RAPHAELLE LUISIER
PRINCIPAL INVESTIGATOR
My Background
I am a computational biologist initially trained as a Bioengineer. My research interests include bioinformatics, visual analytics and machine/deep learning applied to neuroscience and health informatics.
I earned a Master of Science in Bioengineering and Biotechnology at the Swiss Federal Institute of Lausanne (EPFL, Switzerland, 2009), and a PhD in Bioinformatics from the Basel University (Switzerland, 2013). Before joining Idiap in 2019, I was leading several research projects at the Francis Crick Institute (London, UK) on RNA metabolism in developing neurons and its impact on disease using high content genomic data.
I started my own research group in December 2019, which focuses on developing computational and informatics methods for integrative analysis of transcriptomic, imaging and digital data to improve the understanding and diagnosis of complex disorders such as neurodegenerative diseases and cancer. I am also an SIB Swiss Institute of Bioinformatics Group Leader since 2022 and an EPFL Lecturer since 2023.
My Vision
My vision is to transform our understanding and treatment of devastating and incurable human diseases by adapting cutting-edge computational methods inspired from various signal processing fields such as computer vision and language processing to longitudinal biological and clinical data.
The methods developed by myself and my research group have enabled for example to identify the earliest events underlying drug-induced liver tumor development [1,2,3,4] and to challenge current dogma related to the regulation and roles of non-coding portions of mRNA such as introns [5,6,7] and 3' untranslated regions (3' UTRs) [8,9].
My goal is synergise with researchers of various expertises that are complimentary to my own and required to implement my vision. Specifically my group will continue to develop powerful and innovative data science methods to large-scale genomic, clinical, digital and imaging data to address salient biological questions related to sub-cellular compartmentalisation of RNA and proteins in disease. The close collaboration with clinicians and industry will ensure the translational potential of my research.
REFERENCES
1. Lempiainen, H., Couttet, P., Bolognani, F., Muller, A., Dubost, V., Luisier, R., Del Rio Espinola, A., Vitry, V., Unterberger, E. B., Thomson, J. P., Treindl, F., Metzger, U., Wrzodek, C., Hahne, F., Zollinger, T., Brasa, S., Kalteis, M., Marcellin, M., Giudicelli, F., Braeuning, A., Morawiec, L., Zamurovic, N., Langle, U., Scheer, N., Schubeler, D., Goodman, J., Chibout, S.-D., Marlowe, J., Theil, D., Heard, D. J., Grenet, O., Zell, A., Templin, M. F., Meehan, R. R., Wolf, R. C., Elcombe, C. R., Schwarz, M., Moulin, P., Terranova, R., and Moggs, J. G. Identication of dlk1-dio3 imprinted gene cluster noncoding rnas as novel candidate biomarkers for liver tumor promotion. Toxicol Sci (2013).
2. Luisier, R., Lempiainen, H., Scherbichler, N., Braeuning, A., Geissler, M., Dubost, V., Muller, A., Scheer, N., Chibout, S.-D., Hara, H., Picard, F., Theil, D., Couttet, P., Vitobello, A., Grenet, O., Grasl-Kraupp, B., Ellinger-Ziegelbauer, H., Thomson, J. P., Meehan, R. R., Elcombe, C. R., Henderson, C. J., Wolf, C. R., Schwarz, M., Moulin, P., Terranova, R., and Moggs, J. G. Phenobarbital induces cell cycle transcriptional responses in mouse liver humanized for constitutive androstane and pregnane x receptors. Toxicol Sci (2014).
3. Luisier, R., Unterberger, E. B., Goodman, J. I., Schwarz, M., Moggs, J., Terranova, R., and van Nimwegen, E. Computational modeling identies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion. Nucleic acids research (2014).
4. Unterberger, E. B., Eichner, J., Wrzodek, C., Lempiainen, H., Luisier, R., Terranova, R., Metzger, U., Plummer, S., Knorpp, T., Braeuning, A., Moggs, J., Templin, M. F., Honndorf, V., Piotto, M., Zell, A., and Schwarz, M. Ha-ras and -catenin oncoproteins orchestrate metabolic
programs in mouse liver tumors. Int J Cancer (2014).
5. Luisier, R., Tyzack, G. E., Hall, C. E., Mitchell, J. S., Devine, H., Taha, D. M., Malik, B., Meyer, I., Greensmith, L., Newcombe, J., et al. Intron retention and nuclear loss of sfpq are molecular hallmarks of als. Nature communications (2018).
6. Tyzack, G. E., Luisier, R., Taha, D. M., Neeves, J., Modic, M., Mitchell, J. S., Meyer, I., Greensmith, L., Newcombe, J., Ule, J., Luscombe, N. M., and Patani, R. Widespread fus mislocalization is a molecular hallmark of amyotrophic lateral sclerosis. Brain (2019).
7. Tyzack, G. E., Manferrari, G., Newcombe, J., Luscombe, N. M., Luisier, R., and Patani, R. Paraspeckle components NONO and PSPC1 are not mislocalized from motor neuron nuclei in sporadic ALS. Brain (2020).
8. Andreassi, C.*, Luisier, R.*, Crerar, H., Darsinou, M., Blokzijl-Franke, S., Lenn, T., Luscombe, N. M., Cuda, G., Gaspari, M., Saiardi, A., and Riccio, A. Cytoplasmic cleavage of impa1 3' utr is necessary for maintaining axon integrity. Cell Reports (2021), 108778.
9. Luisier, R., Andreassi, C., Lisa M. Fournier and Riccio, The predicted RNA-binding protein regulome of axonal mRNAs. Genome Research (2023).