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.
Apply Now
Deadline 25 October
Don't forget to mention EuroScienceJobs when applying.
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