People

Principal Investigator

Dr Michael Inouye email (baker) | email (cambridge) | email (turing) | twitter @minouye271



Current2018 - Director, Cambridge Baker Systems Genomics Initiative2018 - Turing Fellow, The Alan Turing Institute2018 - Principal Researcher, Dept of Public Health & Primary Care, University of Cambridge2020 - Munz Chair of Cardiovascular Prediction & Prevention, Baker Heart & Diabetes Institute
2018 - Associate Professor, Dept of Physiology, Anatomy & Microbiology, La Trobe University2017 - Associate Professor, Central Clinical School, Monash University2016 - Associate Professor, Dept of Clinical Pathology & School of BioSciences, University of Melbourne
Previous2017 - 2019 Principal Research Fellow, Baker Heart & Diabetes Institute2014 - 2018 NHMRC RD Wright Fellow2014 - 2018 National Heart Foundation Future Leader Fellow2015 - 2017 Co-Founder / Deputy Director, Centre for Systems Genomics, University of Melbourne2012 - 2017 Senior Research Fellow - Principal Research Fellow (Associate Professor), University of Melbourne2010 - 2014 NHMRC Peter Doherty Fellow2010 - 2012 Postdoctoral Fellow, Walter and Eliza Hall Institute of Medical Research2005 - 2010 Researcher / Genome Analyst, Wellcome Trust Sanger Institute
Education2010 PhD Computational Genomics, Leiden University / Wellcome Trust Sanger Institute Mentors: Leena Peltonen & Gert-Jan van Ommen Thesis: Analysis & algorithms in human disease genomics2005 MSc Biochemistry & Molecular Biology, University of California Los Angeles2004 BSc Biochemistry, University of Washington2004 BSc Economics, University of Washington

Biography

Mike grew up in the Seattle area before beginning undergraduate study in 1999 at the University of Washington, where he graduated with BSc's in biochemistry and economics. As a 19 year-old freshman, Mike began analyzing data from the draft Human Genome Project, 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 (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 analytics for the first wave of genome-wide association studies as well as large-scale studies integrating multi-omic data. After a postdoc at the Walter and Eliza Hall Institute (Melbourne, AU), he was recruited to the faculty at the University of Melbourne in 2012 where he built a research program in systems genomics with a focus on clinical and public health applications. In 2017, Mike was recruited to the Baker Institute and the University of Cambridge to set up a lab spanning Australia and the UK 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 the Munz Chair of Cardiovascular Prediction and Prevention at the Baker Institute, an investigator at Health Data Research UK (Cambridge Site), and a Turing Fellow at the Alan Turing Institute (London).

An interview with Mike about starting a research group

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 György (George) Abrusán (University of Cambridge)

György obtained his M.Sc. in Biology from the University of Debrecen (Hungary), and his Ph.D from Warsaw University (Poland). Initially his bioinformatic work focused on comparative genomics and the biology of transposable elements (TEs), particularly on TE – host coevolution. More recently he worked in computational structural biology, and focused on the factors governing the evolution of quaternary structure of proteins, and their dependence on interactions with their ligands. He has demonstrated that the structure of ligand binding site is a fundamental factor shaping the evolution and function of protein complexes, including folding, allostery or chaperone interactions. He joined the Inouye Lab in 2020, where his research interests include the structural and functional consequences of missense variants.

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 Sol Lim (University of Cambridge)

Sol received her BSc in Mathematics, MSc in Cognitive Sciences, PhD in Neuroscience from Seoul National University. During her PhD, she studied Connectomics in Dynamic Connectome Lab with Prof Marcus Kaiser (Seoul, South Korea and Newcastle, UK), in particular, focusing on the spatial and topological characteristics of the brain network and its development microscopically in synaptic connectivity and macroscopically using mainly Neuroimaging techniques such as diffusion MRI and functional MRI. During the last two years of her PhD, She visited the School of Computing Interdisciplinary Computing and Complex BioSystems (ICOS) research group as a research assistant at Newcastle University, UK. After her PhD, she moved to Bloomington, USA to join Computational Cognitive Neuroscience Lab as a postdoc working with Prof Olaf Sporns at Indiana University and collaborated with network scientists such as Prof Santo Fortunato and Prof Filippo Radicchi on multiscale community detection and multilayer networks applied to human brain networks. She then came back to the UK to join Ed Bullmore’s Brain Mapping Unit group in the Department of Psychiatry, University of Cambridge where she worked on the longitudinal brain imaging data (NSPN consortium: NeuroScience in Psychiatry Network). To continue her adventure, in April 2020 she joined the Cambridge node of the Inouye lab and is investigating various approaches to the analysis of single-cell and bulk functional genomics data.

Dr Jonathan Marten (University of Cambridge)

Jonathan studied Natural Sciences at the University of Cambridge for his BA, following on with an MSci in Systems Biology where he discovered his love of computational biology. After working as a research assistant for the QTL In Health and Disease programme at the MRC Human Genetics Unit in the University of Edinburgh, he began a three-year PhD investigating the genetic regulation of serum urate in humans. In 2019, he began a postdoc at the Cardiovascular Epidemiology Unit in the University of Cambridge, working with RNA sequencing data in the INTERVAL cohort. His interest in functional genomics lead him to join the Cambridge node of the Inouye lab in late 2019.

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 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 CurrentPetar Scepanovic Postdoc May 2019 - Dec 2019 Senior Scientist, Roche LtdMarta Brozynska Research manager Jan 2017 - Sep 2019 Qualified Education Agent CounsellorAlex Tokolyi Bioinformatician Jan 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 Postdoc Dec 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 Postdoc Oct 2014 - Apr 2017 Centenary Fellow, Walter & Eliza Hall Institute Lesley Raven (née Gray) Postdoc Dec 2013 - Mar 2017 Australian Genome Research Facility Danielle Belgrave Visitor Sept 2016 - Dec 2016 Principal Researcher , Microsoft Research UKMichael Walker MSc Feb 2013 - Sept 2016 Research Officer, La Trobe Univ Kristijan Vukovic Endeavour Fellow Feb 2016 - Aug 2016 Marie Curie Fellow / PhD student, in3-Milan Anni Joensuu Visitor Feb 2016 - Mar 2016 PhD student, Univ of HelsinkiAki Havulinna Visitor Aug 2015 Senior Scientist, FIMM, Univ of Helsinki Chris Sibley Postdoc Aug 2014 - Aug 2015 Wellcome Fellow & Group Leader , Univ of Edinburgh Alysha de Livera Postdoc Oct 2014 - Aug 2015 Lecturer, Univ of Melbourne Alexia Rohmer Intern Jan 2015 - June 2015 Engineer, Strasbourg Univ Adrian Hecker Intern Dec 2013 - Feb 2014 MSc student, Univ of Melbourne David Savage Postdoc Feb 2013 - July 2013 Data Mining Analyst, Australian Govt