Systems Genomics‎ > ‎

Members

Principal Investigator


Michael Inouye 
 
Education
2010    PhD    Human Genomics, Leiden University / Wellcome Trust Sanger Institute
                         Mentors: Leena Peltonen & Gert-Jan van Ommen
                         Thesis: Analysis & algorithms in human disease genomics
2005    MSc    Biochemistry & Molecular Biology, University of California Los Angeles
2004    BSc     Biochemistry, University of Washington
2004    BSc     Economics, University of Washington


Current
2018 -             Director, Cambridge Baker Systems Genomics Initiative
2018 -             Turing Fellow, The Alan Turing Institute
2018 -             Principal Researcher, Dept of Public Health & Primary Care, University of Cambridge
2017 -             Head of Systems Genomics Lab, Baker Heart & Diabetes Institute

2018 -             Associate Professor, Dept of Physiology, Anatomy & Microbiology, La Trobe University
2017 -             Associate Professor, Central Clinical School, Monash University
2016 -             Associate Professor, Dept of Clinical Pathology & School of BioSciences, University of Melbourne

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

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. As a 19 year-old freshman, Mike began analyzing data from the initial draft Human Genome, spending several years doing research in gene finding and protein structure prediction. He continued studying protein structure 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. During his postdoctoral fellowship at the Walter and Eliza Hall Institute in Melbourne, Mike continued to apply his genomic expertise to problems in immunology. In 2012, he was recruited to 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 and the University of Cambridge to set up a transnational lab that focuses on core areas of systems genomics, including polygenic risk scores, integrated analysis of multi-omics data and development of analytic tools. He is an investigator at Health Data Research UK, the national institute for data science in healthcare, as well as a Turing Fellow at the Alan Turing Institute, the UK's national institute for data science and artificial intelligence. 





Research Staff



Dr Gad Abraham   (Group Leader, Baker Institute, 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 Rodrigo Canovas  
(Baker Institute)
Rodrigo got his Bachelor (2007) and Master (2010) degree in Computer Science Master at the University of Chile. In collaboration with Prof. Gonzalo Navarro, he worked in the area of succinct data structures and its applications in Bioinformatics focusing in the suffix tree data structure. Later in 2015, he received his PhD at the University of Melbourne, where in collaboration with Prof. Alister Moffat and Andrew Turpin, he explored how succinct data structures can be use to compress genomic files, proving the feasibility of random access to the compressed genetic data without requiring full decompression of large data files. Then he began a Posdoctoral Researcher position at the Lab. of Computer Science, Robotics and Microelectronics of Montpellier (LIRMM) and The Institute of Computational Biology (IBC). There he worked in exploring and improving existing tools while at the same time proposing novel methods and ideas for analyzing sequence data coming from High Throughput Sequencing technologies. Also, during his stay at Montpellier he developed tools to accurate predicting Glycosylphosphatidylinositol (GPI) proteins base on the biological and structural features of known GPI-anchored Proteins. In the Inouye Lab, Rodrigo is doing research in the application of genomic prediction to common disease, particularly autoimmunity.








Dr Sergio Ruiz Carmona   (Baker Institute)
Sergio carried out his MSc and PhD in Barcelona (Barril Lab, www.ub.edu/bl), where he worked with different Structure-Based Drug Design methods with the aim to improve drug design for non-standard targets. Mainly, he was involved in the development and application of virtual screening approaches using molecular docking and other complementary methods. After finishing his PhD in 2017, he stayed as a postdoctoral researcher in the same lab collaborating in projects related to cancer, where he could successfully apply the methods developed during his PhD to find bioactive compounds targeting “undruggable” proteins. He also carried out two short stays in the labs of Dr Andreas Bender (Cambridge, UK) and Dr Peter Kolb (Marburg, Germany), where he learnt about genomics and other computational methods. Sergio joined the Baker Institute in January 2019, where he will study the relationship between genetic variants and their effect on protein structures.











Dr Sam Lambert   (University of Cambridge)
Sam received his BSc in Canada from the University of Guelph where he studied Biological Sciences with stints working with chicken viruses, studying abroad in Singapore, working in a lab in China, and finally doing some nutrigenomics/lipid research. He then moved back home to Toronto to pursue his PhD in Molecular Genetics with Dr. Tim Hughes at the University of Toronto. During his PhD he studied anything and everything to do with transcription factors – developing computational methods to measure and understand the diversity of sequences transcription factors recognize within and between species. Sam joined the Cambridge node of the Inouye lab in January 2019, and is excited to be working on topics related to polygenic (risk) scores for predicting an individual’s disease risk or phenotype based on their genetics.











Dr Guillaume Méric
  
(Baker Institute)
Read more about me here. My research interests are broad and revolve around the ecology and evolution of environmental and pathogenic bacteria in relation to their human or animal hosts. I study different levels of these host-pathogen/host-bacterial interactions, mainly with a microbial population biology angle: how the ecology and environment can impact on bacterial and microbial population evolution, how pathogens emerge from background asymptomatic carried populations, and how microbes jump and transmit between various hosts. For example, I try to understand the impact of host factors (ecology, physiology or immunity) on the evolution and adaptation of the bacterial species they carry. In the Inouye Lab, I'm working on pathogen and antimicrobial resistance gene detection from shotgun metagenomics data and how these relate to host phenotypes (human genetics, metabolomics, incident disease etc). I collaborate closely with Kathryn Holt's lab at the Bio21 Institute.









Dr Artika Nath  
(Baker Institute)
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 Scott Ritchie
   (University of Cambridge)
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 Woei Yuh Saw   (Baker Institute)
Woei Yuh completed her PhD at the National University of Singapore (NUS) in Jan 2019. As part of her PhD, she focused on mapping the degree of natural variation amongst Asian populations, using different biological molecular states which include genomics (for instance, whole genome SNPs data, pharmacogenomics variants, and HLA typing alleles), transcriptomics, and lipidomics. During her PhD, she also worked at the NUS StatGen (Statistical Genetics) Laboratory. She is now a Research Officer in the System Genomics laboratory at Baker Heart and Diabetes Institute. Her main research interest is looking at multi-omics integration together with clinical, diet and environmental data, which she hopes to be able to derive biological insights from the multi-omics and infer links with diseases.










Dr Petar Scepanovic   (University of Cambridge)
Montenegrin of origin, Petar moved to Italy for his undergraduate studies. He obtained BSc in Biotechnology and then MSc in Molecular Biotechnology from University of Turin. During this time, he worked in the cancer biology lab of Prof. Carola Ponzeto and bioinformatics lab of Prof. Paolo Provero, studying the role of Met kinase in the development of rhabdomyosarcoma. After five years in Italy, Petar moved to Switzerland where he obtained his PhD at EPFL in Lausanne. He worked in the lab of Prof. Jacques Fellay studying human genomics of immune system, infection and microbiome, within the framework of Milieu intérieur consortium focusing on healthy individuals. He joined Inouye lab as a postdoc in May 2019 to study the link between polygenic risk scores and the structural proteome in complex diseases.














Dr Alex Smith
  
(Baker Institute)
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 Howard
Tang   (Baker Institute)
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.











Dr Shu Mei Teo   (Baker Institute)
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 Yu Xu   (University of Cambridge)
Yu received his Ph.D. degree in Intelligence Systems at Trinity College Dublin, where he continued working as a research fellow till late 2018. Yu’s Ph.D. research tackled the problem of user expertise inference on social media which aimed to predict the online user’s expertise information via exploiting machine learning techniques, with a focus on the application of probabilistic graph models and multi-task learning algorithms. Prior to that, Yu earned his M.S. degree in Computer Science at Hunan University of Science and Technology, China in 2013. His M.S. research developed novel collaborative filtering and optimal path search algorithms to address the Web service recommendation problem. As a post-doctoral researcher in Inouye Lab, Yu is exploring machine learning and deep learning techniques to address genomic prediction problems including genotype/phenotype imputations, polygenic risk score predictions on human diseases, etc. 











PhD students




Muhamad Fachrul   (University of Melbourne)
Fachrul was born and raised in Jakarta, Indonesia. He finished his undergraduate studies at Indonesia International Institute for Life Sciences (i3L), and was one of the first three students in the country to receive a BSc in Bioinformatics. As an undergrad Fachrul got the opportunity to do internships in Singapore, Melbourne, and Norwich, where he developed an attachment towards transcriptomics. His bachelor’s thesis project was focused on profiling A-to-I RNA editing in cardiomyocytes from the point of view of differentiation and disease states. Fachrul joined Inouye Lab as a PhD student in 2019 (co-supervised by Agus Salim), and his current research interests lie in the biostatistical approaches in analyzing the human microbiome.













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).












Loïc Lannelongue   (University of Cambridge)
Loïc is a PhD student from the MRC Doctoral Programme at the University of Cambridge. Before that, he was trained in Paris at Lycée Saint-Louis and ENSAE ParisTech where he earned a BSc and a french Diplôme d’ingénieur (MSc) studying mainly mathematics and statistics, but also a bit of theoretical physics and economics. Then he completed an MSc in Statistics and Machine Learning at the University of Oxford in 2018. His Master’s thesis focused on developing a Bayesian tree-based algorithm to predict the length of hospital stays for patients. He joined the Inouye Lab after his graduation and is now interested in how Machine Learning can help to best infer Protein-Protein Interaction Networks.











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.












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.











Visiting Scholars



Dr Marika Catapano 
Marika has a background in computational biology applied to molecular genetics. During her PhD in immunogenetics at King's College London, she investigated the pathogenesis of rare immune-mediated diseases. After a postdoc in the Inouye Lab (Cambridge node) as a computational immunobiologist investigating the functional genomics of long-lived plasma cells in the human gut, Marika is now a visiting researcher with a day job at Benevolent AI in London.











Assoc Prof Agus Salim (website)
Agus is an Associate Professor in Mathematics & Statistics at La Trobe University and Chief Biostatistician 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
Marta Brozynska
Research manager
Jan 2017 - Sep 2019
 
Alex Tokolyi
BioinformaticianJan 2019 - Aug 2019
PhD student, Cambridge Univ
Qinqin Huang
PhD student
Sept 2016 - June 2019
Postdoc, Wellcome Sanger Institute
Oneil Bhalala
Bioinformatician
June 2012 - May 2019
Clinical Resident, Melbourne Health
Tingting Wang
PostdocDec 2017 - May 2019
Postdoc, Baker Institute
Amy Hamilton
PhD student
Jan 2015 - July 2018
Research Scientist, St Vincent's Hospital
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
Principal Researcher, 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 2015Wellcome Fellow & Group Leader, Univ of Edinburgh
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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