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Stellenangebote

PhD student (f/m/d) position in Computational Biology/Bioinformatics for translational cancer research with a focus on the analysis of single cell sequencing data

The Department of Internal Medicine II, at the Technische Universität München (TUM) and the Institute of Translational Cancer Research and Experimental Cancer Therapy at TUM and the German Cancer Research Center offers a

 

PhD student (f/m/d) position
in Computational Biology/Bioinformatics for translational cancer research with a focus on the analysis of single cell sequencing data

 

at the Center for Translational Cancer Research (TranslaTUM) in Munich.

 

We are deploying genetic models to study molecular, immunological and translational aspects of pancreatic cancer. We utilize these systems to uncover molecular mechanisms as well as inflammatory and immune pathways that are required for tumor initiation and -progression in vivo (e.g. Nature 2018, 554:62-68; Nat. Commun. 2016, 7:10770; Nat Med. 2014, 20:1340-7; Cancer Cell. 2013,24:15-29, Cancer Cell. 2013,23:406-20, Nat Commun. 2013;4:1630; PNAS 2011, 108:9945-50). During the past decade, our lab has generated a comprehensive resource of pancreatic primary tumors and primary cell cultures. Multiple NGS methods have been performed to decipher the molecular makeup of these tumors. The advertised project focuses on unraveling tumor heterogeneity and its impact on treatment response and resistance using single cell sequencing techniques and will be performed in close collaboration with the Floßdorf lab (Dr. rer. nat. Michael Floßdorf) at TUM.

 

We are an enthusiastic and international team and offer intensive training and mentoring. The successful candidate will have the opportunity to:

                Set up bioinformatics platforms and develop computational pipelines for the analysis of single cell RNA-sequencing and single cell DNA-sequencing datasets

                Integrate these datasets with molecular (WES, WGBS, lcWGS, ChIPseq, ATACseq), phenotypic (e.g. histology) and clinical information

                Apply bioinformatics techniques to published/unpublished data for the analysis and interpretation of omics datasets

                Aid researchers select and use computational and statistical tools relevant to their single cell sequencing projects

 

The successful candidate will interact within a multidisciplinary environment of biologists, clinicians, computational scientists and mathematicians within the TranslaTUM. She/he will work closely with a diverse team to formulate hypotheses and validate predictions using genomic and transcriptomic assays. She/he will be exposed to cutting edge experimental methods to study translational aspects of cancer.

 

We are looking for an exceptional self-motivated computational scientist with a strong analytical background. Previous exposure to and experience with bioinformatics as well interests in molecular aspects of cancer research are an asset, but not required. Due to the interdisciplinary framework and close collaboration with wet-lab scientists, communicative skills are essential.

 

We give priority to severely disabled applicants with essentially equal qualifications. Payment according to tariff (TV-L).

 

We are looking forward for you application!

 

Interested candidates should send a CV with cover letter, certificates, and letters of recommendation by e-mail to: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

 

Univ.-Prof. Dr. med Dieter Saur

Institut für Experimentelle Tumortherapie

Klinik und Poliklinik für Innere Medizin II

Klinikum rechts der Isar der Technischen Universität München

Ismaninger Straße 22

81675 München

 

 

E-Mail: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

3 PhD Student Positions in the Computational Plant Sciences [IMPRS]

THE GRADUATE SCHOOL
 
The International Max Planck Research School (IMPRS) on Understanding Complex Plant Traits using Computational and Evolutionary Approaches is a local collaboration between the Max Planck Institute for Plant Breeding Research (MPIPZ) and the Universities in Cologne and Düsseldorf (Germany). The IMPRS has been established in 2002 and offers an international PhD programme in English. Students are closely supervised through an advisory committee, receive professional training in transferable and applicable skills and are supported to share their scientific insights.
 
THE RESEARCH
 
Our common goal is to understand the molecular basis of complex traits that differ between plant species and confer novel phenotypic characteristics. Computational approaches have become an integral part of our research, reflected by a continuously growing number of related projects and groups. The advertised projects will be performed in the groups of Angela Hancock (www.mpipz.mpg.de/imprs-hancock), Andrea Fulgione & George Coupland (www.mpipz.mpg.de/imprs-fulgione) and Stefan Laurent (www.mpipz.mpg.de/imprs-laurent) and applicants have the opportunity to indicate a preference in the online application process. 

YOUR PROFILE

You are a highly qualified and motivated student from any nationality with an MSc (or equivalent) degree in a related subject such as bioinformatics and population/quantitative genetics. You have a proved track record of academic and research excellence and are fluent in written and spoken English. Additionally, you have experience with one or more programming languages such as Python, Java, C/C++ and R. Applicants still studying should receive their degree not later than 5 months after the interview date in late April 2020.
 
OUR OFFER

We provide an excellent, international and interdisciplinary research environment with state-of-the-art facilities and a renowned faculty. Positions are fully funded for 3 years with possible extension. We are committed to increasing the number of individuals with disabilities in the workforce and encourage applications from such qualified individuals. Further, we seek to increase the number of women in those areas where they are underrepresented and therefore explicitly encourage women to apply.

YOUR APPLICATION

Apply by February 2nd 2020 at gradschool.mpipz.mpg.de. Only applications submitted through the online platform will be considered. Shortlisted candidates will be invited to the MPIPZ for interviews on March April 21-24th 2020. Successful candidates will start their positions preferably on October 1st 2020.

CONTACT

Dr. Stephan Wagner (IMPRS co-ordinator) at Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

Apply online via https://gradschool.mpipz.mpg.de/ and find additional information at http://www.mpipz.mpg.de/imprs/

Postdoc position “Modeling microbial communities of the Southern Ocean” [Royal NIOZ, Texel, the Netherlands]

We are looking for an enthusiastic early career scientist to work as a Post Doc in the research team of dr. Julia Engelmann (department of Marine Microbiology and Biogeochemistry, Royal NIOZ, Texel, the Netherlands). The team’s overarching interest is to understand how marine microbes interact with each other and form communities. The team applies bioinformatic and network biology approaches to marine marker gene, metagenomic and transcriptomic sequencing data to infer these interactions.

LOCATION: NIOZ TEXEL

VACANCY NR.: 2019 – 65

CLOSING DATE: 05-01-2020

THE PROJECT

At the base of the marine food web, microbes act both as primary producers and degraders of organic material. This organic matter fuels life in the oceans. While recent years have seen a tremendous increase in knowledge about diversity, genome composition and metabolic capabilities of microbes living in the ocean, we are still lack insights about how these communities interact and work at the systems level. Computational approaches such as network modeling can be used to generate hypothesis about potential interactions, which can then be validated with functional or other experimental approaches. Potential interactions include for example the provision of nutrients or energy substrates, competition for nutrients or response to signaling molecules. The Post-Doc will focus on elucidating marine microbial inter-species interactions in the Southern Ocean (Rothera, Antarctica; a 2 month expedition in 2021 is planned) and will perform sampling, high-throughput sequencing, network modeling and validation experiments both in the laboratories at Rothera and the NIOZ. One question we aim at answering is how climate change impacts microbial communities and especially their inter-species interactions in the Southern Ocean.

THE CANDIDATE

Do you have a PhD degree in Bioinformatics, Computational Biology, Microbiology, Molecular Ecology, Microbial Ecology, (Bio-)Statistics, or related fields? Are you organized and motivated to work in a vibrant research environment? Do you have computational and experimental (laboratory, field work) skills? Do you have good command of at least one programming language such as R or python and experience with Unix/Linux systems? Then apply for this post! Ideally, you also have experience in the analysis of high throughput genomic data. Due to the international character of the research group and institute, an excellent command of the English language is expected.

CONDITIONS OF EMPLOYMENT

We are offering a full-time position for 3 years, a pension scheme, a yearly 8% vacation allowance, year-end bonus and flexible employment conditions. Conditions are based on the Collective Labour Agreement of Research Centers. The position will be located on Texel. Cost of relocation and help with housing is provided by NIOZ.

FURTHER INFORMATION

Additional information about the vacancy can be obtained from: Dr. Julia Engelmann (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, Research Scientist).

Additional information about the procedure can be obtained from Alexandra Noppeney (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, Sr HR Advisor).

Interviews will be held Jan 16, 2020.

APPLY ONLINE

https://www.workingatnioz.com/job-application.html?id=7486

 

Application deadline: Jan 5, 2020

PhD position (m/f/d) in Computational Neuroimaging at Goethe-University Frankfurt / University Hospital Frankfurt

The laboratory for neuroimaging / the research group of Professor Christine Ecker at University Hospital Frankfurt is looking for a highly motivated and skilled PhD-candidate with a Master’s degree in neuroinformatics, bioinformatics, physics, or a related field.

You will be part of the “Transcranial brain stimulation as innovative therapy for chronic paediatric neuropsychiatric disorders” project (STIPED, https://cordis.europa.eu/project/rcn/207203/factsheet/en) and your tasks will include:

-	Acquisition of neuroimaging data (sMRI, DTI, and rsfMRI)
-	Pre-processing of neuroimaging data using standard neuroimaging software packages and custom pipelines 
-	Reproducible analysis of neuroimaging data using statistical methods and machine learning approaches in Matlab, Python and R
-	Writing research papers and other publications

For more information on the laboratory for neuroimaging, please visit https://www.kgu.de/einrichtungen/kliniken/zentrum-fuer-psychische-gesundheit/psychiatrie-psychosomatik-und-psychotherapie-des-kindes-und-jugendalters/forschungsbereiche/laboratory-of-neuroimaging

The contract is limited to 36 months. Salary and benefits are in accordance with a public service position in Germany (collective agreement TV-G-U E13, 70%). Working language is English or German.

If you have any questions left, please contact Dr. Tim Schäfer (tim.schaefer[at]kgu.de). To apply, send your application (a short letter of motivation, a current CV, and contact data of up to three references) by email to Prof. Christine Ecker (christine.ecker[at]kgu.de). Please provide all documents as a single PDF file.


PhD Position (m/f/d) - Functional Comparative Genomics of Oomycetes

Job offer Ref. # 12-19013

 

The Senckenberg Gesellschaft für Naturforschung (SGN) is a member of the Leibniz Association and is based in Frankfurt am Main, Germany. LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) is a joint venture of the Senckenberg Gesellschaft für Naturforschung (SGN), Goethe-University Frankfurt, Justus-Liebig-University Giessen and Fraunhofer Institute for Molecular Biology and Applied Ecology IME aiming to intensify biodiversity genomics in basic and applied research. We will 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.

 

The Senckenberg Gesellschaft für Naturforschung and the LOEWE-TBG invite applications for a

 

PhD position (m/f/d)

Functional Comparative Genomics of Oomycetes

(TV-H E13, half time position)

 

 

Your tasks

 

·         Library preparation and genome sequencing using latest technologies (including oxford nanopore sequencing)

·         Genome assemblies and annotation

·         Comparative genomics focusing on functional aspects, such as pathogenicity genes and regulatory networks

·         Pattern analyses using standard algorithms and deep learning approaches

 

Your profile

 

·         Master or equivalent Diploma in biology, bioinformatics or related subjects

·         Experience with handling large amounts of sequence data

·         Experience and exceptional interest in comparative genomics and evolutionary biology research

·         Ability to effectively communicate and organize workflows, to closely collaborate in interdisciplinary teams

·         Proficient use of the English language (C1 or native)

 

What is awaiting you?

 

·         An interesting task in a dynamic team of researchers in an international research group

·         Exposure to an additional 20 research groups in the LOEWE excellence centre

·         A workplace close to the city center of Frankfurt, a lively and diverse city with high life quality

·         Flexible working hours –company pension scheme – Senckenberg badge for free entry in museums in Frankfurt a family-conscious personnel policy

 

 

Salary and benefits are in accordance with a public service position in Germany (collective agreement TV-H E13, 50%). The contract shall start as soon as possible and will be limited to 36 months. Equally qualified handicapped applicants will be given preference. The place of work is in Frankfurt am Main at the Senckenberg Biodiversity and Climate Research Centre (SBiK-F). The employer is the Senckenberg Gesellschaft für Naturforschung.

 

We look forward to your application!

 

Please send your application, mentioning the reference of this job offer (ref. #12-19013) by January 15th, 2020 (deadline) by e-mail (attachment in a single pdf document) and including

- 
a cover letter describing your suitability and motivation

a detailed CV

your credentials and certificates

-  and contact details of two potential references to:

  

Senckenberg Gesellschaft für Naturforschung                                                                        

Senckenberganlage 25

60325 Frankfurt

 

E-Mail: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

  

 

For scientific enquiries please get in contact with Prof. Dr. Marco Thines (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).

PhD-Position in Nutritional Medicine & Bioinformatics at University of Kiel

The Research Group for Nutriinformatics at the University of Kiel is seeking a PhD-candidate with a Masters degree in bioinformatics, biostatistics, biotechnology or another study program with a strong focus on quantitative methods in molecular life sciences.

The candidate will apply bioinformatic and systems biology approaches in the field of nutritional medicine. The PhD-Project will be carried out in close collaboration with experimental research labs in Kiel and the University Hospital Schleswig-Holstein. The candidate will have access to large data sets and state-of-the-art experimental and computational facilities to investigate the interplay between human and microbial metabolism and the impact of nutrition.

Together with other world-renowned research institutes in Kiel (e.g. Max-Plank-Institute for Evolutionary Biology and the GEOMAR - Helmholtz Centre for Ocean Research ), Kiel University has become a hot-spot for Microbiome Research. Therefore, Kiel is an ideal location for scientific communication and to further develop essential skill for a career in science and information technology.

Kiel is located in northern Germany directly at the coast of the Baltic sea and offers plenty of opportunities for outdoor activities.

How to apply:
Please refer to the application procedure details in the job announcement (https://www.uni-kiel.de/personal/de/stellen/extern/wiss/dateien-extern-wiss/ausschreibungstext-promotion.pdf). For questions regarding the position please contact Jun.-Prof. Silvio Waschina (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).


Links:

Detailed job offer: https://www.uni-kiel.de/personal/de/stellen/extern/wiss/dateien-extern-wiss/ausschreibungstext-promotion.pdf