Postdoctoral Position in Computational Biology (100%, funded) W/M

About Idiap

Idiap is an independent, not-for-profit, research institute accredited and funded by the Swiss Federal Government, the State of Valais, and the City of Martigny.

Idiap offers competitive salaries and working conditions at all levels in a dynamic, multicultural environment. Idiap is an equal opportunity employer. We specifically encourage women and minorities to apply.

Idiap is located in the town of Martigny in Valais, Switzerland, offering exceptional quality of life, exciting recreational activities, including hiking, climbing and skiing, as well as varied cultural activities. It is within close proximity to Lausanne and Geneva. Although Idiap is located in the French part of Switzerland, English is the official working language.

For frequently asked questions (FAQs) about living in Switzerland, please go to https://www.idiap.ch/en/faq

Job description

Study of aberrant mRNA metabolism in melanoma using scRNA-seq data towards identification of rare tumor subpopulation.

About the position:
The Genomics and Health Informatics group at the Idiap Research Institute in Martigny (Switzerland) has availability for one fully funded postdoctoral candidate to join our efforts to develop a framework to enable easy implementation and evaluation of AS/APA methods to scRNA-seq and then test their utility to identify rare tumor subpopulation in advanced melanoma.

About the project:
We are seeking a highly motivated, ambitious and talented scientist to join our efforts to refine the molecular characterisation of tumor composition and to provide with the high-resolution reconstruction of the seemingly homogenous tumor cell populations underlying heterogenous drug response in melanoma. The postdoc will develop specific and reliable biomarkers for improved patient stratification and tumor classification, and the understanding of the mechanisms responsible for therapy resistance, in particular for drugs in development in Novartis through the integrative analysis of clinical, images of hematoxilin and eosin stained tissue sections, and multiomics data (bulk RNA-sequencing, 10X Genomics single-cell sequencing, Smart-seq 3 full-length single-cell sequencing data, spatial transcriptomics. This position is in collaboration with the Novartis Institutes for Biomedical Research (NIBR, Basel) where the postdoc will have the opportunity to test the developed methods.


About our group:
The Genomics and Health Informatics group develops computational models and statistical methods to interpret large-scale longitudinal data (e.g. transcriptomics, clinical, cellular imaging) to address biological questions related to human disorders. We seek to produce top notch science and foster the development of outstanding, independent scientists through nurturing mentorship and interdisciplinary, collaborative efforts. The group is an associated member of the National Center of Competence and Research (NCCR) RNA and Disease and is also part of the SIB Swiss Institute of Bioinformatics, offering various training possibilities as well as networking opportunities within the Swiss bioinformatics community.

For more information about our group:
https://www.idiap.ch/en/scient...

Key Papers from the lab

Hagemann, C., Tyzack, G. E., Taha, D. M., Devine, H., Greensmith, L., Newcombe, J., Patani, R., Serio, A., & Luisier, R. (2021). Automated and unbiased discrimination of ALS from control tissue at single cell resolution. In Brain Pathology. https://doi.org/10.1111/bpa.12937

Luisier, R., Tyzack, G. E., Hall, C. E., Mitchell, J. S., Devine, H., Taha, D. M., Malik, B., Meyer, I., Greensmith, L., Newcombe, J., Ule, J., Luscombe, N. M., & Patani, R. (2018). Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS. Nature Communications, 9(1), 2010.

Petric-Howe, M., Crerar, H., Neeves, J., Harley, J., Tyzack, G., Klein, P., Ramos, A., Patani, R., & Luisier, R. (2022). Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis. Genome Research. https://doi.org/10.1101/gr.276898.122

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., & Patani, R. (2019). Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis. Brain: A Journal of Neurology, 142(9), 2572–2580.

Tyzack, G. E., Neeves, J., Crerar, H., Klein, P., Ziff, O., Taha, D. M., Luisier, R., Luscombe, N. M., & Patani, R. (2021). Aberrant cytoplasmic intron retention is a blueprint for RNA binding protein mislocalization in VCP-related amyotrophic lateral sclerosis. In Brain (Vol. 144, Issue 7, pp. 1985–1993). https://doi.org/10.1093/brain/awab078

Verzat, C., Harley, J., Patani, R., & Luisier, R. (2022). Image-based deep learning reveals the responses of human motor neurons to stress and VCP-related ALS. Neuropathology and Applied Neurobiology, 48(2), e12770.

Sought profile

The candidate qualifications

• PhD in bioinformatics, computational biology, signal processing, or related field.

• Strong mathematical and computational skills.

• Expert knowledge in Python, Linux and HPC computing environments.

• Proven ability to take ownership of a project and push it forward independently.

• Proactivity and excellent analytical, communication, and organizational skills.

• Outstanding writing and communication skills, with an ability to work both independently and within collaborative teams productively

• Track record of productivity supported by accepted or in press first-author publications in peer-reviewed journals.

• Candidates do not necessarily have to have a biological background but should have a strong desire to directly work with experimental biologists.

• Good knowledge of English.

Required languages

• English - Level advanced

Réf: 84636a25-8c99-4500-be4d-a1a450a0f075