Research Engineer Position in Computational Genomics and Scientific Software

Research Engineer Position in Computational Genomics and Scientific Software

Institut Pasteur

Paris, France

Position:

The Bioinformatics and Biostatistics Hub at Institut Pasteur is hiring a senior research engineer in bioinformatics.

The engineer will dedicate 80% of her/his time to work in the team “sequence bioinformatics” headed by Dr. Rayan Chikhi. The remaining 20% will be devoted to technical contribution, training or teaching activities at the Institut Pasteur Bioinformatics Hub.

Duties:

The main mission of the position is to contribute to the scientific, methodological, and software development of bioinformatics research projects, with a focus on computational genomics, metagenomics, k-mer-based methods, analysis of ancient or degraded data, machine learning, and the scaling of software and analysis pipelines.

The successful candidate will notably be responsible for:

Methodological and software development:

• Develop new methods, software, and analysis pipelines, particularly for large-scale sequencing data, k-mer-based approaches, and machine-learning methods;
• Document, maintain, and disseminate open-source scientific software, reproducible workflows, or tools integrated into shared environments such as Galaxy, where relevant;
• Keep abreast of scientific and technological developments, and evaluate available tools and published methods.

Scientific valorization:

• Contribute to the design, implementation, and writing of collaborative research projects as well as funding applications;
• Participate in the writing, submission, and revision of scientific publications.

Expertise and Advisory:

• Participate to bioinformatics analysis projects submitted to the Bioinformatics and Biostatistics Hub and related to the scientific scope of the position;
• Share, advise and guide users and colleagues on the use of methods, tools, and best practices for the analysis of genomic, metagenomic, and paleogenomic data.

Profile:

The position requires an experienced profile combining methodological research in bioinformatics, scientific software development, and the analysis of large-scale sequencing data, with demonstrated experience in metagenomics, k-mer-based methods, ancient or degraded data analysis, and machine learning.

Candidates must hold at least a Master’s-level degree (or equivalent) in bioinformatics, computer science, data science, computational biology, or a related discipline. Research experience at the PhD, postdoctoral, advanced research engineering, or equivalent level is strongly preferred.

Required skills:

Bioinformatics expertise:

• Strong command of high-throughput sequencing data: genomics, metagenomics, paleogenomics, assembly, mapping, quality control, k-mer-based methods;
• Hands-on experience with machine-learning or deep-learning methods applied to sequencing data.

Software development and infrastructures:

• Strong experience in scientific programming (Python and/or C/C++);
• Command of scientific computing environments: Linux, Bash, Git, HPC, containers, reproducible workflows;
• Development of software/pipelines for vast collections of sequencing data on HPC and/or cloud infrastructures.

Research activity:

• Contribution to scientific projects, publications, and funding applications;
• Scientific writing in English.

Transversal skills:

• Autonomy, rigor, organizational skills, ability to carry a project through to publication;
• Excellent interpersonal skills and teamwork with a wide range of profiles (biologists, computer scientists, platforms...);
• Interest in open science, reproducibility, and tool dissemination.

Previous experience in developing tools for metagenomics, ancient DNA, large genome collections, k-mer-based methods, deep learning, cloud/HPC infrastructures, Galaxy, or reproducible bioinformatics workflows will be considered a significant advantage.

Deadline 25 October