Mots-Clés

deep learning transcription factor JASPAR genomics UniBind

Description

The Computational Biology & Gene Regulation group led by Anthony Mathelier at the NCMM, a part of the Nordic EMBL Partnership for Molecular Medicine, is seeking an ambitious and highly motivated Postdoctoral Fellow or Researcher for a two-year position, starting as soon as possible in 2024. The selected candidate will play a pivotal role in a collaborative project spanning internationally renowned groups, namely those of Drs. Anshul Kundaje at Stanford University, USA, Wyeth Wasserman at the University of British Columbia, Canada, and Anthony Mathelier, NCMM, Norway. The position will be based in Norway. More information about the group can be found at https://mathelierlab.com/.

Join us to not only advance your career but also contribute to meaningful scientific discoveries and resources in the world of computational biology and gene regulation.

Position Description

The selected candidate will contribute to a cutting-edge project aimed at enhancing and expanding computational resources to decipher transcription factor (TF) – DNA interactions. The focus will be on the enhancement of the JASPAR (https://jaspar.elixir.no) and UniBind (https://unibind.uio.no)  databases, which are officially recognized by ELIXIR Norway as Norwegian bioinformatics services. Specifically, the candidate will utilize advanced deep-learning techniques to provide refined models and data crucial for the analysis of disease mutations affecting gene expression.

It is expected that the successful candidate will be able to complete the project in the course of the period of employment.

The candidate can refer to the following publications: https://doi.org/10.1093/nar/gkac1143, https://doi.org/10.1186/s12864-021-07760-6, https://doi.org/10.1038/s41588-021-00782-6, https://doi.org/10.1101/2022.12.20.520743, https://doi.org/10.48550/arXiv.1704.02685, https://doi.org/10.48550/arXiv.1811.00416.

Key responsibilities

• Generation of BPnet deep learning models on ChIP-seq datasets from the GEO database.
• Employing interpretation tools like DeepLIFT and TF-MoDISco to meticulously extract TF-DNA interactions.
• Development of a framework for integrating these models into JASPAR and enriching the UniBind database with high-resolution interactions.

Requirements

The ideal candidate should meet the following criteria:

• Ph.D. in Computational Biology, Bioinformatics, or a related field.
• Proficiency in programming and experience with computational genomics data analysis.
• Experience in machine learning, particularly deep learning techniques.
• Experience in web development for scientific applications or databases; ideally proficiency in frameworks such as Django.
• Ability to collaborate with researchers from different fields and at different career stages.
• Willingness to be part of a team to share knowledge and skills.
• Documented ability to communicate science.
• Excellent written and verbal communication skills in English.

Advantageous skills

• Familiarity with TF-DNA interaction models and genomic interpretation tools would be a distinct advantage.
• Track record of developing reproducible computational pipelines, preferably with workflow management systems like Snakemake or Nextflow would be an advantage.
• Ability to containerize applications using Docker or Singularity for better software management and reproducibility.
• Prior experience with genomic databases, especially JASPAR or UniBind, is desirable.

What we offer

• A salary of NOK 575 400 – 646 000 per annum depending on qualifications in position as Postdoctoral Fellow (position code 1352)/Researcher (position code 1109)
• A stimulating research project that will have an impact on the scientific community.
• A role within an ambitious and multi-disciplinary team that combines the strengths of both experimental and computational sciences, aimed at delivering high-impact research.
• Attractive welfare benefits including a generous pension agreement.
• A family-friendly environment in Oslo, known for its high quality of life, rich cultural scene, and abundant opportunities for outdoor activities.

Collaborative Environment

This position offers the unique opportunity to engage with leading experts in the field and to be part of a supportive and dynamic local and international research environment. The collaboration with the groups of Drs. Kundaje and Wasserman provides an enriching cross-institutional experience.