Statistical Bioinformatics Seminar: Dr Laura Luebbert

Speaker: Dr Laura Luebbert (Broad Institute) 

Abstract: There are an estimated 300,000 mammalian viruses from which infectious
diseases in humans may arise.  They inhabit human tissues such as the lungs, blood, and
brain and often remain undetected.  Efficient and accurate detection of viral infection
is vital to understanding its impact on human health and to make accurate predictions to
limit adverse effects, such as future epidemics.  The increasing use of high-throughput
sequencing methods in research, agriculture, and healthcare provides an opportunity for
the cost-effective surveillance of viral diversity and investigation of virus-disease
correlation.  However, existing methods for identifying viruses in sequencing data rely
on and are limited to reference genomes or cannot retain single-cell resolution through
cell barcode tracking.  We introduce a method that accurately and rapidly detects viral
sequences in bulk and single-cell transcriptomics data based on highly conserved amino
acid domains, which enables the detection of RNA viruses covering up to 10^12 virus
species.  The analysis of viral presence and host gene expression in parallel at
single-cell resolution allows for the characterization of host viromes and the
identification of viral tropism and host responses.  We applied our method to identify
putative novel viruses in rhesus macaque PBMC data that display cell type specificity
and whose presence correlates with altered host gene expression.  

About the speaker: Laura recently completed her Ph.D. in Computational Biology at the
California Institute of Technology in the US.  She recently wrote a pipeline for the
detection of previously unknown viral sequences in NGS data and will apply her work
towards the detection of emerging pathogens as a postdoctoral researcher in the
laboratory of Prof.  Pardis Sabeti at the Broad Institute of MIT and Harvard (with a
joint affiliation with Harvard University).  Laura is passionate about bridging the gap
between biology and bioinformatics, having worked in both wet lab and computer science
roles.  Her first software project, gget, which facilitates access to large genomic
databases, has been downloaded over 100,000 times and has become a worldwide standard in
transcriptomic and proteomic data processing.  

This event will be online.  

Zoom: https://uni-sydney.zoom.us/j/84087321707