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Postdoc position “Modeling microbial communities of the Southern Ocean”

We are looking for a Post-Doc to work for 3 years in the research team of dr. Julia Engelmann in the department of Marine Microbiology and Biogeochemistry at the Royal Netherlands Institute of Sea Research on Texel (The Netherlands). The team applies bioinformatic and network biology approaches to marine marker gene, metagenomic and transcriptomic data. On top of describing microbial communities, we are interested in how the individual species interact with each other. We use modern sequencing approaches and network modeling techniques to infer these interactions.


The Department of Marine Microbiology and Biogeochemistry on Texel performs detailed studies on microbial communities in the marine environment. We study the diversity, physiology and activity of phytoplankton, prokaryotes (archaea and bacteria) and viruses in diverse marine environmental settings by a variety of techniques, including modern genomic techniques.


At the base of the marine food web, microbes act both as primary producers and degraders of organic material. The organic matter they provide feeds the oceans and life on land. While we have seen a tremendous increase in knowledge about the diversity, genome composition and metabolic capabilities of microbial species living in the ocean, we still lack insights about how these communities work at a systems level. Because of the high complexity of many natural communities, inter-species interactions are difficult to study. Computational approaches such as network modeling can be used to generate hypothesis about potential interactions which can then be validated with functional or other experimental approaches. Potential interactions include providing nutrients or energy substrates to another species, competing for nutrients or responding to signaling molecules. The Post-Doc will focus on elucidating marine microbial inter-species interactions in the Southern Ocean (close to Rothera, Antarctica) and perform sampling, high-throughput sequencing, network modeling and validation experiments in the laboratory. Part of the project will address the question of how climate change will impact microbial species abundance and especially their inter-species interactions in the Southern Ocean.


The candidate must hold a PhD degree in Bioinformatics, Computational Biology, Microbiology, Molecular Ecology, Microbial Ecology, Computer Science, (Bio-)Statistics, Physics or related fields and be highly organized and motivated. The position requires both strong computational as well as experimental skills. Candidates with a theoretical background should have at least some experience with microbiology and/or molecular microbial ecology techniques, and candidates with an experimental background need to have proof of computational skills, including excellent command of at least one programming language such as R or python. Experience with Unix/Linux systems is mandatory. The ideal candidate has experience in the analysis of high throughput genomic data. Due to the international character of the research group, excellent command of the English language is expected.


We are offering a fulltime position for 3 years, a pension scheme, a yearly 8% vacation allowance, year-end bonus and flexible employment conditions. Conditions are based on the Collective Labour Agreement of Research Centers. The position will be located on Texel. Cost of relocation and help with housing is provided by NIOZ.


Additional information about the vacancy can be obtained from: Dr. Julia Engelmann (Research Scientist).

Additional information about the procedure can be obtained from Alexandra Noppeney (Sr HR Advisor).



Interviews will be held on Texel, 25 September 2019. 

Postdoctoral Fellow in Computational Biology [Rome, Italy]



Rome, Italy

Staff Category:

Postdoctoral Fellow

Contract Duration:

2 years (renewable)


Postdoc Stipend

Closing Date:

1 October 2019

Reference Number:


The Boulard and Gross Groups are seeking to recruit a Postdoctoral Fellow with experience in computational biology to lead a project at the interface of epigenetics and neuroscience. The project combines the expertise of the Boulard and Gross groups in chromatin biology and neural circuits, respectively, to explore the cell-type specific interplay between transcription factors and the brain epigenome. The successful applicant will be part of a collaborative team of molecular biologists, biochemists, and neuroscientists that are working together on the large-scale exploration of previously uncharacterized transcription factors in mammalian brains.

Your role

The successful applicant will devise and carry out computational analyses of large-scale epigenomic and transcriptomic datasets internally generated, including:

·       developing methods and pipelines to analyze CutnRun and DAP-seq data sets, and

·       integrating, comparing, mining, and visualizing omic data sets.

You have

·       PhD degree in Bioinformatics, Computer Science, Mathematics, or related fields.

·       Solid skillset and experience in bioinformatics:

o   Excellent knowledge of R and biostatistics

o   Experience and proven track record in handling NGS datasets and developing analysis pipelines

·       Outstanding interpersonal and communication skills are essential


You might also have


·       Experience with Unix-based environment and high-performance computing cluster environment is not required, but would be considered an advantage.

·       Experience in motif discovery is not required, but would be considered an advantage.


Why join us

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organization. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits. Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.  

What else you need to know

EMBL is one of the highest ranked scientific research organizations in the world. 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. The Neurobiology and Epigenetics Unit at EMBL Rome studies mammalian physiology from the molecular to the systems level using the laboratory mouse as a model system. We take advantage of a full range of core facilities, including bioinformatics services and a high-performance computing cluster. For more information, please see our website at To apply please submit a cover letter clearly stating your motivation and future research interests/plans and a CV with at least two referees through our online system at Applications are welcome from all nationalities, appointment will be based on merit alone.


2 Stellen als Wissenschaftlicher MitarbeiterIn (m/w/d) (DoktorandIn oder Postdoc) in Bioinformatik [LMU München]

In der Arbeitsgruppe von Prof. Dr. Caroline Friedel an der Ludwigs-Maximilians-Universität München sind frühestens zum 1.10.2019 zwei Stellen als 

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. Eine Bewerbung ist auch bereits jetzt möglich, wenn Master oder Promotion erst in einigen Monaten abgeschlossen werden. Beide Stellen werden durch die DFG gefördert.

Themen der Stellen:

1. Großskalige Untersuchung von Short-Read-Archiven zu Störungen in der Transkriptionsterminierung und zirkulärem Spleißen / 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. 


2. Funktionelle Analyse der Induktion offenen Chromatins stromabwärts von Genen in der HSV-1-Infektion / Functional analysis of downstream open chromatin induced in HSV-1 infection

In früheren Studien haben wir festgestellt, dass HSV-1 Infektion zu einer massiven Störung der Transkriptionsterminierung führt, die mit offenem Chromatin in intergenischen Regionen assoziert ist. In diesem Projekt sollen nun RNA-seq und ChIP-seq Daten aus einer Kollaboration mit Prof. Lars Dölken vom Institut für Virologie der Universität Würzburg analysiert werden und neue Methoden entwickelt werden, um den Mechanismus und auslösenden Faktor für das offene Chromatin zu identifizieren.



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.

University professorship - Bioinformatics - (Salary level W2 )

The University Medical Center Göttingen (UMG) pursues the consistent development of its profile-forming research foci neurosciences, cardiovascular medicine and oncology with translational and
systems-medical approaches and is closely networked on the Göttingen campus with the natural and bioscientific facilities of the university as well as the non-university facilities at the location.

At the UMG there is a

University professorship
(Salary level W2 )

to fill at the earliest possible date. The appointment of the professorship will initially be effected for a period of 5 years with the option for tenure track.

The professorship is associated with the establishment and management of a working group at the Institute of Medical Bioinformatics (Director: Prof. Dr. Tim Beißbarth). The professorship will build a
bridge from Medical Bioinformatics to the Center for Applied Computer Science, the Center for Statistics and the Data Science activities currently under development in Göttingen. An outstanding
doctorate in bioinformatics, computer science, statistics, natural sciences or a related subject with a
strong component in the quantitative analysis of biomedical data is required as well as experience in independent scientific research in the field of bioinformatics or data science after the doctorate, which is documented by relevant publications and/or third-party funding.

The successful candidate will work on the methodical development of analytical methods for biomedical high-throughput data, e.g. methods of machine learning and integrative data analysis.
Experience with Omics data or image data in biomedicine is desirable. In addition, an interest in
collaborations and applications within research alliances in the main research areas of the UMG is
expected. Methodical research in bioinformatics forms the basis for modern Systems Medicine. The
professorship should support the applications of bioinformatics in Systems Medicine through appropriate methodological research.

A positively evaluated junior professorship, habilitation or equivalent academic achievements as well
as commitment to teaching are assumed, as is the willingness to participate in academic self-administration.

Further expected are:

  • a high level of commitment to teaching
  • the readiness for interdisciplinary scientific work
  • the willingness and ability to competitively solicit third-party funded research projects

The further prerequisites for the recruitment of professors are set out in § 25 Lower Saxony
Higher Education Act (NHG) in the currently valid version. Applicants who have completed
their doctorate at the University of Göttingen can generally only be considered if they have
worked outside the UMG for at least two years after completing their doctorate. UMG has the right of appeal.

Applications from scientists from abroad are expressly welcome. The UMG aims to increase the proportion of women and therefore expressly invites qualified women to apply. Severely handicapped persons will be given preferential treatment if they are suitable.

Please submit your application documents until August 25th 2019 online via the following link:

If you have any questions, please do not hesitate to contact us at This email address is being protected from spambots. You need JavaScript enabled to view it..

1 Postdoc in Bioinformatics, 1 Bioinformatician / Computational Scientist, 1 Scientific Software Developer [DKFZ, Heidelberg]

Three open positions in the Bioinformatics and Omics Data Analytics Group at the DKFZ in Heidelberg.   

The new Collaborative Research Centre “Understanding and Targeting Resistance in Glioblastoma” (UNITEGLIOBLASTOMA, SFB1389) is focused on decoding and combating resistance in glioblastoma, a serious and usually fatal brain tumor in children and adults. The goal of the research consortium is to understand the molecular mechanisms of resistance against current therapies and to develop new types of treatment. At the heart of the CRC is the “Core Collection”, for which uniform, integrated data sets from multiple omics analyses, preclinical models, imaging, and clinical data are being generated.

We invite applications of enthusiastic and motivated Bioinformaticians / Computational Scientists / Scientific Software Developers to join the UNITE core work package “Data integration, bioinformatics analysis, and data exploration for precision neurooncology”.

The complete announcements, contact details and information how to apply can be found here:


Research Associate (m/w/d) in Bioinformatics (TV-H E13 100%) [Gießen]

The Professorship for Algorithmic Bioinformatics at Justus Liebig University Giessen invites applications for the full-time position of a Research Assistant.


·        -  Own scientific training; Scientific services in research and teaching according to § 65 HHG; university didactic qualification

·         - Taking on teaching duties according to the teaching obligation ordinance of the state of Hesse

·        -  development of bioinformatic algorithms and sustainable engineering of their implementations in fields like phylogenetics and annotation recruitment in close collaboration with other team members as well as statistical analyses of microbiome big data. 


·         Completed academic studies in a natural science subject as well as teaching experience in the field of bioinformatics / genome research / sequence analysis

·         strong practical skills in genomics, especially in automated microbial genome annotation•fluency in Python would be ideal

·         experiences with high performance computing, grid clusters or clouds as well as routine use of collaborative software engineering tools are highly preferred



Link to complete job description:

Post-doc in Biomedical Data Science (TB) (E13 TV-L, 100%) [Tübingen]

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


Post-doc in Biomedical Data Science (TB) (E13 TV-L, 100%)


starting as soon as possible. The initial fixed-term contract will have an end date of 31st December 2020 with possible extension.

According to WHO there were 558,000 cases of drug-resistant tuberculosis (TB) infections world-wide in 2017 of which 82% were multidrug-resistant. In this project, which is funded through a Horizon 2020 grant by the European Commission, the successful candidate will build a prediction engine that is able to provide treatment decision support for TB-infected patients by applying and extending state-of-the-art machine learning methods. This will be in close collaboration with our Western and Eastern European partners, with a focus on multidrug-resistant strains from Eastern Europe.

The group has extensive knowledge at the interface between statistical machine learning, digital medicine, and computational biology. Nico 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 a Ph.D. or equivalent in Biomedical Data Science, Biometry, Biostatistics, Machine Learning, Bioinformatics, Medical Informatics, Computer Science, Computational Biology or a related life science discipline. Applicants should have an interest in interdisciplinary work. Proven 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

·       Proficiency in Russian language (communication with Eastern European partners)

·       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: Post-Doc application Biomedical Data Science (TB).

Application deadline: 4th August 2019.

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



Ph.D./Posdoc position in computational detection of RNA-DNA triple helices

The Institute for Computational Genomics, RWTH Aachen University
performs cutting edge research on computational and genomic methods
for understanding regulatory and epigenetic processes driving cell
differentiation and diseases (Gusmao, Nature Methods, 2016, Li, Genome
Biology, 2019). This project aims studying RNA-DNA interactions as
mechanisms of transcriptional control. We have recently shown how
long-noncoding RNAs (HOTAIR, GATA6-AS, NEAT1) interacts with DNA via
triple helices to control the expression of genes during cell
differentiation (Kalwa et al., NAR, 2016; Kuo, NAR, 2019; Frank, Cell
Stem cell, 2019).

We are looking for a phd/postdoc candidate to work on sequence
analysis algorithms and statistical models for detection of RNA-DNA
triple helices. This includes the analysis of novel in vitro
transcription experiments and target sequencing protocols, which
capture triple helix forming RNA and DNA molecules. This project will
be performed in collaboration with cell biologists of RWTH Aachen,
University of Cologne and University of Oslo.

Applicants should hold a M.Sc. or Ph.D. in Bioinformatics or Computer
Science. Experience in the analysis of biological sequences and
regulatory genomics is required. The candidate should have solid
programming skills (C, Python and/or R) and acquaintance with
Unix/Linux. Experience with high performance computing is a plus. The
working language of the group is English. The position is a will be
initially for 3 years with possibility of extension. The salary
corresponds to level 13 TV-L.

Interested candidates should send a brief statement of research
interests, CV and the names of three references to This email address is being protected from spambots. You need JavaScript enabled to view it..

2x PhD pos., Comp. biochem./chem. or struct. bioinf., University of Duesseldorf, Gohlke group

Applications are invited for two PhD student positions in the Computational Pharmaceutical Chemistry & Molecular Bioinformatics group (Prof. Dr. Holger Gohlke, at the Heinrich-Heine-University, Düsseldorf, Germany.

PhD student position 1: Overcoming lantibiotics resistance in bacterial pathogens: Nisin as a model system
Topic: Lantibiotics are antimicrobial peptides that are produced by Gram-positive bacteria and bactericidal against other bacteria in the low nanomolar range. Because of their high selectivity and stability, lantibiotics are considered valuable future anti-infective agents. The best-studied lantibiotic is Nisin. Various human pathogenic strains of bacteria have been found to have natural immunity to nisin, attributed to, e.g., the nisin resistance protein (NSR) or ABC transporter NsrFP. By structure-based design, hit molecules have been identified that inhibit NSR, and a structural model of NsrFP has been generated. In this project within the DFG-funded GRK 2158 (, the inhibitory, physicochemical, and pharmacokinetic properties of the hits will be improved by structure-based and computer-aided drug design, analog searches, synthesis, and in vitro and in vivo testing. Furthermore, the mechanism of NsrFP will be scrutinized by molecular simulations with the aim to identify novel compounds that inhibit the transporter. Our group has a strong background in computational pharmaceutical chemistry and molecular informatics and will collaborate with the Smits, Pfeffer, Kalschauer, Stork, Pietruszka and Müller groups of the GRK 2158.
Availability: The position is available as of 01.10.2019.


PhD student position 2: Functional analyses in silico and in vitro of consequences of cholestasis-associated mutations
Topic: Mutations in several genes (ATP8B1, ABCB11, ABCB4, TJP2, NR1H4, MYO5B) contribute to the development of severe forms of intrahepatic cholestasis. Since most mutations are only found in one or two families, their clinical consequences are often unknown. In particular, biological consequences of missense mutations (38-66% of mutations in ATP8B1, ABCB11, and ABCB4 in patients with severe cholestasis) are less clear. In this project performed within the BMBF-funded Hereditary Intrahepatic Cholestasis Translational Network (HIChol), novel missense mutations will be structure-based analyzed for their potential impact on interactions with surrounding residues, substrate and cofactor binding, protein stability, structural dynamics. While molecular models have been established for ABCB11 and ABCB4, and experimental structural information is (in part) available for TJP2, FXR, and MYO5B, a structural model of FIC1 will be generated. In collaboration with the Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital, Heinrich Heine University Düsseldorf, results from molecular modelling and simulations will be tested for selected mutations by transfection of mutated cDNA into polarized hepatoma cell lines and HEK293 cells. Trafficking, subcellular localization, and function will then be studied. The cell culture approach will be used to optimize the predictions from molecular modelling and simulations. Results from this project will allow for classification of detected missense mutations into subgroups according to their cell biological consequences (e.g., maturation, trafficking, targeting, or function), and selected mutations will be further analyzed within HIChol.
Availability: The position is available immediately.

Requirements: Ideal candidates will have a record of excellence and a strong background in computational biochemistry, molecular informatics, and computational structural biology as well as a high interest in working in an interdisciplinary research field, and profound knowledge in state-of-the-art molecular dynamics simulations (Amber) software and molecular modeling.

How to apply: Applicants should submit applications (a one-page letter of motivation why they are interested in the respective project and how they can contribute to the project’s success, a current CV, and contact data of three references) by email to gohlke* Please provide all documents as one PDF file and specify for
which position you are applying.

Detailed information about living and studying in Düsseldorf is provided here:

Bioinformatics PhD [FibroOmics]

This PhD position will provide sophisticated bioinformatics analysis for a new project initiative, FibroOmics, which aims to accelerate improvements in the understanding and treatment of lung fibrosis. This project involves cutting edge molecular and analytical techniques, including single cell RNA sequencing (scRNA-seq), signal deconvolution, therapeutic target discovery, and interactive software development. FibroOmics has strong translational relevance and unique access to patient samples for Omics studies.

The successful candidate will apply and develop sophisticated bioinformatics algorithms, drawing on methodologies of the domains of statistics, computer science and machine learning. Previously published methodologies will be utilized as a starting point, but it should be emphasized that there will be a need for novel algorithm development.

The position will be located at Hannover Medical School (MHH) in the context of its membership in the German Center for Lung Research (DZL, Deutsche Zentrum für Lungenforschung), an association of the leading university and non-university institutions dedicated to translational lung research in Germany. At the DZL site in Hannover (BREATH) biomedical researchers utilize the full spectrum of high throughput molecular techniques (“Omics”) metagenomics, whole genome and exome sequencing, RNA-seq, among others to lung diseases such as cystic fibrosis, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, lung transplantation as well as rare genetic disorders.  This combination of proximity to the clinic with cutting edge Omics applications makes the BREATH site a unique workplace for bioinformaticians to help impacting patient outcomes.

Basic Requirements

·        Master’s degree in Bioinformatics, Molecular Biology, Computer Sciences, Statistics or Mathematics or other related field.

·        Analytical ability founded either in statistics, mathematics, or computer science principles

·        Proficiency in at least one programming / scripting language such as python, c/c++, Java, R, perl etc.

Desired Qualifications

·        Previous experience in Bioinformatics (desired, but optional)

·        Experience working with Next Generation Sequencing technologies (desired, but optional)

·        Expertise in at least one of the relevant interdisciplinary pillars: genetics, molecular biology, machine learning, statistics, computer science, mathematics (at least one is required)

Important Characteristics

·        Strong drive and interest in interdisciplinary approaches

·        A thirst for knowledge

·        Enjoyment of working in a team

·        A desire to hold one’s self to the highest standards of professional and academic excellence

This position offers:

·        A doctoral degree in the natural sciences – Dr. rer. nat. upon successful completion and ample opportunities for writing publications.

·        Salary is in accordance with the Tarifvertrag für den Öffentlichen Dienst der Länder (TV-L)

·        An interdisciplinary and collaborative work environment

·        Comprehensive health-promotion programs

·        Reliable family services, including emergency child care

The position start date is planned for October 1st, 2019.

The MHH is committed to supporting the professional careers of women and applications form women are particularly desired. People with disabilities will be preferred when their qualifications match or exceed those of other applicants.

Please direct inquiries to Dr. David DeLuca, Tel. +49 511-532 7873 and send your applications by email to This email address is being protected from spambots. You need JavaScript enabled to view it.



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