Bioinformatics Data Scientist (m/f/d) - Virtual Patient Engine (VPE)

Join to apply for the Bioinformatics Data Scientist (m/f/d) - Virtual Patient Engine (VPE) role at BioMed X Institute

Join to apply for the Bioinformatics Data Scientist (m/f/d) - Virtual Patient Engine (VPE) role at BioMed X Institute

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About BioMed X

BioMed X is an independent research institute located on the campus of the University of Heidelberg in Germany, New Haven in Connecticut, XSeed Labs in Ridgefield, Connecticut, and a world-wide network of partner locations. Together with our partners, we identify big biomedical research challenges and provide creative solutions by combining global crowdsourcing with local incubation of the world’s brightest early-career research talents. Each of the highly diverse research teams at BioMed X have access to state-of-the-art research infrastructure and is continuously guided by experienced mentors from academia and industry. At BioMed X, we combine the best of two worlds - academia and industry - and enable breakthrough innovation by making biomedical research more efficient, more agile, and more fun.

About Team VPE

The goal of team ‘Next Generation Virtual Patient Engine for Clinical Translation of Drug Candidates’ (VPE) is to develop a versatile computational platform that can predict the efficacy of first- or best-in-class drug candidates in virtual patient populations at an unprecedented accuracy, thereby addressing one of the most critical bottlenecks of the pharmaceutical industry today: a 90% failure rate of new drug candidates during clinical development. In partnership with Sanofi the VPE team will develop innovative artificial intelligence methods to build the virtual patient platform. As a proof-of-concept, the initial platform will focus on chronic immune-mediated diseases such as atopic dermatitis (AD) and inflammatory bowel disease (IBD), where new medication that can address patient heterogeneity is needed.

The Position

We are looking for a talented and curious Bioinformatics Data Scientist to join our team, bringing fresh perspectives and advanced expertise to fuel innovative thinking and scientific excellence. This position is for you if you are passionate about transforming biomedical data into actionable knowledge within a collaborative environment.

The ideal candidate will have:

• PhD or equivalent degree in bioinformatics, computational biology, or computer science.
• You will leverage your advanced computational skills and deep biological knowledge to tackle complex challenges in digital twin technologies.
• You will be part of a dynamic team driving discovery through cutting-edge data science, including the development and application of artificial intelligence, foundation models, and agentic AI systems.

Required skills

• Strong background in Python for statistical analysis, data manipulation, and visualization.
• Experience with developing and implementing scalable, reproducible pipelines for processing and analyzing high-throughput sequencing data (e.g., RNA-seq, scRNA-seq, scATAC-seq, etc.) using workflow management systems such as Nextflow and Snakemake.
• Hands-on experience in handling, processing, integrating, and analyzing large-scale, heterogeneous datasets—including multi-omics data and real-world data (RWD) such as electronic health records (EHRs), and clinical trial data—in the context of biomedical research.
• Familiarity with biological network analysis, pathway enrichment tools, and knowledge graphs.
• Experience in SQL and/or NoSQL databases for managing and querying large-scale datasets.
• Working knowledge of foundation models in life sciences (e.g., ESM2, AlphaFold, Cell2Sentence, Geneformer) and practical experience in incorporating these models into computational workflows.
• Proficiency in using version control with Git, Docker containers and Anaconda; in using code management best practices such as unit testing, linting, and documentation; orchestrating machine learning experiments using cloud computing environments; and using continuous integration and deployment (CI/CD) frameworks.
• Ability to work as part of an interdisciplinary team but also independently.
• Strong problem-solving skills and scientific curiosity.
• Excellent communication, organizational, and interpersonal skills.

Additional skills, good to have

• Experience in applying artificial intelligence methods to biomedical data using AI/ML libraries such as PyTorch and PyTorch Lightning.
• Experience in building serverless data pipelines with AWS EMR, and integrating with other AWS services (e.g. S3).
• Experience working with or developing agentic AI systems is a plus.

What we offer

• The post is offered for a limited term until June 30th, 2028.
• Flexible working hours and hybrid working location.
• Access to a vast scientific network. The team will be working closely with our industry partner Sanofi, including various high profile academic partners, and industry-academia consortiums.
• Opportunities to publish in top academic journals and present at top academic and industry conferences.
• Training in how scientific teams take a high risk and high reward idea from development to early stage productization.
• International, diverse, and positive work atmosphere that fosters personal and professional growth.
• Job ticket, complimentary fresh fruit, soft drinks and chocolate, team recognition events, complimentary Coursera courses, etc.

The position is sponsored by Sanofi and is immediately available.

Please submit your application with the following documents to the attention of Dr. Gurdeep Singh by July 15th 2025 via our online application system https://career.bio.mx/job/2025-BMX-J01:

• Curriculum Vitae outlining scientific interests, research achievements, and a record of publications.
• 2 references will be asked for after submission as a part of the interview process.

At BioMed X we embrace diversity as we consider it the source of innovation. We are committed to equal opportunity in the terms and conditions of employment for all employees and job applicants without regard to race, color, religion, ideology, sex, sexual orientation, age, gender identity or gender expression, national origin, or disability.

To read about us, please visit: https://bmedx.com

Seniority level

• Seniority level

  Mid-Senior level

Employment type

• Employment type

  Full-time

Job function

• Job function

  Research and Science

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