PhD Student (m/f/d) / 12175 / Department of Hematology and Stem Cell Transplantation

PhD Student (m/f/d)
(Entgeltgruppe: EG 13 TV-L)
Einsatzbereich: Department of Hematology and Stem Cell Transplantation
Stellen ID: 12175
Eintritt: Next possible date
Umfang: Teilzeit / 25,025 h
Vertragsart: Befristet
Befristung: 36 months from the start of the project

Ihre Aufgaben

• As part of the project, the candidate will investigate the interplay between cancer cells and their tumor immune microenvironment using longitudinally collected DNA and (single nucleus) RNA sequencing data. This work will be performed in close collaboration with the Institute for Artificial Intelligence in Medicine (IKIM), which provides state-of the art computational infrastructure.
• You will contribute to: Computational analysis of large-scale genomic datasets
• Application and development of computational tools for mutational signature analyses
• Processing of raw sequencing data (particularly Whole Genome Sequencing and single nucleus RNA sequencing) via established computational pipelines
• Scientific publications
• Planning, perfoming and documenting of bioinformatic laboratory work
• Presentation and discussion of results at regular internal and external meetings

Ihr Profil

• We are seeking a highly motivated candidate with a strong background in bioinformatics and computational biology who will develop and apply computational tools to decipher ecotypes and mutational signature dynamics in the context of cancer treatment.
• Diploma or Master's degree in natural or life sciences in good standing
• Proficiency in using Linux/UNIX-based operating systems and working with HPC systems using SLURM
• Experience with R and/or Python for data analysis, visualization, and statistics
• Familiarity with workflow management tools such as Snakemake and/or Next flow
• Strong coding skills, including version control with Git and thorough script documentation
• Experience in analyzing sequencing data, including sequence alignment, quality control, variant calling/filtering, and gene expression analyses
• Familiarity with sequencing databases such as TCGA/ICGC, UCSC, and Ensemble
• Basic understanding of cell biology, molecular biology and cancer biology
• Fluent in scientific English

Freuen Sie sich auf:

• Our group has expertise in the computational analysis of multi-omic datasets, including Glioma Longitudinal Analysis (GLASS) Consortium (Kocakavuk et al. 2023, Neuro Oncol; Kocakavuk et al. 2021, Nature Genetics; Barthel *et al.*2019, Nature; Varn et al. 2022, Cell) and Hartwig Medical Foundation (HMF) datasets (Kocakavuk et al. 2021, Nature Genetics). The GLASS, HMF and other datasets, including ICGC-PCAWG and AACR-GENIE, will be available for analysis.
• Cutting-edge methods for longitudinal, multi-level, and single-cell sequencing in preclinical models and patient biospecimens
• The Emmy Noether Group 'Computational Pathology', led by Emre Kocakavuk, MD, PhD of the Department of Hematology and Stem Cell Transplantation (Chair Prof. Dr. C. Reinhardt), is funded by the German Research Foundation (DFG).
• Graduate School of Biomedical Science (BIOME): Access to its structured PhD lecture and seminar program, interdisciplinary exchange within the BIOME network
• Support and supervision for academic endeavors as needed
• Comprehensive training in state-of-the-art technologies, covering both theory and methodology
• Opportunities for interdisciplinary networking and international collaborations (e.g. as part of the GLASS consortium)
• Supporting and enriching work environment with close interdisciplinary contact to dry-lab/wet-lab researchers as well as Clinician Scientists
• A secure job in the public service of the state of NRW
• Fair payment in accordance with the collective wage agreement (TV-L) incl. annual bonus payment and supplementary company pension scheme
• 30 days of vacation per calendar year (for a full-time position)
• Interdisciplinary work with colleagues from other departments
• Working with modern equipment and certified quality standards
• Family-friendly corporate culture, e.g. company daycare center, vacation program for school-age children, advice and support from the Employee Service Office in all life situations
• Wide range of training and continuing education opportunities, e.g. at the Training Academy of UK Essen
• Health Management, e.g. company integration management, vaccinations, promotion of sports activities
• Attractive fringe benefits, e.g. reduced-price canteen meals, community events, accommodation in student residences

Rahmenbedingungen: Die Eingruppierung richtet sich nach den persönlichen und tariflichen Voraussetzungen., Schwerbehinderte Bewerberinnen / Bewerber und Gleichgestellte i.S. des § 2 Abs. 3 SGB IX werden bei gleicher Eignung bevorzugt berücksichtigt., Im Falle einer schriftlichen Bewerbung reichen Sie Ihre Unterlagen nur als unbeglaubigte Kopien ein und verwenden Sie keine Mappen, da keine Rückgabe erfolgt. Eine Vernichtung entlang der datenschutzrechtlichen Bestimmungen wird zugesichert., Das UK Essen strebt eine Erhöhung des Frauenanteils in Bereichen an, in denen Frauen unterrepräsentiert sind. Sie werden zur Bewerbung aufgefordert und im Sinne des LGGs bei gleicher Qualifikation vorrangig berücksichtigt., Eine Bescheinigung gemäß §23a Infektionsschutzgesetz (IfSG) über den Impf- und Serostatus bzgl. Masern ist erforderlich.