Identifying the micro from the peta: tales of big data in the micro world

Authors

Nikos Kyrpides, PhD, Prokaryote Super Program Head, DOE Joint Genome Institute

Document Type

Presentation

Publication Date

6-26-2017

Comments

Dr. Kyrpides 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 (IMG). He became the Metagenomics Program head in 2010 and leads the Prokaryotic Super Program and the Microbiome Data Science Group 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 with Ross Overbeek at the Argonne National Laboratory. Dr Kyrpides has over 25 years of research experience in sequence analysis, bioinformatics, and microbial genomics and published more than 530 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 focuses 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 Earthʼs Virome, the delineation of host-virus interactions, and the discovery of novel protein families from microbiome data. Dr Kyrpides has received a number of 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.

Abstract

Shotgun sequencing of environmental samples has revealed a new universe of microbial communities (metagenomes) involving previously uncultured organisms, which is expected to further advance our understanding the structure and function of entire microbial communities and expand our current knowledge of genetic and functional diversity of individual micro-organisms. Although most metagenomic studies aim to unveil the genetic and functional novelty present in various environments, current best practices in metagenome analysis tools, and workflows, are suffering from a number of pitfalls, impairing the fulfillment of this objective. 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.

Presentation: 1:09:25

Recommended Citation

Language

English