SysGen Seminar – Kim-Anh Lê Cao – 15th September, 2017

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Andrew Siebel

T: +61 3 8344 0707

Kim-Anh Lê Cao

Centre for Systems Genomics, Mathematics & Statistics, The University of Melbourne

Friday 15th September
FW Jones Theatre, Level 3 Medical Building, The University of Melbourne

Challenges in microbiome data analysis a.k.a. ‘poop analyses'

Our recent breakthroughs and advances in culture independent techniques, such as shotgun metagenomics and 16S rRNA amplicon sequencing have dramatically changed the way we can examine microbial communities. But does the hype of microbiome outweigh the potential of our understanding of this ‘second genome’? There are many hurdles to tackle before we are able to identify and compare bacteria driving changes in their ecosystem. In addition to the bioinformatics challenges, current statistical methods are limited to make sense of these complex data that are inherently sparse, compositional and multivariate.

I will discuss some of the topical challenges in 16S data analysis, including the presence of confounding variables and batch effects, some experimental design considerations, and share my own personal story on how a team of rogue statisticians conducted their own mice microbiome experiment leading to somewhat surprising results! I will also present our latest analyses to identify multivariate microbial signatures in immune-mediated diseases and discuss what are the next analytical challenges I envision.

This presentation will combine the results of exciting and highly collaborative works between a team of eager data analysts, immunologists and microbiologists. For once, the speaker will abstain from talking about data integration, or mixOmics (oops! but if you are interested keep an eye out in PLOS Comp Biol). 

Dr Kim-Anh Lê Cao (NHMRC career development fellow, Senior Lecturer) recently joined the University of Melbourne (Centre for Systems Genomics and School of Mathematics and Statistics). She was awarded her PhD from the Université de Toulouse, France and moved Australia as a postdoctoral research fellow at the Institute for Molecular Bioscience, University of Queensland. She was hired as a research and consultant at QFAB Bioinformatics where she developed a multidisciplinary approach to her research. Between 2014 - 2017 she led a computational biostatistics group at the biomedical research UQ Diamantina Institute. Dr Lê Cao is an expert in multivariate statistical methods and novel developments. Since 2009, her team has been working on implementing the R toolkit mixOmics dedicated to the integrative analysis of `omics' data to help researchers mine and make sense of biological data (

Enquiries: Andrew Siebel (