An enhanced Markov clustering method for detecting protein complexes. - Charalampos N. Moschopoulos; Georgios A. Pavlopoulos; Spiridon D. Likothanassis; Sofia Kossida (BIBE, 2008)

A survey of visualization tools for biological network analysis. - Georgios A. Pavlopoulos; Anna-Lynn Wegener; Reinhard Schneider 002 (BioData Min., 2008)

Arena3D: visualization of biological networks in 3D. - Georgios A. Pavlopoulos; Seán I. O'Donoghue; Venkata P. Satagopam; Theodoros G. Soldatos; Evangelos Pafilis; Reinhard Schneider 002 (BMC Syst. Biol., 2008)

jClust: a clustering and visualization toolbox. - Georgios A. Pavlopoulos; Charalampos N. Moschopoulos; Sean D. Hooper; Reinhard Schneider 002; Sophia Kossida (Bioinform., 2009)

OnTheFly: a tool for automated document-based text annotation, data linking and network generation. - Georgios A. Pavlopoulos; Evangelos Pafilis; Michael Kuhn 004; Sean D. Hooper; Reinhard Schneider 002 (Bioinform., 2009)

GIBA: a clustering tool for detecting protein complexes. - Charalampos N. Moschopoulos; Georgios A. Pavlopoulos; Reinhard Schneider 002; Spiridon D. Likothanassis; Sophia Kossida (BMC Bioinform., 2009)

Data integration and visualization techniques in systems biology. - Georgios A. Pavlopoulos (2009)

A reference guide for tree analysis and visualization. - Georgios A. Pavlopoulos; Theodoros G. Soldatos; Adriano Barbosa-Silva; Reinhard Schneider 002 (BioData Min., 2010)

GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. - Venkata P. Satagopam; Margarita C. Theodoropoulou; Christos K. Stampolakis; Georgios A. Pavlopoulos; Nikolaos Papandreou; Pantelis G. Bagos; Reinhard Schneider 002; Stavros J. Hamodrakas (Database J. Biol. Databases Curation, 2010)

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships. - Adriano Barbosa-Silva; Theodoros G. Soldatos; Ivan L. F. Magalhães; Georgios A. Pavlopoulos; Jean-Fred Fontaine; Miguel A. Andrade-Navarro; Reinhard Schneider 002; José Miguel Ortega (BMC Bioinform., 2010)

Using graph theory to analyze biological networks. - Georgios A. Pavlopoulos; Maria Secrier; Charalampos N. Moschopoulos; Theodoros G. Soldatos; Sophia Kossida; Jan Aerts; Reinhard Schneider 002; Pantelis G. Bagos (BioData Min., 2011)

Visualizing high dimensional datasets using parallel coordinates: Application to gene prioritization. - Thomas Boogaerts; Léon-Charles Tranchevent; Georgios A. Pavlopoulos; Jan Aerts; Joos Vandewalle (BIBE, 2012)

A Simple Genetic Algorithm for Biomarker Mining. - Dusan Popovic; Alejandro Sifrim; Georgios A. Pavlopoulos; Yves Moreau; Bart De Moor (PRIB, 2012)

Towards Better Prioritization of Epigenetically Modified DNA Regions. - Ernesto Iacucci; Dusan Popovic; Georgios A. Pavlopoulos; Léon-Charles Tranchevent; Marijke Bauters; Bart De Moor; Yves Moreau (SETN, 2012)

Mining Cell Cycle Literature Using Support Vector Machines. - Theodoros G. Soldatos; Georgios A. Pavlopoulos (SETN, 2012)

Caipirini: using gene sets to rank literature. - Theodoros G. Soldatos; Seán I. O'Donoghue; Venkata P. Satagopam; Adriano Barbosa-Silva; Georgios A. Pavlopoulos; Ana Carolina Wanderley-Nogueira; Nina da Mota Soares-Cavalcanti; Reinhard Schneider 002 (BioData Min., 2012)

ReLiance: a machine learning and literature-based prioritization of receptor - ligand pairings. - Ernesto Iacucci; Léon-Charles Tranchevent; Dusan Popovic; Georgios A. Pavlopoulos; Bart De Moor; Reinhard Schneider 002; Yves Moreau (Bioinform., 2012)

A bioinformatics e-dating story: computational prediction and prioritization of receptor-ligand pairs. - Ernesto Iacucci; Léon-Charles Tranchevent; Dusan Popovic; Georgios A. Pavlopoulos; Bart De Moor; Reinhard Schneider 002; Yves Moreau (BMC Bioinform., 2012)

Arena3D: visualizing time-driven phenotypic differences in biological systems. - Maria Secrier; Georgios A. Pavlopoulos; Jan Aerts; Reinhard Schneider 002 (BMC Bioinform., 2012)

OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction. - Evangelos Pafilis; Georgios A. Pavlopoulos; Venkata P. Satagopam; Nikolas Papanikolaou; Heiko Horn; Christos Arvanitidis; Lars Juhl Jensen; Reinhard Schneider 002; Ioannis Iliopoulos (BIBE, 2013)

Unraveling genomic variation from next generation sequencing data. - Georgios A. Pavlopoulos; Anastasis Oulas; Ernesto Iacucci; Alejandro Sifrim; Yves Moreau; Reinhard Schneider 002; Jan Aerts; Ioannis Iliopoulos (BioData Min., 2013)

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. - Nikolas Papanikolaou; Georgios A. Pavlopoulos; Evangelos Pafilis; Theodosios Theodosiou; Reinhard Schneider 002; Venkata P. Satagopam; Christos A. Ouzounis; Aristides G. Eliopoulos; Vasilis J. Promponas; Ioannis Iliopoulos (Bioinform., 2014)

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. - Nikolas Papanikolaou; Georgios A. Pavlopoulos; Evangelos Pafilis; Theodosios Theodosiou; Reinhard Schneider 002; Venkata P. Satagopam; Christos A. Ouzounis; Aristides G. Eliopoulos; Vasilis J. Promponas; Ioannis Iliopoulos (Bioinform., 2015)

DrugQuest - a text mining workflow for drug association discovery. - Nikolas Papanikolaou; Georgios A. Pavlopoulos; Theodosios Theodosiou; Ioannis S. Vizirianakis; Ioannis Iliopoulos (BMC Bioinform., 2016)

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. - Georgios A. Pavlopoulos; David Páez-Espino; Nikos Kyrpides; Ioannis Iliopoulos (Adv. Bioinformatics, 2017)

ProteoSign: an end-user online differential proteomics statistical analysis platform. - Georgios Efstathiou; Andreas N. Antonakis; Georgios A. Pavlopoulos; Theodosios Theodosiou; Peter Divanach; David C. Trudgian; Benjamin Thomas; Nikolas Papanikolaou; Michalis Aivaliotis; Oreste Acuto; Ioannis Iliopoulos (Nucleic Acids Res., 2017)

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. - David Páez-Espino; I-Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; Ernest Szeto; Manoj Pillay; Jinghua Huang; Victor M. Markowitz; Torben Nielsen; Marcel Huntemann; T. B. K. Reddy; et al. (Nucleic Acids Res., 2017)

Distributed many-to-many protein sequence alignment using sparse matrices. - Oguz Selvitopi; Saliya Ekanayake; Giulia Guidi; Georgios A. Pavlopoulos; Ariful Azad; Aydin Buluç (SC, 2020)

VICTOR: A visual analytics web application for comparing cluster sets. - Evangelos Karatzas; Maria Gkonta; Joana Hotova; Fotis A. Baltoumas; Panagiota I. Kontou; Christopher J. Bobotsis; Pantelis G. Bagos; Georgios A. Pavlopoulos (Comput. Biol. Medicine, 2021)

Arena3Dweb: interactive 3D visualization of multilayered networks. - Evangelos Karatzas; Fotis A. Baltoumas; Nikolaos A. Panayiotou; Reinhard Schneider 002; Georgios A. Pavlopoulos (Nucleic Acids Res., 2021)

ProteoSign v2: a faster and evolved user-friendly online tool for statistical analyses of differential proteomics. - Evangelos Theodorakis; Andreas N. Antonakis; Ismini Baltsavia; Georgios A. Pavlopoulos; Martina Samiotaki; Grigoris D. Amoutzias; Theodosios Theodosiou; Oreste Acuto; Georgios Efstathiou; Ioannis Iliopoulos (Nucleic Acids Res., 2021)

The human GPCR signal transduction network. - Panagiota I. Kontou; Athanasia Pavlopoulou; Niki L. Dimou; Margarita C. Theodoropoulou; Georgia Braliou; Georgios N. Tsaousis; Georgios A. Pavlopoulos; Stavros J. Hamodrakas; Pantelis G. Bagos (Netw. Model. Anal. Health Informatics Bioinform., 2021)

Extreme-Scale Many-against-Many Protein Similarity Search. - Oguz Selvitopi; Saliya Ekanayake; Giulia Guidi; Muaaz G. Awan; Georgios A. Pavlopoulos; Ariful Azad; Nikos Kyrpides; Leonid Oliker; Katherine A. Yelick; Aydin Buluç (SC, 2022)

NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization. - Mikaela Koutrouli; Evangelos Karatzas; Katerina Papanikolopoulou; Georgios A. Pavlopoulos (Genom. Proteom. Bioinform., 2022)

Exploring microbial functional biodiversity at the protein family level - From metagenomic sequence reads to annotated protein clusters. - Fotis A. Baltoumas; Evangelos Karatzas; David Páez-Espino; Nefeli K. Venetsianou; Eleni Aplakidou; Anastasis Oulas; Robert D. Finn; Sergey Ovchinnikov; Evangelos Pafilis; Nikos Kyrpides; Georgios A. Pavlopoulos (Frontiers Bioinform., 2023)

Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources. - Evangelos Karatzas; Fotis A. Baltoumas; Eleni Aplakidou; Panagiota I. Kontou; Panos Stathopoulos; Leonidas Stefanis; Pantelis G. Bagos; Georgios A. Pavlopoulos (Bioinform., 2023)