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Postdoctoral Researcher position in Bioinformatics [Dortmund]

The Max Planck Institute of Molecular Physiology (Dortmund, Germany) seeks to fill a

Postdoctoral Researcher position in Bioinformatics with a strong background in Statistics (m/w/d)

The position is available immediately in the Department of Chemical Biology (Director: Prof. Dr. Dr. h.c. Herbert Waldmann)


Job description

The department is currently running a multi-parameter phenotypic screening campaign (a.k.a "Cell Painting") of its in-house library at the Max Planck Society's (MPS) screening facility COMAS, also located in Dortmund.

In the Cell Painting assay [1], cells are treated with test compounds, then stained with multiple reagents that are selective for different cell compartments. Microscopic images are taken from the cells and analyzed with the Open Source software CellProfiler [2], eventually resulting in profiles of several hundred features for each compound. The profiles are normalized to controls and compared for similarity against sets of reference compounds with known bioactivity or other test compounds.

The whole analysis and post-processing workflow is implemented in Python / Pandas and is running on clusters of the MPS.

The successful candidate will identify and resolve statistical pitfalls, explore further analysis options for the data, and help synthesis groups of the department interpret their results in the assay, leading to the design of new bioactive compounds.

[1] Bray, M.-A., Singh, S., Han, H., Davis, C. T., Borgeson, B., Hartland, C., Kost-Alimova, M., Gustafsdottir, S. M., Gibson, C. C. & Carpenter, A. E. Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nature Protocols 11, 1757–1774 (2016).
DOI: 10.1038/nprot.2016.105




The successful candidate has:

·         a PhD in Bioinformatics

·         expert knowledge in Statistics

·         expert knowledge of at least one scripting language in the context of data analysis (preferably Python / Pandas)

·         additional knowledge of a cheminformatics toolkit (e.g. RDKit) and experience with Deep Learning (e.g. Keras, PyTorch) would be advantageous


We offer a full-time employment in a modern, international work environment.

The position represents an excellent opportunity to work on bioinformatic projects in a highly relevant chemical biology context within a very distinguished group. The position is available from now on and is limited to two years.

Remuneration is paid in accordance with the collective bargaining agreement of the public service (TVöD Bund), taking account of your qualifications and professional experience. In addition, social benefits correspond to those of the public service.



The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.

Furthermore, the Max Planck Society seeks to increase the number of women in areas where they are underrepresented and therefore explicitly encourages women to apply.

The Max-Planck-Society strives for gender equality and diversity within its workforce.

Applications should be conclusive and complete, including the earliest possible starting date. The application deadline is 19th May 2019.

Please send applications by email in one PDF file to Dr. Axel Pahl (This email address is being protected from spambots. You need JavaScript enabled to view it.) using “Bioinformatics” as the subject.

Links: ;

Research Associate (Postdoc) at the Universität Hamburg (TVL-13, full)

We are looking for a talented Postdoc for the deNBI partner project "EnzymeStructures". The position commences on May 1, 2019 and is renumerated at the salary level TV-L 13.
We are providing  the Webservice ProteinsPlus. If you are interested in Structural Bioinformatics and/or Cheminformatics think about joining us in Hamburg.

More details can be found here.

Research assistant/associate (100%, TV-L E 13)

In the frame of the collaborative research project DBAC (DNA-Barcode Analyzer for CITES Species), financed by the Federal Agency for Nature Conservation (BfN), the University of Bonn invites applications for a

Research assistant/associate (100%, TV-L E 13)

to begin on April 1st, 2019 at the Nees Institute for Plant Biodiversity in the research group of Prof. Dr. Dietmar Quandt.

 DBAC aims to develop a browser based open source analyses platform for DNA-barcode sequences generated via next generation sequencing (NGS). The standalone platform will also be embedded in the online resources of the West German Genome Center (WGGC) at the University of Bonn. Therefore, the applicant should be familiar with programming, NGS and bioinformatics. The research project runs in collaboration with the Institute for Human genetics, University Hospital Bonn (UKB), the Max Planck Institute (MPI) for Plant Breeding Research (MPIPZ), and the Institute for Evolutionary Biology, University of Münster.

The position's requirements are:

·         Diploma, or Master in (Bio)-Informatics or Biology, Plant Science, Evolutionary Biology, or related fields,

·        Preferably a PhD in one of the fields

·         Proven qualifications in programming and bioinformatics

·         Experience with next generation sequencing data and DNA-Barcoding

·         High motivation, active participation, commitment and interaction with the collaborative partners

·         Language skills: English (written and spoken)


Application documents:

·         Letter of motivation

·         Curriculum vitae

·         Transcripts of studies

·         Two letters of recommendation


The temporary position is limited to the duration of the research program and therefore restricted to a maximum duration of 12 months. Starting date of the position is February or latest April 1st, 2019.


The University of Bonn is an equal opportunities employer.



Applications in German or English should be sent in electronic form by March 1st, 2019 to Prof. Dr. Dietmar Quandt at the following e-mail address: This email address is being protected from spambots. You need JavaScript enabled to view it. (subject: DBAC Application).

Computer scientist or bioinformatician with strong computational background (Web development, data and workflow management…)

We are looking for a computer scientist or a bioinformatician with a strong computation background to join the bioinformatics unit of the IEO in Milan. The candidate will evolve in a research environment (next generation sequencing among others). The selected candidate will consolidate our team for the development and maintenance of the bioinformatics resources, and will have the opportunity to support the research groups in setting new tools and pipelines.

Place of employment and work

The candidate will be located at the Department of Experimental Oncology of the European Institute of Oncology in Milan (Italy), one of Europe’s leading research institutes in biomedical research, where he/she will also interact with one of the largest computational biology communities in Italy


The candidate should have good programing skills. Background in bioinformatics would be appreciated but is not mandatory. Experience with containers (docker, singularity), grid computing, web frameworks, spring boot, nextflow, continuous integrations will be appreciated.


For further info or to arrange an informal interview, please write to This email address is being protected from spambots. You need JavaScript enabled to view it.

PhD position - Functional Genomics and Computational Biology

A three-year Ph.D. position (65% E 13 TV-L) is immediately available at the Department of Biology ( at the Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU).

The focus of our research group is on understanding the functional aspects of the human genome in health and disease through the analysis of the different levels of information encoded in the sequence. Some of our publications include:

Li L, Barth NKH, Hirth E, Taher L. Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units, Genome Biol Evol., 2018 (
Taher et al., Sequence signatures extracted from proximal promoters can be used to predict distal enhancers, Genome Biology, 2013 (

We are looking for talented, highly motivated applicants with:
1. A master's degree or equivalent within the field of computational biology, bioinformatics or related fields.
2. Familiarity with bash scripting, Perl (or Python) and R programming.
3. Experience with the analysis of Next-Generation Sequencing data (mainly from Illumina platforms).
4. Strong written and oral communication skills in English.

How to Apply:
The position will remain open until filled. Please email applications to Leila Taher (This email address is being protected from spambots. You need JavaScript enabled to view it.) with the subject "PhD Position". An application package must contain the following documents (please, send all in one PDF file):
1. A letter of interest.
2. A complete curriculum vitae.
3. A short (<10,000 characters) research proposal on the topic "regulatory functions of transposons".
4. Copies of transcripts.
5. Names and contact information for 2-3 references.

Only complete applications will be considered. 

Ph.D. Student in Biomedical Data Science (HIV) (E13 TV-L, 65%)

The Chair for Methods in Medical Informatics (Prof. Dr. Nico Pfeifer), Department of Computer Science at Eberhard Karls University Tübingen, one of eleven German universities distinguished as excellent under the German government’s initiative, is currently looking for a

Ph.D. Student in Biomedical Data Science (HIV) (E13 TV-L, 65%)

starting as soon as possible. The initial fixed-term contract will be for 3 years with possible extension. The position is funded by the Machine Learning Competence Center Tübingen (TUE.AI Center).

According to WHO about 37 million people have been living with HIV/AIDS world-wide at the end of 2017. Since there is no approved curative treatment, infected people have to take life-long anti-retroviral treatments (ART). Due to the high variability of HIV, resistant variants can emerge in patients even if they are under treatment. There are even cross-resistances between different ARTs. Therefore, there is a constant need for new targets. Highly potent and broadly neutralizing antibodies (bNAbs) have been promising candidates to fulfill this need. The goal of this Ph.D. project is to extend the work by Hake and Pfeifer to build an interpretable prediction model that can be used to give decision support for bNAbs treatment by applying and extending state-of-the-art machine learning methods.

The group has extensive knowledge at the interface between statistical machine learning, digital medicine, and computational biology. Nico Pfeifer is a PI in the excellence cluster “Machine Learning: New Perspectives for Science” starting in January 2019. We are developing methods that allow answering new biomedical questions (Speicher and Pfeifer 2015, Proceedings of ISMB/ECCB 2015) and optimize them in close contact with our excellent national and international biomedical partners (Carlson et al. 2016, Nature Medicine, Schoofs et al. 2016, Science, Döring et al. 2016, Retrovirology, Mendoza et al. 2018, Nature).


The ideal candidate will have an M.Sc. or equivalent in Biomedical Data Science, Biometry, Biostatistics, Bioinformatics, Medical Informatics, Computer Science, Computational Biology or a related life science discipline. Applicants should have an interest in interdisciplinary work. Experience in data science and machine learning as well as strong programming/scripting skills (C/C++, R, Matlab, Python, JavaScript, Java) are desirable. Other relevant qualifications include:

  • Background in Statistics

  • Knowledge of the adaptive immune system (especially humoral immune response)

  • Experience with medical data (clinical data, molecular data, …)

  • Experience with high-throughput data (next-generation sequencing)

  • Databases (MySQL, NoSQL)

In case of equal qualification and experience, physically challenged applicants are given preference. The University of Tübingen aims at increasing the share of women in science and encourages female scientists to apply. Candidates will be officially employed by the administration of the University of Tübingen.

Please send your application (including motivation letter, curriculum vitae, transcripts and certificates, and contact details of two academic references) via e-mail to
This email address is being protected from spambots. You need JavaScript enabled to view it. with the subject: Ph.D. student application Biomedical Data Science (HIV).

Application deadline: March 3rd, 2019.

Candidates are encouraged to send their application material early since we will start reviewing applications already before the deadline.


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

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

Your qualifications

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

In addition:

Excellent academic performance

Very good master's degree in Bioinformatics or Biotechnology

Very good knowledge of English

Willingness to move to the university location

For further information: 

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

<a href="">European Galaxy Team</a> is hiring!

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

Current areas of expertise include:

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

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


If you are interested to work with us,  This email address is being protected from spambots. You need JavaScript enabled to view it. (This email address is being protected from spambots. You need JavaScript enabled to view it.) and help us to make science more accessible, reproducible, and transparent.

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

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


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

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


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


Your key responsibilities


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

·         Build interactive applications for multi-OMICS data

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


Your qualifications

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

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

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

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

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


Our offer


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

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

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





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