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Phd Candidate position in Computational Epigenomics

The Bioinformatics Group RWTH Aachen University performs research on computational epigenomic methods. Over the past years, we have developed methods for prediction of cell specific binding sites from DNAse-Seq data (Gusmao et al., Bioinformatics, 2014; Gusmao et al., Nature Methods, 2016) and epigenetic and regulatory networks driving cell differentiation via integrative analysis of ChIP-Seq and RNA-Seq data (Allhoff et al., Bioinformatics, 2015; Lin et al., NAR, 2015).

We invite applicants for Phd Candidate positions in Computational Epigenomics. Candidates will perform research on methods for analysis of single cell epigenomics as ATAC-Seq, DNAse-seq and ChIP-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. in Bioinformatics, Computer Science or related areas. Experience in the analysis of biological sequences, regulatory genomics and/or machine learning is desirable. The candidate should have solid programming skills (C, Python and 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!.


PhD student (f/m) in Neuroscience

The Hospital of the University of Munich, Germany, is one of the largest and most competitive university hospitals in Germany and Europe. 46 specialized hospitals, departments and institutions harbouring excellent research and education provide patient care at the highest medical level with approximately 10.000 employees. The Institute for Stroke and Dementia Research offers a fully funded position available immediately:

PhD student (f/m) in Neuroscience

The ISD is a research institute primarily financed by foundation funds bridging the traditional barriers between academic medicine and basic science in the area of stroke research and related dementias.


The candidate will work closely with the Principal Investigator to perform both experimental and computational approaches. This PhD position will be in an international, dynamic and “open-door” atmosphere, with access to state of the art laboratory facilities and structured training as part of the Graduate School for Systemic Neuroscience (GSN) (, which is a part of Ludwig Maximilian University of Munich (LMU) (ranked as the top university in Germany according to
Times Higher Education World University Rankings).

Your profile:

Applicants should hold a diploma or Master’s degree in a quantitative discipline (e.g. physics, mathematics, computer science, engineering) or biological sciences, preferably with focus on bioinformatics (e.g. biology, medicine, bioengineering) is important. Experience in analysis of functional sequencing data and knowledge of R, Matlab or Python is strongly desired. Sound knowledge of the English language and team-oriented working is crucial for the applicant’s success. Suitable candidate should be highly motivated with an intrinsic interest in disease mechanisms.


We look for a talented individual to join the ISD ( ISD has a modern infrastructure including: brand new fully equipped lab spaces and offices, an animal facility that is fully equipped with surgery rooms, state-of the art imaging equipment. Our group will integrate single-cell transcriptome profiling with in vivo imaging to focus basic research on clinically relevant questions on the prevention, diagnosis and treatment of stroke and cognitive decline.

The position is initially for 2 years, but has the possibility of extension. Salary will be based on German public employment guidelines (TV-L). The Ludwig-Maximilians-University/Klinikum der Universität München is an equal opportunity employer. Individuals of all nationalities, genders, ages, and those with disabilities are encouraged to apply. We give priority to applicants with a disability and essentially equal qualifications. Presentation costs cannot be refunded. Skype interviews for candidates from abroad are welcome for an initial interview.

Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can’t be refunded.

Applicants should submit their complete application documents (including detailed CV, cover letter, copies of latest degree and transcripts, at least 1 references or the contact info of referee/s – all documents within a single PDF file) via email to:
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Prof. (W2) für Bioinformatik von Herz-Kreislauferkrankungen an der Universität Frankfurt

Am Fachbereich Medizin der Johann Wolfgang Goethe-Universität Frankfurt am Main ist im Rahmen des Deutschen Zentrums für Herz-Kreislauf-Forschung im Beamten- bzw. äquivalent im Arbeitsverhältnis eine


Professur (W2) für Bioinformatik von Herz-Kreislauf-Erkrankungen


- befristet auf 6 Jahre - zu besetzen. Die W2-Professur wird vom Deutschen Zentrum für Herz-Kreislauf-Forschung (DZHK) finanziert – der größten Forschungseinrichtung für Herz-Kreislauf-Erkrankungen in Deutschland. Das DZHK konzentriert sich darauf, neue Ansätze aus der Herz-Kreislauf-Forschung in die klinische Praxis zu überführen (Translation), um Diagnose, Prävention und Behandlung von Herz-Kreislauf-Erkrankungen zu verbessern. Das DZHK vereint hervorragende Grundlagenforscher/innen und klinische Forscher/innen aus sieben Standorten in Deutschland. Der/die erfolgreiche Bewerber/in wird DZHK-Professor/-in und Principal Investigator des DZHK ( Die Professur ist eingebettet in das Vascular Research Centre der Goethe-Universität. Die Position soll auch an den Fachbereich Informatik assoziiert werden.


Die Kandidatin/der Kandidat muss auf dem Gebiet der bioinformatischen Datenanalyse ausgewiesen sein. Ein Forschungsschwerpunkt im Bereich der Regulatorischen RNAs (RNA Struktur-Funktionsbeziehung, Analyse nicht codierender RNAs) oder System-Biologie/
Medizin (z.B. Datenintegration) wird ausdrücklich begrüßt. Eine spezielle Expertise in der Analyse des kardiovaskulären Systems ist von Vorteil, aber keine Einstellungsvoraussetzung. Daneben werden Erfahrung in der Lehre und der Leitung einer eigenen Arbeitsgruppe sowie hochkarätige Drittmitteleinwerbung und publikatorische Leistungen vorausgesetzt.


Die Professur ist ausgestattet mit einer Anschubfinanzierung („start-up package“), eigenen Mitteln und uneingeschränktem Zugang zur Infrastruktur des Instituts für kardiovaskuläre Regeneration und der IT-Infrastruktur des Kardiovaskulären Schwerpunktes.


Einstellungsvoraussetzungen sind ein abgeschlossenes Hochschulstudium, pädagogische Eignung, Promotion und Habilitation oder der Nachweis gleichwertiger wissenschaftlicher Leistungen, die auch im Rahmen einer Juniorprofessur oder außerhalb des Hochschulbereichs erbracht worden sein können. Die Goethe-Universität ist bestrebt, den Anteil der Professorinnen zu erhöhen und fordert deshalb entsprechend qualifizierte Frauen nachdrücklich auf, sich zu bewerben. Details zu den Einstellungsvoraussetzungen und rechtlichen Rahmenbedingungen finden Sie unter: 


Wissenschaftlerinnen und Wissenschaftler, die in Forschung und Lehre exzellent ausgewiesen sind und international sichtbare Forschungsleistungen belegen können, sind eingeladen, ihre Bewerbungen nach den Richtlinien des Fachbereichs abzufassen und innerhalb von 4 Wochen nach Erscheinen dieser Anzeige an den Dekan des Fachbereichs Medizin der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, E-Mail: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! (ein zusammenhängendes pdf), zu richten.


Hinweise zur Abfassung Ihrer Bewerbung finden Sie unter folgender Internet-Adresse:


Software Engineer in PhenoMeNal Project

We are seeking to recruit an experienced Software Engineer/Developer to work on the PhenoMeNal H2020 project, to create an e-infrastructure for large-scale computing with medical metabolomics data. You will join the Cheminformatics and Metabolism team at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Genome Campus near Cambridge in the UK.

You will lead the further development, scaling and integration of existing bioinformatics solutions into a European e-infrastructure for analysing medical metabolomics data. This will lead into the development of virtual machine images (VMIs) to sustain various levels of data storage, pre-processing, integration, analysis, and visualisation. The use of VMIs will enable a flexible architecture that can run on local systems within participating and collaborating organisations, and maintain a high level of data security/integrity. Tools, services and associated software included in the different VMI’s will be developed and integrated. The project will integrate well established stand-alone bioinformatics tools and a significant amount of research is necessary to investigate the requirements for interoperability of those tools in a coherent practically useful processing pipeline.

The EBI is part of the European Molecular Biology Laboratory (EMBL) and it is a world-leading bioinformatics centre providing biological data to the scientific community with expertise in data storage, analysis and representation. EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academic and industry.

Qualifications and Experience

You must have experience with the following:

    • Java and associated frameworks like Spring and Hibernate


    • Frontend JavaScript frameworks, like jQuery and AngularJS

    • RESTful Web Services, JSON

    • Maven

    • Continuous Integration, Jenkins

    • Batch / Script / Shell programming

    • Linux/UNIX

    • SQL and NoSQL databases, JDBC

You should also be experienced with agile software development. Familiarity with R, data analysis will be very beneficial. Interest in grid and cloud technologies and interactions with other large-scale EU infrastructures such as the European Grid Initiative is essential.

You will have a strong interest in software engineering along with a strong degree in computer science or a related field. You must be able to work as part of a focussed team, but as the same time be self-driven, trustworthy and able to work independently. You must be a structured worker with good communication skills, and a willingness to travel to European project meetings.


EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation.

We provide a dynamic, international working environment and have close ties with both the University of Cambridge and the Wellcome Trust Sanger Institute.

EMBL-EBI staff also enjoy excellent sports facilities, a free shuttle bus to Cambridge and other nearby centres, an active sports and social club and an attractive working environment set in 55 acres of parkland.


Postdoctoral positions available in the Department for Computational Biology of Infection Research

The Department for Computational Biology of Infection Research Group at HZI is looking for excellent bioinformatics postdocs to work in computational metagenomics and infection research. The two-year postdoc positions are funded with an attractive salary of 100% TVöD E14, with possible extensions depending on performance.

We offer: The lab develops software and algorithms, co-organizes the Critical Assessment of Metagenome Interpretation challenge (CAMI;, hosts the bioinformatics unit of the German centre for infection research ( and collaborates locally, nationally and internationally with biologists and medical experts from universities and research institutes. For instance, we recently characterized the root-associated microbiome in barley (Bulgarelli et al. 2015, Cell Host Microbe), developed accurate taxonomic binning software (Dröge et al., 2015, Bioinformatics), and software to study the evolution of influenza viruses from genomic and phenotypic data sets (Klingen et al., in press, Virus Evolution)  Follow-up projects, as well as newly established collaborations, offer plenty of opportunity for an excellent bioinformatics postdoc to shine.

 Location: The department is part of the Helmholtz Center for Infection Research (, the Braunschweig Integrated Center for System Biology (BRICS) and Technical University of Braunschweig, Germany. Braunschweig is a city with a high density of scientific institutions, many parks and recreational areas and about 250.000 residents. It is centrally located within Germany, with shorter train travel times (30 min, 90 min) to Hannover and Berlin.

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

How to apply: Send your electronic application materials including a letter of motivation, curriculum vitae, copies of your most important publications and addresses of two or three referees to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!. Please add the header ‘comp bio position’ to your application. Note that the HZI is an equal opportunity employer. Qualifications being equal, precedence will be given to candidates with disabilities.


Postdoctoral Fellow in Bioinformatics / Systems Medicine

A more complete PDF version of this job posting is available from the following URL:

We are recruiting postdocs who want to work at the forefront of precision medicine, analyzing and integrating various types of omics data with 3D imaging and wearable device data into systems models of cancer.

Our group is based at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna. It combines advanced technologies (epigenomics, single-cell sequencing, drug screening, mass spectrometry, imaging, etc.) with a deep interest in computational modeling and relevant clinical collaborations. We collaborate closely with physicians at the Vienna General Hospital and the Medical University of Vienna to establish proof-of-concept for precision medicine in several types of cancer.

The Project

For the first time, it is now realistic to follow individual patients in full clinical and molecular detail over the course of diagnosis, first-line treatment and recovery, cure and/or relapse. Prospectively studying representative patients for several cancers, we will combine (i) Omics Profiling including Single-Cell Epigenome/Transcriptome Sequencing, (ii) Patient-specific 3D Culture Models, (iii) Multimodal Imaging, (iv) Digital Pathology and (v) Clinical Phenotyping, in order to establish systems medicine accounts of individual patients. At this level of detail, each patient becomes a powerful study in itself, providing novel insights into complex disease mechanisms and informing personalized therapy.

The Candidate

We are looking for highly motivated and academically outstanding candidates who want to pursue a scientific career in the field of computational and medical epigenomics. A strong candidate may have a background in the computational sciences (bioinformatics, statistics, physics, engineering, etc.) and some prior experience with collaborative research in high-throughput biology. In the same way, we are considering applicants with a background in medicine or in biology (e.g., functional genomics, chemical biology, human genetics, molecular medicine, etc.) who have strong quantitative skills and a keen interest in pursuing systems medicine projects.

The Lab (

The Medical Epigenomics Lab at CeMM pursues an interdisciplinary and highly collaborative research program aimed at understanding the cancer epigenome and establishing its utility for precision medicine. The lab is internationally well-connected and active in several fields:

- Epigenomics. We perform large-scale epigenome mapping in order to dissect the dynamics of cancer development and emerging drug resistance. This work is part of the European BLUEPRINT project and the International Human Epigenome Consortium.

- Technology. Exciting biomedical research is often driven by new technologies. Our lab is therefore heavily invested into technology development, including single-cell protocols, nanopore sequencing, CRISPR, and epigenome editing.

- Bioinformatics. New algorithms and advanced computational methods allow us to accurately infer epigenetic cell states from large-scale datasets, in order to reconstruct the epigenetic landscape that controls cellular differentiation and reprogramming.

- Diagnostics. Using large-scale DNA methylation mapping, bioinformatic prioritization, and functional characterization, we strive to develop clinically relevant biomarkers for informing personalized cancer therapy.

The Principal Investigator (

Christoph Bock is a principal investigator at CeMM, guest professor at the Medical University of Vienna, scientific coordinator of Vienna’s Biomedical Sequencing Facility, and adjunct group leader at the Max Planck Institute for Informatics. Previous appointments include the Max Planck Institute for Informatics (PhD studies) and the Broad Institute of MIT and Harvard (postdoctoral research). CB is a 2009 recipient of the Otto Hahn Medal by the Max Planck Society for pioneering work in computational epigenetics, and he recently received two major career development grants – a New Frontier Group award by the Austrian Academy of Sciences (EUR 1.4 million) and an ERC Starting Grant by the European Research Council (EUR 1.3 million). CB leads Genom Austria, which is the Austrian contribution to the International Network of Personal Genome Projects, and he is a member of several European and global initiatives on epigenetics & precision medicine.

The Institute (

CeMM is an international research institute of the Austrian Academy of Sciences. Driven by medical needs, CeMM integrates basic research and medical expertise to pursue innovative approaches focused on cancer, inflammation, and immune disorders. CeMM is located at the center of one of the largest medical campuses in Europe, within walking distance of Vienna’s historical city center. A study by “The Scientist” placed CeMM among the top-5 best places to work in academia world-wide ( Vienna is frequently ranked the world’s best city to live. It is a United Nations city with a large English-speaking community. The official language at CeMM is English, and more than 30 different nationalities are represented at the institute.

Applicants should submit cover letter, CV, academic transcripts, and contact details of three referees to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!. Please submit your application documents as a single combined PDF, if possible, and refer to the reference code (PD CB) in the subject line. Applications will be reviewed on a rolling basis, and any application received by 15 April 2016 will be considered. Start dates are very flexible.

Postdoctoral Scholar Position in Bioinformatics/Systems Cancer Biology

We are looking for a highly motivated postdoctoral scholar at Stanford University School of Medicine. Our lab is focused on developing novel biomarkers (diagnostic, prognostic, or predictive) toward precision medicine in cancer. We have significant expertise in quantitative image analysis and machine learning applied to multi-modality imaging such as PET, CT, and/or MRI. We are interested in the integrative analysis of imaging and genomic data in cancer, with the goals of discovering fundamental genotype-phenotype connections and transforming clinical care through translational research. We work closely with cancer biologists and oncologists. Our research is generously supported by multiple research grants from the NIH as well as industry.

We are seeking a highly motivated individual with the desire and talent to tackle challenging technical problems in medicine. The project involves the development and/or application of computational algorithms and statistical/machine learning approaches that integrate diverse types of high-throughput molecular data, towards understanding patient specific cancer networks and their response to therapy. The ideal candidate would have training in bioinformatics and/or computational biology, or a related field such as biostatistics, biomedical engineering, electrical engineering, computer science, and physics. Prior knowledge and experience with cancer genomics are preferred but not required. Strong programming skills in R or MATLAB are required.

I am dedicated to mentoring and educating the future leaders in biomedical research. Some major awards recently won by postdocs in the lab include: Resident Clinical/Basic Science Research Award (2014), Basic/Translational Science Award (2015) from the American Society of Radiation Oncologists, and Science Council Research Award (2015) from the American Association of Physicists in Medicine.

Interested applicants should send CV and a brief statement of research to:

Ruijiang Li, PhD, DABR
Assistant Professor
Department of Radiation Oncology
Stanford University
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PhD in Barcelona (students finishing their MSc in Bioinformatics or similar)

Two PhD positions are available in the Barril’s lab (University of Barcelona) in the context of a Marie Curie Initial Training Network (FragNet). Applications from MSc students finishing their Bioinformatics (or related) degree on/before summer 2016 are particularly welcome. 
Prof. Barril ( is a world expert on structure-based drug design. His research combines computational and experimental methods to discover bioactive molecules, with a particular emphasis on novel mechanisms of action.
The Marie Curie fellowships offer a very competitive salary, while the ITN program is designed to provide excellent training and networking opportunities. FragNet will train students on all aspects of fragment-based drug discovery (FBDD), a powerful technique to discover good quality leads. As such, this is an exceptional opportunity for students interested in drug discovery or chemical biology.
A brief description of the projects is provided below. More details about these and other positions in the nertwork can be found in the project’s web page:
Position ESR9 - Construction of a computational platform for fragment evolution. The platform will combine existing chemoinformatics and computational chemistry software to deliver a tool that can effectively navigate chemical space and guide the evolution of fragments into hits.
Position ESR10 - Molecular simulations applied to FBDD. Biased and unbiased molecular dynamics simulations will be used to investigate binding of fragments to their protein targets and to guide the fragment evolution process. 
Note that, as a Marie Curie program, the mobility rule applies. Essentially, this means that the students are not be elegible to carry out their PhD in the same country where they’ve resided for the past few years.
Apply as soon as possible through the project web page. Direct any queries directly to Prof. Barril: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!


PhD student openings in the RNA Bioinformatics Group in Jena

The Research Group RNA Bioinformatics and High Throughput Analysis in Jena is looking for talented and motivated PhD students who are interested in (at least) one of the following topics:

• High throughput sequencing analysis: We are specialized to analyze huge amounts of RNA-Seq data produced by current high-throughput sequencing methods. We are looking for a bioinformatician to process data based on state-of-the-art techniques (quality control, reference mapping, de novo assembly, quantification, visualization) as well as to develop own scripts and tools to find genes differential expressed between certain conditions. Based on RNA-Seq data of a host and its pathogen we try to find out more about the ecology and species barriers in emerging viral diseases by detecting protein- and non-coding genes differential expressed between different combinations of species, tissues and time points post infection.
• Virus bioinformatics: Since the last emerging viral epidemics/pandemics, caused by SARS, MERS and Ebola, viruses are extensively studied in wet lab, however specific bioinformatic tools are still missing. We develop new tools to find conserved RNA secondary structures and RNA-RNA interactions in viral genomes to understand the viral replication. Furthermore we want to facilitate the viral genome assembly. It is a challenging task to assemble viral sequences out of samples, including millions of host sequences. A new challenge is also the design of synthetic viruses with weak clinical symptoms along with still viable viruses. A successful design can be used to produce cheap vaccinations within decent time.
• Monitoring antibody profiles: To rapidly monitor the specific antibody profile of a patient and decide on vaccination, currently used methods of serological analysis need to be improved. We are looking for a bioinformatician to develop better tools for identification of immunodominant domains (epitopes, antigenic determinants) on bacterial, viral and other microbial proteins. In a four-party project, the results of this in silico study will be verified in the diagnostic lab by testing patient sera, and the feedback will be used to refine the epitope identification software.
• Epigenetic regulation by long non-coding RNAs: The project will focus on elucidating lncRNA-genome interactions and their impact on gene regulation in mam- malian cells. The candidate will be involved in developing tools and techniques to detect novel lncRNA/DNA structures genome-wide, to identify the associated binding proteins and to unravel the underlying regulatory mechanisms. The work will include state-of-the-art laboratory techniques (e.g. ChIP, ChRIP, high throughput sequencing, proteomics) and bioinformatical analysis of the data.
• Combined metabolome and transcriptome analysis: In this project we analyse transcriptomics and metabolomics data of cyanobacteria to analyse their fitness regarding the circadian clock. On transcriptomic level we want to identify unknown genes and differentially analyse different time points of the circadian rhythm. On metabolomic level we want to fill the gaps in the metabolic networks. In particular, we want to combine the analysis of both data types to compensate for incompleteness in one of the data sources.
Applicants should have: 
• a Master in bioinformatics, computational biology or a related area,
• a passion for developing and using computational tools and algorithms to analyze large biological data sets,
• good programming skills in a unix environment,
• high motivation and the ability to work both independently and in a team.
Candidates are encouraged to send their application including CV and a short description of research experience and interests to 
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PhD Positions available at IMPRS for Computer Science: Computational Biology and Applied Algorithms

The International Max Planck Research School for Computer Science (IMPRS-CS) is a graduate program jointly run by the Max Planck Institute for Informatics (MPI-INF), the Max Planck Institute for Software Systems (MPI-SWS), and the Computer Science Department at Saarland University. The MPI-INF and the MPI-SWS are among the more than 80 institutes run by the Max Planck Society. The MPIs are Germany's prime basic research facilities with world-class, basic research in the fields of medicine, biology, chemistry, physics, technology, and the humanities. Since 1948, MPI researchers have been awarded 18 Nobel prizes, which testifies to the quality and innovation of MPI research programs.

Educating and training junior scientists is of primary importance for the future of science, research, and innovation. The Max Planck Society, in cooperation with German Universities has launched the International Max Planck Research Schools (IMPRS) initiative. Admitted students receive a first rate, research-oriented education in their chosen area of concentration. They enjoy close supervision by a world-renowned scientist in a competitive, yet collaborative, environment rich in interaction with other students, post-docs, and scientists. The program is fully funded.

Applicants for the PhD program must hold a Master's degree or a Bachelor's degree from a research-oriented institution. Successful candidates will typically have ranked at or near the top of their classes, have already engaged in research and published their results, and be highly proficient in written and spoken English. Applicants are required to deliver a 15-minute research presentation on their Master's project, followed by a question and answer period, in front of the admission committee and other audience members. All admitted students receive financial aid in the form of a support contract (according to TvöD Bund, German Collective Agreement for the Public Sector, Category: Federal).

Applicants to the IMPRS-CS PhD program should fill in the following online form:, and submit their complete documents until 15th February 2016. The respective application talks are currently scheduled for May 2016.

More information on the application process and our institutes, especially Department 3: Computational Biology and Applied Algorithms, can be found online:, and

Andrea Ruffing, IMPRS-CS Coordinator
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+49 681-9325-1800