COLCOM - Postdoctoral Researcher: Genomic Language Models for Bacterial Genomes

Location: University Mohammed VI Polytechnic, College of Computing, Bioinformatics Laboratory, Ben Guerir, Morocco.

Duration:  2 years

About the Lab/Institution:

The Bioinformatics Laboratory conducts research in the fields of bioinformatics, computational biology and computational chemistry and serves the agricultural, environmental and health sectors. The lab also provides bioinformatics consulting and data management services to UM6P researchers and their collaborators. UM6P has state of the art NGS sequencers and mass spectrometry and the largest HPC (High Performance Computing) cluster in Africa. The laboratory aims to leverage these resources to address bioinformatics needs internally and at the African level and to develop innovative research and training programs. For more information about the laboratory, you can visit https://bioinformatics.um6p.ma/ 

Project Description:

We are seeking a highly motivated and talented postdoctoral researcher to join our team to develop a novel GPT-like system for bacterial genomes using cutting-edge genomic language models. This project aims to adapt and extend transformer-based architectures to create a powerful tool for understanding and predicting bacterial genomic sequences. The successful candidate will play a key role in developing and optimizing these models, applying them to diverse bacterial use cases, and contributing to the development of software tools for the broader research community.

Responsibilities:

• Develop and implement transformer-based genomic language models for bacterial genome analysis.
• Train and evaluate models on large-scale bacterial genomic datasets.
• Apply the developed models to address specific research questions, such as gene function prediction, antibiotic resistance analysis, and evolutionary studies.
• Analyze and interpret results, and prepare manuscripts for publication in peer-reviewed journals.
• Collaborate with other researchers within the lab and external collaborators.
• Maintain accurate and organized records of research activities.

Qualifications:

• Ph.D. in Bioinformatics, Computational Biology, Computer Science, Genomics, or a related field.
• Strong background in machine learning, particularly deep learning and natural language processing.
• Experience with transformer-based architectures (e.g., BERT, GPT) is highly desirable.
• Proficiency in Python and relevant machine learning libraries (e.g., TensorFlow, PyTorch).
• Experience with bioinformatics tools and genomic data analysis.
• Strong programming and data analysis skills.
• Excellent communication and writing skills.
• Ability to work independently and as part of a team.

Preferred Qualifications:

• Experience working with bacterial genomic data.
• Knowledge of bacterial genetics and evolution.
• Experience developing software tools for bioinformatics applications.
• Experience with cloud computing platforms.

To Apply:

Please submit the following materials 

• Cover letter outlining your research interests and experience.
• Curriculum vitae (CV) including a list of publications.
• A brief research statement describing your past research and future interests.
• Contact information for three professional references.