Integrative Systems Biology

We are a research group in the Centre for Systems Genomics (@SysGenMelb) and the School of BioSciences at the University of Melbourne (Melbourne, Australia).

The Inouye Lab aims to alleviate the burden of human disease by using its inter-disciplinary strengths in statistics, computation and bioscience to leverage the latest genomic/biomolecular profiling technologies. To achieve this aim, our strategy is to:
  • Uncover the genomic basis of complex disease
  • Understand the pathogenesis of molecular systems
  • Build predictive models for patient stratification and prioritisation
We straddle basic and translational research in diseases with strong immune/inflammatory aetiologies: asthma, cardiovascular and infectious disease. As a pure research group with no service provision we conceive, manage and execute research projects as well as actively collaborate with researchers around Australia, USA, Europe and Asia.

For more about our group's research, see our Research Highlights and Publications.

For inquiries, please contact the Principal Investigator: A/Prof Michael Inouye (minouye [at] unimelb [dot] edu [dot] au)

Or follow Mike on Twitter: @minouye271



Multi-scale and multi-omic research to predict, to understand pathogenesis, and to intervene




News and Events


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Jan 19, 2016: Update on all future news & events
In future, I'll be posting most news and events on Twitter @minouye271 or via the Centre for Systems Genomics website and @sysgenmelb handle. Please check these places for the latest updates!

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Oct 23, 2015: Now published in Cell Systems... 
The Biomarker GlycA Is Associated with Chronic Inflammation and Predicts Long-Term Risk of Severe Infection
Here's the link. We've also posted a summary of the work on the Centre for Systems Genomics website.

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Sept 13, 2015: We've posted the NetRep source code: a tool for rapid, permutation-based testing of gene coexpression network preservation and replication
It's here on GitHub. Give it a try and let us know what you think! The pre-print has been posted on biorxiv, available here.

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July 25, 2015: Now published in Current Opinion in Genetics and Development...

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July 17, 2015: Now published in Genome Medicine Special Issue on Diagnostic Genomics... Genomic prediction of celiac disease targeting HLA-positive individuals
See here for the paper and here for the original pre-print.

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June 8, 2015: The new UoM Centre for Systems Genomics is rapidly taking shape

For more information, please visit our interim website.

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Apr 28, 2015: Submitted for peer review and preprinted in Biorxiv... Systems medicine links microbial inflammatory response with glycoprotein-associated mortality risk
See here for the preprint. Congratulations to Scott Ritchie on his first paper, it's a fantastic achievement! This was another excellent collaboration with numerous universities around Finland (Oulu, Helsinki, Turku, Tampere and others) and was made possible by their unique collaborative environment and unparalleled health system infrastructure.
(Update Sept 13, 2015: Manuscript is in press at Cell Systems)

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Apr 10, 2015: Now published in Cell Host & Microbe... The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development

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Apr 7, 2015: Now submitted... Genomic prediction of celiac disease targeting HLA-positive individuals
See the preprint in biorxiv.org. Congrats to Alexia on her first paper!

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Mar 29, 2015: The Inouye Lab is a founding partner in the upcoming Centre for Systems Genomics at The University of Melbourne!
We are co-locating with other exciting investigators and their groups in this space: Dr Kathryn Holt (bacterial genomics), Prof David Balding (statistical genomics), and Prof Edmund Crampin (systems & computational biology). More updates will be forthcoming!

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Dec 3, 2014:
Now submitted...
The infant airway microbiome in health and disease impacts later asthma development
An amazing collaboration with Kathryn Holt's group, Telethon Kids Institute, University of Wisconsin and Imperial College London has resulted in this groundbreaking work... we've put the pre-print in biorxiv!

(Update Feb 15, 2015: Manuscript now in press at Cell Host & Microbe)

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Nov 20, 2014: Now published...
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
See here for the paper in Genome Medicine. The software is available through github. This has been a fantastic collaboration with Kathryn Holt's group, to keep improving SRST2 give us your feedback here.
(Update Dec 23, 2014: Also see the BMC Blog interview here)

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Sept 5, 2014: We've published our take on where deeply phenotyped cohorts in respiratory disease should be heading: Elucidation of pathways driving asthma pathogenesis: Development of a systems-level analytic strategy
See here for the 'Theory & Hypothesis' paper in Frontiers in Immunology.

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June 26, 2014: The SRST2 manuscript has been posted on bioarxiv: SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
See here for the pre-print on bioarxiv and here for the software.

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Mar 24, 2014: Posted on bioarxiv.org: Towards a molecular systems model of coronary artery disease 
See here for the link. This is a literature review intended for a clinical audience and is in press at Current Cardiology Reports.
(Update Apr 18, 2014: Manuscript now published in Current Cardiology Reports)

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Feb 15, 2014: Just published in PLoS Genetics: Accurate and Robust Genomic Prediction of Celiac Disease Using Statistical Learning 
See here for the link. We've also made the predictive model publicly available. The analysis made extensive use of the SparSNP algorithm. The paper is largely a proof-of-concept; it's our hope that further prospective clinical studies will validate the genomic risk score as a new tool that improves the diagnostic pathway of celiac disease.

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Feb 8, 2014:
Extensive epistasis within the MHC contributes to the genetic architecture of celiac disease has been posted on biorxiv.org
See this link for the preprint. The full manuscript is to be submitted very soon. It has been a long time coming :)

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Feb 7, 2014:
Fast Principal Component Analysis of Large-Scale Genome-Wide Data: The FlashPCA algorithm and software released

See here for software and details. A preprint has been posted on bioarxiv and the manuscript has been submitted.
(Update Apr 10, 2014: Manuscript now published in PLoS ONE)

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Dec 8, 2013:
Postdoctoral opportunity available (updated)

We are looking for a talented individual with a strong analytical background and knowledge of biology/genetics to take a leading role as part of an exciting project to analyse  genomic, transcriptomic and metabolomic data together with clinical measures and outcomes with the aim of deriving new biological insights into the pathogenesis of cardiovascular disease.

You can find more information and application details here. A position description can be obtained here.

Qualified individuals will have previous experience in the analysis of omics data and a strong computing background. If you are interested in a position, please also contact Mike Inouye: minouye [at] unimelb [dot] edu [dot] au

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Sept 27, 2013:
SRST2 algorithm and beta software has been released
It has taken a while but we've finally posted the anticipated follow up, SRST2. See here for details and software. SRST2 is a method and tool for genomic surveillance of bacterial pathogens which is designed for both a research environment as well as the hospital and public health setting. From Illumina whole genome sequencing of an isolate, it performs genomic typing (MLST) as well as drug resistance and virulence gene/allele detection. A manuscript is in preparation.

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