All Stories

  1. 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

  2. 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

  3. Untapped viral diversity in global soil metagenomes

    Article • March 2019, Cold Spring Harbor Laboratory Press

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  4. 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

  5. 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

  6. 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

  7. 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

  8. A thermostable Cas9 with increased lifetime in human plasma

    Article • Nature Communications, November 2017, Nature

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  9. 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

  10. 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

  11. 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

  12. 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

  13. Uncovering Earth’s virome

    Article • Nature, August 2016, Nature

    PhD David Paez-Espino, Dr Nikos C Kyrpides

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

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

    Article • mBio, April 2015, ASM Journals

    Rodolphe Barrangou, PhD David Paez-Espino

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

    Article • Environmental Microbiology, April 2015, Wiley

    PhD David Paez-Espino

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

    Article • Environmental Microbiology, April 2014, Wiley

    PhD David Paez-Espino

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

    Article • Nature Communications, February 2013, Nature

    PhD David Paez-Espino

  23. 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

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

    Article • Environmental Microbiology, January 2011, Wiley

    PhD David Paez-Espino

  25. 10.1093/nar/gks1119

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

    PhD David Paez-Espino