Nikos Kyrpides

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.

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]