Biography:Nikos Kyrpides

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Short description: Greek-American bioscientist (born 1963)
Nikos Kyrpides
Νίκος X. Κυρπίδης
BornNovember 11, 1963
Serres, Greece
Alma materAristotle University of Thessaloniki
Known forMicrobial genomics, metagenomics, Microbiome, Virome, microbiome data science
Scientific career
FieldsBioinformatics, microbiology, virology, computational biology, data science
InstitutionsJoint Genome Institute, Lawrence Berkeley National Laboratory
Academic advisorsCarl Woese, Ross Overbeek
Websitehttps://jgi.doe.gov/our-science/scientists-jgi/nikos-kyrpides/

Nikos Kyrpides (Greek: Νίκος Κυρπίδης) is a Greek-American bioscientist who has worked on the origins of life, information processing, bioinformatics, microbiology, metagenomics and microbiome data science.[1][2][3] He is a senior staff scientist at the Berkeley National Laboratory,[4] head of the Prokaryote Super Program[5] and leads the Microbiome Data Science program[6] at the US Department of Energy Joint Genome Institute.[7]

Education

Kyrpides was born in Serres, Greece, where he studied biology at the Aristotle University of Thessaloniki and received his PhD in molecular biology and biotechnology from the University of Crete. He pursued postdoctoral studies in microbiology with Carl Woese at the University of Illinois at Urbana-Champaign and in bioinformatics with Ross Overbeek at the Argonne National Laboratory. From 1999 to 2004 Kyrpides worked in the biotech industry in Chicago , where he led the development of genome analysis and bioinformatics. He joined the United States Department of Energy Joint Genome Institute (JGI) in 2004 to lead the Genome Biology Program and develop the data management and comparative analysis platforms for microbial genomes and metagenomes. Kyrpides became the Metagenomics Program head in 2010 and founded the Prokaryotic Super Program in 2011, which he still leads with the Microbiome Data Science Group.

Research

Kyrpides's early work focused on the origins and evolution of the genetic code. In collaboration with Christos Ouzounis, he developed a series of hypotheses for the transfer of information from proteins to nucleic acids known as reverse interpretation.[8][9][10] With the advent of genomics, Kyrpides turned his interest to the study and understanding of the last universal common ancestor. With Ouzounis he coined the acronym "LUCA" at a conference organized by Patrick Forterre at Les Treilles, France, and performed some of the first comparative genome analysis to predict the gene content of the LUCA.[11][12] Kyrpides's work on the information processing systems revealed several previously-unsuspected relationships, suggesting new models for the evolution of those processes. He identified previously-undetected relationships between the eukaryotic and bacterial translation machinery, suggesting that the rudiments of translation initiation would have been present at the universal-ancestor stage.[13][14] Kyrpides's work on the evolution of transcription helped change the understanding of the nature and organization of archaeal transcription machinery, which (at the time) was that transcription in Archaea was strictly similar to that in eukaryotes. Kyrpides and Ouzounis demonstrated the parallel existence of a large number of bacterial-type transcription factors in archaeal genomes.[15][16][17]

He led the development of several pioneering data-management systems in microbial genomics and metagenomics, which are widely used in the scientific community (with several thousand users worldwide).[18] These include systems for data management and curation of genome projects and their associated metadata, such as the Genomes OnLine Database (GOLD),[19] and comparative-genomics systems such as ERGO[20] and the Integrated Microbial Genomes (IMG).[21][22]

Kyrpides's current research focuses on microbiome research, with an emphasis on microbiome data science. This includes the understanding of structure and function of various microorganisms and microbial communities and the elucidation of the evolutionary dynamics shaping the microbial genomes. To accomplish that, his group is developing novel computational methods for enabling large-scale comparative analysis and mining and visualizing big data. He proposed and published the first study on the use of standard benchmarking data for the evaluation of method accuracy in metagenomics.[23] This approach has become the standard in the field.[24] Some of Kyrpides's recent research in microbiome data science include the exploration of Earth’s virome,[25][26] the identification of new bacterial phyla[27] the prediction of novel folds using metagenomic sequences,[28] and the discovery and characterization of new protein families from microbiome data.[29]

International initiatives

Kyrpides began the MikroBioKosmos (MBK) initiative in Greece in 2007, with the goal of exploring and commercially using microbial national resources. MikroBioKosmos became a scientific society, with Kyrpides its first president. He is a founding member of two bioinformatics societies in Greece: the Hellenic Society of Computational Biology and Bioinformatics (HSCBB) in 2010 and Hellenic Bioinformatics in 2016. Kyrpides is also a board member[30] of the international Genomic Standards Consortium (GSC),[31] which aims to enable genomic data integration, discovery and comparison with international, community-driven standards.

He began the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project at the JGI and the Microbial Earth Project with Hans-Peter Klenk, Philip Hugenholtz and Jonathan Eisen in 2007,[32] with the goal of improving the genome characterization of phylogenetically-diverse cultured microbes.[33] The latter project evolved into an international effort to sequence all the type strains of bacteria and archaea,[34] through a series of GEBA 1,000-genome projects.[35][36][37][38] The rapid growth of microbial genome sequences at the end of 2010, without a parallel venue for describing those projects in a standardized manner, led to the need for a new scientific forum which would be a clearinghouse for capturing and presenting this information to the community. This idea led Kyrpides, George Garrity and Dawn Field to launch a new scientific journal: Standards in Genomic Sciences (SIGS), which became part of BioMed Central.[39][40]

Kyrpides proposed the development of a Microbial Environmental Genomics Administration in 2009, analogous to NASA, for the study and exploration of the most abundant life on the planet.[41] In 2016, following the enormous growth of microbiome data, he outlined the need for a common infrastructure for microbiome data analysis and proposed the development of a National Microbiome Data Center (NMDC), later renamed to National Microbiome Data Collaborative.[42][43] With Emiley Eloe-Fadrosh, Kyrpides organized the first NMDC workshop to launch this initiative at the Joint Genome Institute. This was followed by additional workshops in 2017 hosted by the American Society for Microbiology to promote the initiative.[44]

Awards and honours

Kyrpides has received several awards, including the 2022 Exceptional Scientific Achievement Award from the Director of Lawrence Berkeley National Laboratory, the 2018 USFCC/J. Roger Porter Award from the American Society for Microbiology,[45] the 2014 van Niel International Prize for Studies in Bacterial Systematics from the International Union of Microbiological Societies (IUMS),[46] a 2007 outstanding-performance award from the Lawrence Berkeley National Laboratory, and the 2012 Academic Excellence Prize from the Empirikion Foundation. He is an elected fellow of the American Academy of Microbiology (AAM) (2014),[47] and has been on the Thomson Reuters list of the world’s most frequently-cited scientists since 2014.[48][49] A bacterial genus (Kyrpidia) was named after Kyrpides in 2011.[50] In 2017, he received an honorary doctorate from the Aristotle University of Thessaloniki.[51]

References

  1. ↑ Search Results for author Kyrpides on PubMed.
  2. ↑ Nikos Kyrpides - Google Scholar
  3. ↑ Ellnines.com
  4. ↑ "Nikos Kyrpides | Biosciences | Berkeley Lab". http://biosciences.lbl.gov/profiles/nikos-kyrpides/. 
  5. ↑ Prokaryote Super Program
  6. ↑ Microbiome Data Science
  7. ↑ About Nikos Kyrpides at the JGI
  8. ↑ Kyrpides N., and Ouzounis C. (1993) Mechanisms of specificity in mRNA degradation: autoregulation and cognate interactions. J.Theor.Biology 163: 373-392. PMID 8246508
  9. ↑ Ouzounis, C., and Kyrpides, N. (1994) Reverse interpretation: a hypothetical selection mechanism for adaptive mutagenesis based on autoregulated mRNA stability. J.Theor.Biology 167: 373-380. PMID 8207952
  10. ↑ Kyrpides, N. and Ouzounis, C. (1995) Nucleic acid-binding metabolic enzymes: Living fossils of stereochemical interactions? J.Mol.Evolution 40: 564-569. PMID 7543949
  11. ↑ Ouzounis, C. and Kyrpides, N. (1996) The emergence of major cellular processes in evolution. FEBS Letters 390: 119-123. PMID 8706840
  12. ↑ Kyrpides N, et al. (1999) Universal protein families and the functional content of the Last Universal Common Ancestor. J.Mol.Evolution 49, 413-423. PMID 10485999
  13. ↑ Kyrpides, N., and Woese, C. (1998) Universally conserved translation initiation factors. Proc. Natl. Acad. Sci. USA 95, 224-228. PMID 9419357
  14. ↑ Kyrpides, N., and Woese, C. (1998). Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families. Proc. Natl. Acad. Sci. USA 95, 3726-3730. PMID 9520434
  15. ↑ Kyrpides, N. and Ouzounis, C. (1995) The eubacterial transcriptional activator Lrp is present in the Archaeon Pyrococcus furiosus. Trends in Biochemistry. 20: 140-141. PMID 7770911
  16. ↑ Kyrpides, N. and Ouzounis, C. (1997) Bacterial sigma-70 transcription factor DNA-binding domains in the archaeon Methanococcus jannaschii. J.Mol.Evolution 45: 706-707. PMID 9419249
  17. ↑ Kyrpides, N. and Ouzounis, C. (1999) Transcription in Archaea. Proc. Natl. Acad. Sci. USA 96, 8545-8550. PMID 10411912
  18. ↑ IMG Registered User count
  19. ↑ Bernal A, et al. (2001) Genomes OnLine Database (GOLD): a monitor of genomes projects worldwide. Nucleic Acids Research 29, 126-127. PMID 11125068
  20. ↑ Overbeek R, et al. (2003) The ERGOTM Genome Analysis and Discovery System. Nucleic Acids Research 31, 164-71. PMID 12519973
  21. ↑ Markowitz VM, et al. (2006) An Experimental Metagenome Data Management and Analysis System. Bioinformatics 22, e359-67. PMID 16873494
  22. ↑ Markowitz VM, et al. (2015) Ten years of maintaining and expanding a microbial genome and metagenome analysis system. Trends in Microbiology 23(11):730-41. PMID 26439299
  23. ↑ Mavromatis K, et al. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods 4, 495-500. PMID 17468765
  24. ↑ Sczyrba A, et al. (2017) Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software. Nature Methods 14(11):1063-1071. PMID 28967888.
  25. ↑ Paez-Espino D, et al. (2016) Uncovering Earth’s Virome. Nature 536(7617):425-30. PMID 27533034,
  26. ↑ Global Viral Diversity Study Results in 16-Fold Increase in Number of Known Viral Genes
  27. ↑ Eloe-Fadrosh EA, et al. (2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nature Communication 7:10476. PMID 26814032.
  28. ↑ Ovchinnikov S, et al. (2017) Protein Structure Determination using Metagenome sequence data. Science 355:294-298. PMID 28104891.
  29. ↑ Pavlopoulos, Georgios A. (2023-10-19). "Unraveling the functional dark matter through global metagenomics" (in en). Nature 622 (7983): 594–602. doi:10.1038/s41586-023-06583-7. ISSN 0028-0836. PMID 37821698. PMC 10584684. https://www.nature.com/articles/s41586-023-06583-7. 
  30. ↑ GSC Board Members
  31. ↑ Field D, et al. (2011) The Genomic Standards Consortium. PLoS Biology 9(6):e1001088. PMID 21713030
  32. ↑ "Microbial Earth Project | Genomic Standards Consortium". http://gensc.org/projects/microbial-earth-project/. 
  33. ↑ Wu, D., et al. (2009) A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. Nature 462: 1056-60. PMID 20033048
  34. ↑ Kyrpides NC, et al. (2014) Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains. PLoS Biology 12(8): e1001920. PMID 25093819
  35. ↑ Kyrpides NC, et al. (2014) Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences. 9(3):1278-84. PMID 25197443.
  36. ↑ Whitman WB, et al. (2015) Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Standards in Genomic Sciences. 10:26. PMID 26203337.
  37. ↑ Mukherjee S, et al. (2017) 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology 35(7):676-683. PMID 28604660.
  38. ↑ "Uncovered: 1000 New Microbial Genomes". 2017-06-12. https://jgi.doe.gov/uncovered-1000-new-microbial-genomes/. 
  39. ↑ Garrity GM, et al. (2009) Standards in Genomic Sciences. Standards in Genomic Sciences. 1(1):1-2.
  40. ↑ Garrity GM, et al. (2011) Alive and well at 100. Standards in Genomic Sciences. 4(1): 1-2. PMID 21475581
  41. ↑ Kyrpides NC. (2009) Fifteen Years of Microbial Genomics: Meeting the Challenges and Fulfilling the Dream. Nature Biotechnology 27, 627 -632. PMID 19587669
  42. ↑ Kyrpides NC, et al. (2016) Microbiome Data Science: understanding our microbial planet. Trends in Microbiology 24(6):425-427. PMID 27197692.
  43. ↑ A Rallying Call for Microbiome Science National Data Management (DOE-JGI, 2016)
  44. ↑ ASM Hosts National Microbiome Data Collaborative Workshop
  45. ↑ Nikos Kyrpides Named 2018 ASM USFCC/J. Roger Porter Awardee
  46. ↑ Tindall BJ and Garrity GM. (2015) The van Niel International Prize for Studies in Bacterial Systematics awarded in 2014 to Nikos C. Kyrpides. Int J Syst Evol Microbiol. 65(Pt 6):2011-2 PMID 26184666
  47. ↑ AAM Fellow
  48. ↑ Six from DOE JGI on 2016 Highly Cited Researchers List (DOE-JGI, 2016)
  49. ↑ Highly Cited: 8 DOE JGI Researchers Make 2015 List (DOE-JGI, 2015)
  50. ↑ Klenk HP, et al. (2011) Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Stand Genomic Sci. 15;5(1):121-34. PMID 22180816
  51. ↑ Nikolaos Kyrpides awarded Honorary Doctor of the Department of Biology of the Aristotle University of Thessaloniki



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