Clinical bioinformatician

CHUV - Centre Hospitalier Universitaire Vaudois Lausanne — Lausanne
01 AprilFach­ver­ant­wortung100%

Clinical bioinformatician

Clinical bioinformatician

The immunopeptidomics unit headed by Dr. Michal Bassani-Sternberg is part of the Oncology department at the University Hospital of Lausanne (CHUV/UNIL). The unit is incorporated into the hiTIDE (human integrated tumour immunology discovery engine) translational research group led by Prof. George Coukos. In addition, the unit is affiliated to the Center of Experimental Therapeutics and to the Ludwig Institute for Cancer Research, and bridges basic cancer-immunology research and exploratory first-in-man clinical trials.

In the immunopeptidomics lab we are developing and implementing experimental and computational proteo-genomics pipelines for antigen discovery by mass-spectrometry-based immunopeptidomics. Our main goal is to identify clinically relevant and novel cancer-specific human leukocyte antigen (HLA) ligands that will guide the dvelopment of personalized cancer immunotherapy.

We are involved in first-in-man phase I clinical trials where we are responsible for identifying neoantigens specific to patient tumor samples, which are then used to identify tumor neoantigen-specific T cells for adoptive T cell therapies. In addition, we pursue fundamental discovery work to elucidate how tumour cells present antigens, and to reveal the molecular bases of tumour immunogenicity. We established a proteo-genomics bioinformatics pipeline for the direct identification of neoantigens by combining genomic information derived from exome-seq analysis with measured immunopeptidomics mass spectrometry data. 

We are now looking for a bioinformatician with established expertise in genomics, transcriptomics and/or proteomics data analysis to join our bioinformatics team to execute and further develop this computational pipeline. Importantly, the bioinformatician will directly support clinical operations related to personalized therapeutic programs. This position offers the opportunity to develop and execute cutting-edge discoveries in an environment of translational research.

Département DO - Dpt d'oncologie Code emploi Administrateur-trice de bases de données - 107010Niveau 10Date d'entrée souhaitée 01-06-2021Type de contrat CDDDate de fin de contrat 31-05-2022Catégorie professionnelle Médico-techniquesLieu LausanneTaux d'activité 80% -100% Date de début de publication 01-04-2021 Date de fin de postulation 31-05-2021 Référence 06935-MT-209-2021 Documents

  • Cahier des charges EN
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The Lausanne University Hospital (CHUV) is one of five Swiss university hospitals. Through its collaboration with the Faculty of Biology and Medicine of the University of Lausanne and the EPFL, CHUV plays a leading role in the areas of medical care, medical research and training.


This position offers the opportunity to develop and execute cutting-edge discoveries in an environment of translational research.


  • Be able to integrate genomics, transcriptomics and immunopeptidomics for antigen discovery through the generation of customized reference databases for proteogenomics, including data visualization and statistical analyses

  • Develop new concepts related to prioritization of neoantigens and clinically relevant antigens, and incorporate the latest developments and trends concerning computational analysis in cancer and immunology research

  • Analyze « Next-Generation Sequencing (NGS) » (whole exome seq, whole genome seq, RNA sequencing), including the application and/or the development of methods for large-scale analysis using publically available datasets

  • Develop and support the research team in statistical analysis of clinical and research data in order to improve the understanding of clinical responses and link it with the immune system of the patients and any correlates to the cancer development and the efficacy of the therapeutic treatment

  • Collaborate with other Hi-TIDE bioinformaticians to develop analytical tools in a quantitative manner based on omics data

  • Document procedures in internal protocols, reporting and discussing results in scientific meetings, both locally and internationally as well as writing scientific research manuscripts and reviews.


  • PhD in computational biology or in bioinformatics with a background in immunobiology and cancer, in applied mathematics and/or in statistics.

  • Expertise in the analysis of Next-generation sequencing (NGS) transcriptomic (RNA-Seq) and MS proteomics data is required.

  • Expertise in bioinformatics, including fluency in Perl, Python, Java and R.

  • Expertise in systems biology/systems medicine, large-scale data analysis, integration and visualization

  • Competence in/familiarity with running Bash/Perl based pipelines in a Linux environment

  • Curiosity about biological and pathological mechanisms, in particular towards immunological phenomenon and in the context of cancer research

  • Proven capacity to interact with biologists and bioinformaticians of the research department to communicate/discuss results, ideas and follow-up of experiments

  • Demonstrated ability to apply new methods of analysis and computational tools

  • Extensive knowledge of public and private databases and relevant analytic tools

  • Excellent written and verbal communication skills required for publications and presentations

  • Proficient in spoken and written English.

Nous offrons

If you become an employee at the Centre Hospitalier Universitaire Vaudois, we will offer you the following :

  • High social benefits

  • Regular salary progression according to job responsibilities

  • Three days of training per year

  • 25 working days of vacation per year

  • Very good restaurants with preferential rates.

Contact et envoi de candidature

 The application should include:

  • Application letter

  • Curriculum vitae, list of qualifications and description of previous research/work

  • Publication list (with three most relevant publications highlighted)

 For further inquiries please contact : Michal Bassani - responsable de l'unité de spectrométrie de masse - 021 314 85 02.

As our applications are processed electronically, would you please apply exclusively by internet, with the « POSTULER » button, at the bottom of the ad. If for any technical reason, you are not able to do it, we invite you to contact our recruitment team, which will assist you (contact : 021.314.85.70).

The CHUV applies the highest quality requirements as part of its recruitment process. In addition, mindful to promote the diversity of our employees we are attentive to the different life courses and strive to ensure equal treatment and avoid any discrimination. We are looking forward to receiving your application.

We thank in advance the employment agencies to take note that applications inserted by them directly on our recruitment platform are not accepted and cannot be billed. Thank you for your understanding.

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