Antrittsvorlesung „Bioinformatics in Infection Research – an overview of the lab’s research activities“ 09.11.2016 | 17:00 Uhr - 18:30 Uhr
Our attention lies on questions related to human health and disease, such as study of gene-phenotype connections within the human microbiome using meta´omics technologies. Secondly, we study the interactions and co-evolution between viral pathogens and their hosts, with a particular focus on influenza viruses. Methodologically, our lab develops software and algorithms combining methods from various fields of computer science and biology, such as machine learning, phylogenetic theory and population genetics.
This is a young research area, which deals with the sequencing and study of whole communities of microorganisms, as opposed to the sequencing of genomes of individual organisms that have been obtained in pure culture. As by estimates less than 1% of all microorganisms can be cultured using standard techniques, the current knowledge of prokaryote biology and the collection of sequenced genomes are strongly biased towards a few, well characterized phyla, while very little is known about the vast majority of the prokaryotic world. Meta´omics has the potential to level this inequality and has already delivered an enormous gain in biological knowledge. The lab co-organizes the Critical Assessment of Metagenome Interpretation challenge (CAMI; https://data.cami-challenge.org/), hosts the bioinformatics unit of the German Centre for Infection Research (www.dzif.de), develops software and algorithms and collaborates locally, nationally and internationally with biologists and medical experts from universities and research institutes. Currently, we are working on methods that allow to predict microbial phenotypes directly from the genomic information of individual microbes and to suggest protein families that are key to their realization.
The lab has combined epidemiological, genetic, antigenic and structural information to determine the antigenicity-altering areas on the protein structure, key sites and amino acid changes. We analyse how these affect the fitness of the viral population with regards to escaping the human immune response. We furthermore develop techniques to study the genomic evolution of viruses on a genome-wide scale, methods to make predictions on which future viral strains may become predominant in the next influenza seasons and methods to determine key areas of the proteins of animal influenza viruses, which could be implicated in the adaptation to the human host and initiation of future pandemic events.
Alice Carolyn McHardy studied biochemistry from 1995 to 2000 at Bielefeld University. She obtained a PhD in computational biology in 2004 and then worked as a postdoc at the Center for Biotechnology at Bielefeld University. From 2005 to 2007 she worked first as a postdoc and then as a permanent staff member in the Bioinformatics and Pattern Discovery Group at the IBM T.J. Watson Research Center in Yorktown Heights, USA. She then became the head of the independent research group for „Computational Genomics and Epidemiology“ at the Max Planck Institute for Computer Science in Saarbrücken. In 2010, she was appointed as Chair of Algorithmic Bioinformatics at Heinrich Heine University in Düsseldorf. Since 2014, she leads the Computational Biology of Infection Research Lab at the Helmholtz Centre for Infection Research in Braunschweig.
Prof. Dr. Alice McHardy, Abteilung Bioinformatik der Infektionsforschung, HZI