Systems Genomics‎ > ‎


Principal Investigator

Michael Inouye
minouye [at] baker [dot] edu [dot] au

Academic degrees
2010    PhD    Human Genomics, Leiden University / Wellcome Trust Sanger Institute
                        Mentors: Leena Peltonen & Gert-Jan van Ommen
2005    MSc    Biochemistry & Molecular Biology, University of California at Los Angeles
2004    BSc     Biochemistry, University of Washington
2004    BSc     Economics, University of Washington

Current Appointments
2017 -             Head of Systems Genomics Lab, Baker Heart & Diabetes Institute
2015 -             Associate Professor (Principal Research Fellow), School of BioSciences, University of Melbourne
2014 -             NHMRC RD Wright & National Heart Foundation Future Leader Fellow

Previous Appointments
2015 - 2017     Founding Core Member / Deputy Director, Centre for Systems Genomics, University of Melbourne
2012 - 2015     Group Leader (Senior Research Fellow), Dept of Pathology / Dept of Microbiology & Immunology, University of Melbourne
2010 - 2012     NHMRC Postdoctoral Fellow, Walter and Eliza Hall Institute of Medical Research
2005 - 2010     Researcher / Genomic Analyst, Wellcome Trust Sanger Institute

2014               Paul Korner Innovation Award, National Heart Foundation (top-ranked fellowship)
2011               Young Investigator Award, International Congress of Human Genetics
2011               Harold Mitchell Foundation Travel Fellow
2010               NHMRC Early Career Awardee - Science at the Shine Dome, Australian Academy of Science

Mike grew up in the Seattle area before beginning undergraduate study in 1999 at the University of Washington, where he later graduated with BSc's in biochemistry and economics. During this time he was also introduced to computational genomics as the initial draft Human Genome was being finished, spending several years doing research in gene finding and protein structure prediction. He continued studying biochemistry as a graduate student at UCLA, but returned to genomics in 2005 when he moved to the Wellcome Trust Sanger Institute in Cambridge, UK. While at Sanger, Mike completed his PhD with Prof Leena Peltonen and Prof Gert-Jan van Ommen and was heavily involved in the first wave of genome-wide association studies, especially the statistical methods thereof. He also led large-scale studies to integrate multi-omic data, and identified a gene co-expression network related to the innate immune response and associated with diverse metabolic traits. In 2010, Mike moved to the Walter and Eliza Hall Institute in Melbourne on a postdoctoral fellowship to continue applying genomic expertise to problems in immunology. In 2012, he joined the faculty at the University of Melbourne where he built a research program in systems genomics with particular focus on clinical and public health problems. In 2017, Mike and his lab were recruited to the Baker Institute where he has close linkages with the University of Melbourne and University of Cambridge.

Research Staff

Dr Gad Abraham (website)
Dr Gad Abraham received the BAppSci(Hons) in computer science from RMIT University in 2005, and a PhD at the University of Melbourne in 2012. He then began a postdoctoral fellowship at the Department of Pathology at the University of Melbourne (2012–2015) and was later awarded an NHMRC Doherty Fellowship, becoming a group leader and Core Member at the Centre for Systems Genomics, School of BioSciences, University of Melbourne (2015–2017). In mid 2017, he joined the Baker Institute as a Group Leader in the Inouye Lab. His main research interest has been the development of genomic (polygenic) risk scores for complex human disease, including coeliac disease and more recently coronary heart disease. Such scores have the potential to stratify individuals by disease risk early in life, better tailoring treatment or lifestyle modifications to individuals, years or decades before disease manifests. He also has an interest in development of computational tools and methods for practical analysis of large genomic and multi-omic datasets.

Dr Marta Brożyńska
Marta finished a Master’s degree in Applied Biotechnology at the Agricultural University in Poland. In her thesis she investigated physiological responses to abiotic stresses of the banana plant. In 2016, she completed a PhD at the University of Queensland in the genomics and phylogenetics of Australian wild rice species. Between her studies, she took up a position as Data Analyst at Era7 Bioinformatics in Spain where her interest and passion for genomics and bioinformatics started. During that time she mainly worked on assembly and annotation of microbial samples. In the Inouye Lab, she has a dual role as both bioinformatics research fellow and project manager.

Dr Shu Mei Teo
Shu Mei’s interest in genetics and bioinformatics started in 2007 with an honours year project on “Methodology research with regards to DNA pooling for SNP genotyping” at the National University of Singapore (NUS) where she graduated with a BSc with a major in Statistics. She subsequently went on to pursue a Ph.D. in genetic and molecular epidemiology at NUS and Karolinska Institutet (joint degree), with a thesis entitled “Statistical Methods for the Detection and Analyses of Copy Number Variants in the Human Genome”. Shu Mei is currently a post-doctoral research fellow at the Department of Pathology and Department of Biochemistry and Molecular Biology at UniMelb. She works on the analysis of microbiome data and the interactions between the microbiome, host genetics and other environmental factors (such as viral infection etc.) on the pathogenesis of childhood asthma. Outside of work, Shu Mei enjoys rockclimbing, hiking, yoga and playing boardgames. She holds a joint position with Kathryn Holt's group at the Bio21 Institute.

Dr Scott Ritchie
Scott grew up in Melbourne before spending several years in the UK and US. He returned to Melbourne to begin undergraduate study at the University of Melbourne in 2008 graduating with a Bachelor in Computer Science in 2010. During his undergraduate he became interested in machine learning and data analysis, and was introduced to Bioinformatics in his final year. This led him to continue with postgraduate study at the University of Melbourne in Bioinformatics, graduating with distinction with an MSc in 2012. During this time he joined the Inouye Lab where he was introduced to systems biology, exploring different methods for constructing gene co-expression networks. In 2017, he completed his PhD also in the Inouye Lab. His current research interests include network analysis, gene expression data, and data visualisation.

Dr Oneil Bhalala
Oneil Bhalala received his Bachelors of Science in Mathematics and Biology from Massachusetts Institute of Technology, Cambridge, MA, USA. He then earned a PhD in neuroscience from Northwestern University, Chicago, IL, USA, while working with John Kessler on the role miR-21 in the astrocytic response to CNS injury and differentiation. He recently completed an MD with Distinction at The University of Melbourne and is currently an intern at the Royal Melbourne Hospital. His research interests include understanding and elucidating mechanisms governing disorders involving cognition, including schizophrenia and Alzheimer's disease. In the Inouye Lab, he is applying machine learning approaches and statistical tools to perform genomic prediction and identify causal loci and pathways in disease.

PhD students

Artika Nath
Artika’s training in genetics started with a BSc (Honours) degree from the University of Otago in New Zealand. Her experience in molecular genetics excited her desire to learn more about how genes contribute to human disease. Her passion towards a genomics based approach for biomedical research was rewarded by a Fulbright Fellowship for a Masters degree in Biological Sciences where she obtained training in genomics profiling and bioinformatics at Georgia Institute of Technology, Atlanta, USA. Artika, joined the Inouye Lab in 2013 after being awarded the Australian Postgraduate Award (APA) and International Postgraduate Research Scholarship (IPRS) to pursue her interest in genomics, immunology and integrative biology.

Dr Howard
Howard graduated from the University of Melbourne in 2012 with MBBS, BMedSc (Hons), and spent a year working as a junior doctor at the Northern Hospital, Epping. He has been involved in a number of clinical research projects around Melbourne. For example he has conducted analysis and provided statistical consultation for surgical researchers studying risk factors for blood transfusion following hip operations, and physical and psychological outcomes following breast reconstruction surgery for breast cancer. Howard has a keen interest in the mathematical modelling of biological processes, and the use of statistical tools to better understand complex biological systems. He is studying for his PhD in systems biology and will be exploring clinical prediction models for asthma, as well as understanding environment-genome interactions that underlie asthma pathogenesis.

Yu Wan
Yu is a joint PhD student with Dr Kathryn Holt (Biochemistry & Molecular Biology) and Prof Justin Zobel (Computing & Information Systems). He completed his bachelor degree in automation at Zhejiang University, China, in 2008. Then he worked as an IP network engineer for two and a half years and an editor of a scientific magazine for another half year. He became a MSc student in bioinformatics at the University of Melbourne in 2013 and joined our lab after his graduation. His research focuses on the network of bacterial horizontal gene transfer, which is closely related to nosocomial transmission of antibiotic-resistance genes and disease outbreaks. Yu immerses himself in microscopy and travelling in his spare time.

Qinqin Huang
Qinqin grew up in a coastal city in China and moved to Beijing for her undergraduate studies in Biological Science at Peking University. There, she developed an interest in genetics and molecular biology and was introduced to bioinformatics in her last year. Her research experience focused on cotton genomes and transcriptomes, but she became more interested in the human genome and its relationship with disease. She joined the Inouye Lab as a PhD student in 2015. Her current research interests mainly lie in gene co-expression networks, eQTL analysis and regulatory pathways. Ultimately, she hopes to uncover the biological mechanisms of common diseases.

Youwen (Owen) Qin
Owen finished his MPhil on Bioinformatics and Biological Statistics in 2015 from the University of Hong Kong with the supervision of Prof Pak Chung Sham and Prof Karen SL Lam.  He studied and worked at Beijing Genomics Institute, Shenzhen for 4.5 years since 2010 when he was the final year undergraduate student at Huazhong University of Science and Technology. Owen's previous research was on the human gut microbiome, including several metagenome-wide association studies on complex diseases, including type 2 diabetes, colorectal cancer, rheumatoid arthritis and gastric cancer. Now he is conducting a PhD in functional and population genomics.

Amy Hamilton
Amy is a joint PhD student with Prof Michael Kamm (St Vincent's Hospital) in the Dept of Medicine at the University of Melbourne. In the Inouye Lab, Amy's focus is the relationship between the gut microbiome and recurrence of Crohn's disease.



Name  Position
Andrew Bakshi
Apr 2016 - Apr 2017
PhD student, VCCC & Monash Univ
Sean Byars
Feb 2014 - June 2017
Postdoc, Univ of Melbourne
Liam Fearnley   
PostdocOct 2014 - Apr 2017
Centenary Fellow, Walter & Eliza Hall Institute
Lesley Raven (née Gray)
Dec 2013 - Mar 2017
Danielle Belgrave
VisitorSept 2016 - Dec 2016
MRC Fellow & Group Leader, Imperial College London
Michael Walker
MScFeb 2013 - Sept 2016
Research Officer, La Trobe Univ
Kristijan Vukovic
Endeavour Fellow
Feb 2016 - Aug 2016
MSc from Univ of Zagreb
Anni JoensuuVisitorFeb 2016 - Mar 2016PhD student, Univ of Helsinki
Chris SibleyPostdocAug 2014 - Aug 2015Safra Fellow & Group Leader, Imperial College London
Alysha de LiveraPostdocOct 2014 - Aug 2015Lecturer, Univ of Melbourne
Alexia RohmerInternJan 2015 - June 2015Engineer, Strasbourg Univ
Adrian HeckerInternDec 2013 - Feb 2014MSc student, Univ of Melbourne
David SavagePostdocFeb 2013 - July 2013Data Mining Analyst, Australian Govt

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