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Bioinformatician/Computational Biologist (m/f) [LMU Munich]

The Klinikum der Universität München (KUM) belongs to the Ludwig Maximilians University Munich (LMU), the leading teaching and research university in Germany, ranking 1st in Germany in the latest Times Higher Education World University Ranking. With the neighbouring Max-Planck, Helmholtz, and Technical University institutions, it can be regarded as a major European science hub. LMU is a large beneficiary of the German excellence initiative, and has hosted more than 40 ERC grants. In total, under the Seventh EU Framework Program the LMU was recipient of 225 projects, in 22 of which it is/was the coordinating institution.

The Division of Infectious Diseases and Tropical Medicine hosts the international Clinical Trials Unit of the German Center for Infection Research (DZIF), which specializes in large human cohort research in the field of vaccines, novel diagnostics and therapeutics.

The Teaching and Research Unit Bioinformatics focuses on developing algorithms for the analysis of large-scale experimental data, in particular applications of next-generation sequencing such as RNA-seq, ChIP-seq or ATAC-seq.

The research group “Geldmacher/von Both” at the Division of Infectious Diseases and Tropical Medicine and the Dr. von Hauner children’s hospital jointly with Prof. C. Friedel at the Teaching and Research Unit Bioinformatics are looking for a highly motivated

Bioinformatician/Computational Biologist (m/f)

Your tasks and area of work:
The main research focus of our "infection & immunity" work group is the characterisation of the human host response to infection, with special emphasis on development of novel Tuberculosis diagnostic tests (Portevin et al. 2014 The Lancet ID), assessment of novel vaccines (Bauer et al. 2017 JV) and basic life sciences (Geldmacher et al. J.Exp.Med 2010, von Both et al. 2018 Sci Rep). The key pathogens for these projects under investigation comprise Mycobacteria spp., HIV and HPV.

Your tasks will include processing, analysis, and interpretation of large-scale next generation sequencing (NGS) datasets from transcriptomics and genomics studies, as well as automated analysis of microscopy images. You will implement analysis pipelines and responsibly drive projects as a computational biologist/ bioinformatician. You will further support supervision of Master and PhD students as well as interpretation of respective results and their publication in scientific journals.

Your qualifications:
- Master/PhD in bioinformatics, computational biology, biostatistics or related fields
- Programming experience for the analysis/processing of NGS datasets
- Experience with R, Linux/Unix OS, databases, and cluster computing
- Ability to work independently and to manage your own projects
- experience in image analysis software (i.e. ImageJ, CellProfiler, Ilastik) would be an advantage.

Our offer to you:
We offer a senior position in an interdisciplinary team of scientists, bioinformaticians, statisticians, and physicians focussing on infection and immunity during large international human cohort studies. Thus, we offer international collaborations, travel opportunities, and networking with key players in the field of infection & immunity research.

Munich is an international centre of both splendid research activities as well as great outdoor opportunities due to its vicinity to the Alps. It also boasts a great environment for families and children.  

Payment according to TVöD (VKA) of the German civil servant pay scale

For sending your application or for geting in touch with any potential enquiries, please contact us via E-Mail (This email address is being protected from spambots. You need JavaScript enabled to view it.) or phone +89 2180 17601.

PhD position in Bioinformatics/Computational Biology (m/f) [LMU Munich]

The Klinikum der Universität München (KUM) belongs to the Ludwig Maximilians University Munich (LMU), the leading teaching and research university in Germany, ranking 1st in Germany in the latest Times Higher Education World University Ranking. With the neighbouring Max-Planck, Helmholtz, and Technical University institutions, it can be regarded as a major European science hub. LMU is a large beneficiary of the German excellence initiative, and has hosted more than 40 ERC grants. In total, under the Seventh EU Framework Program the LMU was recipient of 225 projects, in 22 of which it is/was the coordinating institution.

The Division of Infectious Diseases and Tropical Medicine hosts the international Clinical Trials Unit of the German Center for Infection Research (DZIF), which specializes in large human cohort research in the field of vaccines, novel diagnostics and therapeutics.

The Teaching and Research Unit Bioinformatics focuses on developing algorithms for the analysis of large-scale experimental data, in particular applications of next-generation sequencing such as RNA-seq, ChIP-seq or ATAC-seq.

The research group “Geldmacher/von Both” at the Division of Infectious Diseases and Tropical Medicine and the Dr. von Hauner children’s hospital jointly with Prof. C. Friedel at the Teaching and Research Unit Bioinformatics are looking for a highly motivated

PhD candidate in Bioinformatics/Computational Biology (m/f)

Your tasks and area of work:
The main research focus of our "infection & immunity" work group is the characterisation of the human host response to infection, with special emphasis on development of novel tuberculosis diagnostic tests (Portevin et al. 2014 The Lancet ID), assessment of novel vaccines (Bauer et al. 2017 JV) and basic life sciences (Geldmacher et al. J.Exp.Med 2010, von Both et al. 2018 Sci Rep). The key pathogens for these projects under investigation comprise Mycobacteria spp., HIV and HPV.

The proposed PhD project will include processing, analysis, and interpretation of large-scale next generation sequencing (NGS) datasets from transcriptomics and genomics studies, as well as automated analysis of microscopy images. You will help implementing analysis pipelines and responsibly drive projects as a computational biologist/ bioinformatician. You will further be involved in the interpretation of respective results and their publication in scientific journals.

Your qualifications:
    • Master/diploma in bioinformatics/computational biology or a related subject
    • Programming experience for the analysis/processing of NGS datasets
    • Experience with R, Linux/Unix OS, databases, and cluster computing
    • Experience in image analysis software (i.e. ImageJ, CellProfiler, Ilastik) would be an advantage.

Our offer to you:
We offer a PhD (Dr. rer nat.) position (100%) in an interdisciplinary team of scientists, bioinformaticians, statisticians, and physicians focussing on infection and immunity during large international human cohort studies. Thus, we offer international collaborations, travel opportunities, and networking with key players in the field of infection & immunity research.

Munich is an international centre of both splendid research activities as well as great outdoor opportunities due to its vicinity to the Alps. It also boasts a great environment for families and children.  

Payment according to TVöD 13 (VKA) of the German civil servant pay scale

For sending your application or for geting in touch with any potential enquiries, please contact us via E-Mail (This email address is being protected from spambots. You need JavaScript enabled to view it.) or phone +89 2180 17601.

Software engineering for genome annotation in Greifswald


The Ernst Moritz Arndt University of Greifswald´s Institute of Mathematics and Computer Science offers subject to the budgetary authority for the period from next possible date limited for 3 years a part-time position (50%) as a researcher.

Payment will be made according to pay group 13 TV-L Wissenschaft if the personal and pay group specific qualifications can be provided.

The group of Mario Stanke develops the bioinformatics tool AUGUSTUS, which identifies the genes and their exon-intron structure in newly sequenced genomes. AUGUSTUS is widely used although deficits in usability hamper effective and optimal application by a diverse set of users. The position is in a DFG grant project to improve the user friendliness of AUGUSTUS both for end-users that annotate one or a few genomes and for bioinformaticians who want to integrate AUGUSTUS into other software. A supplementation of the position with further funding is intended.

Job Description:
The candidate shall help improve the usability of AUGUSTUS, e.g. by implementing a repository where users can share parameters with each other or by assembling an automatized pipeline. The applicant will thereby be supported by a software engineer who works on the same project.

Job Specification:
The candidate shall have a Master of Science or "Diplom" in Bioinformatics, Biomathematics, Mathematics, Computer Science or a related field. She or he must have experience in software development and the implementation of efficient algorithms for large data. ln particular, experience in C++ in a Linux environment is required.

Candidates should have a strong interest in interdisciplinary work ranging from biology via physics to medicine. Knowledge of protein-nanoparticle interactions is an advantage.

The University would like to increase the proportion of women in areas in which they are underrepresented and thus applications from women are particularly welcome and will be treated with priority if they have the same qualifications and as long as there are no clear reasons which make a fellow applicant more suitable.

Severly disabled applicants with the same qualifications will be considered with preference.
This announcement is directed at all persons, no matter which gender.

According to § 68 Sub-Section 3 PersVG M-V, the staff council will only be involved in staff matters of the academic or artistic staff on request.

The costs for applying cannot be reimbursed by the state of Mecklenburg-Vorpommern.

The complete application should be e-mailed by 28th February 2018 with reference of the job advertisement Number 18/Sa06 to:

Ernst-Moritz-Arndt-Universität Greifswald
Institut für Mathematik und Informatik
Herrn Prof. Dr. Mario Stanke
Walther-Rathenau-Str. 47
17489 Greifswald

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


Links: https://www.uni-greifswald.de/en/university/information/jobs/current-vacancies/wissenschaftliches-personal/institute-of-mathematics-and-computer-science-18sa06

Doktorandenstelle Software Qualitätssicherung in Göttingen

Am Institut für Informatik der Fakultät für Mathematik und Informatik der Georg-August-Universität Göttingen ist zum nächstmöglichen Zeitpunkt die Stelle einer/eines

wissenschaftlichen Mitarbeiterin/wissenschaftlichen Mitarbeiters

mit 50 % der regelmäßigen wöchentlichen Arbeitszeit (zzt. 19,9 Stunden/Woche) befristet für die Dauer von 3 Jahren zu besetzen. Die Entgeltzahlung erfolgt nach Entgeltgruppe 13 TV-L.

Ihre Aufgaben
• Sie arbeiten in einem Verbundprojekt mit der Universität Greifswald an der Weiterentwicklung des Werkzeugs AUGUSTUS zur Annotation von Genomen.
• Sie forschen im Bereich der Software Qualitätssicherung, insbesondere von Software für maschinelles Lernen.

Ihr Profil
• Sie haben ein überdurchschnittlich abgeschlossenes wissenschaftliches Hochschulstudium in einem relevanten Gebiet, vorzugsweise der Informatik.
• Sie verfügen über gute Programmierkenntnisse (bevorzugt in C++), sowie Erfahrungen mit Softwaretechnik. Wünschenswert sind Vorkenntnisse in den Bereichen Multiprocessing, Softwaretesten, Debian Packeterstellung, Windows Installern, DevOps Technologien und des maschinellen Lernens.
• Sie haben bereits in der Bioinformatik gearbeitet oder Interesse an der Arbeit mit biologischen Daten.
• Sie beherrschen die englische Sprache in Wort und Schrift.
• Sie sind engagiert und haben Freude am wissenschaftlichen Arbeiten im Team.

Die Stelle soll der Qualifizierung des wissenschaftlichen Nachwuchses dienen und bietet die Möglichkeit zur Promotion. Eine Aufstockung der Stelle auf 100 % der regelmäßigen wöchentlichen Arbeitszeit (zzt. 39,8 Stunden/Woche) ist angestrebt.

Die Universität Göttingen strebt in den Bereichen, in denen Frauen unterrepräsentiert sind, eine Erhöhung des Frauenanteils an und fordert daher qualifizierte Frauen nachdrücklich zur Bewerbung auf. Sie versteht sich als familienfreundliche Hochschule und fördert die Vereinbarkeit von Wissenschaft/Beruf und Familie. Die Universität hat sich zum Ziel gesetzt, mehr schwerbehinderte Menschen zu beschäftigen. Bewerbungen Schwerbehinderter erhalten bei gleicher Qualifikation den Vorzug.

Bewerbungen mit den üblichen Unterlagen reichen Sie bis zum 28.02.2018 ausschließlich über das Online-Bewerberportal unter https://lotus2.gwdg.de/uni/uzdv/perso/knr_100310.nsf ein.

Für Rückfragen steht Ihnen Herr Steffen Herbold, Telefon: 0551 / 39 172037, E-Mail: This email address is being protected from spambots. You need JavaScript enabled to view it. zur Verfügung.

Links: http://www.uni-goettingen.de/de/305402.html?cid=100310

PhD position in Bioinformatics group of Prof. Meyer, Berlin

Research in the Meyer group is focused on discovering new mechanisms of
transcriptome regulation in diverse biological settings. We have a particular interest in regulatory mechanisms mediated by RNA-structures and trans RNA-RNA interactions. To this end, we develop and apply new computational methods, algorithms and analysis pipelines to analyse large-scale data sets (e.g. RNA-seq). We develop machine learning techniques, phylogenetic models and a range of probabilistic methods to tackle exciting, fundamental questions in biology. We work in close collaboration with several experimental research groups to investigate biological systems ranging from differentiating stem cells to cells during virus-infection and expect to engage in single-cell studies in the near future.

Our group is part of the Berlin Institute for Medical Systems Biology (BIMSB) of the the Max-Delbruck Centre for Molecular Medicine in Berlin, Germany, which combines state-of-the-art high-throughput technologies with Bioinformatics, molecular biology, biochemistry and engineering to gain acomprehensive and fundamental understanding of different biological systems.

We are looking for an enthusiastic and ambitious new team member who combinesstrong skills in computational method development with a keen desire to investigate exciting biological systems. Key attributes sought are the ability to work alone and as part of a team, excellent attention to detail, solid problem solving skills, and the desire to learn and improve. Furthermore, you should demonstrate your ability to communicate both biological and computational ideas (orally and in writing) and time management to deadlines. The successful applicants will join us in the new BIMSB building in the centre of Berlin, Germany.

Requirements

Essential:
- proficiency in object-oriented programming (C++, Java) and developing software in a
  Unix-based environment
- solid background in and high enthusiasm for computational method development
- solid background in machine learning, statistics and programming in R
- ability to write, understand and maintain complex code
- keen interest in investigating biological systems
- excellent communication skills (oral and written) in English

Desired:
- previous experience of processing and analysing NGS data sets
- prior expertise with investigated biological systems (e.g. stem cells, virus infections)
- familiarity with compute clusters and software development tools

Certificates:
- MSc in Computer Science, Bioinformatics, Genetics or related fields
  (including Statistics, Bioengineering, Physics, Mathematics, Biochemistry)

Salary
Re-numeration according to German TVoeD (Bund/Ost) E13 (50% in first year, 65% in subsequent years).

Application Deadline
Sunday, 25. February 2018

Start Date
as soon as possible

Limitation
The position is initially offered for 3 years, with the possibility for a further extension.


For further information, contact Irmtraud Meyer (This email address is being protected from spambots. You need JavaScript enabled to view it.).

How to apply:
(1) Please submit your complete application as a single pdf-file by email to This email address is being protected from spambots. You need JavaScript enabled to view it. using subject line “Reg.-Nr. 10920/2018” including
•    cover letter
•    CV
•    complete set of university certificates and transcripts
•    names and contact details of 3 referees
(2) Please get 3 letters of recommendation to be sent directly using subject line “Reg.-Nr. 10920/2018” to This email address is being protected from spambots. You need JavaScript enabled to view it. by the application deadline.

The MDC is an equal opportunity employer and supports gender equality.

Links:

Meyer group: www.mdc-berlin.de/meyer

web-server: www.e-rna.org


Post-doc position in Bioinformatics group of Prof. Meyer, Berlin

Research in the Meyer group is focused on discovering new mechanisms of
transcriptome regulation in diverse biological settings. We have a particular interest in regulatory mechanisms mediated by RNA-structures and trans RNA-RNA interactions. To this end, we develop and apply new computational methods, algorithms and analysis pipelines to analyse large-scale data sets (e.g. RNA-seq). We develop machine learning techniques, phylogenetic models and a range of probabilistic methods to tackle exciting, fundamental questions in biology. We work in close collaboration with several experimental research groups to investigate biological systems ranging from differentiating stem cells to cells during virus-infection and expect to engage in single-cell studies in the near future.

Our group is part of the Berlin Institute for Medical Systems Biology (BIMSB) of the the Max-Delbruck Centre for Molecular Medicine in Berlin, Germany, which combines state-of-the-art high-throughput technologies with Bioinformatics, molecular biology, biochemistry and engineering to gain a comprehensive and fundamental understanding of different biological systems.

We are looking for an enthusiastic and ambitious new team member who combines strong skills in computational method development with a keen desire to investigate exciting biological systems. Key attributes sought are the ability to work alone and as part of a team, excellent attention to detail, solid problem solving skills, and the desire to learn and improve. Furthermore, you should demonstrate your ability to communicate both biological and computational ideas (orally and in writing) and time management to deadlines. The successful applicants will join us in the new BIMSB building in the centre of Berlin, Germany.

Requirements

Essential:
- proficiency in object-oriented programming (C++, Java) and developing software in a
  Unix-based environment
- solid background in and high enthusiasm for computational method development
- solid background in machine learning, statistics and programming in R
- ability to write, understand and maintain complex code
- keen interest in investigating biological systems
- excellent communication skills (oral and written) in English
- previous experience of processing and analysing NGS data sets

Desired:
- prior expertise with investigated biological systems (e.g. stem cells, virus infections)
- familiarity with compute clusters and software development tools

Certificates:
- PhD in Computer Science, Bioinformatics, Genetics or related fields
  (including Statistics, Bioengineering, Physics, Mathematics, Biochemistry)

Salary
Re-numeration according to German TVoeD (Bund/Ost) E13, depending on qualification and experience.

Application Deadline
Sunday, 25. February 2018

Start Date
as soon as possible

Limitation
The position is initially offered for 2 years.

For further information, contact Irmtraud Meyer (This email address is being protected from spambots. You need JavaScript enabled to view it.).

How to apply:

(1) Please submit your application as a single pdf-file by email using subject line “ Reg.-Nr. 10921/2018” to This email address is being protected from spambots. You need JavaScript enabled to view it. including
•    cover letter
•    CV
•    complete set of university certificates and transcripts
•    names and contact details of 3 referees
(2) Please get 3 letters of recommendation to be sent directly using subject line “Reg.-Nr. 10921/2018” to This email address is being protected from spambots. You need JavaScript enabled to view it. by the application deadline.

The MDC is an equal opportunity employer and supports gender equality.

Links:

Meyer group: www.mdc-berlin.de/meyer

web-server: www.e-rna.org

Senior Bioinformatics Scientist (m/f) Genome Informatics [Molecular Health GmBH]

We are seeking for our headquarter in Heidelberg a highly motivated

Senior Bioinformatics Scientist (m/f) Genome Informatics

As a member of the Genome Informatics group, you will be responsible for the integration and analysis of data sets from oncology and publication of scientific results. Your tasks will include the evaluation and development of algorithms to analyze data from next-generation sequencing (NGS), up to and including the detection of sequence variations such as, SNVs, indels, and CNVs. In this regard, you will plan and lead projects resulting in scientific publications, conference posters, and marketing material of outstanding quality.

Your skills and qualifications
    • PhD in computational biology, bioinformatics, or related field
    • Several years’ experience with NGS data
    • Up to date with current research
    • Proven excellence in research productivity with numerous peer-reviewed publications and presentations
    • Profound knowledge of NGS algorithms and software
    • Strong proficiency in object-oriented programming (e.g., Python)
    • Work experience in industry is considered as a plus
    • Fluent in English and German (written and spoken)
    • Able to work independently, and are dependable, focused, and team-oriented

We offer
    • An innovative, exciting international company interesting for employees who have the ability to think outside the box and who want to make a difference and strike out in a new direction
    • A challenging, stimulating scientific and professional environment with a focus on innovation and on the continuous development of our company
    • A modern working environment in a new office building with the latest (technical) equipment
    • A multicultural team and attractive company events, together with an open culture of trust
    • Excellent location in the center of Heidelberg
    • Opportunities for personal development in a rapidly growing, global company
    • Competitive compensation and attractive benefits package, flexible working models

Take the first step and join us! We are looking forward to receiving your complete application, in English or German, including your salary expectations and earliest start date. Please send it to Thorsten Vogt at This email address is being protected from spambots. You need JavaScript enabled to view it..           

Working Student in Genome Informatics (m/f) [Molecular Health GmBH]

We are seeking for our headquarter in Heidelberg a highly motivated

Working Student in Genome Informatics (m/f)

As a member of the Genome Informatics group, you will be responsible for the application and further development of computational pipelines for statistical validation of our products. You will support the team with maintenance of software and its application to data sets from genomics.
          
Your skills and qualifications
    • Current Master student with a Bachelor Degree in computational biology, bioinformatics, or related field
    • Up to date with current research
    • Understanding of standard statistical concepts and methods
    • Good understanding of NGS algorithms and software
    • Good skills in object-oriented programming (preferable in Python, R and/or C/C++)
    • Fluent in English or German (written and spoken)
    • Willingness to learn, ability to work independently, focused, and team-oriented
We offer
    • An innovative, exciting international company interesting for employees who have the ability to think outside the box and who want to make a difference and strike out in a new direction
    • A challenging, stimulating scientific and professional environment with a focus on innovation and on the continuous development of our company
    • A modern working environment in a new office building with the latest (technical) equipment
    • A multicultural team and attractive company events, together with an open culture of trust
    • Excellent location in the center of Heidelberg
    • Opportunities for personal development in a rapidly growing, global company

Take the first step and join us! We are looking forward to receiving your complete application, in English or German, including your earliest start date. Please send it to Thorsten Vogt at This email address is being protected from spambots. You need JavaScript enabled to view it..

2 PostDoc positions in Bioinformatics in Freiburg

The Freiburg Galaxy Team works on software development for biomedical high-throughput sequencing data. We currently have open positions on different projects varying from programming to applied data analysis.

Ideal candidates have a PhD in informatics, computational biology or bioinformatics, a strong proficiency in UNIX, Python and JS, and proficiency in software development. A strong background in HTS data analysis and/or RNA research, and interest in new technologies (containers) is desired. Candidates must have excellent verbal and written communication skills (English).

We offer the chance to work with leading, cutting edge technologies both in IT and computational biology and give you the opportunity to broaden your skills using open source technologies within a bioinformatics context. The university offers the development of professional and personal skills and the chance to work in one of the highest ranked scientific research organizations in the world. Come and join our team and contribute to this joint effort and work in a young and international environment.

Positions are for initially 2 years. The salary will be determined in accordance with TVL-E13 (100 %).

Please send your application including a motivation letter, CV, certificates, and 3 references latest until 15.2.2018 via email to Anika Erxleben (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Further information:
http://www.bioinf.uni-freiburg.de
https://usegalaxy.eu