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Stellenangebote

Scientific Programmer / Bioinformatician [ Zimmermann research group, EMBL]

We are seeking a highly motivated scientific programmer and data manager to join the new Zimmermann research group in the Structural and Computational Biology unit. The Zimmermann group combines high-throughput mass spectrometry, bacterial genetics, multi-omics analyses and computational models to investigate the interactions within microbial communities and between microbes and their environment. Your role would be to develop analysis pipelines, infrastructure and data management systems within the group and externally. It includes the development and maintenance of bioinformatics software for different research projects, adaptation of existing code and pipelines, and providing programming and statistics support to the group. The position involves large scale data handling from mass-spectrometry and sequencing experiments (metabolomics, NGS). The duties range from generic bioinformatics and IT support to development of own independent research projects.

Requirements:

—a Ph.D. degree in bioinformatics, computational biology, statistics, or related subjects

—substantial experience in software development and/or scientific computing

—experience with large-scale data analysis and management

—experience with the Linux/Unix shell

—advanced skills in a high level programming language (>2 years of experience)

—ability to work independently and in a team, and at the interface between life sciences and informatics

—willingness to learn new skills and programming languages as projects require

—good communication, interpersonal and English language skills 

Links: https://www.embl.de/jobs/apply_page/?jobId=QHPFK026203F3VBQB688N79SB-1098&langCode=en_GB

2 Phd positions in Computational Biology [Center for Molecular Medicine, Frankfurt]

The group of Prof. Marcel Schulz  is looking to fill the position of two Phd students (E13 TV-G-U, 65%) to start as early as possible at the Computational Epigenomics & Systems Cardiology group at the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, Frankfurt (https://schulzlab.github.io).

Exact payment is based on previous research experience according to the work laws of Goethe University (TV-G-U).

Tasks:

We offer a Phd position for method development for integrative analysis methods targeted for analysis of single cell assays that are conducted with multiple assays simultaneously, for example RNA-seq and DNA methylation or ATAC-seq. Another position is about method development of novel approaches for the prediction of gene expression. Different approaches from Machine Learning should be tested and novel approaches for the interpretability of complex non-linear methods or Deep Learning based approaches should be developed to unravel gene-specific regulatory codes from a large catalogoue of epigenomics data.

Requirements:

·       Masters degree in Bioinformatics, Machine Learning, Computer Science or a related discipline

·       good programming skills

·       experience in the application of machine learning methods is advantageous

·       experience in the analysis of sequencing data is advantageous

·       we are working in an interdisciplinary team and are looking for people with good organizational and communication skills, as well as high creativity to address novel research problems

·       good knowledge of the English language

Please send your application with CV and two names of references latest until 15.06.2019 (preferably by email) to:

Prof. Marcel Schulz, Institut für Kardiovaskuläre Regeneration, Zentrum für Molekulare Medizin, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, E-Mail: marcel.schulz AT em.uni-frankfurt.de

Please do not send original documents by mail, because there will be no return of such documents. All electronic documents should be combined into one pdf document. Travel and application costs are not being reimbursed.

Goethe University is comitted to increase the amount of female researchers and we encourage their application. Applicants with a disability and equal qualifications will be favoured.

 

Postdoc Computational Biology [Center for Molecular Medicine, Frankfurt]

The group of Prof. Marcel Schulz is looking to fill the position of a

Postdoc (E13 TV-G-U, 100%)

to start as early as possible at the Computational Epigenomics & Systems Cardiology group at the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, Frankfurt (https://schulzlab.github.io).

Exact payment is based on previous research experience according to the work laws of Goethe University (TV-G-U).

Tasks:

·       The Postdoc position is part of a large project about the analysis of high-dimensional data to understand gene regulation in heart diseases. It involves the development of new methods for the analysis of single cell data and application of machine learning methods to address problems of data heterogeneity and integration of datasets from different cellular levels (RNA, DNA methylation, chromatin).

 

Requirements:

·       Masters degree in Bioinformatics, Machine Learning, Computer Science or a related discipline

·       Phd degree in Bioinformatics, Machine Learning, Computer Science or a related discipline

·       good programming skills

·       experience in the application of machine learning methods

·       experience in the analysis of sequencing data

·       we are working in an interdisciplinary team and are looking for people with good organizational and communication skills, as well as high creativity to address novel research problems

·       good knowledge of the English language

Please send your application with CV and two names of references latest until 15.06.2019 (preferably by email) to:

Prof. Marcel Schulz, Institut für Kardiovaskuläre Regeneration, Zentrum für Molekulare Medizin, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, E-Mail: marcel.schulz AT em.uni-frankfurt.de

Please do not send original documents by mail, because there will be no return of such documents. All electronic documents should be combined into one pdf document. Travel and application costs are not being reimbursed.

Goethe University is committed to increase the amount of female researchers and we encourage their application. Applicants with a disability and equal qualifications will be favoured. 

13 positions for PhD students available including a computational molecular design topic

Within the Research Training Group "Chemical Biology of Ion Channels (Chembion)" funded by the Deutsche Forschungsgemeinschaft (DFG) and established at the Westfälische Wilhelms-Universität in Münster 13 positions for PhD students, 13 TV-L (65 %) are available.

13 scientists of the Westfälische Wilhelms-Universität Münster have teamed up with their complementary expertise to focus on the chemical biology of ion channels. The interdisciplinary research activities are centered on five topics: ligand recognition, subtype specific modulation, molecular imaging, molecular and cellular physiology, integrative (patho)physiology. Our vision of this interdisciplinary project is to solve physiological questions in the field of ion channels with innovative chemical methods, to bring together the molecular world of chemistry/pharmacy with the function-centered world of medicine and to develop the internationalization of our doctoral students.

One topic is of special interest for the bioinformatics/cheminformatics community: "In-silico studies of ion channels and their modulators using computational molecular design".

Further details can be obtained from the Chembion homepage: www.uni-muenster.de/chembion

 

Wissenschaftlicher MitarbeiterIn (m/w/d) (DoktorandIn oder Postdoc, TV-L E13/100%) in Bioinformatik

In der Arbeitsgruppe von Prof. Dr. Caroline Friedel an der Ludwigs-Maximilians-Universität München ist frühestens zum 1.7.2019 die Stelle einer/s

Wissenschaftlichen Mitarbeiter/in (TV-L 13, 100%)

als Promotions- oder Postdoc-Stelle zu besetzen. Der Beginn der Stelle ist flexibel bis zum 31.3.2020, daher ist eine Bewerbung auch bereits jetzt möglich, wenn Master oder Promotion erst in einigen Monaten abgeschlossen werden.

Diese Stelle ist Teil des durch die DFG geförderten Projektes „Large-scale investigation of short read archives for disruption of transcription termination and circular splicing“.  

Ziel dieses Projektes ist dabei die Entwicklung und Anwendung von neuen Methoden zum Durchsuchen großer Read-Datenbanken wie die NCBI SRA nach Evidenz für Störungen in der Transkriptionsterminierung und speziellen Splicing-Ereignissen.

Kandidatinnen und Kandidaten sollten ein Hochschulstudium (Master/Diplom) bzw. eine Promotion für die Postdoc-Stelle in Bioinformatik oder einem nahe verwandten Fachgebiet absolviert haben oder kurz vor dem Abschluss stehen. Vorausgesetzt werden gute Programmierkenntnisse (Java, Python und/oder Perl) und Interesse an quantitativer Datenanalyse und bioinformatischer Methodenentwicklung. Erfahrungen mit der Analyse von Hochdurchsatz-Daten, insbesondere Next-Generation Sequencing-Daten, wären von Vorteil.

Bewerbungen mit den üblichen Unterlagen (Lebenslauf, Zeugniskopien, Master/Diplom-Arbeit bzw. Doktorarbeit als PDF per Email) bzw. Fragen zur Stellenausschreibung sind zu richten an:

Prof. Dr. Caroline Friedel
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
This email address is being protected from spambots. You need JavaScript enabled to view it.
 
 

 

 

Bioinformatician (full time) [Heidelberg University Hospital ]

We have an opportunity for a a talented and motivated bioinformatician to join the Portugal laboratory in the Parasitology Department of Heidelberg University Hospital.

We are seeking a Bioinformatics Scientist (BSc, MSc or PhD [title and rank will be determined based on experience and degree]) with background in biology, statistics and programming. Expertise in R and familiarity with analytic tools and public genomic and clinical databases.

Project Description: We have recently shown that dry season Plasmodium falciparum infections are maintained asymptomatically during the 6-month dry season in Mali, while P. falciparum-specific humoral responses decrease (Portugal, S. et al. 2017). We are currently investigating parasite transcription and transcriptional regulation, during the dry season through NGS, comparing leucocyte-depleted blood of Malian children with persistent subclinical P. falciparum infections at the end of the dry season, and that of age- and gendermatched Malian children presenting with their first clinical malaria case in the ensuing transmission season.

We aim to investigate parasite transcription, including the expression of genes coding for parasite variant surface proteins on the surface of the host erythrocyte, and RNA-protein-DNA interactome, chromatin accessibility, and epigenetics. The person we seek will be working at the interface of wet lab and field researchers as well as P. falciparum bioinformaticians with whom we collaborate to further develop analytic tools. The ideal candidate should have or quickly develop excellent communication skills and the ability to work with interdisciplinary teams, be fluent in English and be willing to present results internally and externally.

Collaboration Partners: Peter Crompton (NAID, NIH), Boubacar Traore (FMPOS, ICER Mali), Thomas Lavstsen (Copenhagen University), Thomas Otto (University of Glasgow)

Profile of candidate’s qualification:

-           Graduate, Master’s or PhD Degree in Informatics, Biology or related areas;

-           Expertise in bioinformatics and molecular/cellular biology and experience with “Omics” data analysis.

-           Background in Statistics

-           Excellent knowledge of spoken and written English and excellent communication skills and team spirit; organizational skills and ability to keep detailed records of experiments;

-           Critical mind, enthusiasm; and ability to work in multidisciplinary and multicultural teams.

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

Please send your application (including motivation letter, curriculum vitae, transcripts & certificates, and contact details of two academic references) via email by July 15th indicating Bioinformatician call on the email subject.

Postdoc in Computational Biology [HZI]

The Department of Computational Biology for Infection Research at the HZI, led by Prof Dr Alice C. McHardy, is looking for excellent postdocs in computational biology or bioinformatics. 

The goal of our projects is the development of algorithms and computer-aided methods to analyze (meta)-omics data of the human microbiome, viral and bacterial pathogens, and human cell lineages within individual patients, to further personalize medicine in infection research. The methods that we employ or develop in our research are related to the fields of machine learning, phylogenetics and population genetics-. The lab co-organizes the Critical Assessment of Metagenome Interpretation challenge (CAMI; Sczyrba et al., Nature Methods 2017), hosts the bioinformatics unit of the German Center for Infection Research (DZIF; https://www.dzif.de), is part of the new German excellence cluster RESIST (www.dfg.de) and a priority programme on CRISPR-Cas (https://gepris.dfg.de/gepris/projekt/405892038) and collaborates locally, nationally and internationally with biologists and medical experts. The lab’s projects offer plenty of opportunity for an excellent bioinformatics postdoc to shine.

Requirements: The candidate should have a PhD degree in bioinformatics, computational biology, machine learning, biomathematics, computer science, statistics or similar and a competitive publication record. A commitment to reproducible research, the ability to work in a highly interdisciplinary research field and very good programming skills are obligatory. Prior experience in meta’omics, infection research, statistical learning or with the analysis of NGS data sets is advantageous, but not required.

 

 

 

Bioinformatician for single-cell developments in the context of viral infection

The Health Data Science Unit (HDSU, www.hdsu.org) is a newly created unit of the BioQuant and medical Faculty of the University Heidelberg, which focuses on research topics related to digital health and the integration of clinical and genomic datasets. HDSU is one of the major partners of the HighMed medical informatics consortium (www.highmed.org), and leads the effort to set up systems for clinical data integration. A further topic of the unit lies in the analysis of (epi)genomic datasets and single-cell datasets, as part of several consortia. We seek to develop novel approaches for the integration of multi-omics datasets, especially in a single-cell context.

 
Within the DFG-funded transregio project “Determinants and dynamics of elimination versus persistence of hepatitis virus infection” (www.trr179.de), the group of Dr. Carl Herrmann is planning to set up a central single-cell analysis facility, in collaboration with the single-cell Open Lab at BioQuant Heidelberg (https://malone.bioquant.uni-heidelberg.de/scopenlab/). We want to investigate the sources of variability in the cellular response to viral infection, in particular HCV virus, by combining several layers of single-cell omics in various cellular populations.

In this context, we are looking for a bioinformatician to support and coordinate this effort, with a focus on the following points:

· Development and implementation of standard single-cell analysis workflows for scRNA-seq and scATAC-seq datasets in an HPC environment;

· Implementation of such workflows in a cloud infrastructure (de.NBI cloud, ELIXIR,…);

· Development of data integration methods and strategies for multi-omics single-cell datasets;

· Analysis of single-cell datasets (scRNA-seq/scATAC-seq/CITE-seq) generated within the DFG consortium;

· Contribution to training efforts and documentation for external users of these workflows.

We are looking for a candidate with experience in large-scale high-throughput sequencing data such as RNA-seq, ChIP-seq and ATAC-seq, and the ability to set up analysis workflows (preferentially using snakemake). First experience with single-cell datasets as well as a solid statistical background would be a strong plus.

The position is funded for two years, with a possibility for further extension.

Application letters and CVs (as pdfs), together with contact information of two referees should be sent by mail to This email address is being protected from spambots. You need JavaScript enabled to view it.
 

Research Assistant (m/w/d) in Bioinformatics (TV-H E13 100%)

The Professorship for Systems Biology at Justus Liebig University Giessen invites applications for the full-time position of a Research Assistant within a BMBF-funded project.

 

Duties:

·         key tasks involved in the certification of a cloud computing and introduction of the relevant management systems.

·         planning and monitoring of the implementation and provision of cloud-based services.

·         creating a user-oriented repository of predominantly bioinformatics software tools including installation and function testing in OpenStack- and Kubernetes-based environments.

·         maintenance of related comprehensive user documentation.

·         specific project support with both data analysis and development of new software tools for the analysis and visualisation of high-throughput data.

 

Qualifications:

·         A full university education in bioinformatics, informatics or other IT-based subject

·         Wide experience in system administration, especially with Linux operating systems

·         Basic knowledge of the demands of certification processes in the IT field

·         Experience with administration of infrastructure systems and relevant bioinformatics applications and their maintenance and installation

·         Sound knowledge of network infrastructure

·         Experience with the effective use of cloud computing platforms, such as OpenStack or Kubernetes

·         Assured and demonstrable experience with at least one programming language, e.g. Perl, Java, Python

 

Link to complete job description: http://www.inst.uni-giessen.de/stellenmarkt/pdf/stelle0011805.pdf

Full Professorship in Medical Data Science and Services (W3 BBesO grade post)

We are one of the youngest universities in Germany and think in terms of unlimited possibilities instead of possible limitations. Located in the heart of the Ruhr metropolis, our 11 faculties develop ideas for the future. We are strong in research and teaching, we embrace diversity, promote academic potential, and we are highly committed to educational equality.

University Medicine Essen is on its way to becoming a SMART Hospital, where digital technologies will enable employees to further improve patient care, research and education. We are convinced that truly personalized medicine can only be realized, if we combine digitization in medicine with artificial intelligence. We have therefore decided to establish an Institute for Artificial Intelligence (AI) in Medicine. In its founding stage, this institute will be staffed with four professorships dealing with different aspects of AI in medicine. We envision these professorships to synergistically lead the successful development of our innovative concept. It is our aim to identify highly motivated individuals with a broad and complementary range of expertise with whom we undertake this journey.

The Medical Faculty of the

University of Duisburg-Essen

is inviting applications for a

Full Professorship in

Medical Data Science and Services

(W3 BBesO grade post)

The position is newly established and will work in concert with three additional professorship positions (two of them within the framework of the Cancer Research Center Cologne Essen (CCCE)), all related to the use of artificial intelligence in medicine. Upon successful development perpetuation of the professorship is envisioned.

Core tasks of the applicant are (i) enhancing the potential of medical data by enabling interoperability between different systems and locations by means of structurization, harmonization, and annotation (ii) data aggregation of next generation information systems like bioimaging, outputs from multi-omics analyses, and others (iii) strategies for anonymization and nationwide valid patient's consent and data access management (iv) data protection-compliant distributed analytics over multiple national and international sites.

The future job holder should have several years of professional experience in the field of data analysis. Excellent knowledge of relational and non-relational database systems is desirable. Further prerequisites are experience in the development and implementation of cooperations with industry as well as scientific productivity. The applicant should have experience with AI techniques and neuronal networks. Ideally, the applicant is familiar with NLP and related methods.

The future chair will also contribute to the main research focuses of the Medical Faculty and will collaborate with and contribute to ongoing and evolving research consortia. Furthermore, the future chair will possess dedicated teaching skills and use innovative methods in teaching and post-graduate qualification.

Qualifications according to § 36 Hochschulgesetz NRW are required and successful experience with competitive third-party funding applications are mandatory. As the University of Duisburg-Essen puts special emphasis on the quality of academic teaching, concepts on the participation in teaching activities with regard to the profile of the University Duisburg-Essen should be provided.

The Medical Faculty in Essen promotes research particularly in the following areas: Cardiovascular Disease, Oncology, Transplantation Medicine and Translational Neuro- and Behavior Sciences, as well as the bridging disciplines of Immunology and Infectious Diseases. This position is dedicated to the area of Oncology.

The position will be available at the earliest.

Application deadline: 13.06.2019

The University of Duisburg-Essen aims to increase diversity among its faculty members (see http://uni-due.de/diversity) and strives to increase the number of women in such positions; therefore, we especially encourage women with relevant qualifications to apply. Women with the appropriate qualifications will receive preferential consideration. Applications from severely disabled candidates according to § 2 Abs. 3 SGB IX are welcome.

Applications with the usual supporting documents [curriculum vitae, list of scientific publications (see http://www.uni-due.de/imperia /md/content/medizin/formblatt_aufbau_schriftenverzeichnis.pdf)], documents on scientific and professional career, certificate copies, information on third-party funding, participation in academic self-administration, past teaching experience and concepts for teaching, and 5 key publications should be submitted by email (This email address is being protected from spambots. You need JavaScript enabled to view it.) to Univ.-Prof. Dr. J. Buer, Dekan der Medizinischen Fakultät, Universitätsklinikum Essen, Hufelandstr. 55, 45147 Essen.

Furthermore, we need you to fill in our application form at https://www.uni-due.de/med/de/organisation/bewerbungsbogen.php. Further information on the position and its embedding in the University of Duisburg-Essen as well as in the Faculty can be found at https://www.uni-due.de/med/de/organisation/berufungen.php. For general information please visit: https://ai.uk-essen.de.