| Year |
Citation |
Score |
| 2024 |
Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Computational and Structural Biotechnology Journal. 23: 2011-2033. PMID 38765606 DOI: 10.1016/j.csbj.2024.04.060 |
0.694 |
|
| 2023 |
Tzaferis C, Karatzas E, Baltoumas FA, Pavlopoulos GA, Kollias G, Konstantopoulos D. SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data. Computational and Structural Biotechnology Journal. 21: 5382-5393. PMID 38022693 DOI: 10.1016/j.csbj.2023.10.032 |
0.329 |
|
| 2023 |
Karatzas E, Baltoumas FA, Aplakidou E, Kontou PI, Stathopoulos P, Stefanis L, Bagos PG, Pavlopoulos GA. Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources. Bioinformatics (Oxford, England). 39. PMID 37540207 DOI: 10.1093/bioinformatics/btad490 |
0.336 |
|
| 2023 |
Kokoli M, Karatzas E, Baltoumas FA, Schneider R, Pafilis E, Paragkamian S, Doncheva NT, Jensen LJ, Pavlopoulos GA. Arena3D: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. Nar Genomics and Bioinformatics. 5: lqad053. PMID 37260509 DOI: 10.1093/nargab/lqad053 |
0.714 |
|
| 2023 |
Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters. Frontiers in Bioinformatics. 3: 1157956. PMID 36959975 DOI: 10.3389/fbinf.2023.1157956 |
0.67 |
|
| 2022 |
Zafeiropoulos H, Paragkamian S, Ninidakis S, Pavlopoulos GA, Jensen LJ, Pafilis E. PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. Microorganisms. 10. PMID 35208748 DOI: 10.3390/microorganisms10020293 |
0.678 |
|
| 2021 |
Baltoumas FA, Zafeiropoulou S, Karatzas E, Paragkamian S, Thanati F, Iliopoulos I, Eliopoulos AG, Schneider R, Jensen LJ, Pafilis E, Pavlopoulos GA. OnTheFly: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. Nar Genomics and Bioinformatics. 3: lqab090. PMID 34632381 DOI: 10.1093/nargab/lqab090 |
0.736 |
|
| 2021 |
Baltoumas FA, Zafeiropoulou S, Karatzas E, Koutrouli M, Thanati F, Voutsadaki K, Gkonta M, Hotova J, Kasionis I, Hatzis P, Pavlopoulos GA. Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. Biomolecules. 11. PMID 34439912 DOI: 10.3390/biom11081245 |
0.354 |
|
| 2021 |
Thanati F, Karatzas E, Baltoumas FA, Stravopodis DJ, Eliopoulos AG, Pavlopoulos GA. FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. Biology. 10. PMID 34356520 DOI: 10.3390/biology10070665 |
0.338 |
|
| 2021 |
Koutrouli M, Karatzas E, Papanikolopoulou K, Pavlopoulos GA. NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization. Genomics, Proteomics & Bioinformatics. PMID 34171457 DOI: 10.1016/j.gpb.2021.02.005 |
0.335 |
|
| 2021 |
Koutrouli M, Karatzas E, Papanikolopoulou K, Pavlopoulos GA. NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization. Genomics, Proteomics & Bioinformatics. PMID 34171457 DOI: 10.1016/j.gpb.2021.02.005 |
0.335 |
|
| 2021 |
Karatzas E, Baltoumas FA, Panayiotou NA, Schneider R, Pavlopoulos GA. Arena3Dweb: interactive 3D visualization of multilayered networks. Nucleic Acids Research. PMID 33885790 DOI: 10.1093/nar/gkab278 |
0.531 |
|
| 2020 |
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. UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. Nar Genomics and Bioinformatics. 2: lqaa005. PMID 33575553 DOI: 10.1093/nargab/lqaa005 |
0.301 |
|
| 2020 |
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. UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. Nar Genomics and Bioinformatics. 2: lqaa005. PMID 33575553 DOI: 10.1093/nargab/lqaa005 |
0.301 |
|
| 2020 |
Koutrouli M, Karatzas E, Paez-Espino D, Pavlopoulos GA. A Guide to Conquer the Biological Network Era Using Graph Theory. Frontiers in Bioengineering and Biotechnology. 8: 34. PMID 32083072 DOI: 10.3389/Fbioe.2020.00034 |
0.396 |
|
| 2019 |
Sberro H, Fremin BJ, Zlitni S, Edfors F, Greenfield N, Snyder MP, Pavlopoulos GA, Kyrpides NC, Bhatt AS. Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. Cell. 178: 1245-1259.e14. PMID 31402174 DOI: 10.1016/J.Cell.2019.07.016 |
0.317 |
|
| 2018 |
Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG. Bipartite graphs in systems biology and medicine: a survey of methods and applications. Gigascience. 7: 1-31. PMID 29648623 DOI: 10.1093/Gigascience/Giy014 |
0.397 |
|
| 2018 |
Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D, Perry R, Henderson G, Creevey CJ, et al. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology. PMID 29553575 DOI: 10.1038/Nbt.4110 |
0.321 |
|
| 2018 |
Azad A, Pavlopoulos GA, Ouzounis CA, Kyrpides NC, Buluç A. HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks. Nucleic Acids Research. PMID 29315405 DOI: 10.1093/Nar/Gkx1313 |
0.393 |
|
| 2017 |
Pavlopoulos GA, Paez-Espino D, Kyrpides NC, Iliopoulos I. Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. Advances in Bioinformatics. 2017: 1278932. PMID 28804499 DOI: 10.1155/2017/1278932 |
0.456 |
|
| 2017 |
Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC. Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nature Protocols. 12: 1673-1682. PMID 28749930 DOI: 10.1038/Nprot.2017.063 |
0.332 |
|
| 2017 |
Theodosiou T, Efstathiou G, Papanikolaou N, Kyrpides NC, Bagos PG, Iliopoulos I, Pavlopoulos GA. NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks. Bmc Research Notes. 10: 278. PMID 28705239 DOI: 10.1186/S13104-017-2607-8 |
0.435 |
|
| 2017 |
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, et al. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology. PMID 28604660 DOI: 10.1038/Nbt.3886 |
0.323 |
|
| 2017 |
Efstathiou G, Antonakis AN, Pavlopoulos GA, Theodosiou T, Divanach P, Trudgian DC, Thomas B, Papanikolaou N, Aivaliotis M, Acuto O, Iliopoulos I. ProteoSign: an end-user online differential proteomics statistical analysis platform. Nucleic Acids Research. PMID 28520987 DOI: 10.1093/Nar/Gkx444 |
0.391 |
|
| 2017 |
Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Protein structure determination using metagenome sequence data. Science (New York, N.Y.). 355: 294-298. PMID 28104891 DOI: 10.1126/Science.Aah4043 |
0.314 |
|
| 2017 |
Pavlopoulos GA. How to Cluster Protein Sequences: Tools, Tips and Commands Moj Proteomics & Bioinformatics. 5. DOI: 10.15406/Mojpb.2017.05.00174 |
0.345 |
|
| 2016 |
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, et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Research. PMID 27799466 DOI: 10.1093/Nar/Gkw1030 |
0.353 |
|
| 2016 |
Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos GA, Bagos PG. Data and programs in support of network analysis of genes and their association with diseases. Data in Brief. 8: 1036-9. PMID 27508260 DOI: 10.1016/J.Dib.2016.07.022 |
0.377 |
|
| 2016 |
Papanikolaou N, Pavlopoulos GA, Theodosiou T, Vizirianakis IS, Iliopoulos I. DrugQuest - a text mining workflow for drug association discovery. Bmc Bioinformatics. 17: 182. PMID 27295093 DOI: 10.1186/S12859-016-1041-6 |
0.361 |
|
| 2016 |
Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos GA, Bagos PG. Network analysis of genes and their association with diseases. Gene. PMID 27265032 DOI: 10.1016/J.Gene.2016.05.044 |
0.384 |
|
| 2015 |
Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I. Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience. 4: 38. PMID 26309733 DOI: 10.1186/S13742-015-0077-2 |
0.394 |
|
| 2015 |
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I. Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinformatics and Biology Insights. 9: 75-88. PMID 25983555 DOI: 10.4137/Bbi.S12462 |
0.405 |
|
| 2015 |
Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. Bioinformatics (Oxford, England). 31: 979. PMID 25673338 DOI: 10.7490/F1000Research.1096805.1 |
0.704 |
|
| 2015 |
Papanikolaou N, Pavlopoulos GA, Theodosiou T, Iliopoulos I. Protein-protein interaction predictions using text mining methods. Methods (San Diego, Calif.). 74: 47-53. PMID 25448298 DOI: 10.1016/J.Ymeth.2014.10.026 |
0.401 |
|
| 2014 |
Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery. Bioinformatics (Oxford, England). 30: 3249-56. PMID 25100685 DOI: 10.1093/Bioinformatics/Btu524 |
0.753 |
|
| 2014 |
Pavlopoulos GA, Promponas VJ, Ouzounis CA, Iliopoulos I. Biological information extraction and co-occurrence analysis. Methods in Molecular Biology (Clifton, N.J.). 1159: 77-92. PMID 24788262 DOI: 10.1007/978-1-4939-0709-0_5 |
0.441 |
|
| 2013 |
Pavlopoulos GA, Oulas A, Iacucci E, Sifrim A, Moreau Y, Schneider R, Aerts J, Iliopoulos I. Unraveling genomic variation from next generation sequencing data. Biodata Mining. 6: 13. PMID 23885890 DOI: 10.1186/1756-0381-6-13 |
0.578 |
|
| 2013 |
Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, Lin ML, Voet T, Moreau Y, Aerts J. Meander: visually exploring the structural variome using space-filling curves. Nucleic Acids Research. 41: e118. PMID 23605045 DOI: 10.1093/Nar/Gkt254 |
0.409 |
|
| 2013 |
Pavlopoulos GA, Pafilis E, Satagopam VP, Horn H, Arvanitidis C, Jensen L, Iliopoulos I, Schneider R. OnTheFly 2.0 beta: automated annotation of scientific documents F1000research. 4. DOI: 10.7490/F1000Research.1093964.1 |
0.668 |
|
| 2013 |
Pafilis E, Pavlopoulos GA, Satagopam VP, Papanikolaou N, Horn H, Arvanitidis C, Jensen LJ, Schneider R, Iliopoulos I. OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction 13th Ieee International Conference On Bioinformatics and Bioengineering, Ieee Bibe 2013. DOI: 10.1109/BIBE.2013.6701679 |
0.701 |
|
| 2012 |
Sifrim A, Van Houdt JK, Tranchevent LC, Nowakowska B, Sakai R, Pavlopoulos GA, Devriendt K, Vermeesch JR, Moreau Y, Aerts J. Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. Genome Medicine. 4: 73. PMID 23013645 DOI: 10.1186/Gm374 |
0.397 |
|
| 2012 |
Iacucci E, Tranchevent LC, Popovic D, Pavlopoulos GA, De Moor B, Schneider R, Moreau Y. ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. Bioinformatics (Oxford, England). 28: i569-i574. PMID 22962483 DOI: 10.1093/Bioinformatics/Bts391 |
0.482 |
|
| 2012 |
Michalopoulos I, Pavlopoulos GA, Malatras A, Karelas A, Kostadima MA, Schneider R, Kossida S. Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes. Bmc Research Notes. 5: 265. PMID 22672625 DOI: 10.1186/1756-0500-5-265 |
0.523 |
|
| 2012 |
Secrier M, Pavlopoulos GA, Aerts J, Schneider R. Arena3D: visualizing time-driven phenotypic differences in biological systems. Bmc Bioinformatics. 13: 45. PMID 22439608 DOI: 10.1186/1471-2105-13-45 |
0.749 |
|
| 2012 |
Soldatos TG, O'Donoghue SI, Satagopam VP, Barbosa-Silva A, Pavlopoulos GA, Wanderley-Nogueira AC, Soares-Cavalcanti NM, Schneider R. Caipirini: using gene sets to rank literature. Biodata Mining. 5: 1. PMID 22297131 DOI: 10.1186/1756-0381-5-1 |
0.54 |
|
| 2011 |
Moschopoulos CN, Pavlopoulos GA, Iacucci E, Aerts J, Likothanassis S, Schneider R, Kossida S. Which clustering algorithm is better for predicting protein complexes? Bmc Research Notes. 4: 549. PMID 22185599 DOI: 10.1186/1756-0500-4-549 |
0.54 |
|
| 2011 |
Pavlopoulos GA, Hooper SD, Sifrim A, Schneider R, Aerts J. Medusa: A tool for exploring and clustering biological networks. Bmc Research Notes. 4: 384. PMID 21978489 DOI: 10.1186/1756-0500-4-384 |
0.616 |
|
| 2011 |
Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG. Using graph theory to analyze biological networks. Biodata Mining. 4: 10. PMID 21527005 DOI: 10.1186/1756-0381-4-10 |
0.712 |
|
| 2011 |
Moschopoulos CN, Pavlopoulos GA, Likothanassis S, Kossida S. Analyzing protein-protein interaction networks with web tools Current Bioinformatics. 6: 389-397. DOI: 10.2174/157489311798072972 |
0.449 |
|
| 2010 |
Satagopam VP, Theodoropoulou MC, Stampolakis CK, Pavlopoulos GA, Papandreou NC, Bagos PG, Schneider R, Hamodrakas SJ. GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. Database : the Journal of Biological Databases and Curation. 2010: baq019. PMID 20689020 DOI: 10.1093/Database/Baq019 |
0.53 |
|
| 2010 |
Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R. A reference guide for tree analysis and visualization. Biodata Mining. 3: 1. PMID 20175922 DOI: 10.1186/1756-0381-3-1 |
0.613 |
|
| 2010 |
Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM. LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships. Bmc Bioinformatics. 11: 70. PMID 20122157 DOI: 10.1186/1471-2105-11-70 |
0.583 |
|
| 2009 |
Moschopoulos CN, Pavlopoulos GA, Schneider R, Likothanassis SD, Kossida S. GIBA: a clustering tool for detecting protein complexes. Bmc Bioinformatics. 10: S11. PMID 19534736 DOI: 10.1186/1471-2105-10-S6-S11 |
0.562 |
|
| 2009 |
Pavlopoulos GA, Moschopoulos CN, Hooper SD, Schneider R, Kossida S. jClust: a clustering and visualization toolbox. Bioinformatics (Oxford, England). 25: 1994-6. PMID 19454618 DOI: 10.1093/Bioinformatics/Btp330 |
0.541 |
|
| 2009 |
Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R. OnTheFly: a tool for automated document-based text annotation, data linking and network generation. Bioinformatics (Oxford, England). 25: 977-8. PMID 19223449 DOI: 10.1093/Bioinformatics/Btp081 |
0.757 |
|
| 2008 |
Pavlopoulos GA, Wegener AL, Schneider R. A survey of visualization tools for biological network analysis. Biodata Mining. 1: 12. PMID 19040716 DOI: 10.1186/1756-0381-1-12 |
0.612 |
|
| 2008 |
Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R. Arena3D: visualization of biological networks in 3D. Bmc Systems Biology. 2: 104. PMID 19040715 DOI: 10.1186/1752-0509-2-104 |
0.745 |
|
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