Microbiome Research: From Products to Data

(CSE Distinguished Lecture Series)

Nikos Kyrpides

Nikos Kyrpides
Prokaryotic Super Program, Joint Genome Institute, Department of Energy
Monday,  October 16, 2017, 11am
Room 1202, CSE Building

Microbiome Research: From Products to Data

Abstract: Microbiology is experiencing a revolution brought on by recent developments in sequencing technology. The unprecedented volume of microbiome data being generated pose significant challenges with respect to standards and management strategies, but also bear great new opportunities that can fuel discovery. Computational analysis of microbiome samples involving previously uncultured organisms, is currently advancing our understanding of the structure and function of entire microbial communities and expanding our knowledge of genetic and functional diversity of individual micro-organisms. I will describe some of our computational approaches and will emphasize the value of assemblies in enabling the exploration of large metagenomic datasets and the discovery of novelty. I will discuss the results for the discovery of novel phylogenetic lineages as well as the exploration of the viral dark matter.


Dr. Kyrpides was born in Greece where he studied Biology at the Aristotle University of Thessaloniki. He received his PhD in Molecular Biology and Biotechnology from the University of Crete. He then turned into Microbiology pursuing his postdoctoral studies 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 he worked in biotech industry in Chicago, IL, where he led the development of the genome analysis and Bioinformatics core. He joined the DOE Joint Genome Institute in 2004 to lead the Genome Biology Program and the development of the data management and comparative analysis platforms for microbial genomes and metagenomes. He became the Metagenomics Program head in 2010, founded the Prokaryotic Super Program on 2011 which he still leads along with the Microbiome Data Science Group.

Dr Kyrpides has over 25 years of research experience in sequence analysis, bioinformatics, and microbial genomics and published more than 550 papers in the field. He led the development of several pioneering data managements systems in microbial genomics and metagenomics, which are widely used in the community and have several thousand users across the world.

Research in his group is currently focusing 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 that shape the microbial genomes. To accomplish that, his group is developing novel methods for enabling large-scale comparative analysis, as well as mining and visualization of big data. Some of his current projects include the sequencing and comparative analysis of thousands of archaeal and bacterial type strains, uncovering Earth’s Virome, the delineation of host-virus interactions, and the discovery and characterization of novel protein families from microbiome data.

Dr. Kyrpides has received several prestigious awards including the van Niel International Prize for Studies in Bacterial Systematics, an outstanding performance award from Lawrence Berkeley National Laboratory, and the Academic Excellence Prize from Empeirikeion Foundation. He is an elected fellow of the American Academy of Microbiology and he is in the list of the most Highly Cited Researchers from 2014-2016.

Host: CSE Prof. Pavel Pevzner