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

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes. - David Páez-Espino; Simon Roux; I-Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; Marcel Huntemann; T. B. K. Reddy; Joan Carles Pons; Mercè Llabrés; Emiley A. Eloe-Fadrosh; Natalia N. Ivanova; et al. (Nucleic Acids Res., 2019)

VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. - Joan Carles Pons; David Páez-Espino; Gabriel Riera; Natalia Ivanova; Nikos Kyrpides; Mercè Llabrés (Bioinform., 2021)

IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. - Simon Roux; David Páez-Espino; I-Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; T. B. K. Reddy; Stephen Nayfach; Frederik Schulz; Lee Call; Russell Y. Neches; Tanja Woyke; et al. (Nucleic Acids Res., 2021)

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling. - Yekaterina S. Pavlova; David Páez-Espino; Andrew Yu. Morozov; Ilya S. Belalov (PLoS Comput. Biol., 2021)

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)