PhD Fellowship in machine learning for protein function and foundation modeling in biology

Job title:

PhD Fellowship in machine learning for protein function and foundation modeling in biology

Company:

Københavns Universitet

Job description

The Machine Learning for LIfe Science (MLLS) Center invites applications for a PhD Fellow position starting in September 2025, or as soon as possible after that. The position is within the scope of MLLS and the CAZAI projects, both of which are funded by the Novo Nordisk Foundation Data Science Initiative. The Department of Biology and the Pioneer Centre for AI, Faculty of Science at University of Copenhagen will host the PhD candidate.About the MLLS CenterThe Machine Learning for Life Science Center is currently funded by the Novo Nordisk Foundation until the end of 2026. The principal investigators are from the Department of Computer Science and Biology, University of Copenhagen and DTU Compute, Technical University of Denmark and all are working on machine learning methodology inspired by applications in life and natural sciences. The Pioneer Centre for Artificial Intelligence at University of Copenhagen serves as host for the Center’s activities.For more information on the Center’s activities and researchers, please see .About the CAZAI projectCazyme specificity prediction using AI (CAZAI) is a collaborative research project headed by professor Bernard Henrissat, DTU Bioengineering, Technical University of Denmark (DTU) with Co-PIs, professor Ole Winther, Department of Biology, University of Copenhagen (UCPH) and Research engineer Renaud Vincentelli, Aix-Marseille University. CAZAI is funded by the Novo Nordisk Foundation and runs until the end of 2027. The project aims at improving the functional characterization of carbohydrate-active enzymes through predictive machine learning and experimental data collection and validation.The advertised position will have Ole Winther as main supervisor.The PhD projectThe PhD position aims at * improving models for detailed functional predictions for protein in general and carbohydrate-active enzymes in particular and

• developing foundational machine learning models for understanding the interplay between genomics, transcription and disease.

Who are we looking for?The ideal candidate has a background in machine learning, with an MSc preferably in machine learning, bioinformatics, computational biology, or a related field. The candidate has a strong motivation for doing multidisciplinary research as well as for developing machine learning models to advance the state of the art in biological sequence analysis.The projects will include advancing models for sequence-based predictions in general, and for carbohydrate-active enzymes. Using large-scale public datasets, projects will be conducted to train foundational models jointly at DNA and RNA incorporating pertubations with the aim at understanding mechanisms relevant for human disease.Furthermore, the projects will encompass thorough data curation pipelines based on several biological databases, executing various systematic analyses of biological data, and performing experiments related to finetuning of large language models trained on biological sequences.To qualify for this position, you should have a number of the following qualifications:

• Curious mindset with a strong interest in the research themes of MLLS and CAZAI.
• Knowledge and experience in working with protein language models.
• Strong programming skills in Python, with a particular focus on experience in PyTorch.
• Experience with carrying out a bioinformatics workflow pipeline, including thorough data curation, analysis and modeling.
• Experience with Linux, including working in high-performance computing environments.
• Strong background in biology, including knowledge of phylogeny and taxonomy.
• Analytical mindset and ability to work systematically.
• Great ability to work both independently as well as in collaborations.
• Excellent English language skills.
• University-level teaching experience is a plus.

The PhD programmeThe PhD programme offered is three years of full-time study within the framework of (5+3 scheme).Qualifications needed: To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. Computer science, Machine learning, Bioinformatics or other related technical disciplines. For information of eligibility of completed programmes, see and .Terms of employment in the regular programmeEmployment as PhD fellow is full time and for maximum 3 years.Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.The terms of employment and salary are in accordance with the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State (AC). The position is covered by the Protocol on Job Structure.Responsibilities and tasks in the PhD programme● Carry through an independent research project under supervision● Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE● Participate in active research environments, including a stay at another research institution, preferably abroad● Teaching and knowledge dissemination activities● Write scientific papers aimed at high-impact journals● Write and defend a PhD thesis on the basis of your projectWe are looking for the following qualifications:● Professional qualifications relevant to the PhD project● Relevant work experience● Relevant publications● Other relevant professional activities● Curious mind-set with a strong interest in the research themes of MLLS and CAZAI● Excellent English language skillsApplication and Assessment ProcedureYour application, including all attachments, must be in English and submitted electronically by clicking APPLY NOW below.Please include: * A statement describing your research interests, experience and background, and your motivation for applying for a PhD position at the Department of Biology (maximum two pages, text, figures and references included).

• Curriculum vitae including information about your education, experience, any publications, language skills and other skills relevant for the position
• Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If the education is not yet completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
• Publication list (if possible)
• Reference letters (if available)

Application deadline:The deadline for applications is 15 June 2025, 23:59 GMT +1.We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.The further processAfter the deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified whether you will be passed for assessment.The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above-mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at .Interviews with selected candidates are expected to be held in July 2025.QuestionsFor specific information, please contact Ole Winther ( ).General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: .The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri forskning på højt internationalt niveau. Vi søger svar og løsninger på fælles problemer og gør ny viden tilgængelig og nyttig for andre.

Expected salary

Location

København

Job date

Wed, 21 May 2025 05:26:59 GMT

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