097/ICO.0b013e31816313a2.

PMID:
18434843
42.

Tuberculous conjunctivitis in a doctor.

Psathakis K, Mermigkis Ch, Vlachaki E, Pavlopoulos G, Skagias L, Skiadas V, Kokkonouzis I, Tsintiris K.

Int J Tuberc Lung Dis. 2008 Feb;12(2):228. No abstract available.

PMID:
18230260
43.

Videokeratography of keratoconus in monozygotic twins.

Parker J, Ko WW, Pavlopoulos G, Wolfe PJ, Rabinowitz YS, Feldman ST.

J Refract Surg. 1996 Jan-Feb;12(1):180-3.

PMID:
8963810
44.

Calculation of intraocular lens power after radial keratotomy with computerized videokeratography.

Celikkol L, Pavlopoulos G, Weinstein B, Celikkol G, Feldman ST.

Am J Ophthalmol. 1995 Dec;120(6):739-50.

PMID:
8540547
45.
46.
47.

Prophylactic use of acetazolamide to prevent intraocular pressure elevation following Nd-YAG laser posterior capsulotomy.

Ladas ID, Pavlopoulos GP, Kokolakis SN, Theodossiadis GP.

Br J Ophthalmol. 1993 Mar;77(3):136-8.

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