Student / Research Assistant - High- Throughput Effect-Directed Analysis (HT-EDA) in the field of Environmental Toxicology in Leipzig bei Helmholtz Zentrum für Umweltforschung UFZ

Student / Research Assistant (f/m/x) - High- Throughput Effect-Directed Analysis (HT-EDA) in the field of Environmental Toxicology in Leipzig bei Helmholtz Zentrum für Umweltforschung UFZ

Helmholtz-Zentrum für Umweltforschung UFZ

Place of work

Leipzig

Working time

19 hours / week

Contract limitations

limited contract / 3 months (start as soon as possible)

Contact

Your contact for any questions you may have about the job:
Dr. Jana Schor
jana.schor@ufz.de

The UFZ

The Helmholtz Centre for Environmental Research (UFZ) with its 1,100 employees has gained an excellent reputation as an international competence centre for environmental sciences. We are part of the largest scientific organisation in Germany, the Helmholtz association. Our mission: Our research seeks to find a balance between social development and the long-term protection of our natural resources.

The job

Effect-directed analysis has become more efficient through automated and miniaturized fractionation and optimized bioassays in recent years. These advances have allowed researchers to identify new chemical compounds that risk aquatic environments using high-resolution mass spectrometry, liquid chromatography, and non-target screening. Despite these advances, two main challenges remain: first, identifying which features to prioritize for identification among thousands of potential candidates, and
second, determining the most likely structure of the selected features using in-silico fragmentation tools that can generate hundreds of possibilities based on the assigned molecular formula.
Several computational tools that use machine learning to predict chemical activity based on available information, such as ms2 spectra, ionization behavior, and candidate structures, have been developed. These tools have the potential to enhance toxicity driver prioritization and toxicological endpoint prediction greatly and have yet to be explored in the context of EDA.

Your tasks

Aim:
To implement and integrate promising computational tools to refine compound identification workflows within HT-EDA applications, thereby improving toxicity driver compounds' prioritization and identification processes.

Objective – Acitivity 2:
Utilize computational approaches to link structures in the NORMAN Suspect List with potential effects on gene/pathway levels for environmentally relevant endpoints suitable for EDA studies, such as estrogenicity, androgenicity, and neurotoxicity, leveraging the deepFPlearn tool.

Key Responsibilities:

1. Literature Review & Tool Familiarization:

Review existing literature on the deepFPlearn and the deepchem Python packages
Understand the NORMAN Suspect List and environmental endpoints relevant to EDA studies
Learn to operate the Python packages for computational analysis

2. Computational Analysis:

Input the NORMAN Suspect List into deepFPlearn for computational association with environmental endpoints
Analyze compounds for potential effects on gene/pathway levels, focusing on estrogenicity, androgenicity, and neurotoxicity

3. Data Interpretation & Reporting:

Interpret computational findings to identify significant patterns or insights
Draft a preliminary report on methodologies, results, and their implications for HT-EDA
Collaborate on the preparation of findings for potential academic dissemination

We offer

Excellent supervision that supports your personal and professional development
Exciting insights into the work of a leading research institute
The chance to work in interdisciplinary, international teams and benefit from a wide range of perspectives
The opportunity to contribute and actively shape your own ideas and impulses
right from the start
Modern technical equipment and IT service to optimally support your work

Your profile

Enrolled in or recently graduated (B.Sc. or M.Sc.) from a program in environmental science, toxicology, chemistry, bioinformatics, data/computer science, or a related field
Interest in computational toxicology and environmental protection
Experience with computational analysis in Python

Application deadline: 15.08.2024

Diversity and Inclusion

The UFZ has a strong commitment to diversity and actively supports equal opportunities for all employees regardless of their origin, religion, ideology, disability, age or sexual identity.
We look forward to applications from people who are open-minded and enjoy working in diverse teams.

Important

Please submit your application via our online portal with your cover letter, CV (please omit your photo, age, or marital status) and relevant attachments.

Contact

Your contact for any qu