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.

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.

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 30^th September 2024.

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.

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

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.