PhD-Position; f​/m​/d

The Institute of Pathology / LaBo[o]ratory of Nephropathology is offering a

Operational area: Institute of Pathology / LaBo[o]ratory of Nephropathology
Working hours: 75% of the collectively agreed full-time working hours (currently 38.5 hours per week)
Duration/Term of employment: Initially limited till 30.09.2029, with option of prolongation until the completion of the doctoral degree
Start date: as soon as possible
Remuneration/Rates: EG 13 (TV-L)

Project

Title:

Dissecting immune cell crosstalk in autoimmune kidney diseases with spatial transcriptomics and pathomics. Institute for Pathology, RWTH Aachen

Within this project the PhD candidate will interrogate immune cell crosstalk and crescent formation in patients with autoimmune kidney disease (including IgA nephropathy, ANCA-glomerulonephritis and others). The PhD candidate will learn to train and deploy histology segmentation models as part of the Aachen Digital Pathology group, as well as the downstream analysis of morphometric features in conjuncture with spatial transcriptomics.

This PhD-Program is meant to built a new generation of scientists that are rigorously trained in the development and application of cutting-edge computational tools to generate digital biomarkers with translational clinical impact. This combined skillset will enable the candidate to excel in their further academic or industry career after concluding the PhD training.

The PhD-Project is embedded within the section of Translational Nephropathology at the Institute of Pathology, offering a comprehensive training programs for PhD candidates, peer-to-peer mentoring, lectures and lab meetings on translational kidney research, as well as possibilities for networking and presentations at scientific meetings. We are an interdisciplinary and international team of scientists and clinicians with a long-standing focus and expertise in developing novel methods for digital pathology, advanced image analysis and deep learning.

Our hardware equipment comprises high-end computational infrastructure, with several GPUs (NVIDIA DGX A100), CPU clusters and storage systems.

Tasks

• Development of a pathomics model for H&E- and PAS-stained histological slides of autoimmune kidney diseases
• Application and refinement of techniques for joint analysis of pathomics and spatial transcriptomics
• Implementation of biostatistical and machine learning models for predicting clinical outcomes using joint biomarkers
• Writing scientific publications and presentation of scientific data at medical conferences

Your profile

We are looking for a highly motivated and curious PhD candidate who is eager to learn and apply new computational methods, takes ownership of a project, and drives it forward with a structured, reliable working style. Strong communication skills in English (Lecel C1) and enthusiasm for interdisciplinary teamwork are highly valued.

• Applicants should have a master's degree in biology, medicine, or a related field (e.g. engineering, molecular medicine, physics)
• Interested in working at the intersection of computational pathology and multi-omics. Ideally, applicants should have prior experience in either spatial transcriptomics or computer vision, ideally computational pathology approaches
• Development of a pathomics model for H&E- and PAS-stained histological slides of autoimmune kidney diseases
• Application and refinement of techniques for joint analysis of pathomics and spatial transcriptomics
• Implementation of biostatistical and machine learning models for predicting clinical outcomes using joint biomarkers
• Writing scientific publications…