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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
2008 2
2009 3
2010 3
2011 3
2012 5
2013 2
2014 3
2015 6
2016 6
2017 7
2018 3
2019 2
2020 3
2021 10
2022 9
2023 8
2024 1

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72 results

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Page 1
MPRAbase: A Massively Parallel Reporter Assay Database.
Zhao J, Baltoumas FA, Konnaris MA, Mouratidis I, Liu Z, Sims J, Agarwal V, Pavlopoulos GA, Georgakopoulos-Soares I, Ahituv N. Zhao J, et al. Among authors: pavlopoulos ga. bioRxiv [Preprint]. 2023 Nov 22:2023.11.19.567742. doi: 10.1101/2023.11.19.567742. bioRxiv. 2023. PMID: 38045264 Free PMC article. Preprint.
Unraveling the functional dark matter through global metagenomics.
Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E; Novel Metagenome Protein Families Consortium; Iliopoulos I, Konstantinidis K, Tiedje JM, Pett-Ridge J, Baker D, Visel A, Ouzounis CA, Ovchinnikov S, Buluç A, Kyrpides NC. Pavlopoulos GA, et al. Nature. 2023 Oct;622(7983):594-602. doi: 10.1038/s41586-023-06583-7. Epub 2023 Oct 11. Nature. 2023. PMID: 37821698 Free PMC article.
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 NT, Jensen LJ, Pavlopoulos GA. Kokoli M, et al. Among authors: pavlopoulos ga. NAR Genom Bioinform. 2023 May 30;5(2):lqad053. doi: 10.1093/nargab/lqad053. eCollection 2023 Jun. NAR Genom Bioinform. 2023. PMID: 37260509 Free PMC article.
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 NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. Baltoumas FA, et al. Among authors: pavlopoulos ga. Front Bioinform. 2023 Mar 3;3:1157956. doi: 10.3389/fbinf.2023.1157956. eCollection 2023. Front Bioinform. 2023. PMID: 36959975 Free PMC article. Review.
Prediction and Ranking of Biomarkers Using multiple UniReD.
Baltsavia I, Theodosiou T, Papanikolaou N, Pavlopoulos GA, Amoutzias GD, Panagopoulou M, Chatzaki E, Andreakos E, Iliopoulos I. Baltsavia I, et al. Among authors: pavlopoulos ga. Int J Mol Sci. 2022 Sep 21;23(19):11112. doi: 10.3390/ijms231911112. Int J Mol Sci. 2022. PMID: 36232413 Free PMC article.
Blood Transcriptomes of Anti-SARS-CoV-2 Antibody-Positive Healthy Individuals Who Experienced Asymptomatic Versus Clinical Infection.
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. Sfikakis PP, et al. Among authors: pavlopoulos ga. Front Immunol. 2021 Oct 5;12:746203. doi: 10.3389/fimmu.2021.746203. eCollection 2021. Front Immunol. 2021. PMID: 34675930 Free PMC article.
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 AG, Schneider R, Jensen LJ, Pafilis E, Pavlopoulos GA. Baltoumas FA, et al. Among authors: pavlopoulos ga. NAR Genom Bioinform. 2021 Oct 6;3(4):lqab090. doi: 10.1093/nargab/lqab090. eCollection 2021 Dec. NAR Genom Bioinform. 2021. PMID: 34632381 Free PMC article.
Molecular Epidemiology of SARS-CoV-2 in Greece Reveals Low Rates of Onward Virus Transmission after Lifting of Travel Restrictions Based on Risk Assessment during Summer 2020.
Kostaki EG, Pavlopoulos GA, Verrou KM, Ampatziadis-Michailidis G, 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. Kostaki EG, et al. Among authors: pavlopoulos ga. mSphere. 2021 Jun 30;6(3):e0018021. doi: 10.1128/mSphere.00180-21. Online ahead of print. mSphere. 2021. PMID: 34190583 Free PMC article.
NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization.
Koutrouli M, Karatzas E, Papanikolopoulou K, Pavlopoulos GA. Koutrouli M, et al. Among authors: pavlopoulos ga. Genomics Proteomics Bioinformatics. 2022 Jun;20(3):578-586. doi: 10.1016/j.gpb.2021.02.005. Epub 2021 Jun 24. Genomics Proteomics Bioinformatics. 2022. PMID: 34171457 Free PMC article.
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. Karatzas E, et al. Among authors: pavlopoulos ga. Comput Biol Med. 2021 Aug;135:104557. doi: 10.1016/j.compbiomed.2021.104557. Epub 2021 Jun 8. Comput Biol Med. 2021. PMID: 34139436
Arena3Dweb: interactive 3D visualization of multilayered networks.
Karatzas E, Baltoumas FA, Panayiotou NA, Schneider R, Pavlopoulos GA. Karatzas E, et al. Among authors: pavlopoulos ga. Nucleic Acids Res. 2021 Jul 2;49(W1):W36-W45. doi: 10.1093/nar/gkab278. Nucleic Acids Res. 2021. PMID: 33885790 Free PMC article.
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 AG, Tavernarakis N, Amoutzias GD, Pavlopoulos GA, Aivaliotis M, Nikoletopoulou V, Tzamarias D, Karagogeos D, Iliopoulos I. Theodosiou T, et al. Among authors: pavlopoulos ga. NAR Genom Bioinform. 2020 Feb 11;2(1):lqaa005. doi: 10.1093/nargab/lqaa005. eCollection 2020 Mar. NAR Genom Bioinform. 2020. PMID: 33575553 Free PMC article.
A Guide to Conquer the Biological Network Era Using Graph Theory.
Koutrouli M, Karatzas E, Paez-Espino D, Pavlopoulos GA. Koutrouli M, et al. Among authors: pavlopoulos ga. Front Bioeng Biotechnol. 2020 Jan 31;8:34. doi: 10.3389/fbioe.2020.00034. eCollection 2020. Front Bioeng Biotechnol. 2020. PMID: 32083072 Free PMC article. Review.
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. Seshadri R, et al. Among authors: pavlopoulos ga. Nat Biotechnol. 2018 Apr;36(4):359-367. doi: 10.1038/nbt.4110. Epub 2018 Mar 19. Nat Biotechnol. 2018. PMID: 29553575 Free PMC article.
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. Mukherjee S, et al. Among authors: pavlopoulos ga. Nat Biotechnol. 2017 Jul;35(7):676-683. doi: 10.1038/nbt.3886. Epub 2017 Jun 12. Nat Biotechnol. 2017. PMID: 28604660
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. Efstathiou G, et al. Among authors: pavlopoulos ga. Nucleic Acids Res. 2017 Jul 3;45(W1):W300-W306. doi: 10.1093/nar/gkx444. Nucleic Acids Res. 2017. PMID: 28520987 Free PMC article.
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. Ovchinnikov S, et al. Among authors: pavlopoulos ga. Science. 2017 Jan 20;355(6322):294-298. doi: 10.1126/science.aah4043. Science. 2017. PMID: 28104891 Free PMC article.
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. Paez-Espino D, et al. Among authors: pavlopoulos ga. Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30. Nucleic Acids Res. 2017. PMID: 27799466 Free PMC article.
Uncovering Earth's virome.
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC. Paez-Espino D, et al. Among authors: pavlopoulos ga. Nature. 2016 Aug 25;536(7617):425-30. doi: 10.1038/nature19094. Epub 2016 Aug 17. Nature. 2016. PMID: 27533034
DrugQuest - a text mining workflow for drug association discovery.
Papanikolaou N, Pavlopoulos GA, Theodosiou T, Vizirianakis IS, Iliopoulos I. Papanikolaou N, et al. Among authors: pavlopoulos ga. BMC Bioinformatics. 2016 Jun 6;17 Suppl 5(Suppl 5):182. doi: 10.1186/s12859-016-1041-6. BMC Bioinformatics. 2016. PMID: 27295093 Free PMC article.
Network analysis of genes and their association with diseases.
Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos GA, Bagos PG. Kontou PI, et al. Among authors: pavlopoulos ga. Gene. 2016 Sep 15;590(1):68-78. doi: 10.1016/j.gene.2016.05.044. Epub 2016 Jun 2. Gene. 2016. PMID: 27265032
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. Gkouskou KK, et al. Among authors: pavlopoulos ga. Oncogene. 2016 May 12;35(19):2496-505. doi: 10.1038/onc.2015.307. Epub 2015 Aug 17. Oncogene. 2016. PMID: 26279300
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. Papanikolaou N, et al. Among authors: pavlopoulos ga. Bioinformatics. 2015 Mar 15;31(6):979. doi: 10.1093/bioinformatics/btv029. Epub 2015 Feb 11. Bioinformatics. 2015. PMID: 25673338 No abstract available.
Prediction of miRNA targets.
Oulas A, Karathanasis N, Louloupi A, Pavlopoulos GA, Poirazi P, Kalantidis K, Iliopoulos I. Oulas A, et al. Among authors: pavlopoulos ga. Methods Mol Biol. 2015;1269:207-29. doi: 10.1007/978-1-4939-2291-8_13. Methods Mol Biol. 2015. PMID: 25577381 Review.
Protein-protein interaction predictions using text mining methods.
Papanikolaou N, Pavlopoulos GA, Theodosiou T, Iliopoulos I. Papanikolaou N, et al. Among authors: pavlopoulos ga. Methods. 2015 Mar;74:47-53. doi: 10.1016/j.ymeth.2014.10.026. Epub 2014 Oct 28. Methods. 2015. PMID: 25448298 Review.
Unraveling genomic variation from next generation sequencing data.
Pavlopoulos GA, Oulas A, Iacucci E, Sifrim A, Moreau Y, Schneider R, Aerts J, Iliopoulos I. Pavlopoulos GA, et al. BioData Min. 2013 Jul 25;6(1):13. doi: 10.1186/1756-0381-6-13. BioData Min. 2013. PMID: 23885890 Free PMC article.
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. Soldatos TG, et al. Among authors: pavlopoulos ga. BioData Min. 2012 Feb 1;5(1):1. doi: 10.1186/1756-0381-5-1. BioData Min. 2012. PMID: 22297131 Free PMC article.
Which clustering algorithm is better for predicting protein complexes?
Moschopoulos CN, Pavlopoulos GA, Iacucci E, Aerts J, Likothanassis S, Schneider R, Kossida S. Moschopoulos CN, et al. Among authors: pavlopoulos ga. BMC Res Notes. 2011 Dec 20;4:549. doi: 10.1186/1756-0500-4-549. BMC Res Notes. 2011. PMID: 22185599 Free PMC article.
Using graph theory to analyze biological networks.
Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG. Pavlopoulos GA, et al. BioData Min. 2011 Apr 28;4:10. doi: 10.1186/1756-0381-4-10. BioData Min. 2011. PMID: 21527005 Free PMC article.
A reference guide for tree analysis and visualization.
Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R. Pavlopoulos GA, et al. BioData Min. 2010 Feb 22;3(1):1. doi: 10.1186/1756-0381-3-1. BioData Min. 2010. PMID: 20175922 Free PMC article.
GIBA: a clustering tool for detecting protein complexes.
Moschopoulos CN, Pavlopoulos GA, Schneider R, Likothanassis SD, Kossida S. Moschopoulos CN, et al. Among authors: pavlopoulos ga. BMC Bioinformatics. 2009 Jun 16;10 Suppl 6(Suppl 6):S11. doi: 10.1186/1471-2105-10-S6-S11. BMC Bioinformatics. 2009. PMID: 19534736 Free PMC article.
jClust: a clustering and visualization toolbox.
Pavlopoulos GA, Moschopoulos CN, Hooper SD, Schneider R, Kossida S. Pavlopoulos GA, et al. Bioinformatics. 2009 Aug 1;25(15):1994-6. doi: 10.1093/bioinformatics/btp330. Epub 2009 May 19. Bioinformatics. 2009. PMID: 19454618 Free PMC article.
Arena3D: visualization of biological networks in 3D.
Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R. Pavlopoulos GA, et al. BMC Syst Biol. 2008 Nov 28;2:104. doi: 10.1186/1752-0509-2-104. BMC Syst Biol. 2008. PMID: 19040715 Free PMC article.