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Bioinformatiker für nationales NGS Zentrum in Kiel

Das Institut für Klinische Molekularbiologie möchte ab sofort zwei Stellen im Bereich der Bioinformatik besetzen. Der Hauptfokus der Stellen wird die wissenschaftliche Betreuung des "Competence Centre for Genomic Analysis" (CCGA) sein. Das Zentrum wurde kürzlich als eines von vier nationalen NGS Infrastrukturen der DFG ausgewählt und wird in diesem Rahmen deutschlandweite NGS Dienstleistungen über ein breites Spektrum an Taxa und Anwendungen anbieten.

Die erfolgreichen Bewerber(innen) werden im Rahmen ihrer Tätigkeit die am CCGA durchgeführten Sequenzierprojekte betreuen, beginnend mit der initialen Projektplanung bis hin zur Datenbearbeitung und Auslieferung. Zusätzlich zu den Service-Aufgaben besteht die Möglichkeit zur Teilnahme an einer Vielzahl von anspruchsvollen wissenschaftlichen Projekten und den damit einergehenden Möglichkeiten zur beruflichen Weiterqualifikation in der Bioinformatik.

Die vollständige Stellenausschreibung ist zu finden unter: https://www.uksh.de/Karriere/Stellenangebote-nr-20180486.html

Systementwickler/in im Bereich (Bio)informatik [CCGA Kiel]

Als größtes akademisches Zentrum für Hoch-Durchsatz Sequenzierung (Next Generation Sequencing, NGS) wurde das Institut für Klinische Molekularbiologie (IKMB) kürzlich in einer Initiative der DFG zu einem der 4 in Deutschland geförderten Kompetenzzentren für die Standardisierung und Zentralisierung von NGS Technologien ernannt.

Das hierfür im IKMB neu gegründete „Competence Center for Genomic Analysis” (CCGA) sucht nun schnellstmöglich einen Systementwickler im Bereich Bioinformatik und BioIT-Services, um das vorhandene Team bei der Entwicklung und Erweiterung von benötigten Infrastrukturen und Services zu unterstützen. Neben dem CCGA, welcher u.a. die neuste Generation von NGS-Instrumenten einsetzen wird (Illumina NovaSeq6000), betreibt das IKMB Hoch-Durchsatz-Plattformen für Genotypisierung sowie Genexpressionsanalyse und ist darüber hinaus eng mit der lokalen Biobank PopGen vernetzt. Für die Bereiche Bioinformatik, IT und Datenmanagement hält das IKMB aktuell mehr als 2PB Speicherkapazität und ein „high-performance compute cluster“ (HPC) mit mehr als 1000 cores bereit.

Die volle Stelleanzeige ist erreichbar unter: https://www.uksh.de/Karriere/Stellenangebote-nr-20180487.html

 

Open PhD position in Epigenetics (Marie Sklodowska-Curie Innovative Training Network EpiDiverse)

EpiDiverse is a Marie Skłodowska-Curie Innovative Training Network aimed to study of epigenetic variation in wild plant species. Within this network, a PhD position at the Institute of Applied Genomics (IGA) -Technology Services in Udine (Italy) became available lately. If you are a biologist with interest and some background in bioinformatics, or know someone with that interest, please feel free to apply or forward this information.

Your Benefits:

    Fully funded PhD position for 3 years
    Europe-wide research network (Netherlands, Germany, France, Spain, Czech Republic, Italy and Austria)
    Participating companies (Roche Diagnostics, ecSeq Bioinformatics and IGA-TS)
    Spend up to 12 month at other groups or companies within the network for joint projects (all expenses are covered)
    Get an interdisciplinary training
    Do fundamental research with experts in the field

Information about the specific research project can be found here.

The position will be staffed as soon as possible. So, hurry up!

Email your application directly to This email address is being protected from spambots. You need JavaScript enabled to view it.

Postdoc position in animal genetics/population genomics [Veterinärwissenschaftliches Department, LMU München]

The Population Genomics Group at the Department of Veterinary Sciences, LMU Munich, is seeking a Postdoctoral Research Associate at the earliest possible date. The full-time position is limited to 3 years with a possible extension. The position is intended to facilitate the qualification of young scientists and offers the possibility to habilitate. Payment is according to salary group E13 TV-L. Part-time employment is possible.

The research focus of the Population Genomics Group is on functional and neutral genetic diversity in livestock populations as the basis for sustainable future development in animal breeding. Our functional genomic analyses include the detection of causal mutations behind precisely defined mono- or polygenic phenotypes with regard to production quality and animal welfare as well as domestication research and analyses of genetic diversity in modern and historical samples.

Tasks:
- assistance in current research projects of the working group
- conception and direction of own projects in the research field of the working group including acquisition of funding
- assistance in grant writing
- co-supervision of PhD students
- participation in teaching, especially by offering electives from the own area of expertise

Requirements:

- a PhD in bioinformatics or a different field (veterinary medicine, animal breeding, wildlife biology or similar) with strong bioinformatic focus, preferably in the field of animal genetics or population genomics
- experience with software for NGS data analysis, good ability to independently conduct (population-)genomic and bioinformatic/statistical data analyses
- experience with programming and/or scripting languages like R, Python, Java etc.
- experience with Bayesian statistics (e.g. ABCtoolbox and/or BEAST) is an advantage but not a prerequisite
- practical experience in molecular genetic lab work is an advantage but not a prerequisite
- experience in publishing in international journals
- fluent language skills in English

The Population Genomics Group is currently located at the English Garden in Munich. It is expected to move to Martinsried (close to the Gene Center of the LMU) in 2018.

Your workplace is centrally located in Munich and easy to reach by public transportation. We offer an interesting and responsible job with good opportunities for further education and personal development. Equally qualified disabled applicants will be preferred. Female candidates are encouraged to apply.

Please send your complete application as a single PDF (CV, motivation statement and research experience, record of study, certificates) until June 20th, 2018 to:


PD Dr. habil. Ivica Medugorac

AG Populationsgenomik
Veterinärwissenschaftliches Department
LMU München
Veterinärstraße 13
80539 München

This email address is being protected from spambots. You need JavaScript enabled to view it. (CC to: This email address is being protected from spambots. You need JavaScript enabled to view it.)

For further information about the position, please contact Dr. Medugorac via e-mail or phone (+49 89 2180 3310).

 

PhD student/Postdoc bioinformatics ERC project [Heinrich Pette Institute – Leibniz Institute for Experimental Virology (2)]

The position focuses on developing software based on available open source code to facilitate spectral assignment and interpretation on a newly developed mass spectrometry system. Data created will allow high resolution structural proteomics using structural modelling. We are searching for exceptional, highly motivated candidates holding at least a Master degree in bioinformatics and related disciplines with experience in software development and computational modelling. Experience in any of the following areas will be considered an asset: structural biology, biophysics, virology, mass spectrometry and related data analysis. The position is initially funded for four years.

We offer the opportunity to perform cutting-edge research in an extremely stimulating work environment equipped with state-of-the-art technology. All positions have the possibility for extension after the initial funding period. Payment and social benefits will be in accordance with the regulations of the German TV-AVH (salary agreement for public service employees). The Heinrich-Pette-Institute is an international research institute with English as the working language. For further information please visit the website, http://www.hpi-hamburg.de, or contact Dr. Charlotte Uetrecht (This email address is being protected from spambots. You need JavaScript enabled to view it.).

The Heinrich-Pette-Institute promotes the professional equality between women and men. Handicapped applicants with equal qualifications will be given preferential treatment.

Please send your application by September 30, 2018. Please indicate the position of interest and your earliest possible starting date. Applications providing a motivating cover letter, a CV and the names of at least two referees in a single PDF should be sent via regular or electronic mail to:


Heinrich Pette Institute
Mrs Anke Metzger
Personnel Department
Martinistraße 52
20251 Hamburg
This email address is being protected from spambots. You need JavaScript enabled to view it.

PhD student/Postdoc virology ERC project [Heinrich Pette Institute – Leibniz Institute for Experimental Virology (1)]

The Heinrich Pette Institute – Leibniz Institute for Experimental Virology in Hamburg, Germany, invites applications for three positions in the junior research group "Dynamics of viral structures" of Dr. Charlotte Uetrecht.The group studies functions and interactions of viral proteins. Using advanced mass spectrometric techniques, especially native mass spectrometry (MS), structural information of viral protein complexes is derived in a time-resolved manner.

The position focuses on studies of coronaviral replication/transcription complexes with new mass spectrometric approaches. We are searching for exceptional, highly motivated candidates holding at least a Master degree in biology, biochemistry or other life science related disciplines with experience in virology. Experience in any of the following areas will be considered an asset: structural biology, biophysics, structural proteomics/mass spectrometry, lasers, instrument development, cell biology, or protein purification. The position is initially funded for four years.

We offer the opportunity to perform cutting-edge research in an extremely stimulating work environment equipped with state-of-the-art technology. All positions have the possibility for extension after the initial funding period. Payment and social benefits will be in accordance with the regulations of the German TV-AVH (salary agreement for public service employees). The Heinrich-Pette-Institute is an international research institute with English as the working language. For further information please visit the website, http://www.hpi-hamburg.de, or contact Dr. Charlotte Uetrecht (This email address is being protected from spambots. You need JavaScript enabled to view it.).

The Heinrich-Pette-Institute promotes the professional equality between women and men. Handicapped applicants with equal qualifications will be given preferential treatment.

Please send your application by September 30, 2018. Please indicate the position of interest and your earliest possible starting date. Applications providing a motivating cover letter, a CV and the names of at least two referees in a single PDF should be sent via regular or electronic mail to:

Heinrich Pette Institute
Mrs Anke Metzger
Personnel Department
Martinistraße 52
20251 Hamburg

Research Scientists Bioinformatics (m/f) [University Medical Center Hamburg-Eppendorf, Ref: 2018-344A]

We are seeking scientists with a background in Bioinformatics or in a closely related discipline. The main focus of the open position will be the analysis of high-throughput sequencing (NGS) for the II. Medical Clinic and the Children's Cancer Center. The position will be embedded in the Bioinformatics Core group.

Main tasks:
 - Analysis of high-throughput sequencing data
 - Development of workflows and tools for sequence data processing
 - Consultation on issues of sequencing and sequence data analysis

Candidate profile:
 - Successfully completed studies in Bioinformatics, Biostatistics or in a closely related scientific subject
 - Good command of Linux and at least one of the following programming languages: Ruby, R, Python, Java, Perl
 - Good oral and written communication skills in English
 - Ability to clearly explain methods and results to scientists of other disciplines
 - Desirable skills: competent handling of various sequence data, good understanding of statistical methods and their application to large data sets, and knowledge of machine learning techniques

We offer a work environment which provides equal opportunities regardless of age, gender, sexual identity, disability, origin or religion. This commitment is confirmed by signing the “Diversity Charter of German Companies”. We explicitly strive for an increased proportion of women in leading positions, particularly for employees in research and education. Female applicants will be treated preferentially in case of equivalent qualification. The same applies in case of minor representation of a certain gender in the advertising section. Applicants with severe disability will be treated preferentially in case of equivalent suitability, qualification and professional performance.

We look forward to receiving your application by June 17th 2018.

Please send your complete application to: This email address is being protected from spambots. You need JavaScript enabled to view it. (reference number: 2018-344A) or submit online using our job portal: www.uke.jobs

For further information please contact Prof. Dr. Mascha Binder (#49-(0)40-7410-58787) or Prof. Dr. Martin Horstmann (#49-(0)40-42605-1211).

1 Postdoctoral scientist and 2 PhD students in Bioinformatics/Computational Biology [Innsbruck, Austria]

On a project funded by the European Research Council (ERC) we are recruiting

one postdoc and two PhD students with background in bioinformatics, computational biology, data science, or engineering.

The goal of the project is to identify determinants of resistance to immunotherapy and develop personalized in silico and in vitro models for predicting responses to combination therapy in colorectal cancer. Towards this goal we are systematically interrogating tumor-immune cell interactions using data-driven modeling and knowledge-based mechanistic modeling, and are generating key quantitative data to train and validate algorithms using perturbation experiments with patient-derived tumor organoids and cutting-edge technologies for multidimensional profiling. The candidates will analyze next-generation sequencing data, phosphoproteomics data, and metabolomics data from tracer studies, and investigate rewiring of signaling networks and metabolic reprograming of T cells. The anticipated outcome is a precision immuno-oncology platform that integrates tumor organoids with high-throughput and high-content data for testing drug combinations, and machine learning for making therapeutic recommendations for individual patients.

The Division of Bioinformatics (www.icbi.at) is at the Biocenter of the Medical University of Innsbruck, Austria (www.i-med.ac.at)

Innsbruck (Capital of the Alps, www.innsbruck.info): Doing science where others spend their vacation.

Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.

PhD position in NGS data analysis of bacterial zoonoses

As a Federal Research Institute and independent higher Federal Authority under the Federal Ministry for Food and Agriculture, the research of the Friedrich-Loeffler-Institut (FLI) focusses on the health, nutrition, housing, genetic diversity, and welfare of farm animals.

The Institute for Bacterial Infections and Zoonoses in Jena offers a position as a

PhD in Bioinformatics („Doktorandin/Doktorand“)

with 65% of the weekly working time for 36 months starting as soon as possible. The employment will be based on the Federal Civil Service Act (TVöD) and its related regulations. In case of fulfilment of the relevant requirements, the salary will refer to TVöD 13 (east).


The applicant will be responsible for

Implementing Pipelines for the automatic processing of data from Whole Genome Sequencing (WGS) of Salmonella and Campylobacter isolates with the aims of:

1. Genotyping and outbreak analysis

2. Characterization of plasmids

3. Prediction of resistance to antibiotics

4. Determination of genetics reasons for resistance to antibiotics

5. Processing of metagenomics data

The successful candidate has

-          A PhD in Bioinformatics, Systems Biology, Computational Biology or similar fields

-          Knowledge  in bioinformatics programming (Snakemake, Shell,R/Python/Perl, …)

-          High communication skills

Advantages are

- Experience with Linux-servers

- Experience in analyzing WGS data (Spades, Prokka…) and metagenomc data (Kraken, Metaphlan…)

- Experience with genotyping methods (cgMLST, canonical SNPs…)

- Experience in the prediction of plasmids (plasmidfinder, …) and resistances (resistancefinder, CARD…)

We offer the possibility to gain deep theoretical knowledge and practical experience in the above-mentioned fields and thereby to help spreading of dangerous human and animal diseases. Moreover, we offer the possibility to graduate at the Faculty of Mathematics and Informatics at the Friedrich-Schiller-University, Jena.

The Friedrich-Loeffler-Institut dedicates to increase the proportion of female employees. Applications by women are therefore encouraged. Individuals with disabilities are preferred in case of equal qualification. Only a minimal level of physical qualification is required. Part of the work falls within security areas, which requires both; a security check according to German law (Sicherheitsüberprüfungsgesetz) and special health protection protocols. Personal and health eligibility is therefore required.

For further details please contact Dr. Linde, by phone: 03641-804 2320 or by E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it..

Applications including significant documents should be send to Friedrich-Loeffler-Institut, Fachbereich Personal, Postfach 1318 in 17466 Greifswald-Insel Riems, Germany (refer to “code xx/18”). Email applications will only be considered as a pdf sent to This email address is being protected from spambots. You need JavaScript enabled to view it.. Please state subject: Stelle 18/18. Deadline for submissions is the 31.05.2018.

Bioinformatician: Computational Proteomics [Ruhr-University Bochum]

The Medical Bioinformatics group of the Medizinischen Proteom-Centers / Ruhr-University Bochum is currently looking for a

Bioinformatician.

For more information, please visit the following web site:
https://www.ruhr-uni-bochum.de/mpc/stellen/index.html.en

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