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Computational Genomics Scientist / Bioinformaticion (d/w/m) - Axelios I / SbX & Spatial Diagnostics

Charite Kampagne Discovery 3
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Work time
full-time

Employment period
limited

Application deadline
15.07.2026

Deployment location Charité
BIH Berlin Mitte; Campus Virchow-Klinikum, Wedding

Jobcode
7725

Salary group
E14

 

Unternehmensbeschreibung

The Berlin Institute of Health at Charité (BIH) is dedicated to biomedical translation. Its mission is to translate research findings into personalized prevention, diagnostics, and therapies to benefit patients and provide the scientific community with effective tools. With approximately 750 employees, the BIH specializes in translational method development, precision medicine, regenerative therapies, and biomedical data science. Closely integrated with Charité, the BIH promotes excellent research and facilitates the accelerated transfer of new discoveries into clinical practice through its supporting platforms and programs. Through these efforts, the BIH builds strong partnerships and fosters innovation-driven medicine in both national and international contexts.

The Berlin Institute of Health at Charité is seeking a highly qualified Bioinformatician / Computational Genomics Scientist to join the Spatial Diagnostics Platform (led by Dr. Dr. René Hägerling and Dr. Oliver Klein) at the earliest possible date. The position is full-time (38.5 hours/week) and fixed-term until 31 December 2029.

The Spatial Diagnostics Platform integrates 3D histopathology, spatially guided genomics, proteomics/glycomics, and AI-driven data integration to develop innovative approaches for precision diagnostics, companion diagnostics, and translational oncology research.

This is a unique key position offering the opportunity to help establish one of the first university medical implementations of the Axelios-I technology and to integrate it into a clinically relevant, automated multi-omics analysis pipeline. The role goes far beyond routine bioinformatics support: we are looking for a scientist who can combine emerging sequencing technologies, reproducible computational analysis, and clinically relevant translational research questions at the highest level.

The position is embedded within the BIH/Charité ecosystem, providing extensive opportunities for collaboration with experts in human genetics, pathology, oncology, the Core Unit Bioinformatics, IT, imaging, proteomics, and other translational partners. In addition, the role involves close collaboration with industrial partners in the fields of sequencing technologies, laboratory automation, data analysis, and clinical translation

Das erwartet Sie

  • Establishment, operation, and continuous development of the Axelios-I sequencing platform within the Spatial Diagnostics Platform, including standardized data processing, quality control, and result reporting.
  • Development and maintenance of reproducible analysis pipelines for whole-genome sequencing (WGS) data based on SbX and established sequencing technologies—from raw or unaligned sequencing data through alignment, variant calling, and variant annotation to structured delivery of analytical results.
  • Analysis of next-generation sequencing (NGS) data for research and clinically oriented applications in human genetics and cancer genetics, with a particular focus on whole-genome sequencing (WGS), FFPE samples, liquid biopsies, DNA methylation data, structural variants, mosaic disorders, and low-allele-frequency variants.
  • Analysis of next-generation sequencing (NGS) data for research and clinically oriented applications in human genetics and cancer genetics, with a particular focus on whole-genome sequencing (WGS), FFPE samples, liquid biopsies, DNA methylation data, structural variants, mosaic disorders, and low-allele-frequency variants.
  • Development, automation, and validation of bioinformatics workflows for data quality control, alignment, variant calling, annotation, data export, reporting, and reanalysis of failed or problematic samples; active participation in root-cause analysis and continuous process improvement.
  • Definition, implementation, and monitoring of quality metrics for sequencing data and variant analyses, including sample identity verification, data quality assessment, sequencing coverage, artifact detection, traceability, and comprehensive documentation.
    Integration of genomic data with clinical, histopathological, and spatial multi-omics datasets to establish spatially guided sequencing workflows and support multimodal clinical decision-making.
  • Management and quality assurance of data flows between the platform, laboratory information and data management systems, collaborating partners, and centralized computational infrastructures; automation of data import, export, archiving, and quality assurance reporting.
  • Close collaboration with partners across the BIH/Charité ecosystem as well as with industrial collaborators in the areas of sequencing technologies, workflow integration, laboratory automation, benchmarking, and translational validation.
  • Scientific development of the platform, including contributions to peer-reviewed publications, third-party funded research projects, national and international collaborations, and the supervision and mentoring of students, doctoral researchers, and visiting scientists.

Das bringen Sie mit

  • Master's degree (or equivalent) in Bioinformatics, Computational Biology, Genomics, Medical Informatics, Data Science, or a related discipline with an excellent academic record; a PhD is advantageous.
  • Several years of experience in next-generation sequencing (NGS) data analysis, ideally including whole-genome sequencing (WGS), structural variant analysis, cancer genomics, human genetics, liquid biopsy, FFPE samples, DNA methylation, and low-allele-frequency variant analysis.
  • In-depth understanding of sequencing data processing and analysis, including raw data quality control, alignment, variant calling, annotation, coverage and uniformity assessment, sample identity verification, artifact and error detection, reanalysis, and preparation of analytical reports.
  • Proven experience with reproducible bioinformatics analyses, workflow management, and tool orchestration, including hands-on expertise with workflow management systems such as Nextflow or Snakemake. Experience with workflow validation, quality assurance, and data management is essential.
  • Excellent programming skills, particularly in Python and Bash, together with solid proficiency in R for statistical analysis, data visualization, and exploratory data analysis. Experience with Git, well-documented code, code review practices, and the development of tested, maintainable analysis pipelines is expected.
  • Experience working in Linux environments, including high-performance computing (HPC) clusters and workload managers such as SLURM. Experience with container technologies such as Docker and Singularity/Apptainer is considered an advantage.
  • Experience with accelerated genomics platforms or clinical-grade bioinformatics environments (e.g., DRAGEN, Parabricks, or comparable solutions) is desirable but not required.
  • A strong interest in emerging sequencing technologies, particularly SbX/Axelios I, and the ability to rapidly translate novel technologies into robust, scalable, and well-documented bioinformatics workflows.
  • A strong commitment to scientific quality, with the ability to work independently, apply a structured and systematic approach, and transform complex clinical and scientific questions into reliable computational solutions.
  • Excellent communication skills in both German and English, with enthusiasm for interdisciplinary collaboration across clinical departments, laboratory teams, bioinformatics, IT, pathology, imaging, multi-omics research groups, industrial partners, and academic collaborators.

Das bieten wir Ihnen

  • A unique leadership opportunity to help establish a new, internationally visible Spatial Diagnostics infrastructure at the Berlin Institute of Health (BIH) at Charité.
  • The opportunity to work on one of the first university medical implementations of the Axelios-I technology and to shape its bioinformatics applications from the very beginning.
  • Cutting-edge research and technology development at the interface of genomics, 3D histopathology, spatial and multi-omics technologies, artificial intelligence, laboratory automation, and clinical translation.
  • Extensive opportunities for interdisciplinary collaboration across the BIH/Charité ecosystem, together with close partnerships with leading industrial collaborators.
  • The opportunity to contribute to clinically relevant applications in oncology, human genetics, pathology, dermatology, and related disciplines, with strong integration into translational research and the long-term prospect of advancing patient-centered precision diagnostics.
  • Pay group E14 TVöD VKA-K. The classification is based on qualifications, the respective experience level is calculated on the basis of professional experience. The annual salary (gross) is stated for a full-time position without special or additional payments. The collective agreement can be found here.
  • Additional benefits customary in the public sector (including annual special payment, company pension scheme (VBL), capital-forming benefits)
  • Flexible working hours and the option of working remote 
    30 vacation days per year (with a five-day week)
    Various support offers to balance work and family life (childcare, cooperation with voiio)
  • Training and further education opportunities
  • Mobile citizens' office on site
  • Corporate benefits (travel, leisure, shopping, etc.), Wellhub, JobRad
  • Very easily accessible and attractive workplace at the Rahel Hirsch Center for Translational Medicine, Luisenstr. 65, 10117 Berlin and CVK Förster Str. 15, 13353 Berlin

Wir leben Vielfalt!

We welcome applications from people with diverse backgrounds, regardless of gender, nationality, ethnic and social origin, religion and ideology, disability, age, sexual orientation and identity. Applications from women are expressly encouraged. Severely disabled and equivalent applicants will be given special consideration if they have the same qualifications and suitability.
We believe that diverse teams representing a wide range of experiences, perspectives and backgrounds enrich our research and work.

Please submit your application via our online application form with a letter of motivation, curriculum vitae (without photo, without age statement and without information about your marital status) and other relevant attachments (such as employer references, degree certificates, etc.).

Note: If you have a foreign degree, please submit proof of recognition of your degree in Germany with your application. The proof can be obtained via the anabin database. Please note that it may be necessary to obtain a certificate assessment from the ZAB. You can find more information here.

Proof of measles immunity / measles vaccination is a prerequisite for employment for those born after 1970.

You can find more information about BIH here.

Application

 

Everyone is welcome at the Charité, regardless of age, religion, gender, gender identity, sexual orientation, nationality, disability, ethnic or social background. We are committed to equal opportunities and inclusion.

For data protection reasons, we only accept applications via our application portal. The contact details provided below are intended solely for inquiries.

Apply now

Ansprechperson

For technical or role-related questions regarding the job posting, please contact Mr Dr. Johannes Hartl (Email: johannes.hartl@bih-charite.de).

For questions regarding the application process, please contact Denise Bornschein by email at jobs@bih-charite.de.

More information

Data protection information

The Charité would like to point out that personal data is stored and processed at various locations at the Charité premises (e.g. specialty department, personnel representatives, HR department) as part of and for the purposes of the application process. Furthermore, the data may be transferred or processed within the group and to external bodies (e.g. authorities) to protect legitimate interests. By submitting your application, you agree to our data protection policy and terms of use for application procedures, which you can find here.

Additional information

Charité – Universitätsmedizin Berlin makes its personnel decisions based on suitability, ability and professional performance. The Charité aims to increase the proportion of women in management positions and therefore strongly encourages women to apply. Women with equivalent qualifications will be given priority within the scope of legal possibilities. Applications from people with a migration background who meet the recruitment requirements are expressly encouraged. Severely disabled applicants with equal qualifications will be given preference. A police good-conduct certificate, in some cases an extended good-conduct certificate, is required at the time of recruitment. Unfortunately, application documents can be returned only if a sufficiently stamped envelope is enclosed. Any incurred travel expenses cannot be reimbursed.