Systems Genomics‎ > ‎

Members

Principal Investigator

Education
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 Los Angeles
2004    BSc     Biochemistry, University of Washington
2004    BSc     Economics, University of Washington


Current
2017 -             Head of Systems Genomics Lab, Baker Heart & Diabetes Institute
2018 -             Principal Researcher (eq Reader), Department of Public Health & Primary Care, University of Cambridge
2017 -             Associate Professor, Department of Clinical Pathology & School of BioSciences, University of Melbourne
2017 -             Associate Professor, Central Clinical School, Monash University
2018 -             Associate Professor, Department of Physiology, Anatomy & Microbiology, La Trobe University

Previous
2014 - 2018     NHMRC RD Wright Fellow
2014 - 2018     National Heart Foundation Future Leader Fellow
2015 - 2017     Co-Founder / Deputy Director, Centre for Systems Genomics, University of Melbourne
2012 - 2017     Senior Research Fellow - Principal Research Fellow (Associate Professor), University of Melbourne
2010 - 2014     NHMRC Peter Doherty Fellow
2010 - 2012     Postdoctoral Fellow, Walter and Eliza Hall Institute of Medical Research
2005 - 2010     Researcher / Genome Analyst, Wellcome Trust Sanger Institute

Honours
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, Australian Academy of Science (Science at the Shine Dome)

Biography
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 was recruited to the Baker Institute where he has set up a transnational lab with the University of Cambridge that focuses on core areas of systems genomics, including integrated analysis of multi-omics data, polygenic/genomic risk effects on biological pathways, and development of analytic tools.





Research Staff



Dr Gad Abraham (Group Leader, 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 is both the lab's research manager and bioinformatician.










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 in the Inouye lab at the Baker Institute with close links to the Holt lab at the Bio21 Institute. 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.








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 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. Artika graduated with a PhD from the University of Melbourne in 2017 and completed an AMSI internship with CSL Research Ltd. She rejoined the Inouye Lab in late 2017 as a postdoctoral researcher.










Dr Tingting Wang

Tingting completed her PhD in computer science at La Trobe University, Melbourne. Her PhD subject was 'Computationally efficient genomic prediction on the whole genome sequence data in dairy cattle' and involved the development of computationally efficient genomic prediction methods using machine learning and data mining algorithms. In 2016, Tingting was a postdoctoral researcher at the Department of Economic Development, Jobs, Transport and Resources under a project titled 'MIRprofit: integrating very large genomic and milk mid-infrared data to improve profitability of dairy cows'. In December 2017, Tingting joined the Inouye Lab at the Baker Institute to apply her skills to human genetics, where she is working on the development of algorithms and pipelines for human genomic prediction as well as functional genomics with the Drew and Calkin Labs.








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. As a bioinformatician 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.













Dr Alex Smith

Alex was initially trained as a “French engineer” with a specialisation in Applied Statistics in Rennes. He obtained a CEA PhD scholarship to work on metabolic networks and prokaryote comparative genomics, devising a method to search for candidate genes for sequence-orphan enzymatic activities, as well as integrating evolutionary relationships to inform a high-throughput exploration of the enzymatic activities of a newly-discovered protein family. He followed his wife to New Zealand, where he worked as a biostatistics post-doc for the Sleep/Wake Research Center, before being recruited by the Malaghan Institute of Medical Research to initiate a bioinformatics workforce there, with as a main project the analysis of RNA-seq data from mouse dendritic cells stimulated with parasite material. A third post-doctoral position - this time in Switzerland - saw Alex seeking to identify long intergenic non-coding RNAs involved in driving or maintaining the cell cycle by exploring publicly-available single-cell data of staged mESCs. Alex has again crossed the world and has taken a position at the Baker Institute of Melbourne, where he is working with both the Meikle and Inouye labs on integrating lipidomics and GWAS data. Alex loves to tinker in R and gnaw at datasets until he can get everything out of them, and enjoys helping people out with their experimental designs and statistical analyses.








Dr Rodrigo Canovas




















Dr Guillaume Méric















PhD students



Dr Howard
Tang (University of Melbourne)
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
(University of Melbourne)
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
(University of Melbourne)
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
(University of Melbourne)
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 (University of Melbourne)
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.
















Jason Grealey
(Baker Institute / La Trobe University)
Jason was born and raised in Northern Ireland. He attended the University of Edinburgh where he obtained a first class qualification in the Master of Theoretical Physics, a five year integrated course. During his Master's project he was introduced to the world of applied mathematics, such as computational physics and bioinformatics, and knew that this was the area in which he wanted to do research. Enjoying the academic climate in Australia, Jason is utilising neural networks approaches for the improved prediction and classification of molecular traits. Jason is part of the new Baker / LTU program, where his co-supervisor is Prof Agus Salim (LTU Dept of Maths & Stats).













Yang Liu
(University of Melbourne)
Yang was born and raised in Shandong, China and moved to the U.S. during high school.  She received her Bachelors of Science in Biomedical Engineering with a concentration on electronic & computer engineering from Georgia Institute of Technology, Atlanta, USA. Then she completed her Master of Bioinformatics at the University of Queensland, Brisbane, Australia, where she developed an interest in genomic risk prediction of complex human diseases. She is now studying for her PhD in the Inouye Lab. Her current research interest is in using machine learning for prediction and classification of diseases based on genotype and phenotype data.















Visiting Scholars


Assoc Prof Agus Salim (website)
Agus is an Associate Professor in Mathematics & Statistics at La Trobe University and has a part-time appointment at the Baker Institute. In the Inouye Lab, he's collaborating on methods for genomic prediction as well as other statistical and machine learning problems.









Alumni

Name  Position
Duration
Current
Andrew Bakshi
Bioinformatician
Apr 2016 - Apr 2017
PhD student, VCCC & Monash Univ
Sean Byars
Postdoc
Feb 2014 - June 2017
Postdoc, Univ of Melbourne
Liam Fearnley   
PostdocOct 2014 - Apr 2017
Centenary Fellow, Walter & Eliza Hall Institute
Lesley Raven (née Gray)
Postdoc
Dec 2013 - Mar 2017
Australian Genome Research Facility
Danielle Belgrave
VisitorSept 2016 - Dec 2016
MRC Fellow & Group Leader, Imperial College London / Microsoft Research UK
Michael Walker
MScFeb 2013 - Sept 2016
Research Officer, La Trobe Univ
Kristijan Vukovic
Endeavour Fellow
Feb 2016 - Aug 2016
Marie Curie Fellow / PhD student, in3-Milan
Anni JoensuuVisitorFeb 2016 - Mar 2016PhD student, Univ of Helsinki
Aki Havulinna
Visitor
Aug 2015
Senior Scientist, FIMM, 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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