PhD in Toxin Prediction using Machine Learning (m/f/x)

Institution
Faculty of Medicine - Data Science to Toxicology at the Walther Straub Institute
Start date
as soon as possible
Application deadline
31 May 2022
Remuneration group
TV-L E13 (65%)
Contract duration
a structured project for 3-years

As part of our efforts to bring Data Science to Toxicology at the Walther Straub Institute (Medical faculty, LMU - Munich), we are using Natural Language Processing algorithms to predict bacterial toxins. The predictions will be complemented with laboratory experiments designed to confirm the toxic capabilities on eukaryotic cells. During this project we will be working with the TUM research group from Prof. Rost, who will guide us in the development of the predictor and the creation of a Computational Toxicology Summer School. The position is directly dependent on the availability of the funding, and your elegibility for working visa stipulated under German Laws.

Requirements

We are looking for a highly motivated Biologist, Microbiologist, Cell Biologist or Biochemist with a Master in Science, interested in learning and applying Machine Learning algorithms to biological problems as part of the PhD studies. As part of an an international group, the candidate should feel comfortable speaking and writing in English, be open minded, and feel enriched when exposed to cultural differences.

In addition, the PhD candidate should:

  • have laboratory experience, preferably working in sterile conditions and cell culture,
  • have some programming experience, preferably with R or Python,
  • have a strong statistical knowledge,
  • be able to express complex concepts in simple terms,
  • consider Open Science principles essential for a successful and reproducible science and scientific process,
  • enjoy teaching,
  • have a curious and analytical mind.
  • Document every step and process under the FAIR principles for data stipulated by the Open Science initiative.
  • Create, curate and analyze Datasets that will be used for training of Machine Learning Algorithms.
  • Learn and apply Machine Learning algorithms.
  • Actively participate in the design, development and teaching of the Computational Toxicology Summer School.
  • Perform toxicological experiments in a Biosafety level 2 lab on unicellular model organisms and cell culture. There will be no multicellular animal experimentation.

The obligations of the PhD candidate are:

  • Document every step and process under the FAIR principles for data stipulated by the Open Science initiative.
  • Create, curate and analyze Datasets that will be used for training of Machine Learning Algorithms.
  • Learn and apply Machine Learning algorithms.
  • Actively participate in the design, development and teaching of the Computational Toxicology Summer School
  • Perform toxicological experiments in a Biosafety level 2 lab on unicellular model organisms and cell culture. There will be no multicellular animal experimentation.

Benefits

As a young research group, we are offering:

  • A structured project (3-years) combining traditional biological studies with State-of-the-art research in Machine Learning.
  • Working in collaboration with the Bioinformatics group or Prof. Rost from the TUM.
  • Intensive and personalized training in areas of programming and Machine Learning.
  • Salary (65%) based on TV-L E13 and the social benefits guaranteed under German Working laws.

Also possible in a part-time capacity.

People with disabilities who are equally as qualified as other applicants will receive preferential treatment.

Contact

What to send:
If you are interested, please send a Motivational video (no longer than three minutes) or a Motivational letter, together with your signed CV, University certifications, and two references. All written documents have to be merged into one PDF document. If you choose to send the Motivational Video instead of the motivational letter, please send it compressed and not bigger than 10 MB.

The process:
As soon as we confirm the completeness of your application, we will let you know after May 31st, 2022, that the selection process has started and the status of your application. We will then schedule an interview (online or on-site) to get to know you and you can ask all questions you have regarding the position and the group. The final candidate will be chosen before the 1st of July, 2022, in order to start with the contract process. The planned start date is the 1st of September, 2022.

Where to send it:
Please send your application addressed to Dr. Luisa F. Jiménez-Soto before May 31st, 2022.

If you have questions:

If you have questions regarding the project or the application, please feel free to contact Dr. Luisa F. Jiménez-Soto.

Email: l.jimenez@lmu.de

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