Associate Professor
Dimitri Perrin
Faculty of Science,
School of Computer Science
Biography
Dr Dimitri Perrin is Associate Professor in the School of Computer Science at the Queensland University of Technology, where he leads the Biomedical Data Science group (more details on biomedicaldatascience.com). He is also a Chief Investigator in the QUT Centre for Data Science, co-leading the Health and Biological Systems Domain. Prior to joining QUT, he worked as a FPR Fellow in the Laboratory for Systems Biology (RIKEN, Japan) and as an IRCSET Marie-Curie Research Fellow with the Centre for Scientific Computing & Complex Systems Modelling (Dublin City University, Ireland) and the Department of Information Networking (Osaka University, Japan). His research interests are in developing new approaches to analyse, understand and optimise biomedical and social systems. His work therefore spans the areas of modelling and simulation, computational biology and bioinformatics, and data analysis. Recent projects include gene editing (CRISPR), high-resolution biomedical imaging (CUBIC), and mobile apps for health research. Dimitri Perrin holds a Master’s Degree (Diplôme d'Ingénieur) in Computer Engineering from ISIMA (Aubière, France), a M.Sc. in Computing from Université Blaise Pascal (Clermont-Ferrand, France), and received his Ph.D. in Computing from Dublin City University (Dublin, Ireland). For up-to-date publications and current projects, please check Dr Perrin's group website.Personal details
Positions
- Associate Professor
Faculty of Science,
School of Computer Science
Keywords
Data Science, Complex Systems, Bioinformatics, Computational Biology, Modelling and Simulation, CRISPR, Parallel Computing, Next-Generation Sequencing, Applied Machine Learning, Biomedical Imaging
Research field
Artificial Intelligence and Image Processing, Other Information and Computing Sciences, Biochemistry and Cell Biology
Field of Research code, Australian and New Zealand Standard Research Classification (ANZSRC), 2008
Qualifications
- PhD in Computer Science (Dublin City University)
Professional memberships and associations
Teaching
Dr Dimitri Perrin has extensive experience in teaching, recognised by a Senior Fellowship of the Higher Education Academy (2020). Current teaching:
- IFN564: Data structures and algorithms
- IFN646: Biomedical Data Science
- IFN703/4: Advanced Project / Advanced Project 2
Publications
- Cleves, P., Tinoco, A., Bradford, J., Perrin, D., Bay, L. & Pringle, J. (2020). Reduced thermal tolerance in a coral carrying CRISPR-induced mutations in the gene for a heat-shock transcription factor. Proceedings of the National Academy of Sciences of the United States of America, 117(46), 28899–28905. https://eprints.qut.edu.au/207993
- Bradford, J. & Perrin, D. (2019). A benchmark of computational CRISPR-Cas9 guide design methods. PLoS Computational Biology, 15(8). https://eprints.qut.edu.au/208021
- Bradford, J. & Perrin, D. (2019). Improving CRISPR guide design with consensus approaches. BMC Genomics, 20. https://eprints.qut.edu.au/208020
- Roomkham, S., Hittle, M., Cheung, J., Lovell, D., Mignot, E. & Perrin, D. (2019). Sleep monitoring with the Apple Watch: Comparison to a clinically validated actigraph. F1000Research, 8, 1–19.
- Stephansen, J., Olesen, A., Olsen, M., Ambati, A., Leary, E., Moore, H., Carrillo, O., Lin, L., Han, F., Yan, H., Perrin, D. & other, a. (2018). Neural network analysis of sleep stages enables efficient diagnosis of narcolepsy. Nature Communications, 9, 1–15. https://eprints.qut.edu.au/123954
- Tatsuki, F., Sunagawa, G., Shi, S., Susaki, E., Yukinaga, H., Perrin, D., Sumiyama, K., Ukai-Tadenuma, M., Fujishima, H., Ohno, R., Tone, D., Ode, K., Matsumoto, K. & Ueda, H. (2016). Involvement of Ca2+-dependent hyperpolarization in sleep duration in mammals. Neuron, 90(1), 70–85. https://eprints.qut.edu.au/95240
- Sunagawa, G., Sumiyama, K., Ukai-Tadenuma, M., Perrin, D., Fujishima, H., Ukai, H., Nishimura, O., Shi, S., Ohno, R., Narumi, R., Shimizu, Y., Tone, D., Ode, K., Kuraku, S. & Ueda, H. (2016). Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene. Cell Reports, 14(3), 662–677. https://eprints.qut.edu.au/91686
- Susaki, E., Tainaka, K., Perrin, D., Yukinaga, H., Kuno, A. & Ueda, H. (2015). Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging. Nature Protocols, 10(11), 1709–1727. https://eprints.qut.edu.au/88909
- Tainaka, K., Kubota, S., Suyama, T., Susaki, E., Perrin, D., Ukai-Tadenuma, M., Ukai, H. & Ueda, H. (2014). Whole-body imaging with single-cell resolution by tissue decolorization. Cell, 159(4), 911–924. https://eprints.qut.edu.au/82687
- Susaki, E., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T., Yokoyama, C., Onoe, H., Eguchi, M., Yamaguchi, S., Abe, T., Kiyonari, H., Miyawaki, A., Yokota, H. & Ueda, H. (2014). Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell, 157(3), 726–739. https://eprints.qut.edu.au/82685
QUT ePrints
For more publications by Dimitri, explore their research in QUT ePrints (our digital repository).
Awards
- Type
- Funding Award
- Reference year
- 2012
- Details
- Foreign Postdoctoral Fellowship (http://www.riken.jp/en/careers/programs/fpr/)
- Type
- Funding Award
- Reference year
- 2010
- Details
- Complexity-NET grant (ERA-NET, FP6) for the Complexity of Interdependent Epigenetic Signals in Cancer Initiation (CIESCI) project.
- Type
- Funding Award
- Reference year
- 2009
- Details
- IRCSET-Marie Curie International Mobility Fellowships in Science Engineering and Technology
Selected research projects
- Title
- Safer gene editing tools for Australian livestock and biotech industries
- Primary fund type
- CAT 1 - Australian Competitive Grant
- Project ID
- DP210103401
- Start year
- 2021
- Keywords
- Title
- Deep Learning and Physiology Based Approach to Derive and Link Obstructive Sleep Apnoea Phenotypes and Symptomatology
- Primary fund type
- CAT 1 - Australian Competitive Grant
- Project ID
- 2001729
- Start year
- 2021
- Keywords
Projects listed above are funded by Australian Competitive Grants. Projects funded from other sources are not listed due to confidentiality agreements.
Supervision
Current supervisions
- Optimising the computational performance of CRISPR-Cas guide design tools
PhD, Principal Supervisor
Other supervisors: Professor Chris Drovandi - Data in Intensive Care: Machine Learning and Informed Decision-Making
PhD, Principal Supervisor
Other supervisors: Professor David Lovell - Indexing and Search of Extreme-Scale Genomic Collections
PhD, Associate Supervisor
Other supervisors: Associate Professor Jim Hogan
Completed supervisions (Doctorate)
Supervision topics
- Information retrieval and coding methods for large scale bioinformatics
- Representation learning for anti-microbial resistance
- Scalable software solutions for improving the CRISPR gene editing system
- Hierarchical visualisation of large social networks
- Designing a digital health platform to manage health and well-being
- Visualisation of CRISPR targets
- High-performance bioinformatic analysis of gene editing targets using Python Standard Libraries
- High-performance scoring of CRISPR targets