PhD and PostDoc Positions
Current PostDoc or PhDpositon
Quantum Bioinformatics (Post-doc or Ph.D. position)
Description
Join our new Quantum Bioinformatics team at Cosy.Bio (cosy.bio) in lovely Hamburg, Germany! We seek an Algorithm Engineer to experiment with the power of quantum computing for combinatorial optimization problem solving in Systems Medicine.
Start date: As soon as possible.
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Qualifications
Key Skills and Qualifications:
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Mathematical and Algorithmic Expertise: Strong foundation in mathematics, with experience in algorithm development and optimization, particularly for data analysis in biomedical contexts.
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Interest in Quantum Computing: No prior experience required, but a strong interest in learning and applying quantum computing principles to biomedical data analysis.
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Programming Skills: Proficiency in programming languages like Python or R, with experience in data analysis and algorithm implementation.
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Biomedical Data Analysis: Familiarity with biomedical data structures and computational techniques for extracting and analyzing complex datasets.
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Collaboration Skills: Ability to work effectively in interdisciplinary teams.
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Communication Skills: Clear written and verbal communication for both technical and non-technical audiences.
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Eagerness to Learn: Willingness to engage with new technologies, particularly quantum computing, during the PhD.
Requirements:
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Master's degree (or equivalent) in Mathematics, Computer Science, Physics, or a related field.
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Strong background in algorithm development, optimization, and mathematical modeling.
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Interest in quantum computing and its applications, but no prior experience required.
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Proficiency in relevant programming languages (e.g., Python, R) and experience with data analysis or computational models.
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Strong analytical and problem-solving skills, with the ability to work independently and as part of a team.
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Excellent communication and interpersonal skills, with the ability to collaborate with researchers from diverse backgrounds.
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Fluency in English, with the ability to communicate technical concepts to both technical and non-technical audiences.
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Start date
As soon as possible
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How to Apply
Please email Dr. Mhaned Oubounyt with your CV : mhaned.oubounyt@uni-hamburg.de
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Contact
Current PostDoc positon
Postdoctoral Researcher for LLMs in Bioinformatics in Hamburg, Germany
The Institute for Computational Systems Biology (CoSy.Bio) headed by Prof. Jan Baumbach at the University of Hamburg is pioneering the integration of cutting-edge AI technologies into bioinformatics. We're on a mission to fundamentally change how biomedical research is conducted.
We're seeking an exceptional international postdoctoral researcher to spearhead the development of transformative LLM-powered solutions that will reshape the landscape of biomedical data processing. Your work will be at the forefront of making advanced biomedical analyses accessible to researchers worldwide.
Key Focus Areas:
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Full Stack Development
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Large Language Models (LLMs) Implementation
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LLM Applications in Bioinformatics
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Technical Expertise Required:
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Advanced proficiency in full stack development
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In-depth knowledge of LLMs and their practical applications
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Experience in developing and deploying LLM-based solutions
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Familiarity with bioinformatics tools and omics data analysis (preferred)
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Responsibilities:
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Design and develop full stack applications integrating LLMs for bioinformatics use cases
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Implement and optimize LLM-based solutions for biomedical data interpretation
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Create user-friendly interfaces that make complex bioinformatics tools accessible
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Develop APIs for seamless integration of LLM capabilities into existing bioinformatics workflows
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Collaborate with interdisciplinary teams to push the boundaries of AI in bioinformatics
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Contribute to high-impact publications and present at international conferences
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Interested?
Please send us an expression of interest by email including your CV, a detailed description of your full stack and AI project experiences, and contact information for 2-3 references: Dr. Fernando Delgado Chaves <Fernando.miguel.delgado-chaves@uni-hamburg.de> and Prof. Jan Baumbach <jan.baumbach@uni-hamburg.de>
Looking forward to reading your mail!
Current PhD project opportunity
LPAMS - Large Peptide Aggregation Models for Structural Modelling of Protein Aggregation
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Supervisors: Prof. Meytal Landau (DESY), Prof. Jan Baumbach (UHH)
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Protein misfolding diseases, e.g., Alzheimer’s or Parkinson’s, are accompanied by aggregates of peptides (e.g., amyloid fibrils), which acquire varied three-dimensional (3D) structural configurations. Such fibrils are not limited to human diseases but are also found across the tree of life, perhaps originating in the prebiotic era. Different 3D structural configurations of fibrils correlate with distinct biological activities. For example, the cross-α fibril structure of the peptide uperin 3.5 (secreted by Australian toadlet) has a protective role against bacterial infections. Understanding the rules that translate the sequence of a peptide to its corresponding 3D fibril structure has applications in, e.g., developing drugs for protein misfolding diseases or bacterial infections. One way to learn such rules is to make associations between the 3D structures of fibrils and their constituting peptides. However, the number of 3D structures of fibrils enabling such associations is limited. Wet lab experiments to produce 3D fibril structures are time-consuming and costly. In this project, we will build upon the recent artificial intelligence (AI)-based protein structure predictions (e.g., AlphaFold) as foundation models to develop a fine-tuned AI model for more accurate 3D fibril structure prediction, i.e., a Large Peptide Aggregation Model. The known/predicted 3D fibril structures will be used to learn an association between their functional properties and the sequence characteristics of their constituting peptides, which will then be validated experimentally.
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Requirements:
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Master's degree in computer science, software engineering, or related fields
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advanced programming skills in any language
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experience in computer science or bioinformatics, preferably with prior knowledge in life science systems / biochemistry
Position:
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University of Hamburg
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100% EGR. 13 (TV-L) position for three years, pending approval of funding
The University of Hamburg offers flexible working hours and work-life balance opportunities.
The Free and Hanseatic City of Hamburg promotes equal opportunity. As women are currently underrepresented in this job category at University of Hamburg according to the evaluation conducted under the Hamburg act on gender equality (Hamburgisches Gleichstellungsgesetz, HambGleiG), we encourage women to apply for this position. Equally qualified and suitable female applicants will receive preference.
Severely disabled and disabled applicants with the same status will receive preference over equally qualified non-disabled applicants.
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Please apply here: The Helmholtz Graduate School for the Structure of Matter (dashh.org)
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For inquiries, please email jan.baumbach[a.t_))uni-hamburg.de.
Are you passionate about delving into the complexities of biological systems using cutting-edge computational methods? CoSy.Bio offers exciting PhD and PostDoc positions for motivated individuals who are eager to contribute to groundbreaking research in computational systems biology.
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As a PhD candidate at CoSy.Bio, you will have the opportunity to work alongside leading experts in the field, exploring diverse research avenues ranging from network and systems medicine to privacy-preserving artificial intelligence tools for precision medicine. You will be encouraged to pursue innovative research projects, develop novel methodologies, and collaborate with peers and mentors to advance scientific knowledge in systems biology.
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As a postdoc at CoSy.Bio, you will have the opportunity to lead and collaborate on cutting-edge research projects, working closely with our team of experts to address key challenges in systems biology. Whether your expertise lies in artificial intelligence, network analysis, drug repurposing, or privacy-preserving methodologies, we welcome applications from candidates with diverse backgrounds and research interests.
Why join CoSy.Bio as PhD or PostDoc?
Are you Interested?
Send the following information to management-cosybio[a.t_))lists.uni-hamburg.de:
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your CV,
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a letter of motivation including your research interests,
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a list of your publications, and
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the contact details of preferably three researchers that agreed to provide letters of reference.
Please send it to us as a single PDF.
Postdoctoral Fellowships
Humboldt Research Fellowship
Through the Humboldt Research Fellowship, the Alexander von Humboldt Foundation sponsors researchers with above-average qualifications from across the globe. As a fellow, you will benefit from individual support from the Humboldt Foundation and our diverse sponsorship portfolio. We are happy to host you here in Hamburg, let us know.
In 2023, Professor Jan Baumbach was appointed a Humboldt Scout through the Henriette Herz-Scouting-Program.
Marie Skłodowska-Curie Actions
The Postdoctoral Fellowships action targets researchers holding a PhD who wish to carry out their research activities abroad, acquire new skills and develop their careers. We are happy to be our host organisation when you apply.