All Stories

  1. Author Correction: VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data

    Article • Nature Communications, September 2025, Springer Science + Business Media

    PhD David Paez-Espino

  2. Expanding diversity of virome associated with ammonium-oxidizing archaea and related lineages

    Article • August 2025, Cold Spring Harbor Laboratory Press

    PhD David Paez-Espino

  3. VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data

    Article • Nature Communications, March 2025, Springer Science + Business Media

    PhD David Paez-Espino

  4. Diversity of reverse-transcriptase-containing viruses through global metagenomics

    Article • hLife, January 2025, Tsinghua University Press

    Professor Andrew McMinn, PhD David Paez-Espino

  5. VITAP: A High Precision Tool for DNA and RNA Viral Classification Based On Meta-omic Data

    Article • May 2024, Springer Science + Business Media

    PhD David Paez-Espino

  6. A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

    Article • November 2023, Cold Spring Harbor Laboratory Press

    PhD David Paez-Espino

  7. A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages

    Article • February 2022, Cold Spring Harbor Laboratory Press

    PhD David Paez-Espino

  8. Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants

    Article • Nature Communications, September 2021, Springer Science + Business Media

    PhD David Paez-Espino

  9. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

    Article • Nature Microbiology, June 2021, Springer Science + Business Media

    PhD David Paez-Espino

  10. Author Correction: A genomic catalog of Earth’s microbiomes

    Article • Nature Biotechnology, April 2021, Springer Science + Business Media

    Dr Susannah Green Tringe, Gerard Muyzer, PhD David Paez-Espino

  11. Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling

    Article • PLoS Computational Biology, March 2021, PLOS

    PhD David Paez-Espino

  12. Individuals at risk for developing rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential

    Article • February 2021, Cold Spring Harbor Laboratory Press

    PhD David Paez-Espino

  13. Publisher Correction: A genomic catalog of Earth’s microbiomes

    Article • Nature Biotechnology, November 2020, Springer Science + Business Media

    Dr Nikos C Kyrpides, Dr Susannah Green Tringe, PhD David Paez-Espino

  14. A genomic catalog of Earth’s microbiomes

    Article • Nature Biotechnology, November 2020, Springer Science + Business Media

    Dr Nikos C Kyrpides, Dr Susannah Green Tringe, Gerard Muyzer, PhD David Paez-Espino

  15. IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses

    Article • Nucleic Acids Research, November 2020, Oxford University Press (OUP)

    Dr Nikos C Kyrpides, PhD David Paez-Espino

  16. A scoutRNA Is Required for Some Type V CRISPR-Cas Systems

    Article • Molecular Cell, August 2020, Elsevier

    Dr Nikos C Kyrpides, PhD David Paez-Espino

  17. Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

    Article • The ISME Journal, July 2020, Springer Science + Business Media

    Dr Nikos C Kyrpides, PhD David Paez-Espino

  18. ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic

    Article • Environmental Microbiology, April 2020, Wiley

    PhD David Paez-Espino

  19. In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs

    Article • The Science of The Total Environment, January 2020, Elsevier

    PhD David Paez-Espino

  20. Diversity, evolution, and classification of virophages uncovered through global metagenomics

    Article • Microbiome, December 2019, Springer Science + Business Media

    PhD David Paez-Espino, Dr Nikos C Kyrpides, Dr Susannah Green Tringe

  21. Untapped viral diversity in global soil metagenomes

    Article • March 2019, Cold Spring Harbor Laboratory Press

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  22. IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

    Article • Nucleic Acids Research, November 2018, Oxford University Press (OUP)

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  23. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

    Article • Science, October 2018, American Association for the Advancement of Science

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  24. Investigation of recombination-intense viral groups and their genes in the Earth’s virome

    Article • Scientific Reports, July 2018, Springer Science + Business Media

    PhD David Paez-Espino

  25. Murine colitis reveals a disease-associated bacteriophage community

    Article • Nature Microbiology, July 2018, Springer Science + Business Media

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  26. A thermostable Cas9 with increased lifetime in human plasma

    Article • Nature Communications, November 2017, Nature

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  27. Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

    Article • Nature Protocols, July 2017, Nature

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  28. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

    Article • Nature Biotechnology, June 2017, Springer Science + Business Media

    PhD David Paez-Espino, Prof. Jonathan A. Eisen, Dr Nikos C Kyrpides

  29. A thermostable Cas9 with increased lifetime in human plasma

    Article • May 2017, Cold Spring Harbor Laboratory Press

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  30. Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

    Article • Advances in Bioinformatics, January 2017, Hindawi Publishing Corporation

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  31. Uncovering Earth’s virome

    Article • Nature, August 2016, Nature

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  32. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

    Article • Standards in Genomic Sciences, February 2016, Springer Science + Business Media

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  33. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

    Article • Nature Communications, January 2016, Nature

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  34. Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

    Article • Environmental Microbiology, December 2015, Wiley

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  35. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

    Article • Standards in Genomic Sciences, October 2015, Springer Science + Business Media

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  36. Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation

    Article • The ISME Journal, June 2015, Nature

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  37. CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus

    Article • mBio, April 2015, ASM Journals

    Rodolphe Barrangou, PhD David Paez-Espino

  38. The two paraloguephoN(phosphinothricin acetyl transferase) genes ofPseudomonas putidaencode functionally different proteins

    Article • Environmental Microbiology, April 2015, Wiley

    PhD David Paez-Espino

  39. Functional coexistence of twin arsenic resistance systems inPseudomonas putida KT2440

    Article • Environmental Microbiology, April 2014, Wiley

    PhD David Paez-Espino

  40. Strong bias in the bacterial CRISPR elements that confer immunity to phage

    Article • Nature Communications, February 2013, Nature

    PhD David Paez-Espino

  41. The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes

    Article • Nucleic Acids Research, November 2012, Oxford University Press (OUP)

    PhD David Paez-Espino

  42. Monitoring biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins

    Article • Environmental Microbiology, January 2011, Wiley

    PhD David Paez-Espino

  43. 10.1093/nar/gks1119

    Article • BioMetals, January 2009, Springer Science + Business Media

    PhD David Paez-Espino