Your Job:
DNA replication is a biological process of producing two identical copies of DNA from one original DNA molecule. It occurs in all living organisms and plays the most essential role in biological inheritance. The process is initiated from multiple genomic locations which are still poorly understood even for buddying yeast. In this project one is expected to work on the implementation of the existing language models, e.g. DNABERT in order to predict locations of budding yeast replication origins, thereby avoiding sophisticated feature extraction which are the current state of the art. Your tasks in detail:
- Preprocessing data extracted from the yeast origin databases (OriDB, SGD, deORI)
- Determining the appropriately pre-trained language model to work with the data (DNABERT)
- Fine-tuning the model
- Assessing explainability of the model primarily by extracting attention weights
- Extending the model beyond budding yeast application
Your Profile:
- Completed Bachelor Degree in the field of computer science, biology, physics, mathematics or a comparable course of study
- Completed qualification to enroll for your Master thesis
- Programming skills in Python required (Numpy, Pandas, Scikit-learn, preferably Pytorch/Tensorflow)
- Familiarity with statistical and machine learning concepts
- Interest in working with genomic data
- Willingness to learn and ability to think outside of the box
- Independent and responsible way of working
Our Offer:
We work on the very latest issues that impact our society and are offering you the chance to actively help in shaping the change! We support you in your work with:
- An interesting and biologically relevant topic for your thesis with possibilities of expanding and generalizing it
- Ideal conditions for gaining practical experience alongside your studies
- An interdisciplinary collaboration on projects in an international, committed and collegial team
- Excellent technical equipment and the newest technology
- Qualified support through your scientific colleagues
- The chance to independently prepare and work on your tasks
- A large research campus with green spaces, offering the best possible means for networking with colleagues and pursuing sports alongside work
- A temporary position for 6 months
- Flexible work (location) arrangements, e.g. remote work
- Flexible working hours as well as a reasonable remuneration
In addition to exciting tasks and a collaborative working atmosphere at Jülich, we have a lot more to offer: https://go.fzj.de/benefits
We welcome applications from people with diverse backgrounds, e.g. in terms of age, gender, disability, sexual orientation / identity, and social, ethnic and religious origin. A diverse and inclusive working environment with equal opportunities in which everyone can realize their potential is important to us.