Bioinformatiker (m/w/d) (Bioinformatiker/in)

The Fraunhofer-Gesellschaft currently operates 76 institutes and research units throughout Germany and is a leading applied research organization. Around 32 000 employees work with an annual research budget of 3.4 billion euros.

A new working group in the field of clinical microbiome research currently being established at the Fraunhofer-Institute for Translational Medicine and Pharmacology ITMP in Frankfurt am Main. This group encompasses a research platform focused on the development of microbiota-based therapies. Within this group, the bioinformatic analysis of data sets and, in particular, the development of prediction models for complex microbial communities and their interactions will play a central role. Accordingly, we are looking for a bioinformatician as a postdoc to support our interdisciplinary team.

Bioinformatician / Postdoc - Microbiome Research Microbiome analysis and integration of -omics and clinical data

Fusion and integration of -omics data with clinical data
Complementary metagenomic analysis of existing samples from biobanks and collections
Execution of statistical and bioinformatic analyses of complex data sets in a medical context

Development of new bioinformatic tools and analysis strategies

Application of established bioinformatics tools and solutions, including those for predicting nutrient competition among microorganisms and other mechanisms of colonization resistance
Development of new analysis strategies, tools, and predictive models to support the group’s objectives
Validation and benchmarking of these tools and models using various data sets
Application of the developed solutions to identify potential Live Biotherapeutic Products (LBPs)

Support of the working group

Organization and management of data from microbiome studies, including quality assurance and data preparation
Documentation, visualization and publication of research findings in scientific journals as well as presentation in lectures and conferences
Assistance in securing third-party funding and preparation of grant proposals for clinical studies

A scientific degree in bioinformatics, biology, or a comparable field and a completed PhD or (at the time of application) submitted PhD, ideally with a strong focus on health sciences
Solid knowledge of programming languages such as Python, R and Bash; additional experience with high-performance computing (HPC) is an advantage
Experience in analyzing of sequence data (e.g., tools like QIIME2, MetaPhlAn, Kraken or HUMAnN) and proficiency with MS Office
Understanding of microbiological or molecular biological fundamentals
Interest in the human microbiome and clinical research
Advantageous: Experience in project and data management
Good command of German and English (spoken and written)
A high level of initiative and team spirit

Opportunity for scientific work in a highly innovative and patient-relevant topic
Integration into a competent, friendly, and committed team
A collegial work atmosphere and the freedom to implement your own ideas
Flexible working hours (flexitime model), remote work options, as well as various support measures to balance private life and career
Excellent professional and personal development, opportunities through a variety of internal training programs
30 days paid annual leave, plus Christmas and New Year's Eve as company holidays
Personal retirement benefits (VBL) and additional (social) benefits of public service, such as annual special payment
Capital-forming benefits
Subsidies for public transport (Deutschlandticket)
Corporate benefits: offers from well-known manufacturers and brands
Access to the extensive Fraunhofer network

The Fraunhofer-Gesellschaft (www.fraunhofer.com) currently operates 76 institutes and research institutions throughout Germany and is the world's leading applied research organization. Around 30 000 employees work with an annual research budget of 2.9 billion euros.

A new working group in the field of clinical microbiome research currently being established at the Fraunhofer-Institute for Translational Medicine and Pharmacology ITMP in Frankfurt am Main. This group encompasses a research platform focused on the development of microbiota-based therapies. Within this group, the bioinformatic analysis of data sets and, in particular, the development of prediction models for complex microbial communities and their interactions will play a central role. Accordingly, we are looking for a bioinformatician as a postdoc to support our interdisciplinary team.

What you will do

Microbiome analysis and integration of -omics and clinical data

- Fusion and integration of -omics data with clinical data
- Complementary metagenomic analysis of existing samples from biobanks and collections
- Execution of statistical and bioinformatic analyses of complex data sets in a medical context

Development of new bioinformatic tools and analysis strategies

- Application of established bioinformatics tools and solutions, including those for predicting nutrient competition among microorganisms and other mechanisms of colonization resistance
- Development of new analysis strategies, tools, and predictive models to support the group´s objectives
- Validation and benchmarking of these tools and models using various data sets
- Application of the developed solutions to identify potential Live Biotherapeutic Products (LBPs)

Support of the working group

- Organization and management of data from microbiome studies, including quality assurance and data preparation
- Documentation, visualization and publication of research findings in scientific journals as well as presentation in lectures and conferences
- Assistance in securing third-party funding and preparation of grant proposals for clinical studies

What you bring to the table

- A scientific degree in bioinformatics, biology, or a comparable field and a completed PhD or (at the time of application) submitted PhD, ideally with a strong focus on health sciences
- Solid knowledge of programming languages ​​such as Python, R and Bash; additional experience with high-performance computing (HPC) is an advantage
- Experience in analyzing of sequence data (e.g., tools like QIIME2, MetaPhlAn, Kraken or HUMAnN) and proficiency with MS Office
- Understanding of microbiological or molecular biological fundamentals
- Interest in the human microbiome and clinical research
- Advantageous: Experience in project and data management
- Good command of German and English (spoken and written)
- A high level of initiative and team spirit

What you can expect

- Opportunity for scientific work in a highly innovative and patient-relevant topic
- Integration into a competent, friendly, and committed team
- A collegial work atmosphere and the freedom to implement your own ideas
- Flexible working hours (flexitime model), remote work options, as well as various support measures to balance private life and career
- Excellent professional and personal development, opportunities through a variety of internal training programs
- 30 days paid annual leave, plus Christmas and New Year's Eve as company holidays
- Personal retirement benefits (VBL) and additional (social) benefits of public service, such as annual special payment
- Capital-forming benefits
- Subsidies for public transport (Deutschlandticket)
- Corporate benefits: offers from well-known manufacturers and brands
- Access to the extensive Fraunhofer network

We value and promote the diversity of our employees' skills and therefore welcome all applications - regardless of age, gender, nationality, ethnic and social origin, religion, ideology, disability, sexual orientation and identity. Severely disabled persons are given preference in the event of equal suitability.

The weekly working time is 39 hours. This position is initially limited to 2 years and is also available on a part-time basis. Appointment, remuneration and social security benefits based on the public-sector collective wage agreement (TVöD). Additionally Fraunhofer may grant performance-based variable remuneration components.

With its focus on developing key technologies that are vital for the future and enabling the commercial utilization of this work by business and industry, Fraunhofer plays a central role in the innovation process. As a pioneer and catalyst for groundbreaking developments and scientific excellence, Fraunhofer helps shape society now and in the future.
Interested? Apply online now. We look forward to getting to know you!

Ms. PD Dr. med. Lena Biehl
[email protected]
Fraunhofer Institute for Translational Medicine and Pharmacology ITMP
www.itmp.fraunhofer.de

Requisition Number: 77775                Application Deadline:

Ms. PD Dr. med. Lena Biehl
[email protected]

ERC-funded PhD and Postdoc Positions in Comparative Genomics

(full time / part-time options available)

The Hiller Lab at the LOEWE Center for Translational Biodiversity Genomics (TBG) in Frankfurt, Germany has two openings for a PhD student and/or a Postdoc to work on the BATPROTECT project to investigate the genomic basis of long healthspans, disease resistance, and viral tolerance in bats.

BATPROTECT
is a 6-year funded ERC synergy grant project that will use bats as natural models of healthy aging and disease tolerance to elucidate the molecular mechanisms behind bats’ exceptional longevity and resistance to viral and age-related diseases. BATPROTECT brings together a team of global leaders in bat biology and ageing (Emma Teeling, Dublin), bat immunology and virology (Linfa Wang, Singapore), evolution and genomics (Michael Hiller, Frankfurt), and ageing model organisms (Bjoern Schumacher, Cologne) that will jointly investigate aging and immune responses in bats from the wild and captive colonies, discover genes with evolutionary importance for longevity and disease resistance, and functionally validate longevity and immune regulators in stem and differentiated cells of bats and model organisms, with the ultimate goal to uncover new directions to improve human healthspan and disease outcome.

The Project
The overall goal is to uncover the genomic basis of exceptional healthspans and disease tolerance in bats, understand the evolution of these traits, and identify key molecular targets for functional validation. To this end, we will assemble ~150 new reference-quality bat genomes using HiFi and HiC sequencing to better cover the diversity of bats, generate comparative transcriptomic datasets, and analyze these data using our established methods repertoire (TOGA and others). Work includes phylogenomics, performing comparative screens to identify key adaptations in coding and non-coding (miRNA) genes as well as differences in gene expression patterns across the bat phylogeny, associating genomic changes with longevity and viral reservoir status traits, identifying novel bat genes, and investigating endogenized viral elements. The exact project will be defined based on the interests of the applicants.
The PhD student and postdoc will work closely with other members of the BATPROTECT team, the Hiller lab, and other Bat1K collaborators. We also offer exchanges with the other BATPROTECT labs as well as yearly retreats with all project members.

Your profile
• Master or PhD degree in bioinformatics/computational biology, genomics or a related area
• Solid programming skills in a Linux environment, experience with shell scripts and Unix tools
• Strong interest in comparative genomics, experience in comparative genomics is an advantage
• English in written and oral form

Our lab
The mission of our lab is to understand how nature's fascinating phenotypic diversity has evolved and how it is encoded in the genome. Work in the lab includes sequencing and assembly of reference-quality genomes, genome alignment and gene annotation, development and application of comparative genomic methods to discover differences in genes and gene expression, and the use of statistical approaches to link phenotypic to genomic changes.

Our lab is part of TBG (https://tbg.senckenberg.de/) and the Senckenberg Research Society (https://www.senckenberg.de/en/), and is based near the city center of Frankfurt am Main, Germany. TBG provides access to cutting-edge computational (large HPC clusters, genome browser) and lab infrastructure to sequence and analyze genomes. English is the working language in our lab.

Senckenberg and TBG provide
• Flexible working hours – opportunities for mobile working – leave of absence due to family reasons (certified by “auditberufundfamilie”) – parent-child office – annual special payment – company pension scheme – Senckenberg badge for free entry in museums in Frankfurt. – leave of 30 days/year
• Frankfurt is a vibrant and highly international city at the heart of Europe that combines a skyscraper skyline with ample parks and green areas. The Economist 2022 index ranked Frankfurt among the top 10 most livable cities worldwide.

Place of employment: Frankfurt am Main
Working hours: Full-time (40 hours/week) / part-time options are available
Type of contract: funding is available for 6 years
Postdoc: initially limited to 2 years
PhD: initially limited to 3 years
Start date: flexible, ideally summer of 2024
Salary and benefits: according to the collective agreement of the State of Hesse (TV-H), pay grade E13 (PostDoc 100%, PhD: 75%)

Senckenberg is committed to diversity. We benefit from the different expertise, perspectives and personalities of our staff and welcome every application from qualified candidates, irrespective of age, gender, ethnic or cultural origin, religion and ideology, sexual orientation and identity or disability. Women are particularly encouraged to apply, as they are underrepresented in the field of this position; in the case of equal qualifications and suitability they will be given preference. Applicants with disabilities (“Schwerbehinderung”) will be given preferential consideration in case of equal suitability. Senckenberg actively supports the compatibility of work and family and places great emphasis on an equal and inclusive work culture.

The Senckenberg Gesellschaft für Naturforschung is a member of the Leibniz Association and is based in Frankfurt am Main, Germany. LOEWE-TBG is a joint venture of Senckenberg with five partner institutes from the Federal State of Hesse, aiming to intensify biodiversity genomics in basic and applied research. We establish a new and taxonomically broad genome collection to study genomic and functional diversity across the tree of life and make genomic resources accessible for societal demand driven applied research.

How to apply
Please send us your application documents containing
• a CV with publication list and contact information for at least two references
• a summary of previous research experience (max 1 page)
• and copies of certificates, transcripts and grades
in electronic form (as a coherent PDF file) by June 07th 2024 to [email protected] quoting the reference number #12-24005, or apply through the online application form on our homepage.

Senckenberg Gesellschaft für Naturforschung
Senckenberganlage 25
60325 Frankfurt a.M.
E-Mail: [email protected]

For more information about the lab and the project, please contact Prof. Dr. Michael Hiller ([email protected]) or visit the lab webpage https://tbg.senckenberg.de/hillerlab/. An overview about our publications is available here: https://tbg.senckenberg.de/hillerlab/publications/

For more information about the Senckenberg Gesellschaft für Naturforschung, please visit www.senckenberg.de