请输入您要查询的百科知识:

 

词条 Nikos Kyrpides
释义

  1. Education

  2. Research

  3. {{anchor|International Initiatives}}International initiatives

  4. {{anchor|Awards and Honours}}Awards and honours

  5. References

{{Infobox scientist
| name = Nikos Kyrpides
| native_name = Νίκος X. Κυρπίδης
| native_name_lang =
| image =
| image_size =
| birth_date = November 11, 1963
| birth_place = Serres, Greece
| death_place =
| fields = Bioinformatics, microbiology, computational biology, data science
| workplaces = Joint Genome Institute
| alma_mater = Aristotle University of Thessaloniki
| academic_advisors = Carl Woese, Ross Overbeek
| known_for = Microbial genomics, metagenomics, microbiome data science
| website = https://jgi.doe.gov/about-us/organization/prokaryote-super-program/nikos-kyrpides/
}}Nikos Kyrpides (Greek: Νίκος Κυρπίδης) is an American bioscientist of Greek descent 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 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 characterization of new protein families from microbiome data.

{{anchor|International Initiatives}}International initiatives

Kyrpides began the MikroBioKosmos (MBK) initiative in Greece in 2007,[29] with the goal of exploring and commercially using microbial national resources. MBK 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).[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]

{{anchor|Awards and Honours}}Awards and honours

Kyrpides has received several awards, including 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 newly-described bacterial genus (Kyrpidiae) was named after Kyrpides in 2011.[50] In 2017, he received an honorary doctorate from the Aristotle University of Thessaloniki.[51]

{{Scholia|author}}{{clear}}

References

1. ^[https://www.ncbi.nlm.nih.gov/pubmed/?term=Kyrpides Search Results for author Kyrpides on PubMed.]
2. ^[https://scholar.google.com/citations?user=0FuZRPYAAAAJ&hl=en Nikos Kyrpides - Google Scholar]
3. ^[https://www.ellines.com/en/achievements/636-he-researches-the-usefulness-of-bacteria/ Ellnines.com]
4. ^{{Cite web | url=http://biosciences.lbl.gov/profiles/nikos-kyrpides/ | title=Nikos Kyrpides | Biosciences | Berkeley Lab}}
5. ^[https://jgi.doe.gov/about-us/organization/prokaryote-super-program/ Prokaryote Super Program]
6. ^[https://jgi.doe.gov/our-science/scientists-jgi/microbiome-data-science Microbiome Data Science]
7. ^[https://jgi.doe.gov/about-us/organization/prokaryote-super-program/nikos-kyrpides/ About Nikos Kyrpides at the JGI]
8. ^Kyrpides N., and Ouzounis C. (1993) [https://www.ncbi.nlm.nih.gov/pubmed/8246508 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) [https://www.ncbi.nlm.nih.gov/pubmed/8207952 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) [https://www.ncbi.nlm.nih.gov/pubmed/7543949 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) [https://www.ncbi.nlm.nih.gov/pubmed/8706840 The emergence of major cellular processes in evolution]. FEBS Letters 390: 119-123. {{PMID|8706840}}
12. ^Kyrpides N, et al. (1999) [https://www.ncbi.nlm.nih.gov/pubmed/10485999 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) [https://www.ncbi.nlm.nih.gov/pubmed/9419357 Universally conserved translation initiation factors.] Proc. Natl. Acad. Sci. USA 95, 224-228. {{PMID|9419357}}
14. ^Kyrpides, N., and Woese, C. (1998). [https://www.ncbi.nlm.nih.gov/pubmed/9520434 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) [https://www.ncbi.nlm.nih.gov/pubmed/7770911 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) [https://www.ncbi.nlm.nih.gov/pubmed/9419249 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) [https://www.ncbi.nlm.nih.gov/pubmed/10411912 Transcription in Archaea.] Proc. Natl. Acad. Sci. USA 96, 8545-8550. {{PMID|10411912}}
18. ^[https://img.jgi.doe.gov/usermap.html IMG Registered User count]
19. ^Bernal A, et al. (2001) [https://www.ncbi.nlm.nih.gov/pubmed/11125068 Genomes OnLine Database (GOLD): a monitor of genomes projects worldwide.] Nucleic Acids Research 29, 126-127. {{PMID|11125068}}
20. ^Overbeek R, et al. (2003) [https://www.ncbi.nlm.nih.gov/pubmed/12519973 The ERGOTM Genome Analysis and Discovery System.] Nucleic Acids Research 31, 164-71. {{PMID|12519973}}
21. ^Markowitz VM, et al. (2006) [https://www.ncbi.nlm.nih.gov/pubmed/16873494 An Experimental Metagenome Data Management and Analysis System.] Bioinformatics 22, e359-67. {{PMID|16873494}}
22. ^Markowitz VM, et al. (2015) [https://www.ncbi.nlm.nih.gov/pubmed/26439299 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) [https://www.ncbi.nlm.nih.gov/pubmed/17468765 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) [https://www.ncbi.nlm.nih.gov/pubmed/28967888 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) [https://www.ncbi.nlm.nih.gov/pubmed/27533034 Uncovering Earth’s Virome.] Nature 536(7617):425-30. {{PMID|27533034}},
26. ^[https://www.genomeweb.com/sequencing/global-viral-diversity-study-results-16-fold-increase-number-known-viral-genes#.WtPlxIgbOUk Global Viral Diversity Study Results in 16-Fold Increase in Number of Known Viral Genes]
27. ^Eloe-Fadrosh EA, et al. (2016) [https://www.ncbi.nlm.nih.gov/pubmed/26814032 Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.] Nature Communication 7:10476. {{PMID|26814032}}.
28. ^Ovchinnikov S, et al. (2017) [https://www.ncbi.nlm.nih.gov/pubmed/28104891 Protein Structure Determination using Metagenome sequence data.] Science 355:294-298. {{PMID|28104891}}.
29. ^History of Mikrobiokosmos Initiative
30. ^GSC Board Members
31. ^Field D, et al. (2011) [https://www.ncbi.nlm.nih.gov/pubmed/21713030 The Genomic Standards Consortium.] PLoS Biology 9(6):e1001088. {{PMID|21713030}}
32. ^{{Cite web | url=http://gensc.org/projects/microbial-earth-project/ | title=Microbial Earth Project | Genomic Standards Consortium}}
33. ^Wu, D., et al. (2009) [https://www.ncbi.nlm.nih.gov/pubmed/20033048 A phylogeny-driven genomic encyclopedia of Bacteria and Archaea.] Nature 462: 1056-60. {{PMID|20033048}}
34. ^Kyrpides NC, et al. (2014) [https://www.ncbi.nlm.nih.gov/pubmed/25093819 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) [https://www.ncbi.nlm.nih.gov/pubmed/25197443 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) [https://www.ncbi.nlm.nih.gov/pubmed/26203337 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) [https://www.ncbi.nlm.nih.gov/pubmed/28604660 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. ^{{Cite web | url=https://jgi.doe.gov/uncovered-1000-new-microbial-genomes/ | title=Uncovered: 1000 New Microbial Genomes| date=2017-06-12}}
39. ^Garrity GM, et al. (2009) Standards in Genomic Sciences. Standards in Genomic Sciences. 1(1):1-2.
40. ^Garrity GM, et al. (2011) [https://www.ncbi.nlm.nih.gov/pubmed/21475581 Alive and well at 100.] Standards in Genomic Sciences. 4(1): 1-2. {{PMID|21475581}}
41. ^Kyrpides NC. (2009) [https://www.ncbi.nlm.nih.gov/pubmed/19587669 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) [https://www.ncbi.nlm.nih.gov/pubmed/27197692 Microbiome Data Science: understanding our microbial planet.] Trends in Microbiology 24(6):425-427. {{PMID|27197692}}.
43. ^[https://jgi.doe.gov/rallying-call-microbiome-science-national-data-management/ A Rallying Call for Microbiome Science National Data Management] (DOE-JGI, 2016)
44. ^[https://www.asm.org/index.php/asm-news/item/6953-asm-hosts-national-microbiome-data-collaborative-workshop ASM Hosts National Microbiome Data Collaborative Workshop]
45. ^[https://jgi.doe.gov/nikos-kyrpides-named-2018-usfccj-roger-porter-awardee/ Nikos Kyrpides Named 2018 ASM USFCC/J. Roger Porter Awardee]
46. ^Tindall BJ and Garrity GM. (2015) [https://www.ncbi.nlm.nih.gov/pubmed/26184666 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. ^[https://www.asm.org/index.php/aam-fellows/aam-fellows/fellows-elected-in-2014/item/4742-nikos-kyrpides AAM Fellow]
48. ^[https://jgi.doe.gov/doe-jgi-on-2016-highly-cited-researchers-list-clarivate/ Six from DOE JGI on 2016 Highly Cited Researchers List] (DOE-JGI, 2016)
49. ^[https://jgi.doe.gov/highly-cited-doe-jgi-researchers-make-2015-list/ Highly Cited: 8 DOE JGI Researchers Make 2015 List] (DOE-JGI, 2015)
50. ^Klenk HP, et al. (2011) [https://www.ncbi.nlm.nih.gov/pubmed/22180816 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. ^[https://www.auth.gr/en/node/24284 Nikolaos Kyrpides awarded Honorary Doctor of the Department of Biology of the Aristotle University of Thessaloniki]
{{Authority control}}{{DEFAULTSORT:Kyrpides, Nikos}}

6 : American microbiologists|Microbiomes|Greek biologists|Living people|Bioinformatics|1963 births

随便看

 

开放百科全书收录14589846条英语、德语、日语等多语种百科知识,基本涵盖了大多数领域的百科知识,是一部内容自由、开放的电子版国际百科全书。

 

Copyright © 2023 OENC.NET All Rights Reserved
京ICP备2021023879号 更新时间:2024/11/17 22:57:26