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Stellenangebote

High-throughput virus discovery related to human cancer and other diseases

The recent revolution in nucleic acid sequencing technologies, collectively referred to as "next-generation sequencing"(NGS), opened up unprecedented opportunities to discover novel viruses. It is becoming increasingly evident that the spectrum of currently known virus species just represents the tip of an iceberg. We developed and optimized a highly sensitive and specific method of viral sequence detection in unprocessed NGS data. By use of high performance computing we provided the proof of principle for the feasibility of our strategy in a recent study describing the discovery of a whole new family of non-enveloped fish viruses shedding light on the long-term coevolution of hepatitis B viruses with their vertebrate hosts over a period of 420 million years (Lauber et al., Cell Host & Microbe 2017). Due to the global medical importance, we will now put a major emphasis on the search for unknown human viruses in NGS data related to cancer, as well as some other specified diseases that might be linked to infectious agents, such as autoimmune and neuro-inflammatory disorders. We hypothesize that a substantial proportion of human viruses yet have escaped detection, particularly if they are transmitted vertically and/or cause only mild acute symptoms (if at all), while being able to establish latent long-term infections. Any such viruses could represent etiologic agents involved in the development of human disease without being so far recognized due to the temporal delay between primary infection and disease onset.

Your qualifications

Applicants should hold a Master degree in Bioinformatics or Biotechnology. We are looking for a highly motivated candidate with strong skills in scientific programming and expertise in handling and analyzing NGS data. Advanced knowledge in fundamental virology is advantageous. 

In addition:

Excellent academic performance

Very good master's degree in Bioinformatics or Biotechnology

Very good knowledge of English

Willingness to move to the university location

For further information:

 

https://hectorfellowacademy.applicationportal.org/home.html 

https://www.sciencedirect.com/science/article/pii/S1931312817303025?via%3Dihub 

The European Galaxy Team is looking for a software engineer (100%)

<a href="https://galaxyproject.eu">European Galaxy Team</a> is hiring!

We have a wide variety of active projects and are searching for a software engineer (100%), system analysts/administrators (100%), data analyst (100%), and a community and/or research manager (100%).

Current areas of expertise include:

  • Distributed computing and systems programming. We are engaged in the development of workflow systems, cloud computing based solutions, and other projects involving high performance and data intensive computing.
  • Web-based visualization and visual analytics. We are building web interfaces for visual analysis of large data sets that leverage cutting edge web technologies.
  • Machine learning and cheminformatics. We want to make machine learning and cheminformatics more accessible and reproducible.
  • Linux containers technologies and software management with conda. We are heavily involved in <a href="https://bioconda.github.io/">bioconda</a>, <a href="https://conda-forge.org/">confda-forge</a>and <a href="https://biocontainers.pro">biocontainers</a> to build the new scientific stack for reproducible research.
  • Train the next generation of data scientists. We aim to democratize bioinformatics infrastructure and knowledge. We are passionate about training and education across the world.

Regardless of your areas of expertise we seek talented, self-motivated individuals to join<a href="https://usegalaxy-eu.github.io/freiburg/people">our team</a>. <a href="https://galaxyproject.org">Galaxy</a>is developed in an academic research environment, and members of the European Galaxy team work closely with researchers on projects at the leading edge of data-intensive science. Galaxy is written in Python, but also makes substantial use of JavaScript, Canvas, and other modern Web technologies. Many of the analysis components of Galaxy are performance critical and are implemented in C and other languages as well. Galaxy makes extensive use of Conda packages and Containers and can utilize the  <a href="https://www.denbi.de/cloud">de.NBI Cloud</a> as well as the <a href="https://www.hpc.uni-freiburg.de/nemo">NEMO supercomputer</a> .

 

If you are interested to work with us,  Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) and help us to make science more accessible, reproducible, and transparent.

Bioinformatics Scientist (f/m/d): Full-time and permanent with a keen interest in applying state of the art bioinformatics to target ID and drug discovery

We are applying advanced methods in transcriptomics, proteomics, CRISPR and compound screening to generate large volumes of biological data. In close collaboration with wet-lab and with project scientists the bioinformatics team analyzes these data to generate knowledge about gene function and compound activities in various disease areas. As integral part of the data analysis, we develop our own algorithms and tools according to project needs.

 

Evotec is a leader in the discovery and development of novel small molecule drugs with operational sites in Europe and the US. The Company has built substantial drug discovery expertise and an industrialized platform that can drive new innovative small molecule compounds into the clinic. In addition, Evotec has built a deep internal knowledge base in key therapeutic areas including neuroscience, pain, inflammation, oncology, metabolic and infectious diseases. Leveraging these skills and expertise the Company intends to deliver superior science-driven discovery alliances with pharmaceutical and biotechnology companies.

At our subsidiary in Goettingen, the bioinformatics team is looking for a dedicated and professional Bioinformatics Scientist (f/m/d) Full-time and permanent with a keen interest in applying state of the art bioinformatics to target ID and drug discovery.

 

We are applying advanced methods in transcriptomics, proteomics, CRISPR and compound screening to generate large volumes of biological data. In close collaboration with wet-lab and with project scientists the bioinformatics team analyzes these data to generate knowledge about gene function and compound activities in various disease areas. As integral part of the data analysis, we develop our own algorithms and tools according to project needs.

 

Your key responsibilities

 

·         Multi-OMICS data analysis, e.g. single cell and high throughput RNA-Seq

·         Build interactive applications for multi-OMICS data

·         Work with researchers in interdisciplinary project teams in multiple research programs

 

Your qualifications

·         Hold a master degree or PhD in bioinformatics, informatics or biostatistics

·         Demonstrated strong programming skills in at least two programming languages (e.g. R, Python, JavaScript)

·         Proficiency in working with bioinformatics tools and understanding of common bioinformatics algorithms

·         Knowledge of software development methodology (version control, testing, documentation) is a plus

·         Excellent interpersonal and communication skills and the ability to work independently in a fast-paced work environment

·          

Our offer

·          

·         A permanent position within a vigorous and exciting professional environment promoted by an open culture and a spirit of community

·         A diverse, international workforce with a dynamic working environment that fosters creativity, innovations and teamwork

·         Capital-forming benefits, holiday pay and annual bonus payment depending on performance

 

Link: https://evotecgroup.wd3.myworkdayjobs.com/en-US/Evotec_Career_Site/job/Goettingen/Bioinformatics-Scientist_REQ-00114

 

 

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Bioinformatik - Doktoranden / Postdoc Positionen im Centre for the Advanced Study of Collective Behaviour

The Centre for the Advanced Study of Collective Behaviour will create a global hotspot for the integrated study of collective behaviour across a wide range of species and scales of organisation. With English as the working language, it will be a global hub for scientists seeking to create a synergistic, interdisciplinary environment for the study of collective behaviour. Establishing collective behaviour as an integrative field, the Centre will bring together international researchers from biology, computer science, social psychology, physics, and behavioural economics to work closely on addressing common questions across species boundaries. The Centre is recruiting up to 25 PhD and Post-doc positions in collective behaviour, including positions in Bioinformatics, Computer Science and related areas.  Candidates should be interested in interdisciplinary research. Detailed information can be found here: https://www.exc.uni-konstanz.de/collective-behaviour/open-positions/

Links:
https://www.exc.uni-konstanz.de/collective-behaviour/open-positions/

Biostatistician: Centre for Statistical Data Analysis

Location: EMBL Heidelberg, Germany

Staff Category: Staff Member

Contract Duration: 3 years (renewable)

Grading: 6, 7 or 8; depending on experience and qualifications

Closing Date: 10 March 2019

Reference Number: HD01456

 

EMBL is an international research organization covering many fields of modern biology. Five Computational Centres provide expertise, advice, and training for scientists across EMBL. We are looking for a statistician or data scientist to Head the EMBL Centre for Statistical Data Analysis.

 

Your role

 

Your responsibilities will include:

 

• Statistical consulting for EMBL researchers

• Teaching short courses on computational statistics / data science in biology

• Collaboration on selected research projects with EMBL research groups

 

As statistician/data scientist, you will be interested in statistical applications in modern biology, in computational method development for new technologies (single cell ‘omics, imaging, proteomics, microfluidics), in data visualization and data integration, and in method benchmarking and teaching. You will be co-affiliated with the research group of Wolfgang Huber (see https://www.huber.embl.de/).

 

The position also offers the opportunity to help shape future developments of ‘data science’ in biology, such as publication and communication best practices.

 

You have

 

A PhD or equivalent qualification in a quantitative science (statistics, mathematics, computer science, physics) with solid theoretical foundations in probability and applied statistics and some experience in data analysis of modern biological data. As our ideal candidate you should enjoy teamwork and be excited by providing consulting and teaching services at an advanced level in a world-class research environment. Excellent communication skills in written and spoken English are required.

 

You might also have

 

Candidates should have a solid understanding of programming concepts and multiple languages, including advanced R. Proficiency with scientific authoring frameworks such as LaTeX, Rmarkdown and HTML5 is a plus.

 

Why join us

 

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, as well as financial support for relocation and installation, including your family and the availability of an excellent child care facility on campus. EMBL has a large thriving community of bioinformaticians, working in close collaboration with experimental scientists and with strong links to other local scientists and institutions.

 

What else do I need to know

 

We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

 

Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research.

 

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

 

Ph.D. Student in Translational Immunoinformatics (Lung Diseases)

The Institute of Computational Biology is globally recognized for innovations in data analysis and modeling of biological systems, anchored at the Helmholtz Zentrum Munich and the Technical University Munich.

For our research team "Translational Immunoinformatics" we are currently looking for a

PhD Candidate for the Project: "Cell Fate Modeling in Chronic Lung Diseases” (E13 TV-L)

Job Description

The Ph.D. project will focus on the characterization of genetic factors describing pulmonary fibroblasts in chronic lung diseases and the identification of transcriptional factors that can be used to reprogram diseased lung fibroblasts to healthy lung epithelial cells.

 

The aims of the projects involve:

Identifying biomarkers that lead to fibroblast formation in the lung for early risk assessment

Developing a risk prediction model using the identified biomarkers

Modeling longitudinal mass cytometry data to describe the reprogramming path of fibroblasts to epithelial cells

Analyzing and integrating simultaneously collected single-cell RNA-seq data

 

The Ph.D. candidate will have the opportunity to be integrated into the experimental partner lab to help develop novel analytical strategies in direct interaction with the members of the experimental lab.

 

 Your Qualifications

 

A Master’s Degree in Biostatistics, Bioinformatics, Statistics or related fields (with significant experience in Bioinformatics)

Experience in multivariate statistics and Bayesian modeling

Excellent programming skills (R, Python, C/C++)

Scientific curiosity and ability to work independently

Highly motivated to work in a young and multi-disciplinary, collaborative environment

Fluent in spoken and written English

 

The following qualifications are considered advantageous:

 

Experience with NGS (transcriptomic and genomic) analysis

Basic understanding of mass cytometry analysis

Basic understanding of single-cell RNA-Seq analysis

 

Our Offer

 

At the Helmholtz Zentrum München, you can contribute together with leading researchers to the investigation of the development, prevention, and treatment of environmental diseases such as diabetes, chronic lung diseases, and allergies. To further promote your professional development, we offer extensive and targeted research training and career programmes. We support the reconciliation between work and private life with flexible working time models, occupational health management, day care facility for children, a childcare subsidy, Elder Care, as well as other counseling and support services.

Remuneration and benefits are following the collective agreement for the public service (EG 13 50% TV EntgO Bund). Also, there is also the possibility of granting an allowance amounting to 15% if the necessary conditions are fulfilled.

The position is (initially) limited to three years.

The activity involves specialized knowledge and experiences specific to own scientific skills.

As a holder of the Total E-Quality Award, we promote equality of opportunity. Applications from women are welcome. Qualified applicants with physical disabilities will be given preference.

Please apply through our online application system with a motivation letter, curriculum vitae, transcripts and certificates, and contact details of two academic references.

Apply now: https://fragebogen.candibase.de/helmholtz/mainform.php?param=28723aca288cb003ca4914689782604a&lang=en

Ph.D. Student in Translational Immunoinformatics (Diabetes)

The Institute of Computational Biology is globally recognized for innovations in data analysis and modeling of biological systems, anchored at the Helmholtz Zentrum Munich and the Technical University Munich.

For our research team "Translational Immunogenetics" we are currently looking for a

PhD Candidate for the Project: "Effects of Non-Conventional Epitopes in Type 1 Diabetes"(E13 TV-L)

Job Description

The Ph.D. project will focus on studying the effects of non-conventional epitopes on type 1 diabetes progression and their potential therapeutic exploitation.

The aims of the projects involve:

Developing bioinformatics pipelines to identify non-conventional epitopes derived from alternative splice forms, fusion proteins, and post-translational modifications

Developing predictive models to estimate the effect of post-translational modifications on HLA-epitope affinity

Investigating the prevalence and impact of non-conventional epitopes on disease progression and their interplay with the T-cell population

Developing optimization models for computer-aided vaccine design for type 1 diabetes

 

Your Qualifications

Master’s Degree in Bioinformatics, Biostatistics, Informatics or related fields (with significant experience in Bioinformatics)

Experience with NGS (transcriptomic and genomic) analysis

Experience in machine learning

Excellent programming skills (R, Python, C/C++)

Scientific curiosity and ability to work independently

Highly motivated to work in a young and multi-disciplinary, collaborative environment

Fluent in spoken and written English

 

The following qualifications are considered advantageous:

Basic understanding of the immune system

Know How in combinatorial optimization

 

Our Offer

At the Helmholtz Zentrum München, you can contribute together with leading researchers to the investigation of the development, prevention, and treatment of environmental diseases such as diabetes, chronic lung diseases, and allergies. To further promote your professional development, we offer extensive and targeted research training and career programmes. We support the reconciliation between work and private life with flexible working time models, occupational health management, day care facility for children, a childcare subsidy, Elder Care, as well as other counseling and support services.

Remuneration and benefits are following the collective agreement for the public service (EG 13 50% TV EntgO Bund). Also, there is also the possibility of granting an allowance amounting to 15% if the necessary conditions are fulfilled.

The position is (initially) limited to three years.

The activity involves specialized knowledge and experiences specific to own scientific skills.

As a holder of the Total E-Quality Award, we promote equality of opportunity. Applications from women are welcome. Qualified applicants with physical disabilities will be given preference.

Please apply through our online application system with a motivation letter, curriculum vitae, transcripts and certificates, and contact details of two academic references.

 

 Apply now: https://fragebogen.candibase.de/helmholtz/mainform.php?param=627807ce092170db5005d4c6df6be3b8&lang=en

 

(Bio-)Informatician, Natural Scientist as Projectmanager (m/f) [University Medical Center Göttingen]

The Institute for Medical Bioinformatics is looking for a

(Bio-)Informatician, Natural Scientist as Projectmanager (m/f)

The job is to be filled initially for 2 years. Remuneration is based on TV-L (up to E12). Later prolongation in form of a permanent position is desired.

About us

At the Institute for Medical Bioinformatics of the University Medical Center Göttingen, methods are being developed and applied in collaborative biomedical research projects in order to improve diagnostics and therapy decisions through molecular and genomic data.

Your tasks

    • Independent project and data management at the institute, e.g. setting-up and maintaining the necessary management systems, participation in the application for third-party funded projects, management of projects and consortia, as well as preparation of project reports.

    • Scientific interest and participation in research projects. For the job holder, there is a longer term possibility to prepare a bioinformatic dissertation.

Your profile:

    • Completed university or applied university studies (computer science, bioinformatics, engineering or natural sciences).

    • Very good English skills.

    • In-depth IT knowledge - database systems (SQL), Linux, scripting languages. 

    • Ideally, experience in project management.

    • Ideally, experience in scientific work

    • Organizational skills, good time management and independent working methods.

    • Teamwork and a high level of commitment

    • Safe and friendly manner, professionalism, discretion and loyalty combined with high resilience.

Contact for applications 

Your application should include a letter of motivation in English. Please send your application (preferably as a single PDF file) by e-mail at latest 15.01.2019 to:

 

Prof. Dr. Tim Beißbarth

University Medical Center Göttingen

Institute for Medical Bioinformatics

Goldschmidtstraße 1

37077 Göttingen

Tel.: 0551 / 39-14912

Fax: 0551 / 39-14914

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Web: http://www.bionf.med.uni-goettingen.de 

 

 

 

 

 

 

 

 

 

 

 

Wissenschaftliche Mitarbeiterin/ Wissenschaftlichen Mitarbeiter [Universität Bielefeld ]

Ihre Aufgaben
Die Arbeitsgruppe Bioinformatik und Medizinische Informatik beschäftigt sich mit der Integration und Analyse von molekularbiologischen und medizinischen Datenquellen. Ein aktueller Arbeitsbereich befasst sich mit der Entwicklung von neuartigen Methoden zur Vorhersage genetisch bedingter Interaktionen von Arzneimitteln.
Der Stelleninhaberin/dem Stelleninhaber obliegen Forschungstätigkeiten im Bereich der Informationsfusion und/oder Datenvisualisierung durchführen und darauf aufbauend biomedizinische Informationssysteme zur Analyse von Arzneimittel Interaktionen konzipieren und implementieren. Dadurch soll das existierende Forschungsprogramm (KALIS) für die Identifikation und Reduktion von Arzneimittel Interaktionen unter Berücksichtigung der molekularen Wirkmechanismen weiterentwickelt werden (75 %).
Zudem nimmt die Stelleninhaberin/der Stelleninhaber Aufgaben im Rahmen der Lehre und Betreuung von Bachelor-und Masterstudierenden wahr (25 %).

Ihr Profil
Das erwarten wir
-abgeschlossenes wissenschaftliches Hochschulstudium der Bioinformatik oder einer angrenzenden Disziplin (Masterabschluss als auch Bachelorabschluss ist möglich)
-selbstständiges, eigenverantwortliches und engagiertes Arbeiten
-ausgeprägte Organisations-und Koordinationsfähigkeit
-kooperative und teamorientierte Arbeitsweise
Das wünschen wir uns
-Erfahrungen im Bereich molekularer Wirkmechanismen und biochemischer Prozessmodellierung
-Erfahrungen im Bereich der Datenintegration und Informationsfusion

-Erfahrung bei der Betreuung von studentischen Projekt-oder Abschlussarbeiten

-Publikationstätigkeit und Erfahrungen im Bereich der Entwicklung und Implementierung webbasierter Informationssysteme

Unser Angebot
Die Vergütung erfolgt je nach persönlicher Qualifizierung bis zur Entgeltgruppe 13 des Tarifvertrages für den öffentlichen Dienst der Länder (TV-L). Die Stelle ist gemäß §2 Absatz 1 Satz 1 WissZeitVGfür die Dauer von drei Jahren befristet (entsprechend den Vorgaben des WissZeitVGund des Vertrages über gute Beschäftigungsbedingungen kann sich im Einzelfall eine abweichende Vertragslaufzeit ergeben). Die Beschäftigung ist der wissenschaftlichen Qualifizierung förderlich. Es handelt sich um eine Vollzeitstelle. Auf Wunsch ist grundsätzlich auch eine Stellenbesetzung in Teilzeit möglich, soweit nicht im Einzelfall zwingende dienstliche Gründe entgegenstehen.
Die Universität Bielefeld legt Wert auf Chancengleichheit und die Entwicklung ihrer Mitarbeiterinnen und Mitarbeiter. Sie bietet attraktive interne und externe Fortbildungen und Weiterbildungsmaßnahmen. Zudem können Sie eine Vielzahl von Gesundheits-, Beratungs-und Präventionsangeboten nutzen. Die Vereinbarkeit von Beruf und Familie hat einen hohen Stellenwert.

Interessiert?
Wir freuen uns über Ihre Bewerbung per Post an die untenstehende Anschrift oder per E-Mail unter Angabe der Kennziffer wiss18342 in einem einzigen pdf-Dokument an Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! bis zum 2Wochen nach Veröffentlichung. Bitte verzichten Sie auf Bewerbungsmappen und reichen Sie ausschließlich Fotokopien ein, da die Bewerbungsunterlagen nach Abschluss des Auswahlverfahrens vernichtet werden. Weitere Informationen zur Universität Bielefeld finden Sie auf unserer Homepage unter www.uni-bielefeld.de. Bitte beachten Sie, dass Gefährdungen der Vertraulichkeit und der unbefugte Zugriff Dritter bei einer Kommunikation per unverschlüsselter E-Mail nicht ausgeschlossen werden können. Informationen zur Verarbeitung von personenbezogenen Daten finden Sie unter
http://www.uni-bielefeld.de/Universitaet/Aktuelles/Stellenausschreibungen/2018_DS-Hinweise.pdf.

Bewerbungsanschrift
Universität Bielefeld
Technische Fakultät, AG Bioinformatik/Med. Informatik
Herrn Prof. Dr. Ralf Hofestädt
Postfach 10 01 31
33501 Bielefeld
Ansprechpartner
Prof. Dr. Ralf Hofestädt
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PhD Student position (65% E13, 3 years, available immediately) in the newly established group for Computational Systems Medicine

PhD Student position (65% E13, 3 years, available immediately) in the newly
established group for Computational Systems Medicine at the Chair of
Experimental Bioinformatics, Technical University of Munich, Freising, Germany.

Project description:
Diseases are currently defined and diagnosed based on symptoms (e.g.,
hypertension, depression) or affected organs (e.g., heart failure,
nephropathy). Clearly, there is a lack of mechanistic understanding of diseases
that could improve disease definitions and allow for more informed selection
and development of therapies. To achieve such understanding we develop
integrative bioinformatics methods leveraging network analysis, machine
learning techniques and statistical approaches. Your work will focus on the
development of graph-based machine learning techniques to identify disease- and
patient-specific dysregulated subnetworks.

What you should have:
- Degree in bioinformatics, molecular biology, computer science, or similar
- Solid understanding of molecular biology
- Experience with omics data analysis, graph theory / network biology, and machine learning
- Strong programming skills in Python, R, and / or Java
- Familiarity with Linux and HPC environments
- Fluency in written and spoken English
- Strong commitment and motivation, ability to work collaboratively

What we offer:
At the Chair of Experimental Bioinformatics you will find a
supportive and productive research environment with a young, dynamic team of
more than 20 international researchers at different stages in their career and
education. Find us online at: https://www.exbio.de and
https://compsysmed.de.

Send your application including your CV, grades, publications (if any) and two
reference letters to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.