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Nikos Kyrpides

Kyrpides

Nikos C. Kyrpides, Ph.D
Microbiome Data Science Group Lead

Dr. Kyrpides joined the DOE Joint Genome Institute in 2004 to lead the Genome Biology Program and the development of the comparative analysis platforms for microbial genomes and metagenomes (IMG). He became the Metagenomics Program head in 2010 and has the combined Microbial Genomes and Metagenomes Program since 2011. Prior to joining the DOE Joint Genome Institute, Dr. Kyrpides led the development of the genome analysis and Bioinformatics core at Integrated Genomics Inc. in Chicago, IL. He did his postdoctoral studies with Carl Woese at the University of Illinois at Urbana-Champaign and at Argonne National Laboratory. Dr. Kyrpides’ research focus on Microbiome Research with an emphasis on Microbiome Data Science. His group is developing novel methods for enabling large-scale comparative analysis, as well as mining and visualization of big data.

Education

  • BA in Biology, Aristotle University of Thessaloniki, Greece
  • PhD in Molecular Biology and Biotechnology, University of Crete, Greece

Awards and Service

  • Thomson Reuters Highly Cited Researcher (Biology & Biochemistry) (2014-2023)
  • Lawrence Berkeley National Laboratory Outstanding Scientific Achievement Award (2022)
  • ASM’s USFCC/J. Roger Porter Award (2018)
  • Honorary Doctorate from the Aristotle University of Thessaloniki (2017)
  • The van Niel International Prize for Studies in Bacterial Systematics (2012-2014)
  • American Academy of Microbiology Fellow (2014)
  • Academic Excellence Prize Award, Empeirikeion Foundation (2012)
  • 2007: Outstanding Performance Award, Lawrence Berkeley National Laboratory
  • Scientific Advisory Boards: UniProt; Elixir-GR; Microbiomes in Transition (MinT), PNNL; EarthCube Oceanography & Geobiology Environmental Omics (ECOGEO) RCN, USA; AgreenSkills programme, France; Meta-omics of microbial ecosystems, INRA, France; A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics (MICROME); Metagenomics of the Human Intestinal Tract (MetaHIT); Community Cyber-infrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA).

Publications

  1. Pavlopoulos GA et al. (2023) Unraveling the functional dark matter through global metagenomics. Nature. 622(7983):594-602.
  2. Camargo AP. et al. (2023) Identification of mobile genetic elements with geNomad. Nat Biotechnol. Epub.
  3. Neri U. et al. (2022) Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell. 185(21):4023-4037
  4. Nayfach S, et al. (2021) Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat Microbiol. 6(7):960-970.
  5. Nayfach S, et al. (2021) CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature Biotechnol. 39(5):578-585.
  6. Nayfach S, et al. (2021) A genomic catalog of Earth’s microbiomes. Nature Biotechnol. 39(4):499-509
  7. Danko D, et al. 2021. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. 8674:00585-7.
  8. Nayfach S et al. 2021. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature Biotechnol. 39:578-585
  9. Nayfach S. et al. 2021. A genomic catalog of Earth’s microbiomes. Nature Biotechnol. 39:499-509.
  10. Harrington et al. 2020. A scoutRNA Is Required for Some Type V CRISPR-Cas Systems. Mol Cell. S1097-2765
  11. Schulz F, et al. 2020. Giant virus diversity and host interactions through global metagenomics. Nature. 578:432-436
  12. Roux S. et al. 2019. Cryptic inoviruses are pervasive in bacteria and archaea across Earth’s biomes. Nature 4:1895-1906
  13. Sberro H. et al. 2019 Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. Cell. 178(5):1245-1259.
  14. Wright AV et al. 2019. A Functional Mini-Integrase in a Two-Protein-type V-C CRISPR System. Mol Cell. S1097-2765: 31069-4.
  15. Nyfach et al. 2019. Novel insights from uncultivated genomes of the global human gut microbiome . Nature. 568(7753):505-510.
  16. Roux S et al 2018. Minimum Information about an Uncultivated Virus Genome (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses Nature Biotechnol. 37:29-37.
  17. Harrington et al. 2018. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science. 362:839-842.
  18. Seshadri R. et al. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol.36(4):359-367.

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