Graduate Project Assistant (Diploma/Master)

EURAXESS Ireland; Linz; On-site; EUR 38,000 - 46,000; Part time

Benefits offered by this job

Campus environment

Public transport access

Educational opportunities

Research infrastructure

Sports classes

Job summary

Johannes Kepler University Linz seeks a Graduate Project Assistant to develop and maintain bioinformatics and biostatistics pipelines for spatial transcriptomics and multiplex spatial phenotyping. You will collaborate with LIMICS, the Sorbonne AI center, and SIRIC CURAMUS hubs in Paris, and lead ML/DL approaches for digital pathology.

The role involves handling RNA, protein, and image data, coordinating with wet-lab colleagues, and contributing to teaching and student supervision as part of an

Qualifications

• Completed diploma or master's degree in computer science, life sciences, medicine or related computational field with biomedical focus.
• Strong programming and data analysis skills relevant to bioinformatics and digital pathology.
• Experience with ML/DL for image analysis and omics data integration; GPU-accelerated computing is a plus.

Responsibilities

• Develop and maintain bioinformatics and biostatistics pipelines for spatial transcriptomics and multiplex spatial phenotyping.
• Integrate and analyze RNA, protein and imaging data with QC, normalization and annotation.
• Lead ML/DL approaches for digital pathology including segmentation and phenotyping.
• Collaborate internationally (Linz/Paris) and with clinical AI teams; support data readiness and experimental design.
• Manage HPC workflows for WSI and large spatial datasets; use GPU-accelerated methods as needed.
• Document results and contribute to teaching and supervision of students.

Skills

Programming

Bioinformatics

Machine Learning

Python

GPU computing

Data Visualization

Education

Diploma/Master's degree

Tools

QuPath

Python

GPUs

Job description

Department of Pathology and Molecular Pathology

Organisation/Company Johannes Kepler University Department Department of Pathology and Molecular Pathology Research Field Computer science Medical sciences Researcher Profile First Stage Researcher (R1) Positions PhD Positions Application Deadline 16 Nov 2026 - 23:59 (Europe/Vienna) Country Austria Type of Contract Temporary Job Status Part-time Hours Per Week 30 Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Reference Number 60900-2026-002133 Is the Job related to staff position within a Research Infrastructure? No

Offer Description

The world is changing at an ever-faster pace. At the Johannes Kepler University Linz, we work on technologies and the ideas of tomorrow on a daily basis. At the same time, we educate over 27,000 young people to meet the demands of today’s job market. In short, we are Upper Austria's largest institution for education and research. Are you interested in being a part of shaping the future of Austria's most attractive campus university? We currently have a job opening for a:

Graduate Project Assistant (must hold a Diploma/Master's degree) for a 30-hour/week (part-time), three-year position

Organizational unit:

Department of Pathology and Molecular Pathology

Entry date:

01/07/2027

Job Reference Number:

60900-2026-002133

Job Duties:

• Develop and maintain robust bioinformatics and biostatistics pipelines for spatial transcriptomics and multiplex spatial phenotyping, in collaboration with LIMICS, the Sorbonne Center for AI, and SIRIC CURAMUS hubs in Paris
• Integrate and analyze RNA, protein, and whole-slide imaging data; perform quality control, normalization, cell/tissue-level annotation, and advanced visualization of new data types arising from spatial technologies
• Lead machine learning and deep learning approaches for digital pathology, including segmentation, phenotyping, and feature engineering from segmented tissue compartments; extend existing classifiers and analysis pipelines (e.g., QuPath-based workflows)
• Apply in-situ multi-omics platforms (data side); collaborate with wet-lab colleagues for experimental design and data readiness
• Manage high-performance computing workflows for whole-slide images and large spatial datasets; use GPU-accelerated methods as required by ML/DL pipelines
• Collaborate within an international network with annual on-site meetings (Linz/Paris), weekly virtual lab meetings, and a planned several-month research stay in Paris to deepen in-situ transcriptomics, bioinformatics, and statistics skills
• Document and present results in internal meetings, conferences, and publications; contribute to teaching and co-supervision of students
• Established digital pathology pipelines (e.g., QuPath, python) for multiplex immunofluorescence, segmentation, phenotyping, and spatial neighborhood analyses; machine learning classifiers for tissue compartmentalization already in development
• International collaboration with Sorbonne University teams (CRSA, SIRIC CURAMUS) and dedicated support for bioinformatics/AI pipeline setup and integration
• Close collaboration with the Clinical Research Institute Medical Artificial Intelligence

Your Qualifications:

• The successful candidate must hold a completed diploma or master's degree in computer science, life sciences, medicine, or related fields (or closely aligned computational fields with a strong interest in biomedical applications)
• Strong programming skills and computational expertise aligned with bioinformatics, statistics, and computational pathology for spatial omics and digital pathology data processing
• Experience with machine learning/deep learning for image analysis and/or omics integration; familiarity with pipeline development and GPU-accelerated computing is an advantage
• Ability to collaborate with interdisciplinary teams and to communicate effectively in English; German B1 or willingness to learn German is expected (English B2)
• Independent, reliable, and team-oriented working style

What We Offer:

• On the basis of full-time employment (40 hours/week) the minimum salary in accordance with the collective agreement is € 3,776.10 gross per month (14 x per year, CA Job Grade: B1)
• Attractive campus environment with good public transportation connections
• Attractive continual educational opportunities
• State-of-the-art research infrastructure
• Dynamic research environment
• Exercise and sports classes (USI)
• ...and much more

The Johannes Kepler University wishes to increase the proportion of academic female faculty and, for this reason, especially welcomes applications by qualified women. If applicants are equally qualified, a woman will be given preference for this position. The university welcomes applications from qualified applicants with disabilities. These applications will be given special consideration.