Research Engineer Position in Bioinformatics at Institut Pasteur Paris

Institut Pasteur

Research Engineer Position in Bioinformatics at Institut Pasteur Paris

France

Closing in 22 days

Position:

The Bioinformatics and Biostatistics Hub at Institut Pasteur is hiring a research engineer in bioinformatics, for an ERC-funded 4.5-year-long “CDI projet” contract with the potential to evolve into a full CDI after this time.

The engineer will dedicate 80% of her/his time to work in the team headed by Dr. Deczkowska (www. aleksdelab.com). The remaining 20% will be devoted to technical contribution, and training and teaching activities at the Institut Pasteur Bioinformatics Hub.

The Hub

The Hub provides analytical support to research units and platforms at the Institut Pasteur and is committed to this mission through:

Collaboration on scientific projects submitted by research teams of our institute to the Hub.

Training scientific staff from the Institut Pasteur Paris or other Institutes of the International Pasteur Network.

Development of tools and applications to be shared with the broader scientific community.

Direct interaction with scientists upon specific inquiries.

Deczkowska lab

The Deczkowska lab opened in April 2021 and currently hosts a research engineer, three post-docs, two students, and an administrative assistant as well as a part-time bioinformatician, who will introduce the selected candidate to the position. We collaborate with other labs in neuroscience and immunology departments, as well as core facilities. Our research focuses on exploring different ways via which the immune system can shape the brain function in health and disease. Manipulation of the immune system is used as a therapeutic approach in e.g. oncology. Our vision is to use it in neurological diseases, such as Alzheimer's disease.

To reach this goal, we study how peripheral signals, such as immune cells present at the brain borders, shape brain physiology, how the dysfunction of such communication pathways can contribute to brain aging or disease, and how we can exploit such pathways to cure the brain. We especially focus on the immune niche of the choroid plexus (one of the brain borders), and the skull bone marrow in the contexts of brain development, circadian rhythms, microbiota composition, Alzheimer's disease, and stroke. We use both mouse models and human samples (Baruch, Deczkowska et al., Science, 2014; Schwartz & Deczkowska, TrendsImmune, 2016; A Deczkowska, O Matcovitch-Natan et al, Nat.Comms. 2017; Deczkowska et al., Nat.Neurosci. 2018; Deczkowska et al., Cell. 2018, 2020).

Candidate's Job Description

Analysis, visualization, presentation, and interpretation of high- throughput data generated using spatial transcriptomics (Stereo-Seq), scRNA-seq, bulk RNA-seq, proteomics, metabolomics, epigenetics, and other -omics approaches by members of the Brain-Immune Communication lab, collaborators, as well as from publicly available datasets.

Active contribution to the design of the experiments, projects, and data analysis and interpretation as a support to project leaders, especially from the statistics and analysis point of view.

Continually identifying novel tools and annotation databases to improve the analysis's efficiency, sensitivity, and functionality.

Identifying and improving bioinformatics tools to help automate workflows for routine bioinformatics analyses and instruct lab members on simpler tools, so they can perform some analysis independently, depending on the needs.

Writing, updating, and improving custom scripts for analysis of data derived from high-throughput techniques.

Presentation of data in lab meetings, conferences, manuscripts. Contribution to the writing of manuscripts from the lab.

Maintenance of the infrastructure of the lab informatics facilities and data, including a web server, workstation, compute cluster accounts, sequencing data, remote storage, public databases.

Candidate's qualifications

Master's degree in bioinformatics, computational biology, computer science, engineering, biological sciences, or another related discipline, preferably with some years of experience as a bioinformatician.

Experience in scientific programming in the area of genomics and next- generation sequencing analysis (previous experience with single-cell transcriptomics and spatial transcriptomics analysis is a plus.

Must have excellent programming skills in languages such as Python and R.

Must be familiar with tools and processes for reproducibility and maintainability in software development and data analysis (such as Git, docker, …).

Must have the ability to perform data analysis and plotting in R.

Must have experience in -omics data analysis and know how to visualize such data.

Must have knowledge of commonly used bioinformatics packages.

Familiarity with biological data repositories such as the UCSC Genome Browser and NCBI.

Ability to multitask while working independently, exercising sound judgment in meeting deadlines, maintaining well-documented and tested code, and thoroughly documenting analysis results.

Must have good communication skills focusing on teamwork and creating usable and accessible research software tools.

Experience with data mining and machine learning will be appreciated.

English is our working language. Knowledge of French is optional.

To apply:

Click on the following link and select the corresponding profile “Metabolomics data analysis” when this will be proposed:

https: // hub-jobs2023-fall.pasteur.cloud

Please, submit your updated CV and a cover letter (motivation letter). You may indicate contact information for reference letters (3 max.). They will be automatically contacted when you validate your application.

We are a team committed to foster a fair, inclusive and diverse work environment. Diversity has been scientifically established as a key factor to improve scientific objectivity. Hence, all applicants will be evaluated solely based on qualification regardless of gender, gender identity, sexual orientation, race or disability.