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Stellenangebote

Professorship (W3) for Computational Systems Biology

We are happy to announce a new Bioinformatics Professorship (W3) at the Universität Hamburg with a focus on Systems Biology. Possible research topics include modeling of cellular networks and systems in the context of infection processes; modeling of resistance formation; and simulation of cell systems. The consolidation and integration of large sets of heterogeneous biological data should form an essential part of the research.

The position is located in the Informatics Department and Center for Bioinformatics in Hamburg offering established study programs in Computing in Science and Bioinformatics. It is also part of the upcoming Leibniz-WissenschaftsCampus InterAct strengthening connection to Leibniz-Institutes in the field of infection and structural biology and the Center for Structural Systems Biology (CSSB) on the DESY Campus.

A complete announcement can be fould here:

https://www.uni-hamburg.de/en/uhh/stellenangebote/professuren/22-08-19-w3-2309en.pdf

Researcher (f/m/d) at Freiburg University

Biological Anthropology at Albert Ludwig University Freiburg is looking for a highly motivated

Researcher (f/m/d)

within a DFG-funded project developing scientific software for research in biological anthropology.

Our research project ″Establishing Semantic Research Data Modelling in Biological Anthropology″ aims to improve research data management and curation in biological anthropology by providing appropriate infrastructure. This involves creating a web-based information system for acquisition and tracking of osteological data and subsequent research using the curated data base.

The main task will be adaptation of an existing software framework for a domain-specific RDF ontology. This work will mainly concern the front end but might entail framework adjustments. The primary sub-tasks will be

    • Designing the software concept with us

    • Autonomous implementation of said software concept

    • Testing and optimising the software

    • Tight collaboration with international project partners

 

We offer

    • advanced training to improve individual skills in semantic information systems

    • opportunities for active participation in international conferences

 

Qualifications and requirements

We expect a very high level of self-organisation as well as a creative and solution-oriented mindset. Applicants will be responsible to keep to the production schedule and should be capable of excellent time management, of working in a team and of actively communicating both in-house and with partners abroad. Compliance with predefined workflows is mandatory.

The project is experimental in nature and specific to modelling osteological research data in biological anthropology. As a consequence, we are looking for a creative and open-minded collaborator instead of targeting applicants with specific qualifications.

 

Required skills

    • Master or equivalent degree

    • Experience with semantic web technologies (RDF, SPARQL) OR experience in software development

    • Excellent oral and written knowledge of English

 

Desired qualifications

    • Background in biological or related sciences

    • Adequate knowledge of the code versioning system git

    • Knowledge of the programming language TypeScript

 

The position is limited to two years. Payment and benefits will be according to the German TV-L pay scale (E 13). A first evaluation of applications is scheduled for 31 August 2019. The search will be continued until the position is filled.

Freiburg University seeks to increase the number of women in areas in which they are under-represented and therefore explicitly encourages women to apply. The University Freiburg is also committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.

We look forward to receiving your application. Please upload your documents as a compressed archive file – including a letter of motivation, CV, research statement (max. 1 page), a list of publications and contact information of two references – to our portal:

https://ckan.anthropologie.uni-freiburg.de/owncloud/index.php/s/U5Dbib2uDBjYBeL

For further inquiries, please contact Dr. Stefan Schlager (phone +49 / 761 / 203 – 5522; Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!)

 

Links:

http://ckan.anthropologie.uni-freiburg.de/dataset/a0524158-9711-438a-8953-ab1e674a12b6/resource/12038ede-43a7-4d8f-bee9-1a7f2aff55f3/download/employmentnotice-researcherbiologicalanthropology.pdf

 

4 PhD positions in Bioinformatics at Bielefeld University

The graduate school "Digital Infrastructure in the Life Sciences" (DILS) of the newly established "Bielefeld Institute for Bioinformatics Infrastructure" (BIBI) at Bielefeld University, Germany, offers four PhD positions (3 years, 100% TV-L E13) starting October 2019.

The institute's research program focuses on scientific and service aspects in the area of bioinformatics infrastructure in close cooperation with the "German Network for Bioinformatic Infrastructure" (de.NBI) as well as the "Information Centre for Life Sciences" (ZB MED).

The qualification program of the DILS graduate school includes a joint research program, dedicated courses, workshops, retreats, etc.

Candidates must demonstrate broad background in the interdisciplinary field of bioinformatics in general and deep knowledge in the area they apply for (see project descriptions for detailed requirements). Good communication skills and knowledge of the English language is required, whereas German is not necessary.

The application deadline is 31 July 2019. Application instructions, project descriptions, contact information, and other details can be found on the institute's website.

Links: http://bibi.uni-bielefeld.de

 

 

 

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. 

Details: https://www.bio.ifi.lmu.de/aktuelles/stellenangebote/friedel_sra_mining/sra_details.html 

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.

Details: https://www.bio.ifi.lmu.de/aktuelles/stellenangebote/friedel_sra_mining/details_chromatin.html

Voraussetzungen: 

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
Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!
 
 

(Bio-) Informatiker*in am Max-Planck-Institut für Verhaltensbiologie in Radolfzell/Konstanz

Sie werden in einem Projekt eingesetzt, das Teil des neuen, landesweiten Netzwerks bioDATEN (http://www.biodaten.info/) ist. Dort erarbeiten wir in einem interdisziplinären Team aus Biologen, Informatikern und Informationswissenschaftlern Schnittstellen dieser Disziplinen in der Analyse großer *omics Datensätze. Das Teilprojekt in Konstanz befasst sich mit der Ökologie und Evolution der Immungene von Vögeln. Dabei nehmen wir an den globalen Projekten B10K (https://b10k.genomics.cn/) und VGP https://vertebrategenomesproject.org/ teil.

 

Links: https://ab.iwww.mpg.de/177862/job_full_offer_13636535

Data Scientists in Bioinformatics (m/f/d) (100%) [Dr. rer. nat. Catherine Drescher Cluster of Excellence ImmunoSensation2]

Data Scientists in Bioinformatics (m/f/d) (100%)

The two positions are initially limited to three years with the possibility of extension.

ImmunoSensation2 is a Cluster of Excellence funded by Germany’s Excellence Strategy at

theUniversity of Bonn. Its scientists are dedicated to investigating innate immunity beyond the

boundaries of classical immunology. In a joint effort, immunologists, neurobiologists, systems

biologists and mathematicians from the University of Bonn and the German Center for

Neurodegenerative Diseases (DZNE) of the Helmholtz Association aim to investigate the status of the

immune system, the metabolism and the nervous system connect in health and disease.

ImmunoSensation2 is embedded in the outstanding research environment of the University of Bonn,

the University Hospital and the DZNE. Furthermore, ImmunoSensation2 is internationally connected

and maintains research partnerships with Australia (Melbourne University), Japan (Osaka University,

Waseda University, Kyoto University) and the Netherlands (Radboud University, Nijmegen).

The announced position will be integrated into the Core Unit for Bioinformatics Data Analysis (CUBA)

of the Medical Faculty at the University of Bonn, which provides quantitative and computational

analyses, training and consultation for all members of the faculty. CUBA benefits from a shared

computing infrastructure and exchange of expertise due to its embedding and liaison with the Institut

für Medizinische Biometrie, Informatik und Epidemiologie (IMBIE) and the Institute for Genomic

Statistics and Bioinformatics (IGSB). It operates in close collaboration with other core units like the

NGS, flow cytometry and mass spectrometry core. The unit aims to establish a platform for

computational biology, to facilitate quantitative approaches and to share and offer validated methods,

expertise and resources. These methods will continuously evolve according to the needs of

collaborators and progress in science to provide state-of-the-art bioinformatics and data analyses.

 

Your tasks:

 

Analysis and processing of high-volume data sets such as next generation sequencing

Design, implementation and application of tailored analysis workflows

Statistical analysis and visualization

Interaction and collaboration with researchers

o Consultation regarding the planning and design of experiments

o Presentation and reporting of results

o Recommendation of publicly available resources and tools

Working in a team with bioinformatic and computational colleagues

Selection and adaption of (bioinformatical) methods and tool

Training courses and education

 

Your profile:

 

Master or PhD in bioinformatics, computational biology, computer science,

statistics, mathematics or any other related field

Strong expertise in the analysis of next generation sequencing data (NGS), such as single

cell genomics, RNA-Seq, ChIP-Seq and ATAC-Seq

Profound knowledge of statistics, data analysis and visualisation techniques

Proficiency in programming, e.g. with R/Bioconductor or Python

Experience with Linux and high-performance computing (HPC)

Background in molecular biology concepts and an interest in immunology

Knowledge of high-throughput image analysis (FACS ImageStream) is considered a plus

Good communication and presentation skills and fluency in written and spoken English

Team player capable of adapting to a rapidly evolving and interdisciplinary

research environment

 

We offer:

Outstanding research opportunities

Collaborative work environment

Salary according to the German salary scale TV-L (EG 13)

Supplementary benefits (e.g. pension plan according to VBL)

A “Jobticket” (subsidized public transport)

 

The University of Bonn is committed to diversity and equal opportunity. It is certified as a family-

friendly university. It aims to increase the proportion of women in areas where women are under-

represented and to promote their careers in particular. It therefore urges women with relevant

qualifications to apply. Applications will be handled in accordance with the

Landesgleichstellungsgesetz (State Equality Act). Applications from suitable individuals with a certified

serious disability and those of equal status are particularly welcome.

Applicants should send their application in a single pdf file (max. 5 MB), including a motivation letter,

CV, scanned academic degrees, a list of publications and the contact details of two references. More

information on the scientific projects and project leaders can be found

at www.immunosensation.deand information on CUBA can be found at https://cores.ukb.uni-

bonn.de/bioinformatics/

 

Further details will also be provided during the recruitment process. Applications will be accepted on

rolling basis and successful candidates can begin on August 1, 2019 or later.

Please send your application by email using the reference number 350_2019_FABI to:

Dr. rer. nat. Catherine Drescher

Cluster of Excellence ImmunoSensation2

University Hospital Bonn

Venusberg-Campus 1,

53127 Bonn

Email: applications_immunosensation(at)ukbonn.de

www.immunosensation.de

 

Lead Bioinformatician (m/f/d) for high-throughput genome assembly and annotation [Job offer ref. # 12-19005]

Job offer ref. # 12-19005

The Senckenberg Gesellschaft für Naturforschung (SGN) is a member of the Leibniz Association and is based in Frankfurt am Main, Germany. LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) is a joint venture of the Senckenberg Gesellschaft für Naturforschung (SGN), Goethe-University Frankfurt, Justus-Liebig-University Giessen and Fraunhofer Institute for Molecular Biology and Applied Ecology IME aiming to intensify biodiversity genomics in basic and applied research. We will establish a new and taxonomically broad genome collection to study genomic and functional diversity across the tree of life and make genomic resources accessible for societal-demand driven applied research.

The Senckenberg Gesellschaft für Naturforschung and the LOEWE-TBG invite applications for a

 

Lead Bioinformatician (m/f/d)

for high-throughput genome assembly and annotation

(100%)

 

Your tasks:

·         Lead a team of bioinformaticians to develop, maintain and run high-throughput pipelines for the assembly and annotation of de novo genomes from diverse eukaryotes

·         Implementing and documenting the work-flow from receiving data, issue assembled genomes to users and archiving data in public databases

·         Communication with user groups, service providers and external database managers

 

Your profile:

·         PhD in Bioinformatics or related subjects

·         Experience with de novo genome assembly of non-model organisms and developing large scale, high-throughput procedures for de novo genome assembly and annotation

·         Proven understanding of comparative genomics or evolutionary biology research preferably in non-model organisms

·         Familiarity in leading a service orientated unit and excellent communication skills

 

What is awaiting for you?

·         A central role in an innovative large-scale genomics project with the opportunity to create an own research profile

·         A motivated and dynamic team of international researchers at an internationally recognized biodiversity research institution

·         An opportunity to build a central research and service unit within LOEWE-TBG and Senckenberg

·         Excellent opportunities to expand your scientific network across disciplines

·         Flexible working hours – annual special payment – company pension scheme – 30 days holidays

 

Salary and benefits are according to a full time public service position in Germany                   (TV-H E14/15 according to qualification and experience). The contract should start as soon as possible and will initially be limited to December 31th, 2021. The Senckenberg Gesellschaft für Naturforschung support equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. The place of employment is in Frankfurt am Main, Germany. The employer is the Senckenberg Gesellschaft für Naturforschung.

Please send your application, mentioning the reference of this job offer (ref. #12-19005) before July 28th, 2019 by e-mail (attachment in a single pdf document) and including a cover letter detailing research interests and experience, a detailed CV and a copy of your certification to:

 

Senckenberg Gesellschaft für Naturforschung

Senckenberganlage 25

60325 Frankfurt am Main

E-Mail: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

 
 

 

 

Wissenschaftlicher Mitarbeiter (w/m/d) im Bereich Bioinformatik [Tierärztliche Hochschule Hannover]

Am Institut für Tierzucht und Vererbungsforschung der Tierärztlichen Hochschule Hannover ist ab dem 01. Oktober 2019 eine Stelle als

wissenschaftlicher Mitarbeiter (w/m/d) im Bereich Bioinformatik

mit 65% der vollen Arbeitszeit zu besetzen. Die Stelle ist auf drei Jahre befristet. Ein Promotionsvorhaben auf der Stelle wird unterstützt und ausdrücklich erwünscht.

Aufgaben sind die die Mitarbeit in aktuellen Forschungsaktivitäten der Arbeitsgruppe „Genomics and Bioinformatics of Infectious Diseases“. Dazu zählen vor allem die Weiterentwicklung und Anwendung von statistisch-bioinformatischen Methoden für die Analyse von High-Throughput-Sequenzdaten und High-Throughput-Genexpressionsdaten (NGS-, Microarrays-Daten).

Voraussetzung für eine Bewerbung ist ein abgeschlossenes wissenschaftliches Hochschulstudium mit Masterabschluss in Bioinformatik, Biostatistik oder einem vergleichbaren Fach. Darüber hinaus werden Kenntnisse in der Shell-Programmierung unter Linux sowie in der Programmierumgebung R

erwartet.

Die Vergütung erfolgt nach E 13 TV-L.

Schwerbehinderte Bewerberinnen und Bewerber werden bei gleicher Eignung vorrangig berücksichtigt. Bitte senden Sie Ihre aussagekräftige Bewerbung per E-Mail bis spätestens 31.07.2019 an Herrn Prof. Dr. Klaus Jung (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!), Institut für Tierzucht und Vererbungsforschungs, Tierärztliche Hochschule Hannover. Weitere Auskünfte zu der Stelle werden gerne über diese E-Mail- Adresse erteilt.

 

Ihre personenbezogenen Daten werden vertraulich behandelt (www.tiho-hannover.de/ds-bew).]

2 PhD and 1 postdoc position in computational chemistry / machine learning [Norway.]

Two PhD positions and one postdoc position are available at the University of Bergen and , Western Norway University of Applied Sciences . All positions are associated with the RESPOND3 project “Towards better computational approaches and responsible innovation strategies in early drug discovery: application to antibiotics and COPD”. The project is a cross disciplinary collaboration between research groups at the Centre for Advanced studies in Biomedical Innovation Law at the University of Copenhagen, the Department of Computing, Mathematics and Physics at the Western Norway University of Applied Sciences as well as the Department of Biomedicine and the Department of Chemistry at University of Bergen. The main focus of RESPOND3 will be hit and lead optimization for targets for antibiotics (SAM riboswitch) and chronic obstructive pulmonary disease (proteinase 3) guided by the use of computational methods as well as the development of new scoring functions using machine learning. The entire project is embedded in a responsible research and innovation strategy.

One of the available PhD positions is in the group of Prof. Nathalie Reuter at the Department of Chemistry, University of Bergen. The main tasks of this position are:

- Modelling of target-compound interactions for compounds targeting serine proteases, and compounds targeting riboswitches;

- Quantification, through the use of molecular dynamics simulations and free energy calculations, of the relative affinity of datasets of compounds for the two above-mentioned targets;

- Contributions to development and validation of multi-site lambda dynamics, using experimental affinity data generated by the project.

- Application of multi-site lambda dynamics to ligand discovery and design for the targets noted above.

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/172204/phd-position-in-computational-chemistry

 

The other PhD position is in the group of Prof. Ruth Brenk at the Department of Biomedicine, University of Bergen.

The main objectives of this position are:

- to derive data sets for the development of new scoring functions for protein-ligand interactions with machine learning methods

- to retro- and prospectively evaluate the derived scoring functions

- to design ligands with improved affinities for the targets in the RESPOND3 project

- to supervise master students

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/172060/phd-structure-based-design-machine-learning

 

The postdoc position is in the group of Prof. Alexander Selvikvåg Lundervold, Faculty of Engineering and Science, Western Norway University of Applied Sciences.

The main objectives of this position are:

- Development of new scoring functions for protein-ligand interactions using both in-house data and publicly available data sets.

- Attempts at combatting the tendency for scoring functions to exploit uninteresting features in the training data (data leakage) using e.g. various debiasing techniques. The improved scoring functions will be evaluated prospectively.

- Investigation of the the potential for machine learning methods in de novo structure generation (e.g. using variants of generative adversarial networks).

- Assist in the supervision of MSc students and PhD candidates.

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/172249/postdoctoral-fellow-in-drug-discovery-and-machine-learning

 

Scientific Programmer / Bioinformatician [EMBL, Heidelberg]

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

Requirements:

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

—substantial experience in software development and/or scientific computing

—experience with large-scale data analysis and management

—experience with the Linux/Unix shell

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

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

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

—good communication, interpersonal and English language skills

 

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