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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.

Bioinformatics - PhD / Postdoc positions im Centre for the Advanced Study of Collective Behaviour

The Centre for the Advanced Study of Collective Behaviour will create a global hotspot for the integrated study of collective behaviour across a wide range of species and scales of organisation. With English as the working language, it will be a global hub for scientists seeking to create a synergistic, interdisciplinary environment for the study of collective behaviour. Establishing collective behaviour as an integrative field, the Centre will bring together international researchers from biology, computer science, social psychology, physics, and behavioural economics to work closely on addressing common questions across species boundaries. The Centre is recruiting up to 25 PhD and Post-doc positions in collective behaviour, including positions in Bioinformatics, Computer Science and related areas.  Candidates should be interested in interdisciplinary research. Detailed information can be found here:


Biostatistician: Centre for Statistical Data Analysis

Location: EMBL Heidelberg, Germany

Staff Category: Staff Member

Contract Duration: 3 years (renewable)

Grading: 6, 7 or 8; depending on experience and qualifications

Closing Date: 10 March 2019

Reference Number: HD01456


EMBL is an international research organization covering many fields of modern biology. Five Computational Centres provide expertise, advice, and training for scientists across EMBL. We are looking for a statistician or data scientist to Head the EMBL Centre for Statistical Data Analysis.


Your role


Your responsibilities will include:


• Statistical consulting for EMBL researchers

• Teaching short courses on computational statistics / data science in biology

• Collaboration on selected research projects with EMBL research groups


As statistician/data scientist, you will be interested in statistical applications in modern biology, in computational method development for new technologies (single cell ‘omics, imaging, proteomics, microfluidics), in data visualization and data integration, and in method benchmarking and teaching. You will be co-affiliated with the research group of Wolfgang Huber (see


The position also offers the opportunity to help shape future developments of ‘data science’ in biology, such as publication and communication best practices.


You have


A PhD or equivalent qualification in a quantitative science (statistics, mathematics, computer science, physics) with solid theoretical foundations in probability and applied statistics and some experience in data analysis of modern biological data. As our ideal candidate you should enjoy teamwork and be excited by providing consulting and teaching services at an advanced level in a world-class research environment. Excellent communication skills in written and spoken English are required.


You might also have


Candidates should have a solid understanding of programming concepts and multiple languages, including advanced R. Proficiency with scientific authoring frameworks such as LaTeX, Rmarkdown and HTML5 is a plus.


Why join us


EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, as well as financial support for relocation and installation, including your family and the availability of an excellent child care facility on campus. EMBL has a large thriving community of bioinformaticians, working in close collaboration with experimental scientists and with strong links to other local scientists and institutions.


What else do I need to know


We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.


Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research.


Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.


Ph.D. Student in Translational Immunoinformatics (Lung Diseases)

The Institute of Computational Biology is globally recognized for innovations in data analysis and modeling of biological systems, anchored at the Helmholtz Zentrum Munich and the Technical University Munich.

For our research team "Translational Immunoinformatics" we are currently looking for a

PhD Candidate for the Project: "Cell Fate Modeling in Chronic Lung Diseases” (E13 TV-L)

Job Description

The Ph.D. project will focus on the characterization of genetic factors describing pulmonary fibroblasts in chronic lung diseases and the identification of transcriptional factors that can be used to reprogram diseased lung fibroblasts to healthy lung epithelial cells.


The aims of the projects involve:

Identifying biomarkers that lead to fibroblast formation in the lung for early risk assessment

Developing a risk prediction model using the identified biomarkers

Modeling longitudinal mass cytometry data to describe the reprogramming path of fibroblasts to epithelial cells

Analyzing and integrating simultaneously collected single-cell RNA-seq data


The Ph.D. candidate will have the opportunity to be integrated into the experimental partner lab to help develop novel analytical strategies in direct interaction with the members of the experimental lab.


 Your Qualifications


A Master’s Degree in Biostatistics, Bioinformatics, Statistics or related fields (with significant experience in Bioinformatics)

Experience in multivariate statistics and Bayesian modeling

Excellent programming skills (R, Python, C/C++)

Scientific curiosity and ability to work independently

Highly motivated to work in a young and multi-disciplinary, collaborative environment

Fluent in spoken and written English


The following qualifications are considered advantageous:


Experience with NGS (transcriptomic and genomic) analysis

Basic understanding of mass cytometry analysis

Basic understanding of single-cell RNA-Seq analysis


Our Offer


At the Helmholtz Zentrum München, you can contribute together with leading researchers to the investigation of the development, prevention, and treatment of environmental diseases such as diabetes, chronic lung diseases, and allergies. To further promote your professional development, we offer extensive and targeted research training and career programmes. We support the reconciliation between work and private life with flexible working time models, occupational health management, day care facility for children, a childcare subsidy, Elder Care, as well as other counseling and support services.

Remuneration and benefits are following the collective agreement for the public service (EG 13 50% TV EntgO Bund). Also, there is also the possibility of granting an allowance amounting to 15% if the necessary conditions are fulfilled.

The position is (initially) limited to three years.

The activity involves specialized knowledge and experiences specific to own scientific skills.

As a holder of the Total E-Quality Award, we promote equality of opportunity. Applications from women are welcome. Qualified applicants with physical disabilities will be given preference.

Please apply through our online application system with a motivation letter, curriculum vitae, transcripts and certificates, and contact details of two academic references.

Apply now:

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