| Uncovering Earth's Virome D Paez-Espino, EA Eloe-Fadrosh, GA Pavlopoulos, AD Thomas, ... Nature, 2016 | 974 | 2016 |
| Using graph theory to analyze biological networks GA Pavlopoulos, M Secrier, CN Moschopoulos, TG Soldatos, S Kossida, ... BioData mining 4, 1-27, 2011 | 872 | 2011 |
| Protein structure determination using metagenome sequence data DB Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios ... Science 355 (6322), 294-298, 2017 | 524 | 2017 |
| Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection R Seshadri, SC Leahy, GT Attwood, KH Teh, SC Lambie, AL Cookson, ... Nature biotechnology 36 (4), 359-367, 2018 | 472 | 2018 |
| Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies A Oulas, C Pavloudi, P Polymenakou, GA Pavlopoulos, N Papanikolaou, ... Bioinformatics and biology insights 9, BBI. S12462, 2015 | 463 | 2015 |
| A survey of visualization tools for biological network analysis GA Pavlopoulos, AL Wegener, R Schneider Biodata mining 1, 12, 2008 | 254 | 2008 |
| 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life S Mukherjee, R Seshadri, NJ Varghese, EA Eloe-Fadrosh, ... Nature biotechnology 35 (7), 676, 2017 | 241 | 2017 |
| IMG/VR: A database of cultured and uncultured DNA Viruses and Retroviruses D Paez-Espino, IMA Chen A, K Palaniappan, A Ratner, K Chu, E Szeto, ... Nucleic Acids Research, 2016 | 211 | 2016 |
| A guide to conquer the biological network era using graph theory M Koutrouli, E Karatzas, D Paez-Espino, GA Pavlopoulos Frontiers in bioengineering and biotechnology 8, 34, 2020 | 205 | 2020 |
| Large-scale analyses of human microbiomes reveal thousands of small, novel genes H Sberro, BJ Fremin, S Zlitni, F Edfors, N Greenfield, MP Snyder, ... Cell 178 (5), 1245-1259. e14, 2019 | 198 | 2019 |
| Bipartite graphs in systems biology and medicine: a survey of methods and applications GA Pavlopoulos, PI Kontou, A Pavlopoulou, C Bouyioukos, E Markou, ... GigaScience 7 (4), giy014, 2018 | 167 | 2018 |
| HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks A Azad, GA Pavlopoulos, CA Ouzounis, NC Kyrpides, A Buluç Nucleic acids research 46 (6), e33-e33, 2018 | 147 | 2018 |
| Arena3D: visualization of biological networks in 3D GA Pavlopoulos, S O'Donoghue, V Satagopam, T Soldatos, E Pafilis, ... BMC systems biology 2 (1), 104, 2008 | 136 | 2008 |
| Non-targeted virus sequence discovery pipeline and virus clustering for metagenomic data D Paez-Espino, GA Pavlopoulos, NN Ivanova, K NC Nature Protocols, 1673–1682, 2017 | 123 | 2017 |
| Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future GA Pavlopoulos, D Malliarakis, N Papanikolaou, T Theodosiou, A Enright, ... GigaScience 4 (38), 2015 | 122 | 2015 |
| A reference guide for tree analysis and visualization GA Pavlopoulos, TG Soldatos, A Barbosa-Silva, R Schneider BioData mining 3, 1-24, 2010 | 112 | 2010 |
| Protein–protein interaction predictions using text mining methods N Papanikolaou, GA Pavlopoulos, T Theodosiou, I Iliopoulos Methods 74, 47-53, 2015 | 101 | 2015 |
| Unraveling genomic variation from next generation sequencing data GA Pavlopoulos, A Oulas, E Iacucci, A Sifrim, Y Moreau, R Schneider, ... BioData Mining 6 (13), 2013 | 83 | 2013 |
| Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms EMN Laurent, Y Sofianatos, A Komarova, JP Gimeno, PS Tehrani, DK Kim, ... BioRxiv, 2020.08. 28.272955, 2020 | 68 | 2020 |
| Medusa: A tool for exploring and clustering biological networks GA Pavlopoulos, S Hooper, A Sifrim, R Schneider, J Aerts BMC Research Notes 4 (1), 384, 2011 | 66 | 2011 |
| Diversity, evolution, and classification of virophages uncovered through global metagenomics D Paez-Espino, J Zhou, S Roux, S Nayfach, GA Pavlopoulos, F Schulz, ... Microbiome 7, 1-14, 2019 | 60 | 2019 |
| Empirical comparison of visualization tools for larger-scale network analysis GA Pavlopoulos, D Paez-Espino, NC Kyrpides, I I. Advances in Bioinformatics 2017, 8, 2017 | 58 | 2017 |
| Arena3D: visualizing time-driven phenotypic differences in biological systems M Secrier, GA Pavlopoulos, J Aerts, R Schneider BMC Bioinformatics 13 (1), 45, 2012 | 58 | 2012 |
| Prediction of miRNA Targets. A Oulas, N Karathanasis, A Louloupi, GA Pavlopoulos, I Iliopoulos, ... Methods Mol Biol, doi: 10.1007/978-1-4939-2291-8_13, 2015 | 49 | 2015 |
| LAITOR-Literature Assistant for Identification of Terms co-Occurrences and Relationships A Barbosa-Silva, T Soldatos, I Magalhães, GA Pavlopoulos, JF Fontaine, ... BMC bioinformatics 11 (1), 70, 2010 | 48 | 2010 |
| Apolipoprotein AI inhibits experimental colitis and colitis-propelled carcinogenesis KK Gkouskou, M Ioannou, GA Pavlopoulos, K Georgila, A Siganou, ... Oncogene 35 (19), 2496-2505, 2016 | 46 | 2016 |
| ProteoSign: an end-user online differential proteomics statistical analysis platform G Efstathiou, AN Antonakis, GA Pavlopoulos, T Theodosiou, P Divanach, ... Nucleic Acids Research, 2017 | 43 | 2017 |
| Network analysis of genes and their association with diseases PI Kontou, A Pavlopoulou, NL Dimou, GA Pavlopoulos, PG Bagos Gene 590 (1), 68-78, 2016 | 43 | 2016 |
| jClust: a clustering and visualization toolbox GA Pavlopoulos, CN Moschopoulos, SD Hooper, R Schneider, S Kossida Bioinformatics 25 (15), 1994-1996, 2009 | 37 | 2009 |
| NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks T Theodosiou, G Efstathiou, N Papanikolaou, NC Kyrpides, PG Bagos, ... BMC Research Notes 10, 278, 2017 | 36 | 2017 |
| GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques VP Satagopam, MC Theodoropoulou, CK Stampolakis, GA Pavlopoulos, ... Database 2010, baq019, 2010 | 35 | 2010 |
| FLAME: a web tool for functional and literature enrichment analysis of multiple gene lists F Thanati, E Karatzas, F Baltoumas, DJ Stravopodis, AG Eliopoulos, ... Biology 10 (7), 665, 2021 | 34 | 2021 |
| Human gene correlation analysis (HGCA): A tool for the identification of transcriptionally coexpressed genes I Michalopoulos, GA Pavlopoulos, A Malatras, A Karelas, MA Kostadima, ... BMC Research Notes 5 (1), 265, 2012 | 34 | 2012 |
| Which clustering algorithm is better for predicting protein complexes? CN Moschopoulos, GA Pavlopoulos, E Iacucci, J Aerts, S Likothanassis, ... BMC Res Notes 4 (1), 549, 2011 | 34 | 2011 |
| GIBA: a clustering tool for detecting protein complexes C Moschopoulos, GA Pavlopoulos, R Schneider, S Likothanassis, ... BMC bioinformatics 10 (Suppl 6), S11, 2009 | 34 | 2009 |
| DrugQuest-a text mining workflow for drug association discovery N Papanikolaou, GA Pavlopoulos, T Theodosiou, IS Vizirianakis, ... BMC bioinformatics 17, 333-341, 2016 | 33 | 2016 |
| Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease A Sifrim, JKJ Van Houdt, LC Tranchevent, B Nowakowska, R Sakai, ... Genome Medicine 4, 73, 2012 | 33 | 2012 |
| Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation CJ Cooper, K Zheng, KW Rush, A Johs, BC Sanders, GA Pavlopoulos, ... Communications biology 3 (1), 320, 2020 | 32 | 2020 |
| BioTextQuest + : a knowledge integration platform for literature mining and concept discovery N Papanikolaou, GA Pavlopoulos, E Pafilis, T Theodosiou, R Schneider, ... Bioinformatics 30 (22), 3249-3256, 2014 | 32 | 2014 |
| Biological information extraction and co-occurrence analysis GA Pavlopoulos, VJ Promponas, CA Ouzounis, I Iliopoulos Biomedical literature mining, 77-92, 2014 | 31 | 2014 |
| Distributed many-to-many protein sequence alignment using sparse matrices O Selvitopi, S Ekanayake, G Guidi, G Pavlopoulos, A Azad, A Buluc Proceedings of the International Conference for High Performance Computing …, 2020 | 24 | 2020 |
| OnTheFly: a tool for automated document-based text annotation, data linking and network generation GA Pavlopoulos, E Pafilis, M Kuhn, SD Hooper, R Schneider Bioinformatics 25 (7), 977-978, 2009 | 22 | 2009 |
| Distinct transcriptional profile of blood mononuclear cells in Behçet’s disease: insights into the central role of neutrophil chemotaxis KM Verrou, NI Vlachogiannis, G Ampatziadis-Michailidis, P Moulos, ... Rheumatology 60 (10), 4910-4919, 2021 | 21 | 2021 |
| Unraveling the functional dark matter through global metagenomics GA Pavlopoulos, FA Baltoumas, S Liu, O Selvitopi, AP Camargo, ... Nature 622 (7983), 594-602, 2023 | 20 | 2023 |
| Arena3Dweb: Interactive 3D visualization of multilayered networks. E Karatzas, FA Baltoumas, NA Panayiotou, R Schneider, GA Pavlopoulos Nucleic Acid Research, 2021 | 19 | 2021 |
| OnTheFly 2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis FA Baltoumas, S Zafeiropoulou, E Karatzas, S Paragkamian, F Thanati, ... NAR Genomics and Bioinformatics 3 (4), 2021 | 18 | 2021 |
| An enhanced Markov clustering method for detecting protein complexes CN Moschopoulos, GA Pavlopoulos, SD Likothanassis, S Kossida 2008 8th IEEE International Conference on BioInformatics and BioEngineering, 1-6, 2008 | 17 | 2008 |
| Biomolecule and bioentity interaction databases in systems biology: a comprehensive review FA Baltoumas, S Zafeiropoulou, E Karatzas, M Koutrouli, F Thanati, ... Biomolecules 11 (8), 1245, 2021 | 15 | 2021 |
| PREGO: a literature and data-mining resource to associate microorganisms, biological processes, and environment types H Zafeiropoulos, S Paragkamian, S Ninidakis, GA Pavlopoulos, ... Microorganisms 10 (2), 293, 2022 | 13 | 2022 |
| Interpreting the omics ‘era’data GA Pavlopoulos, E Iacucci, I Iliopoulos, P Bagos Multimedia Services in Intelligent Environments: Recommendation Services, 79-100, 2013 | 13 | 2013 |
| Darling: a web application for detecting disease-related biomedical entity associations with literature mining E Karatzas, FA Baltoumas, I Kasionis, D Sanoudou, AG Eliopoulos, ... Biomolecules 12 (4), 520, 2022 | 12 | 2022 |
| Blood Transcriptomes of Anti-SARS-CoV-2 Antibody-Positive Healthy Individuals Who Experienced Asymptomatic Versus Clinical Infection PP Sfikakis, KM Verrou, G Ampatziadis-Michailidis, O Tsitsilonis, ... Frontiers in Immunology 12, 746203, 2021 | 11 | 2021 |
| ProteoSign v2: a faster and evolved user-friendly online tool for statistical analyses of differential proteomics E Theodorakis, AN Antonakis, I Baltsavia, GA Pavlopoulos, M Samiotaki, ... Nucleic acids research 49 (W1), W573-W577, 2021 | 11 | 2021 |
| Caipirini: using gene sets to rank literature TG Soldatos, SI O'Donoghue, VP Satagopam, A Barbosa-Silva, ... BioData mining 2011 (4), 10, 2011 | 11 | 2011 |
| IL-6 signaling attenuates TNF-α production by plasmacytoid dendritic cells in rheumatoid arthritis G Papadaki, P Goutakoli, I Tiniakou, JR Grün, A Grützkau, ... The Journal of Immunology 209 (10), 1906-1917, 2022 | 10 | 2022 |
| 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 EG Kostaki, GA Pavlopoulos, KM Verrou, G Ampatziadis-Michailidis, ... mSphere, 2021 | 9 | 2021 |
| NORMA-The network makeup artist: a web tool for network annotation visualization M Koutrouli, E Karatzas, K Papanikolopoulou, GA Pavlopoulos Genomics Proteomics and Bioinformatics, 2021 | 9 | 2021 |
| Exploring Networks in the STRING and Reactome Database M Koutrouli, P Hatzis, GA Pavlopoulos Systems Medicine Integrative, Qualitative and Computational Approaches 3 …, 2020 | 9 | 2020 |
| Meander: visually exploring the structural variome using space-filling curves GA Pavlopoulos, P Kumar, A Sifrim, R Sakai, ML Lin, T Voet, Y Moreau, ... Nucleic acids research 41 (11), e118-e118, 2013 | 9 | 2013 |
| Visualizing High Dimensional Datasets Using Parallel Coordinates: Application to Gene Prioritization T Boogaerts, LC Tranchevent, GA Pavlopoulos, J Aerts, J Vandewalle IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE), 2012 | 9 | 2012 |
| Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey A Galanis, P Vardakas, M Reczko, V Harokopos, P Hatzis, EMC Skoulakis, ... Molecular Ecology Resources,, 2022 | 8 | 2022 |
| VICTOR: A visual analytics web application for comparing cluster sets E Karatzas, M Gkonta, J Hotova, FA Baltoumas, PI Kontou, CJ Bobotsis, ... Computers in Biology and Medicine, 104557, 2021 | 8 | 2021 |
| UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network T Theodosiou, N Papanikolaou, M Savvaki, G Bonetto, S Maxouri, ... NAR Genomics and Bioinformatics 2 (1), lqaa005, 2020 | 8 | 2020 |
| How to cluster protein sequences: tools, tips and commands GA Pavlopoulos MOJ Proteomics Bioinform 5 (5), 10.15406, 2017 | 7 | 2017 |
| A Simple Genetic Algorithm for Biomarker Mining D Popovic, A Sifrim, GA Pavlopoulos, Y Moreau, B De Moor Lecture Notes in Computer Science, 222-232, 2012 | 7 | 2012 |
| Data and programs in support of network analysis of genes and their association with diseases PI Kontou, A Pavlopoulou, NL Dimou, GA Pavlopoulos, PG Bagos Data in Brief, 2016 | 6 | 2016 |
| Arena3Dweb: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration M Kokoli, E Karatzas, FA Baltoumas, R Schneider, E Pafilis, ... NAR Genomics and Bioinformatics 5 (2), lqad053, 2023 | 5 | 2023 |
| ReLiance: a machine learning and literature-based prioritization of receptor—ligand pairings E Iacucci, LC Tranchevent, D Popovic, GA Pavlopoulos, B De Moor, ... Bioinformatics 28 (18), i569-i574, 2012 | 5 | 2012 |
| Analyzing protein-protein interaction networks with web tools. C N. Moschopoulos, GA Pavlopoulos, S Likothanassis, S Kossida Current Bioinformatics, 6 (4), 389-397, 2011 | 5 | 2011 |
| Drug genetic associations with COVID-19 manifestations: a data mining and network biology approach T Charitou, PI Kontou, IA Tamposis, GA Pavlopoulos, GG Braliou, ... The Pharmacogenomics Journal 22 (5), 294-302, 2022 | 4 | 2022 |
| The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies E Karatzas, M Koutrouli, F Baltoumas, K Papanikolopoulou, C Bouyioukos, ... Bioinformatics Advances, 2022 | 4 | 2022 |
| The Network Analysis Profiler (NAP v2.0): A web tool for visual topological comparison between multiple networks M Koutrouli, T Theodosiou, I Iliopoulos, G Pavlopoulos EMBnet.journal 26, e943, 2021 | 3 | 2021 |
| Erratum to: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (Nat. Biotechnol. 35, 676–683 (2017)) S Mukherjee, R Seshadri, NJ Varghese, EA Eloe-Fadrosh, ... Nature Biotechnology 36 (4), 368, 2018 | 3 | 2018 |
| OnTheFly 2.0: a tool for automatic annotation of files and biological information extraction E Pafilis, GA Pavlopoulos, VP Satagopam, N Papanikolaou, H Horn, ... IEEE, 2013 | 3 | 2013 |
| Nucleic Quasi-Primes: Identification of the Shortest Unique Oligonucleotide Sequences in a Species I Mouratidis, MA Konnaris, N Chantzi, CSY Chan, A Montgomery, ... bioRxiv, 2023.12. 12.571240, 2023 | 2 | 2023 |
| kmerDB: A Database Encompassing the Set of Genomic and Proteomic Sequence Information for Each Species I Mouratidis, FA Baltoumas, N Chantzi, C Chan, A Montgomery, ... bioRxiv, 2023 | 2 | 2023 |
| Ageotypes revisited: the brain and central nervous system dysfunction as a major nutritional and lifestyle target for healthy aging MG Grammatikopoulou, E Skoufas, S Kanellakis, D Sanoudou, ... Maturitas 170, 51-57, 2023 | 2 | 2023 |
| Exploring microbial functional biodiversity at the protein family level-from metagenomic sequence reads to annotated protein clusters FA Baltoumas, E Karatzas, D Paez-Espino, NK Venetsianou, E Aplakidou, ... Frontiers in Bioinformatics 3, 19, 2023 | 2 | 2023 |
| Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources E Karatzas, F Baltoumas, E Aplakidou, P Kontou, P Stathopoulos, ... Bioinformatics, 2023 | 2 | 2023 |
| Extreme-scale many-against-many protein similarity search O Selvitopi, S Ekanayake, G Guidi, MG Awan, GA Pavlopoulos, A Azad, ... SC22: International Conference for High Performance Computing, Networking …, 2022 | 2 | 2022 |
| The human GPCR signal transduction network P Kontou, A Pavlopoulou, N Dimou, M Theodoropoulou, G Braliou, ... Network Modeling Analysis in Health Informatics and Bioinformatics 10 (1), 1-12, 2021 | 2 | 2021 |
| Mining Cell Cycle Literature Using Support Vector Machines T Soldatos, G Pavlopoulos Lecture Notes in Computer Science, 278-284, 2012 | 2 | 2012 |
| NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes FA Baltoumas, E Karatzas, S Liu, S Ovchinnikov, Y Sofianatos, IM Chen, ... Nucleic Acids Research, 2023 | 1 | 2023 |
| Protocol for unbiased, consolidated variant calling from whole exome sequencing data KM Verrou, GA Pavlopoulos, P Moulos STAR protocols 3 (2), 101418, 2022 | 1 | 2022 |
| A bioinformatics E-dating story: Computational prediction and prioritization of receptor-ligand pairs E Iacucci, LC Tranchevent, D Popovic, GA Pavlopoulos, B De Moor, ... BMC Bioinformatics 13, 2012 | 1 | 2012 |
| APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19 G Gavriilidis, V Vasileiou, S Dimitsaki, G Karakatsoulis, A Giannakakis, ... bioRxiv, 2024.01. 11.575161, 2024 | | 2024 |
| MPRAbase: A Massively Parallel Reporter Assay Database J Zhao, FA Baltoumas, MA Konnaris, I Mouratidis, Z Liu, J Sims, ... bioRxiv, 2023 | | 2023 |
| SCALA: A complete solution for multimodal analysis of single cell next generation sequencing data C Tzaferis, E Karatzas, FA Baltoumas, GA Pavlopoulos, G Kollias, ... Computational and Structural Biotechnology Journal 21, 5382-5393, 2023 | | 2023 |
| Discovery, diversity and distribution of functional dark matter through global metagenomics. GA Pavlopoulos Nature 622, 2023 | | 2023 |
| Prediction and Ranking of Biomarkers Using multiple UniReD I Baltsavia, T Theodosiou, N Papanikolaou, GA Pavlopoulos, ... International Journal of Molecular Sciences 23 (19), 11112, 2022 | | 2022 |
| Τεχνικές Δικτυακών Υπογραφών για τον Προσδιορισμό Φαρμάκων στην Πνευμονική Ίνωση Α Δελής, Ε Καρατζάς, Α Ντούλας, Γ Παυλόπουλος, Μ Γαζούλη, ... | | 2020 |
| SARS-CoV-2 spike D614G variant exhibits highly efficient replication and transmission in hamsters (preprint) BWY Mok, CJ Cremin, SY Lau, S Deng, P Chen, AJ Zhang, ACY Lee, ... | | 2020 |
| Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics (preprint) L Lin, G Yeo, CJ Donahue, RA Davey, V Macwan, DK Kim, JJ Knapp, ... | | 2020 |
| Immune response to vaccine candidates based on different types of nanoscaffolded RBD domain of the SARS-CoV-2 spike protein (preprint) D Lainscek, T Fink, V Forstneric, I Hafner-Bratkovic, S Orehek, Z Strmsek, ... | | 2020 |
| Silicon Nitride Inactivates SARS-CoV-2 in vitro (preprint) CW Lehman, R Flur, K Kehn-Hall, BJ McEntire, BS Bal, RM Bock, ... | | 2020 |
| In silico και in vivo ανάλυση της αντιγραφής και επιδιόρθωσης του DNA Ζ Λυγερού, Σ Μαξούρη, Γ Ανδρουλάκης, Ι Ζαρκάδης, Α Παπαχατζοπούλου, ... | | 2019 |
| Elixir-GR kick-off meeting: Managing and analyzing life sciences data B Savakis, N Blomberg, P Tsanakas, J Vondrasek, C Durinx, G Kotoulas, ... | | 2018 |
| Towards better prioritization of epigenetically modified DNA regions. E Iacucci, D Popovic, GA Pavlopoulos, L Tranchevent, B De Moor, ... Lecture Notes in Computer Science, 270-277, 2012 | | 2012 |
| Molecular Omics P Kontou, A Pavlopoulou, N Dimou, M Theodoropoulou, G Braliou, ... | | |
| Multi-Modal SARS-CoV-2 Proteins Interactomics Unveil Spatial Patterns of Invasion Featuring 151 Contacts with Human Proteins Essential for Infection G Dugied, E Laurent, M Attia, JP Gimeno, K Bachiri, ... | | |
Reinhard SchneiderProf. Bioinformatics, University of Luxembourg, Head of Bioinformatics Core Facility, LuxembourgVerified email at uni.lu
