People

Principal Investigator

Prof Michael Inouye email (cambridge) | email (baker) | twitter @minouye271



Current roles2022 - Theme Lead, Data Science and Population Health, NIHR Cambridge Biomedical Research Centre 2021 - Director of Research (i.e. Research Professor), Dept of Public Health & Primary Care, University of Cambridge2021 - Professorial Fellow (Hon.), Baker Dept of Cardiometabolic Health, University of Melbourne2020 - Munz Chair of Cardiovascular Prediction & Prevention, Baker Heart & Diabetes Institute2018 - Director, Cambridge Baker Systems Genomics Initiative

Previous2018 - 2021 Turing Fellow, The Alan Turing Institute2018 - 2020 Principal Researcher, Dept of Public Health & Primary Care, University of Cambridge2017 - 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 & Gertjan 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, 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.

An interview with Mike about starting a research group

Support Staff

John-Luis Moretti (Administration Officer, Baker Institute)

After completing a Bachelor of Science at Monash University, John-Luis completed a Masters in Biomedical Science research with Geoff Head at the Baker Institute and Roger Evans at Monash University. Since then he has worked at Monash University as a teaching assistant and at the Baker Institute as a surgical assistant. He is currently at the Baker Institute working with the Laboratory Operations team and as an Administration Officer for the Systems Genomics, and Computational and Clinical Informatics labs.

Research Staff

Dr Emma Bonglack (University of Cambridge)

Emmanuela completed her PhD with Micah Luftig at Duke University, developing a novel targeted therapeutic strategy to treat lymphomas caused by EBV related viruses, which often have limited options for treatment in the clinic. As a Schmidt Science Fellow in Mike Inouye’s lab, she is crossing disciplines to integrate multi-omics and advanced statistical methods to study the role of iron-deficiency anemia in cardiometabolic diseases, in ancestrally diverse global populations. Emmanuela’s interest in global health developed during her PhD and as a result of her growing up in Cameroon, where the negative impacts of poor health infrastructure and limited resources could be seen all around. Given the growing burden of chronic diseases and the high prevalence of iron deficiency in LMICs like Cameroon, Emmanuela hopes her research will advance our understanding of the unique factors that drive chronic/cardiometabolic diseases in diverse but underrepresented regions/populations.

Dr Carles Foguet (University of Cambridge)

Carles received his bachelor's degree in Biochemistry from the University of Barcelona, where he developed an interest in Systems Biology. To pursue this interest, he enrolled in the Biohealth Computing Erasmus Mundus master program, enabling him to take courses in bioinformatics at the University of Turin and to develop new modelling tools at the Joseph Fourier University. Next, he pursued a Ph.D. in Biotechnology at the University of Barcelona. During his Ph.D., he developed new approaches to model metabolism at a genome-scale by integrating multiple layers of omics data and an algorithm to integrate transcriptomics with stable isotope-resolved metabolomics and contributed to the PhenoMeNal project. He joined the Cambridge node of the Inouye lab in April 2021, where he works on the analysis of genomic and multi-omic datasets across HDRUK.

Dr Xilin Jiang (University of Cambridge)

I am a statistical geneticist working on the genetic architecture of complex diseases and its implications in clinical practice. Specifically, my research focuses on constructing risk factors using many variables that each have a small effect on diseases. The variables include genotype data, proteomic data, gene expression data and hospitalisation data (EHR). I like to think of disease as a stochastic process and disease risk on the “liability” scale. In statistical terminology, my research involves Bayesian inference for high dimensional data, longitudinal analysis and causal inference. I got my DPhil in Genomic Medicine and Statistics from Oxford University, funded by a Rhodes Scholarship and a Wellcome Trust studentship. I delivered the scholar address (name for a student speech delivered at the scholarship graduating ceremony) for the Rhodes scholar class of 2017. At the beginning of Pandemic, I worked as a consultant to the Gates Foundation and China CDC. Before my DPhil I worked on neural imaging modelling, analysing both structure and functional MRI data. I received my BSc from Fudan University.

Dr Joanna Kaplanis (Wellcome Sanger Institute / University of Cambridge)

Joanna grew up in London before moving to the US in 2008 where she received her BA in Applied Mathematics and MSc in Biostatistics from Harvard University. During this time she was introduced to human genetics while working as a research assistant in Yaniv Erlich's lab where she analysed large social media generated family trees to understand the genetic architecture of longevity. Following this, she moved back to the UK in 2015 to undertake her PhD at the Wellcome Sanger Institute with Matt Hurles where she focussed on understanding the rates and patterns of germline mutation as well as their role in rare developmental disorders. In 2021 she started her post-doc jointly with Gosia Trynka and Mike Inouye where her project is focussed on integrating functional genomics data and polygenic scores to identify disease relevant cell types.

Dr Martin Kelemen (University of Cambridge)

Martin received his BSc at University College London where he studied Human Genetics with a final year project focusing on genetic risk prediction and writing extensions for LDAK, supervised by the method's author Doug Speed. He then completed his PhD on the Mathematical Genomics and Medicine programme, supervised jointly by Carl Anderson at the Wellcome Trust Sanger Institute and by Chris Wallace at the University of Cambridge. Martin's PhD project was centred on finding evidence for epistasis using deep learning methods and improving the accuracy of polygenic risk scores by exploiting shared genetic effects between related diseases. He joined the unit as a postdoc to lead a project on building a risk model for abdominal aortic aneurysm that integrates polygenic scores and conventional risk factors. His current research focuses on exploring the effect of the environment and genetic variation on the transferability of polygenic risk scores across ancestries, working jointly with Mike and Prof Adam Butterworth (Public Health and Primary Care). In his free time Martin enjoys life drawing and listening to trashy Italo disco hits from the 80's.

Loïc Lannelongue (University of Cambridge)

Loïc is now a postdoctoral research associate in biomedical data science. Previously, he was as a PhD student in the MRC Doctoral Programme (Inouye Lab) at the University of Cambridge studying both green computing and protein-protein interaction networks. 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.

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.

Yang Liu (Baker Institute)

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. At Melbourne University, she studied for her PhD in the Inouye Lab using machine learning for prediction and classification of diseases based on genotype and phenotype data. She has continued her studies as a postdoc in the lab.

Dr Douglas Loesch (AstraZeneca / University of Cambridge)

Doug grew up near Philadelphia in the US. He worked as an educator for 8 years with a focus on students with special needs. He then pursued a research career at the University of Maryland (Baltimore), earning a PhD in human genetics and epidemiology under the guidance of Prof Timothy O’Connor. His research has primarily focused on Parkinson disease in South America and has participated in several collaborative initiatives that sought to improve diversity in genomics research. He is now a postdoctoral fellow at the Centre for Genomics Research at AstraZeneca and a visiting research at the Cambridge University. His interests include exploring how genomics can inform clinical care and what we can do to address issues pertaining to equity in biomedical research, especially with regards statistical genetics.

Dr Guillaume Méric (Baker Institute, Group Leader)

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 Elodie Persyn (University of Cambridge)

Dr Elodie Persyn studied agricultural engineering in Rennes (France) and obtained a Masters degree in Cellular and Molecular Biology and in Applied Statistics. She did a PhD in Nantes (France) with Richard Redon, Christian Dina and Lise Bellanger on rare variant association studies. She developed research interests in genetic epidemiology and population genetics with the comparison of statistical methods and the application to complex traits. After her PhD, she moved to the UK to join Cathryn Lewis’ team in King’s College London as a post-doctoral researcher. In collaboration with Hugh Markus from the University of Cambridge, she studied the genetics of brain imaging biomarkers of small vessel disease through the analysis of UK Biobank data. Currently, in the Inouye Lab, she is investigating the integration of multi-omics data from the INTERVAL study (https://www.intervalstudy.org.uk/).

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.

Manika Singh (Baker Institute)

Manika received her B.Sc. degree in Genetics, Biochemistry, and Zoology from Bangalore University and her M.Sc. degree in Bioinformatics from Sikkim Manipal University, India. She received a Bioinformatics National Certification (BINC) fellowship from the department of Biotechnology (DBT), India, and joined as a junior research fellow at the Institute of Bioinformatics, Bangalore. During this time, she learned the analysis of next-generation sequencing datasets and worked on various genomics and proteomics projects. Next, she received a CSIRO data61 scholarship to pursue a Ph.D. at the Queensland University of Technology, Brisbane. During her Ph.D., she developed a novel pipeline for isoform-level multi-omics integration in a mouse model of behaviour. In 2022, she joined the Inouye lab to work on the analysis of genomics and muti-omics datasets.

Dr Jingqin Wu (Baker Institute)

Jingqin Wu received her PhD degree in 2009 and her MSc degree in 2002 both from the University of Sydney. After her PhD graduation, she has worked at the University of Newcastle and the University of Sydney as a research fellow. In 2011, she was awarded the NHMRC early career fellowship. Her research focused on using the state-of-the-art genomic technology to answer biological questions. For example, she has worked on QacA-mediated multidrug resistance in Staphylococci, HIV-host interactions in relation to disease status and therapy effects, genome-wide association study of schizophrenia, and comparative genomics on fungi pathogen. Her multidisciplinary skills (e.g. molecular biology, genomics, and bioinformatics) build up her integrative thinking with a broad research vision. In 2021, she joined the Inouye and Meikle Labs at the Baker Institute as a bioinformatician exploring polygenic risk score and metabolic risk score predictions on human diseases.

Dr Ruidong Xiang (Baker Institute)

Ruidong has broad research interests related to statistical genomics. He has worked with genomic and phenotypic data from plants, animals and humans. He uses functional and evolutionary information to improve genome-wide mapping and prediction of complex traits. He has extensive experience in analysing pleiotropy (variants affecting >1 traits) and molecular phenotypes such as mapping gene expression eQTL, RNA splicing sQTL and metabolomic mQTL. His past work includes the development of the Functional-And-Evolutionary Trait Heritability (FAETH) score to rank genome-wide sequence variants and using Bayesian genome-wide fine-mapping to select core markers to customise a biology-informed SNP chip. More recently, he has developed new methods/analysis framework to link omics data and complex traits (scholar page). At the Inouye Lab, he will develop and/or apply advanced statistical methods to understand the link between multi-omics and human diseases.

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

Claire Coffey (University of Cambridge)

Claire grew up in Birmingham, UK, and completed her BSc in Computer Science at the University of Birmingham. As part of this degree, she also studied at the University of British Columbia and the University of Waterloo. Wanting to apply her interest in artificial intelligence to real-world problems, Claire worked as an AI research and development consultant at a start-up where she was an inventor on 2 patents. She then completed her MPhil in Advanced Computer Science at the University of Cambridge, for which she was awarded the DeepMind Cambridge Scholarship, and her research focused on analysing the fairness of machine learning algorithms (supervised by Neil Lawrence). Claire is now working on her PhD in Health Data Science at Inouye Lab, with a studentship from Health Data Research UK, The Alan Turing Institute, and the Wellcome Trust. Her PhD research focuses on investigating, quantifying, and improving the fairness of medical risk prediction algorithms to ensure these are not discriminating against minority subgroups of society. She is supervised by Mike Inouye, Angela Wood, and Sam Lambert.

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.

Alex Tokolyi (University of Cambridge / Wellcome Sanger Institute)

Alex grew up in Melbourne, Australia, completing undergraduate degrees at Monash University in Computer Science and Science (Microbiology and Molecular biology). During this he had the opportunity through a CSL-funded UROP internship to pursue bioinformatics research at the Australian Regenerative Medicine Institute, creating systems to explore spatial transcriptomic data. Alex then joined the lab of Kathryn Holt at the Bio21 Institute of the University of Melbourne for a year-long honours project on bacterial genomics, analysing how plasmids share genes between each other and different bacterial species. He then joined the Inouye lab to analyse the network interactions of genomic and environmental data from asthma patients, before beginning his PhD at the Sanger Institute in the University of Cambridge. Currently Alex is supervised by Emma Davenport and Mike Inouye, and looks at the variation in the human response to immune conditions such as sepsis, and the interaction of this with resident microbes.

Zhengyang Zhu (University of Cambridge)

Yang was born in China and moved to Singapore during secondary and high school. He completed his BSc in Biomedical Sciences and MSc in Epidemiology at Imperial College London. His Masters' project was to investigate renal safety profiles of HIV-1 patients after switching drug regimen in collaboration with Gilead Sciences Inc., which spurred his interest in data science in the context of infectious diseases. His current research focusses on the application of GWAS in infectious diseases, particularly infections with known comorbidities.

Alumni

Name Position Duration CurrentSergio Ruiz Carmona Bioinformatician Jan 2019 - Nov 2022 Clinical Data Analyst, Murdoch Childrens Research InstituteHoward Tang Postdoc Aug 2015 - Sept 2022 Sam Lambert Postdoc Jan 2019 - July 2022 Assistant Professor (tenured), Cambridge UnivRodrigo Canovas Postdoc Jan 2018 - Apr 2022 Research Scientist, CSIROJason Grealey PhD student Mar 2018 - Sept 2021 Postdoc, Children's Cancer InstituteArtika Nath Postdoc Mar 2013 - Jan 2022 Bioinformatician, Cancer Alliance QueenslandGyorgy Abrusan Postdoc Mar 2020 - Mar 2022Shu Mei Teo Postdoc Mar 2013 - July 2021 Statistician, Cancer Council VictoriaAlex Smith Postdoc (Meikle) Jan 2018 - Mar 2021 Gad Abraham Group Leader Feb 2012 - Mar 2021 Senior Scientist, CSL ResearchYouwen (Owen) Qin PhD student Sept 2016 - Sept 2020 Research Scientist, BGI-ShenzhenJonathan Marten Postdoc Nov 2019 - Aug 2020 Statistical Geneticist, Genomics PLCMarika Catapano Postdoc Feb 2019 - Oct 2019 Senior Bioinformatics Data Scientist, BenevolentAIPetar 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 2015 - June 2019 Staff Scientist, 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 Research Fellow, 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 Senior Bioinformatician, Australian Genome Research Facility Danielle Belgrave Visitor Sept 2016 - Dec 2016 Senior Staff Scientist, DeepMindMichael 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 Senior Researcher, Finnish Institute of Health & WelfareAki Havulinna Visitor Aug 2015 Chief Researcher, Finnish Institute of Health & Welfare 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