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Stellenangebote

Bioinformatics / Computational Biology Staff, ETH Zurich

The Institute of Microbiology at ETH Zurich is seeking a highly qualified and experienced staff bioinformatician / computational biologist who is motivated to support and stimulate collaborative work between its members.

The institute is composed of interdisciplinary research groups that work under the unifying theme of microbial interactions. We study host-microbe and microbiome interactions in diverse systems at all scales of biological organization including the ocean, humans, mice, plants, sponges, and fungi. By developing and applying cutting-edge technology in the area of next generation sequencing, mass spectrometry, imaging, multi-parameter flow cytometry and single-cell approaches, our institute provides a unique opportunity for data-integrative research and collaborations.

More detailed information can be found at: http://www.micro.biol.ethz.ch/.

The motivation of the candidate is to provide strong support for ongoing research projects, and to foster bioinformatic skills among the institute’s students and research staff. The candidate has excellent organisational skills and is able to effectively communicate results to individuals with diverse scientific backgrounds.
The post holder will be embedded in the Microbiome Research group at the Institute of Microbiology providing an environment of complementary expertise and infrastructure for high-performance computational analysis.

Essential qualifications include:
-    postgraduate degree in bioinformatics or related field
-    excellent communication, teamwork and organisational skills
-    excellent skills biological / statistical data analysis (including machine learning)
-    experience in NGS data analysis: (meta)genomics, (meta)transcriptomics
-    advanced programming skills (e.g., Python/Perl, R, UNIX/bash scripting)

The following additional qualifications will be advantageous:
-    background in population genetics / microbial ecology / phylogenetics
-    experience in analysis of antibody sequence libraries (Ig-seq)
-    experience in image data analysis
-    experience in metabolomics/proteomics data analysis
-    experience in web/database development (HTML, PHP, JavaScript, CSS, SQL)

Notes:
Applications will be considered until 31/12/2017 and reviewed on an on-going basis. Therefore, the post may be filled before the deadline. Informal inquiries should be directed by email to Prof. Dr. Shinichi Sunagawa (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).


Links:
https://www.ethz.ch/content/dam/ethz/special-interest/biol/micro-biol/inst-of-microbiology-dam/documents/positions/SS%20Open%20Positions/Staff_Bioinf_position.pdf

Scientific staff for newly founded institute: PhDs/PostDocs/CoreUnitLeader

The newly founded Institute for Genomic Statistics and Bioinformatics (IGSB, www.igsb.uni-bonn.de) at the University of Bonn, Germany, is seeking for outstanding scientific staff (PhD candidates/postdocs/CoreUnitGroupLeader).
The goal of the IGSB is to improve health care by applying artificial intelligence in the analysis of biomedical data. We design, implement and evaluate methods and tools that leverage the knowledge and cognitive skills of investigators in order to enable the interpretation of massively heterogeneous data sets that integrate genomic and clinical information.
All of our research projects are highly interdisciplinary and are being conducted in close cooperation with computational or experimental domain experts providing an excellent opportunity for collaborative research.
Our institute is situated on Venusberg, the Campus of the Medical School Bonn and is part of a vibrant community of scientists, physicians, and engineers, whose goal is to advance the boundaries of knowledge. The institute has recently been founded to lead development of computational and informatics techniques to address pertinent challenges in modern biological sciences and medicine. PhD candidates will be enrolled in the Bonn International Graduate School, BIGS.

DESIRED SKILLS AND EXPERIENCE
Responsibilities of postdocs
The postdoctoral fellows will be responsible for applying novel methodologies to analyze biomedical big data sets, including genomic and imaging data. There is a focus on collaborative projects with other research institutes such as the Departments of Human Genetics and Immunology, or the DZNE. Other responsibilities include day-to-day project management, including coordination with collaborators and other team members, as well as the writing of manuscripts. Contribution to the grant writing efforts of the lab are expected.
Basic Requirements
Postdoc Candidates must have a PhD degree in a quantitative field such as bioinformatics, computer science, physics, or related fields and a track-record of publication in the top journals or conferences of their field. Hands-on experience with management, analysis, and visualization of biomedical data is required for this position. Excellent programming skills and working knowledge of state-of-the-art software development techniques are essential. The candidates interested in these positions must be highly motivated, willing to learn and demonstrate initiative in assigned tasks. Excellent written and verbal communication skills are crucial.

Responsibilities of group leader "Core Unit Bioinformatics Data Analysis" (CUBA)
This CUBA group leader will head a team of three bioinformaticians (in the beginning) and manage projects in a highly collaborative environment. The position will directly interface with faculty and investigators within the Medical Campus Bonn. CUBA has a particular focus on analysis of medium size -omics projects including NGS, FACS and proteomics data.

Basic Requirements
PhD and a minimum of 3 years post-graduate high-level experience in bioinformatics, computational biology, or statistical genetics in industry or academia and demonstrated skill in working within collaborative groups.

ABOUT THE EMPLOYER
The Institute for Genomic Statistics and Bioinformatics has been founded in September 2017 to deepen our understanding of genome biology and advancing personalized medicine. IGSB an entity of University Bonn, one of the eminent research universities in Germany with an excellent international reputation. Since 2006, it has been successful in gaining funding through the Excellence Initiative set out by the federal government and state and the DFG (Deutsche Forschungsgemeinschaft), acquiring two Clusters of Excellence and two Graduate Schools ( Hausdorf Center for Mathematics and Immunosensation).

HOW TO APPLY
Candidates should submit their CV, a research statement, PDFs of their three best papers, and contact information for three regerences to pkrawitz at uni-bonn.de with [PDH], [PostDoc], or [CUBA] in the subject.

Research Assistant / PostDoc [Uni Marburg, Project Group of Dr. Sobetzko]

The Project Group of Dr. Sobetzko, which is part of the Department of Chromosome Biology, Prof. Dr. Torsten Waldminghaus, is seeking for a

Research Assistant.

The full time position, limited to 2 years, is operated by the DFG-funded project „DNA from the coding perspective“. Salary and benefits are according to a public service position in Germany (TV-H E13). Further extension of the contract is possible and depends on a successful application for extension of the project. It can therefore not be garateed.

Gene regulation is the central element to concert complex cellular mechanisms of a living cell. In this project, we want to apply RNA-seq and DNA-seq data to investigate the role of DNA sequence composition in organizing regulatory networks and physical information transfer by gene neighborhood relations. We will develop comparative genomics approaches to tackle these questions. Furthermore, we will monitor the evolution of the regulatory system in strains with network defects for about 20,000 generations using DNA- and RNA-seq. At our graduate school the candidate will be trained to professionally present results and hypotheses within SYNMIKRO and on international conferences and workshops.
In the frame of this third party founded project the opportunity for scientific work is given. The results are available outside for further application.

The limitation of the contract complies to § 2 Abs. 2 WissZeitVG.The successful candidate must hold a MSc, Diploma, PhD or a related qualification in Bioinformatics. Further, the candidate should demonstrate an outstanding scientific record and should be trained in at least one computer language (e.g. Java or Python). Theoretical knowledge in analyzing transcriptomics data and practical experience in statistical analysis using R or MatLab are essential. Theoretical knowledge in the disciplines of microbiology and genetics are welcome.
For informal project enquiries don’t hesitate to contact Dr. Sobetzko via Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.

Scientist (m/f) "(Bio-)Informatics / cloud computing" [Bochum]

The Department Bioinformatics of the Medizinisches Proteom-Center
offers a job position for a scientist (m/f) in the field "(Bio-)Informatics / cloud computing".

Activities:
•    Adoption / further development of scientific analysis software in the field ‚Bioinformatics for Proteomics‘ for the usage in cloud infrastructures (e. g. de.NBI-cloud)
•    Support in the establishment of scientific cloud infrastructures (e. g. authentication and authorization infrastructure service, resource distribution / governance)
•    Technical support of scientists in applying analysis software in the cloud

Job profile:
You have knowledge and / or experience in the following fields of Computer Science / Bioinformatics:
•    Administration of Linux operating systems, Linux script-programming
•    OpenStack
•    Distributed computing and Virtualisation

Preferable are knowledge and interest in:
•    Administration of Windows operating systems
•    authentication and authorization infrastructure systems
•    Bioinformatics of Proteomics
•    Bioinformatics algorithms / analysis software for high-throughput- / Omics data
•    Object oriented programming (e. g. Java, C++)

Details can be found here (in German):
https://www.stellenwerk-bochum.de/jobboerse/wissenschaftl-mitarbeiterin-bio-informatikerin-bio-informatiker-bo-2017-09-08-139523 
http://tinyurl.com/yc27nlfv

Two Bioinformaticians (f/m) for clinical research unit [Münster]

The new DFG Clinical Research Unit ‘Male Germ Cells: from Genes to Function’ (CRU326) investigates in translational projects human male germ cell function in health and disease at the genetic, epigenetic, and molecular level.

The Clinical Research Unit consists of clinicians and basic researchers from the local Centre of Reproductive Medicine and Andrology, Department of General Paediatrics, Institutes of Human Genetics, Cell Biology, and Medical Informatics, and the Max-Planck-Institute of Molecular Biomedicine.

More information on the Clinical Research Unit and projects can be found under:
http://www.male-germ-cells.de

In a joint project, the groups of Prof. Frank Tüttelmann, Institute of Human Genetics, and Prof. Martin Dugas, Institute of Medical Informatics are seeking two postdocs to start at the earliest opportunity on a 3 year funded period with the possibility for extension.

Two Bioinformaticians (f/m)
Ref.: 13644

Full-time (100%)
Employment is funded at 100% of TV-L E14, conditional to previous experience and qualifications

The project entitled “Coordination and integrated analysis of OMICs data” focuses on the identification of epi-/genetic changes associated with male infertility. The project will be conducted in a strong translational setting, in which clinicians, scientists and bioinformaticians are working together closely and involve next-generation sequencing techniques and bioinformatics.

Required qualifications:

  • University degree (required) in Bioinformatics or Medical Informatics (PhD level desired),
  • experience in analyses of Next Generation Sequencing data (required),
  • excellent programming skills (required) in at least one language (ideally R and Java desired),
  • fluency and excellent communication skills in English (and German) (required),
  • strong commitment to research and development in a translational setting (required).

We offer:

  • the setting of an interdisciplinary Clinical Research Unit
  • an international, multidisciplinary, and creative working environment,
  • state-of-the-art research facilities (e.g. High Performance Computing capacity),
  • excellent possibilities for career development and networking.

For further information please contact:
Prof. Frank Tüttelmann, phone: +49 251 83 55411 or e-mail frank.tuettelmann(at)­ukmuenster(dot)­de or
Prof. Martin Dugas, phone: +49 251 83 55262 or e-mail martin.dugas(at)­ukmuenster(dot)­de.

Applications including a short summary of your research background (max. 1 page), CV and publication list, and a letter of recommendation of your scientific supervisor should be sent with reference number via email in one pdf-file until 22.09.2017 to bewerbung(at)­ukmuenster(dot)­de.

Applications from female candidates are particularly encouraged. In the case of equal qualifications, competence and specific achievements, women will be considered on preferential terms within the framework of the legal possibilities unless reasons specific to an individual male candidate predominate. Handicapped candidates with equal qualifications will be given preference.


Links: http://www.male-germ-cells.de

Postdoc Position in Evolutionary Genomics [Max Planck Institute, Dresden]

The Research Group “Computational Biology and Evolutionary Genomics” at the Max Planck Institute in Dresden, Germany has a Postdoc opening.
 
Project description:
The postdoc will utilize numerous sequenced mammalian genomes to discover the genomic basis of repeatedly evolved phenotypic differences. By focusing on natural phenotypes that resemble human diseases, we aim at connecting basic evolutionary with translational research to identify novel genes associated with genetic disorders. The postdoc will apply and further develop our genomics methods, and analyze the results by integrating biomedical knowledge and functional genomics data. Promising candidate genes will be tested experimentally, either by the Postdoc or in collaboration. The Postdoc will work closely with other members of the lab and our institute on the computational and experimental aspects. Funding is according to the German TVöD scale.
 
Our group:
We combine computational biology, comparative genomics and experiment to investigate how nature's fascinating phenotypic diversity evolved and how it is encoded in the genome. On the computational side, we generate high-quality genome alignments, apply comparative methods to discover key differences in genes and regulatory elements, and use statistical approaches to associate genomic to phenotypic differences. On the experimental side, we use RNA-seq, ATAC-seq, functional assays and CRISPR-Cas9 to reveal the molecular function of genomic regions and to test causality between genomic and phenotypic differences.
 
Our group is located at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) and we are jointly affiliated with the Max Planck Institute for the Physics of Complex Systems (MPI-PKS), both in Dresden. Both institutes are highly interactive and interdisciplinary workplaces, provide an international atmosphere with English as working language and access to cutting-edge computational and experimental infrastructure and facilities. The MPI-CBG was awarded one of the “Best Places To Work for Postdocs” in 2011.
 
Requirements:
Applicants with a background in both computational and biological sciences are encouraged to apply. 
Applicants with a computational background should have a strong interest in integrating experiments in their research and a desire to deeply understand the biology underlying mammalian phenotypes and human disease. Applicants with a biological background should be experienced in using text file processing tools in a Linux shell environment and should have good programming skills, for example in a scripting language. Excellent communication skills and a strong publication record is expected. Previous experience in large-scale genomic data analysis is an advantage. 
 
How to apply:
If interested, please email (i) your CV including publication list and contact information for at least two references and (ii) a summary of previous research experience (max 1 page) to Michael Hiller (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!).


Links: 
Further information: https://www.mpi-cbg.de/hiller

Wissenschaftliche/r Mitarbeiter/in Ingenieurinformatik / Bioinformatik / Angewandte Mechanik

Das Institut für Bioprozess- und Analysenmesstechnik e. V. ist ein außeruniversitäres Forschungsinstitut des Freistaates Thüringen. Im Rahmen des Forschungsprofils „Biotechniques at Interfaces“ werden Projekte zu technischen Systemen für die Lebenswissenschaften bearbeitet, bei denen Wechselwirkungen zwischen der biologischen und technischen Komponente dieser Systeme eine besondere Rolle spielen.

Vorzugsweise ab dem 01.10.2017 ist die folgende Stelle in Vollzeit neu zu besetzten: Wissenschaftliche/r Mitarbeiter/in Ingenieurinformatik / Bioinformatik / Angewandte Mechanik

Nach erfolgreicher Einarbeitung sind Sie verantwortlich für die selbstständige Bearbeitung von Forschungs- und Entwicklungsprojekten im Bereich der Programmierung von Softwaresystemen und deren Anpassung an die gestellten Anforderungen. Wesentlicher Bestandteil der Arbeiten bildet der Entwurf, die Umsetzung und die Testung von numerischen Algorithmen, Routinen und  Programmen für das Design und die Optimierung von humanen lasttragenden Knochenimplantaten. Von Interesse sind daher profunde Kenntnisse der Programmiersprachen C, C++ und FORTRAN, der Optimierung von Bauteilen mit Hilfe genetischer / evolutionäre Algorithmen sowie der Auslegung von neuronalen Netzen zur Entscheidungsfindung.

Erforderlich sind Erfahrungen im Bereich der Programmierung und numerischen Mathematik. Von Vorteil sind darüber hinaus Kenntnisse auf dem Gebiet der Finite-Elemente-Methode (FEM) zur Modellierung und Simulation komplexer Systeme, der theoretischen und experimentellen Mechanik sowie Grundkenntnisse in der Biomechanik.

Sie verbinden Flexibilität und Eigeninitiative mit einer teamorientierten, wissenschaftlichen Arbeitsweise bei der Erarbeitung von anwendungsorientierten Problemlösungen im Rahmen von Forschungsprojekten. Wir bieten Ihnen dafür ein attraktives und abwechslungsreiches Betätigungsfeld in einer interdisziplinären und engagierten Forschungsgruppe. Die Möglichkeit zur Promotion ist gegeben. Die Stelle wird nach TV-L vergütet und ist nach derzeitiger Bewilligungslage zunächst bis zum 30.09.2020 befristet. Vorgesehen ist bei entsprechender Eignung die Weiterbeschäftigung in weiteren Projekten. Für weitere Informationen steht Ihnen der Leiter des Fachbereiches Biowerkstoffe Herr Prof. Dr. Liefeith (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) gern zur Verfügung.

Unser Institut ist bestrebt, die Anzahl der wissenschaftlichen Mitarbeiterinnen zu erhöhen. Die Bewerbung von Frauen ist daher ausdrücklich erwünscht. Bei gleicher Eignung und Erfüllung der o.g. Anforderungen werden Bewerber mit einer anerkannten Behinderung gemäß § 2 SGB IX bevorzugt berücksichtigt.

Ihre ausführliche Bewerbung mit den üblichen Unterlagen richten Sie bitte mit dem Betreff „Bioinformatiker/-in K06/2017“ bis zum 31.08.2017 an:

Institut für Bioprozess- und Analysenmesstechnik e.V.
Rosenhof
37308 Heilbad Heiligenstadt
Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

www.iba-heiligenstadt.de]

Bioinformatics Postdoc @ Roche (NGS, Machine learning, Antibody)

Postdoctoral Research Fellow Bioinformatics/ Biostatistics in the
environment of machine learning on antibody NGS data (m/f)

The jobholder will work in the environment of two departments within
Pharma Research and Early Development (pRED): in the wet-lab
laboratories of Large Molecule Research at Roche Penzberg, Antibody
Next Generation Sequencing (NGS) data will be generated and in the Data
Science group of pREDi Penzberg these data are processed, analyzed and
visualized. In doing so, you will be using profound and state-of-the-
art bioinformatics/biostatistics, data analysis, data integration, and
data visualization methods. One key element of the antibody
characterization project, which you will own, is the in silico
prediction of specific antibody properties to foster the lead
identification process within the discovery units.

This position requires the application and development of data
analytics solutions based on machine learning, statistical analysis or
mathematical and predictive modelling techniques to allow project teams
to draw scientific conclusions from large-scale antibody NGS data.


Key responsibilities include, but are not limited to the following
tasks:

- You will work as a bioinformatics/biostatistics researcher (m/f)
within Roche Pharma Research, developing machine learning approaches
for binding properties prediction. Furthermore you will get the unique
opportunity to validate your findings by wet-lab experiments.
- Other key responsibilities comprise the development of data analysis
and prediction algorithms on antibody NGS data by the application of
appropriate machine learning techniques
- It will be your responsibility to cooperate both with wet lab
scientists and data scientists to generate and analyze antibody NGS
data
- The publication of results belongs to your tasks and will be
supported


Who you are

You’re someone who wants to influence your own development. You’re
looking for a company where you have the opportunity to pursue your
interests across functions and geographies. Where a job title is not
considered the final definition of who you are, but the starting point.
- You hold a PhD in bioinformatics or a related relevant field
- In addition, you have excellent programming skills with knowledge of
at least one of the following programming languages: Java, Matlab, R or
similar
- You are experienced in working with next generation sequencing data,
favorably antibody datasets
- We can trust in your experience with statistics, machine learning
including deep learning and/or data mining
- Your knowledge on bioinformatics data integration and large-scale
data analysis is up-to-date
- You have a solid background in protein biology, especially antibody
biology
- Basic knowledge of protein structure is essential and antibody
modeling experience is of advantage
- You are able to perform standard wet-lab experiments with guidance
and you are eager to learn new techniques
- You can prove your scientific excellence with a number of
publications
- You are well known for your strong team spirit and your willingness
to work in international teams
- In addition you are interested to work interdisciplinary and you are
ready to learn and explore new fields
- Excellent English skills, written and spoken, complete your profile

This position is limited to a timeframe of two years.


Link: http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-3409739846

Postdoc in Systems Genetics in the Gagneur lab [TU Munich]

RESPONSIBILITIES

We seek a talented and motivated post-doc to develop computational methods for identifying regulatory genetic variants influencing the risk of common diseases. Research topics include: integration of rare and common regulatory effects on expression level and isoform choices, modeling of rare regulatory variants using deep learning based mechanistic models, and analysis of the role of cryptic splicing in common diseases. The developed methods will be applied to cardiovascular disorders in collaboration with Prof. Heribert Schunkert, Head of the German Heart Center, and to schizophrenia, in collaboration with Dr. Michael Ziller, group leader at the Max Planck Institute of Psychiatry.

The position is funded for 2 years. The salary is according to the TV-L (German academic salary scale).

REQUIREMENTS

Candidates must either hold a PhD in computational biology or bioinformatics, or hold a PhD in physics, statistics, or applied mathematics with practical experience in high-dimensional data analysis. Experience in quantitative genetics is a plus. Applicants must have a proven publication record and an interest for translational research.

ABOUT US

The Gagneur lab is interested in how gene expression is encoded in genomes, and how to leverage this knowledge to understand the basis of genetic diseases. To this end, we employ statistical modeling of ‘omics data and work in close collaboration with experimentalists. Relevant recent work includes establishing RNA-sequencing as a powerful companion to genome sequencing for genetic diagnosis of Mendelian disorders [1], modeling of RNA metabolism from sequence [2, 3], and deep learning modeling of cis-regulatory elements [4].

We are located at the faculty of informatics of the Technical University of Munich. The TUM together with other excellent research institutions in Munich offer a dynamic, interactive and international research environment. With plenty of cultural attractions, green areas, and the proximity of the Alps, Munich provides a superb quality of life.

References
[1] Kremer et al. Genetic diagnosis of Mendelian disorders via RNA sequencing, Nature communications, 2017
[2] Eser. et al, Determinants of RNA metabolism in the S. genome, Mol. Syst. Biol., 2016
[3] Schwalb et al. TT-seq maps the human transient transcriptome, Science, 2016
[4] Avsec et al., CONCISE: Convolutional Neural network for CIS-regulatory Elements, https://github.com/gagneurlab/concise and http://www.biorxiv.org/content/early/2017/07/18/165183

HOW TO APPLY

Applications including a cover letter, CV, and references must be sent to Julien Gagneur (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) until September 15th 2017.


Julien Gagneur
Associate professor of Computatonal Biology
Faculty of Informatics
Technical University of Munich

www.gagneurlab.in.tum.de
Twitter: @gagneurlab

Phd Candidate/Postdoctoral position in Single Cell Computational Epigenomics [RWTH Aachen]

The Bioinformatics Group RWTH Aachen University performs research on computational methods for analysis of epigenomics and transcriptomics data. Over the past years, we have developed methods for prediction of cell specific binding sites from open chromatin data (Gusmao et al., Bioinformatics, 2015; Nature Methods, 2016), inference of regulatory networks driving cell differentiation (Lin et al., NAR, 2015; Allhoff et al., Bioinformatics, 2015) and prediction of long noncoding RNA regulation via DNA-RNA interaction (Kalwa et al., NAR, 2016).

We invite applicants for a Phd Candidate/Postdoctoral position in one of the following topics:

1) Machine learning methods for the analysis of single cell epigenomics data.

2) Sequence analysis algorithms for detection of interactions of long non-coding RNAs with DNA.

Candidates will perform research on methods for analysis of single cell epigenomics and transcriptomics scATAC-Seq, scRNA-Seq and scBS-seq. These projects will be performed in collaboration with stem cell and medical specialists from the RWTH Aachen University.

Applicants should hold a M.Sc./Ph.D. in Bioinformatics or Computer Science. Experience in the analysis of biological sequences, regulatory genomics and/or machine learning is required. The candidate should have solid programming skills (C, Python and/or R) and acquaintance with Linux. Experience with high performance computing is a plus. The working language of the group is English.

 Interested candidates should send a brief statement of research interests, CV and the names of three references to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!.

 The Bioinformatics Research Group (costalab.rwth-aachen.de) is supported by the Interdisciplinary Center for Clinical Research Aachen (IZKF) and hosted by the Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Hospital and the Helmholtz Institute for Biomedical Engineering, RWTH Aachen.