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Veröffentlicht: 3. September 2024
PostDoc or PhD Position- Analysis of Cell Free DNA in Aggressive B Cell Lymphomas
At the University Hospital of Giessen and Marburg, Institute of Pathology, Gießen we are seeking a PostDoc or PhD for the Department of Molecular Cytology and Functional Genomics
The position is initially limited to 3 years, part-time (75%).
Research Environment
Molecular Cytology and Functional Genomics
The Department of Molecular Cytology and Functional Genomics employs a multidisciplinary approach combining genetic, cell biological, and biochemical investigations to identify and functionally characterize the transforming events involved in the pathogenesis of B‑cell lymphomas. The results of these studies lead to improved diagnosis of these diseases and are used to develop prognostic markers for therapy. In addition, new therapeutic strategies are designed and validated in preclinical studies.
Research Project — Liquid Biopsies of Aggressive B‑cell Lymphoma
After determining the genetic lesions of a B‑cell lymphoma at the time of diagnosis, high-throughput sequencing is subsequently performed using blood samples from these patients, both during and after therapy. The so-called liquid biopsy procedure usually allows for the detection of tumor DNA in the blood of patients at the beginning of therapy. Studies with these methods in NHL patients show that there is a correlation between the response to therapy and the detectability of tumor DNA in the blood. Accordingly, the detection of tumor DNA in the blood allows the course of therapy to be monitored closely. After completion of therapy, the ultrasensitive detection of circulating tumor DNA allows early predictions of possible relapses or transformations of the B‑cell lymphoma.
Your profile
- Master or PhD degree in bioinformatics/computational biology, genomics or a related area
- Extensive experience with at least one programming language (e.g., R, Python, etc.).
- You have an interest in interdisciplinary collaboration.
- Dedication, team spirit, and a high degree of responsibility.
- Very good English skills, both written and spoken.
We Offer
- A scientific project in the field of translational cancer research.
- Excellent, interdisciplinary supervision by a Principal Investigator and Postdocs, as well as support for the sustainable development of your scientific profile.
- Opportunity to pursue a doctorate (PhD).
- Opportunity to analyze a broad spectrum of high-throughput sequencing data (including analysis of circulating tumor DNA using PhasED-Seq, exome sequencing, RNA-seq, etc.).
- Focus institute “Liquid Biopsy” within the framework of the “CCC Hessen” initiative.
- Innovative concepts in digital higher education.
- Support for external continuing education and training.
How to apply:
Please send your application documents to roland.schmitz@patho.med.uni-giessen.de until October 20th, 2024, including:
a CV with publication list (if available)
a summary of previous research experience (max 1 page)
copies of certificates, transcripts and grades
For more information about the lab and project, please contact Prof. Dr. rer. nat. Roland Schmitz roland.schmitz@patho.med.uni-giessen.de.
Veröffentlicht: 2. September 2024
PhD Position in Bioinformatics of the Microbiome
Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam
closing date: 29.09.2024
Are you fascinated by the microbiome and its interaction with the human host? Microbiome research has flourished in the last decade, thanks in no small part to the relative ease with which large volumes of metagenomics sequencing data can be generated. Bioinformatics method development has advanced, but to this date, the human microbiome is mostly studied in terms of ‘who’s there’, followed by indicators of microbial metabolism and some specific molecular classes, such as antibiotics resistance. Long-standing biomedical knowledge says that an important part of the interaction between microbes and especially with hosts are determined by structural interactions, but this has been all but ignored. State of the art bioinformatics methods can tackle this challenge! Do you want to address this oversight with us?
In this PhD project, the objective is to develop and extend bioinformatics methods that can mine metagenomic sequencing datasets for features that are related to the physical interaction with human cells, and particularly the immune system. For this, you will make use of classical bioinformatics and machine learning approaches to detect features of interest in sequence and protein structural data. Having applied your new methods to metagenomics data, you will also test what kind of statistical considerations are important for interpreting the results.
Apply via our website: https://vacatures.uva.nl/UvA/job/PhD-Position-in-Bioinformatics-of-the-Microbiome/802049802/
The advertised position is under the supervision of dr. Anna Heintz-Buschart of the Biosystems Data Analysis group at the Swammerdam Institute for Life Sciencesat the University of Amsterdam (UvA). The group has a broad profile in bioinformatics, multivariate statistics and modelling with a growing focus on microbiome research, for example in lively collaborations within UvA’s research priority areas Personalized Microbiome Health and System Biology Host-Microbiome Interaction and the Dutch Holomicrobiome Initiative.
What are you going to do?
You will receive training in and are expected to:
• complete a PhD thesis within the official appointment duration of four years;
• design, apply and benchmark bioinformatics algorithms, tools, and workflows to predict central aspects of host-microbiome interactions based on metagenomics sequencing data of the human microbiome;
• analyse existing and novel metagenomics datasets using your and existing methods;
• document your work in an accessible, open science manner;
• publish the findings in peer-reviewed manuscripts and as part of your PhD thesis;
• participate in the Faculty of Science PhD training program;
• be an active member of the Biosystems Data Analysis group, including by supervision of BSc or MSc students.
What do we require?
You have:
• a MSc degree in bioinformatics; or in data science, informatics, or related subjects with a strong biological or biomedical component; or in the life or biomedical sciences with a strong informatics component;
• hands-on experience in omics data analysis and coding skills – experience with microbiome data and machine learning are a plus;
• fluency in English, written and spoken, and the confidence to use it in scientific communication and publications;
• enthusiasm for human bioinformatics in microbiome research in a diverse team and the ability to take ownership of the research project;
Our selection will be based on your academic track record, your skills and ambition, and your enthusiasm and ideas for this research project.
Apply via our website: https://vacatures.uva.nl/UvA/job/PhD-Position-in-Bioinformatics-of-the-Microbiome/802049802/
Our offer
We offer a temporary contract for 38 hours a week, preferably starting on 1-12-2024, for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.
Based on a full-time appointment (38 hours per week) the gross monthly salary will range from € 2.872 in the first year to €3.670 (scale P) in the last year. This is exclusive 8% holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable.
Are you curious about our extensive package of secondary employment benefits like our excellent opportunities for study and development? Take a look here.
Questions?
Do you have questions about this vacancy? Or do you want to know more about our organisation?
Please contact: Dr. Anna Heintz-Buschart, Assistant Professor, email a.u.s.heintzbuschart@uva.nl.
Apply via our website: https://vacatures.uva.nl/UvA/job/PhD-Position-in-Bioinformatics-of-the-Microbiome/802049802/
About the Faculty of Science and the Swammerdam Institute for Life Sciences
The Faculty of Science has a student body of around 7,000, as well as 1,600 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.
The Swammerdam Institute for Life Sciences (SILS) is located at the vibrant Amsterdam Science Park. SILS is one of eight institutes of the University of Amsterdam’s Faculty of Science (FNWI). With around 240 employees, SILS carries out internationally high-quality life science research and provides educatihttps://sils.uva.nl/on within various university programs. Research is also carried out in close cooperation with the medical, biotech, chemical, flavor, food & agricultural, and high-tech industries, and revolves around 4 main themes, Cell & Systems biology, Neurosciences, Microbiology and Green Life Sciences.
Application
Do you recognize yourself in the job profile? Then we look forward to receiving your application by 29 September 2024. Apply via our website: https://vacatures.uva.nl/UvA/job/PhD-Position-in-Bioinformatics-of-the-Microbiome/802049802/
Applications in .pdf should include:
• a cover letter where you explain your motivation and suitability for this position in your own words and your CV;
• contact details of two academic referees.
Please mention the months (not just years) in your CV when referring to your education and work experience.
A knowledge security check can be part of the selection procedure (for details: national knowledge security guidelines).
The UvA is an equal-opportunity employer. We prioritize diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.
Veröffentlicht: 2. September 2024
Bioinformatician — Omics for Precision Medicine
The Bioinformatics and Computational Pathology Group at the Institute of Pathology, Erlangen, develops computational approaches for the analysis of omics, digital, and molecular pathology data, to dissect regulatory networks in development and disease (https://www.nephropathologie.uk-erlangen.de/forschung-und-lehre/bioinformatics-and-computational-pathology/).
Within the group, we are looking for a
Bioinformatician (f/m/d)
whose primary task will be to support to activities of the Center for Personalized Medicine Erlangen (ZPM; https://www.zpm.uk-erlangen.de/). In addition, there will be the possibility to develop own research projects and apply for local junior research funding.
The goal of the ZPM is to search for targeted cancer treatments that match the molecular properties of the tumour tissue of each patient. In the framework of the “Model Project Genome Sequencing”, this will be based on whole-genome sequencing of the patient’s tumor tissue.
Your tasks will include:
- setting up, maintaining, and running pipelines for sequencing data analyses (targeted panels, whole-exome and whole-genome sequencing);
- closely interacting with ZPM colleagues to develop databases and pipelines for somatic variant annotation and interpretation;
- closely interacting with bioinformaticians within regional and national networks (e.g., BZKF, DNPM).
Qualifications:
- academic degree (MSc or equivalent) in bioinformatics, informatics, computational or life sciences;
- familiarity with working in a Linux/Unix environment;
- very strong programming skills (e.g., Python, Perl, R);
- excellent communication skills and fluency in English;
- prior experience in the analysis of next-generation sequencing data is advantageous.
Applications should be submitted via the following page https://www.karriere.uk-erlangen.de/en/job/bioinformatician-m-f-d-8901/ and include: letter of interest, curriculum, copies of certificates, list of publications (if applicable), as well as contact information of at least two references. Contact for further information: Dr. Fulvia Ferrazzi, tel. +49–9131–8543677.
The position is full time, initially available for 2 years, with the possibility of extension. Pay grade is determined according to TV‑L E13.
The starting date is the earliest possible timepoint. Deadline for applications is 30th September 2024.
Veröffentlicht: 29. August 2024
2 PostDoc or PhD positions in machine learning for precision oncology
The Biomedical Network Science Lab (BIONETS Lab, https://bionets.tf.fau.de) at the Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU, https://fau.eu) and the Department of Pediatrics and Adolescent Medicine at the University Hospital Erlangen (UKER, https://www.uk-erlangen.de/en/) offer 2 postdoctoral or doctoral researcher positions at the intersection of graph-based machine learning, precision oncology, and federated learning.
Position information
Using real-world data from actual patients (>50 million laboratory test results from >500,000 patients), you will design, implement, and validate (graph-based) machine learning models for diagnosis and prognosis in pediatric oncology. Moreover, you will develop federated counterparts of the machine learning models to enable privacy-preserving model training on decentrally available data. You will work on a highly interdisciplinary project and will continuously collaborate with bioinformaticians, clinical oncologists, and industrial software developers.
Research environment
The BIONETS Lab is part of the new Department Artificial Intelligence in Biomedical Engineering at FAU (AIBE, https://aibe.tf.fau.de), which was established as a cornerstone of the health node of the Bavarian High-Tech Agenda. Research at the BIONETS Lab focuses on the development of algorithms and ML models for systems biology, while UKER’s Department of Pediatrics and Adolescent Medicine has strong expertise in the large-scale quantitative analysis of multi-centre laboratory test result data in pediatric oncology (e.g., the PEDREF study, https://www.pedref.org/).
Requirements
All candidates should demonstrate strong research passion, scientific curiosity, and a highly independent work style. Candidates applying for a PhD position should have a Master’s degree in computer science, bioinformatics, applied mathematics, or a related field with above-average grades. Candidates applying for a postdoctoral researcher position should additionally have a PhD in one of these fields and an excellent publication record. Proficiency in both written and spoken English and strong programming skills are essential. Additional desirable qualifications include knowledge or experience in one or several of the following fields:
- Machine learning / deep learning
- Graph-based algorithms and machine learning models
- Federated learning
- Biomedical data science
Position details and application instructions
Positions can start as soon as possible. Funding is available through TV‑L E13 positions (100 %) with a duration of 2 years. Extension may be possible, depending on availability of funding. Candidates should apply with a motivation letter (max. 1 page), an academic CV, a list of publications (especially relevant for PostDoc candidates), the contact details of preferably three researchers who agreed to provide letters of reference, and a transcript of record of their Master’s degree. Please combine these documents in a single PDF and send them to Prof. Dr. David B. Blumenthal (david.b.blumenthal@fau.de) and to PD Dr. Jakob Zierk (jakob.zierk@uk-erlangen.de) in a single email with the subject “<your surname> application FLabNet”. Applications will be accepted until the positions are filled.
Veröffentlicht: 19. August 2024
ERC-funded PhD and Postdoc Positions in Comparative Genomics
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.
About BATPROTECT
This 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
- Good 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
- 30 vacation days/year
- Location in central Frankfurt. Frankfurt is a vibrant and highly international city at the heart of Europe that combines a
skyscraper skyline with historic buildings and multiple parks and green areas. Senckenberg is right next to the botanical garden and famous Palmengarten. The Economist 2022 index ranked Frankfurt among the top 10 most livable cities worldwide.
Place of employment: Frankfurt am Main, Germany
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 in Fall 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 your application documents to recruiting@senckenberg.de until September 8th, 2024, including:
- a CV with publication list and contact information for at least two references
- a summary of previous research experience (max 1 page)
- copies of certificates, transcripts and grades
in electronic form (as a coherent PDF file) quoting the reference number #12–24005‑1. Or apply through the online application form on our homepage, also quoting the reference number.
For more information about the lab and the project, please contact Prof. Dr. Michael Hiller (michael.hiller@senckenberg.de) 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
Veröffentlicht: 7. August 2024
Bioinformatics PhD Position at the Med Uni Graz, Austria
This bioinformatics project is part of an exciting consortium initiative (LYMPHO-CHECK), focusing on the immunomodulatory effects of the NR4A1/p53 axis in diffuse large B cell lymphoma. As a key member of the LYMPHO-CHECK initiative, the PhD student will leverage bioinformatics methods and data analysis techniques to explore this interesting axis in relation to the tumour microenvironment and immune evasive mechanisms.
Details of the position and the application process are provided here: https://www.medunigraz.at/phd/application/
Project Title: The immunomodulatory effects of the NR4A1/p53 axis in diffuse large B cell lymphoma (Feichtinger)
Application Deadline: September 10, 2024
We look forward to receiving your application!
Veröffentlicht: 24. July 2024
Junior Professor of Artificial Intelligence in Protein Science
The University of Bayreuth is a research-oriented university with internationally competitive, interdisciplinary focus areas in research and teaching. The Faculty of Biology, Chemistry & Earth Sciences at the University of Bayreuth is currently seeking to appoint a
Junior Professor of Artificial Intelligence in Protein Science (salary grade W1) with tenure track to W3
to commence as soon as possible. This is a fixed-term civil service position.
We are looking for a dynamic and creative scholar with the ability to work independently and a high potential for development in research and teaching. Applicants should be active and visible in the field of artificial intelligence and structure-based protein biochemistry and complement and strengthen the university’s profile in the field of biochemistry. Future-oriented and innovative research priorities of the successful applicant include for example the prediction of molecular properties such as structure and/or interactions of biological macromolecules, the development of novel methods and applications in the field of AI- / ML-supported visualization and characterization of biomacromolecular complexes and their dynamics, or generative molecular design. Expected are additionally a very good publication record in recognized journals or through conference contributions, the willingness to acquire external funding, and an interest in interdisciplinary collaborations.
The successful applicant will have the potential for outstanding teaching performance in the field of ML / AI as well as biochemistry and will show willingness for undergraduate and research-oriented teaching in both German and English, teaching export and the development of new master’s programmes. Social and leadership skills and the willingness to be involved in academic self-governance are also expected.
The complete vacancy notice including further information on the formal employment requirements can be found at www.uni-bayreuth.de/en (University / Work at the University / Job Vacancies).
Applications (CV, outlining education and academic career, list of publications, list of courses taught, research plan, experience obtaining external funding, as well as copies of certificates and diplomas) are to be addressed to the dean of the Faculty of Biology, Chemistry & Earth Sciences Prof. Dr. Cyrus Samimi and submitted via https://uni-bayreuth.berufungsportal.de by September 13, 2024. Applicants are welcome to direct questions and requests for further information to the Dean at dekanat.bcg@uni-bayreuth.de. Application documents will be deleted in accordance with data protection law following the conclusion of the appointment process.
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