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Bioinformatician / neuroscience / Heidelberg

About BioMed X

The BioMed X Innovation Center is an exciting new collaboration model at the interface between academia and industry (Nat Biotechnol. 2015 33(1):20-1). At our center, distinguished early-career scientists recruited from all over the world work jointly on novel pre-clinical research projects in the fields of biomedicine, molecular biology, cell biology and diagnostics.

About Team BMP (Brain Microcircuits in Psychiatric Diseases)

The main aim of the team, headed by Dr. Michal Slezak, is to understand biological correlates of phenotypes related to human psychiatric diseases. Using advanced behavioural, genetic and physiological approaches combined with computational methods we identify genes underlying glial dysfunction and we use this knowledge to rescue disease-related phenotypes.

The position

We are offering a senior postdoctoral position for an enthusiastic researcher to broaden our think-tank. The ideal candidate has a PhD in bioinformatics, a proven track record evidenced by prior publications and is capable of independent thinking. The main responsibilities include:

  • Statistical analysis of data obtained from cell type- and brain-region-specific gene expression data from rodent models and 
    human brain samples, as well as cell cultures differentiated from patient-specific induced pluripotent stem cells (iPSC)
  • Integration of data from these distinct models with public databases, to validate original findings in the context of the cell type, brain region and disease (e.g. GSEA)
  • Pathway analysis to conclude genetic networks and signaling pathways affected by a disease state or targeted genetic manipulation (e.g. IPA)
  • Contribution to the design of experimental strategies to translate the results of transcriptional surveys to phenotypic studies
  • Collaboration with bioinformatics experts of the industry partner, Boehringer Ingelheim
  • Monitoring the field of psychiatric research for novel methods and pathways of interest

Required skills

  • PhD in the area of bioinformatics, computational biology, systems biology or similar
  • Knowledge in statistical methods in the context of biological systems
  • Prior experience with RNAseq analysis
  • Advanced programming skills in R and/or Python
  • Independent and creative thinking
  • Very good work organization skills
  • Experience to work in interdisciplinary teams
  • Excellent communication skills in English

Additional preferred skills

  • Experience in analysis of NGS data in the context of neuroscience
  • Experience in high-throughput screening methods
  • Experience in mining, integration and analysis of high-throughput datasets

Candidates are requested to submit

  • 1-page cover letter explaining the reasons of interest to join our team
  • Curriculum Vitae outlining scientific interests, research achievements, a record of publications, future personal goals and extra-scientific passions
  • 1- 2 reference letters

What we offer

The current post is offered for a limited term until 31 July 2020. BioMed X is a multidisciplinary and international research institution with a very collegial and flexible working environment. As part of the remuneration package we offer a competitive salary, access to training and lecture courses in house as well as in neighboring research institutions on the Life Science Campus in Heidelberg. Team recognition events, such as our annual two-day retreat, joint luncheons and after work events, a Summer and a Christmas party are just some of the other perks our fellows enjoy. The position is sponsored by Boehringer Ingelheim. Please submit your application to the attention of Dr. Michal Slezak before 15th April 2019 via the online application system on this website. Applicants will be interviewed upon incoming documents, hence please get in touch as soon as you decide to apply.

Contact:

 

Dr. Michal Slezak Phone: +49 6221 4261163 Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Wissenschaftliche/r Mitarbeiter-in [Gießen]

 An der Professur für Systembiologie mit dem Schwerpunkt Genomik, Proteomik und Transkriptomik, Fachbereich Biologie und Chemie,

ist im Rahmen eines drittmittelfinanzierten BMBF-Projektes eine volle Stelle mit einer/einem

 

Wissenschaftlichen Mitarbeiterin/Mitarbeiter

 

zum nächstmöglichen Zeitpunkt befristet bis zum 31.12.2021 zu besetzen.

Bei Vorliegen der tariflichen Voraussetzungen erfolgt die Vergütung nach Entgeltgruppe 13 Tarifvertrag Hessen (TV-H).

 

Aufgaben:

Zertifizierung einer Cloud-Computing-Infrastruktur, Einführung der entsprechenden Managementsysteme.

Planung und Überwachung der Implementierung und Bereitstellung Cloud-basierter Services.

Erstellung einer Benutzer-orientierte Sammlung von bioinformatischen Software-Tools inkl. Installation und Funktionstest in OpenStack- und Kubernetes-basierten Umgebungen.

Pflege der Benutzerdokumentation.

Unterstützung bei Datenanalyse sowie Entwicklung neuer Softwaretools für die Analyse und Visualisierung von Hochdurchsatzdaten.

 

Anforderungsprofil:

Abgeschlossenes wissenschaftliches Hochschulstudium in der Bioinformatik / Informatik oder einem anderen IT-nahen Fach.

Umfangreiche Erfahrung im Bereich Systemadministration, insbes. mit Linux-Betriebssystemen.

Weitere Kenntnisse siehe komplette Ausschreibung.

 

 

Link zur kompletten Ausschreibung: http://www.inst.uni-giessen.de/stellenmarkt/pdf/stelle0011741.pdf

Wissenschaftlicher Mitarbeiter (m/w/d) Bioinformatik / Genetische Epidemiologie / Biometrie

Vollzeit - JobID: P0025V114

baldmöglichst für den Bereich Bioinformatik / Genetische Epidemiologie / Biometrie im Institut für Human­genetik (Direktor: Prof. Dr. med. Christian Schaaf) gesucht.

Die Stelle ist zunächst befristet auf zwei Jahre. Eine anschließende Weiterbeschäftigung ist vorgesehen.

Ihre Aufgaben und Perspektiven

  • Unterstützung bei bioinformatischen Projekten
  • Statistische Beratung
  • Koordination der EDV-Angelegenheiten des Instituts
  • Datenschutzansprechpartner
  • Mitwirkung bei wissenschaftlichen Projekten
  • Einwerbung von Drittmitteln


Es besteht die Möglichkeit zur eigenständigen Forschung. Die Vergütung erfolgt nach TV-L.

Ihr Profil

  • Studium in Bioinformatik / Genetische Epidemiologie / Statistik oder verwandten Bereichen
  • Ausgewiesene Erfahrungen im selbstständigen wissenschaftlichen Arbeiten, bevorzugt mit einer erfolgreich abgeschlossenen Promotion
  • Fundierte Erfahrungen mit bioinformatischen Fragestellungen im Bereich Analyse von OMICS-Daten in Diagnostik und Forschung
  • Erfahrungen mit statistischen Verfahren in der Genetik
  • Organisationvermögen, Initiative, Kommunikationsfähigkeit, Teamgeist

Wir bieten Ihnen

  • Zielorientierte individuelle Fort- und Weiterbildungsmöglichkeiten
  • Gezielte Einarbeitung
  • Jobticket
  • Möglichkeit der Kinderbetreuung (Kinderkrippe und Kindergarten) sowie Zuschuss zur Ferienbetreuung für Schulkinder
  • Aktive Gesundheitsförderung
  • Betriebliche Altersvorsorge
  • Zugriff auf die Universitätsbibliothek und andere universitäre Einrichtungen (z. B. Universitätssport)

Kontakt & Bewerbung

Für Rückfragen zu den Tätigkeiten wenden Sie sich bitte an Dr. Christine Fischer unter Tel. 06221 56-5060, This email address is being protected from spambots. You need JavaScript enabled to view it..

Interessiert?


Wir freuen uns auf Ihre Bewerbung bis zum 30.04.2019 per E-Mail (mit einem einzigen PDF-Dokument).

Universitätsklinikum Heidelberg
Institut für Humangenetik
Prof. Dr. C. Schaaf, Direktor 
Im Neuenheimer Feld 366
69120 Heidelberg
This email address is being protected from spambots. You need JavaScript enabled to view it.

Veröffentlichung: 01.04.2019

Wir stehen für Chancengleichheit. Schwerbehinderte werden bei gleicher Eignung vorrangig eingestellt. Das Universitätsklinikum strebt eine generelle Erhöhung des Frauenanteils in allen Bereichen und Positionen an, in denen Frauen unterrepräsentiert sind. Qualifizierte Frauen sind daher besonders aufgefordert, sich zu bewerben. Vollzeitstellen sind grundsätzlich teilbar, soweit dienstliche oder rechtliche Gründe nicht entgegenstehen.

 

 

Link zur Ausschreibung:  https://karriere.klinikum.uni-heidelberg.de/stellenangebot/8238/Wissenschaftlicher-Mitarbeiter-%28m%7Cw%7Cd%29-Bioinformatik-%7C-Genetische-Epidemiologie-%7C-Biometrie.html

PhD Positions in Data Science and Bioinformatics in Heidelberg

Are you interested in solving fascinating biological or medical questions computationally?

 

At the German Cancer Research Center (DKFZ) in Heidelberg, Germany’s largest biomedical research institute, computational scientists work at the forefront of cancer research. They combine inter­disciplinary approaches from physics, biology, bioinformatics and statistics to analyze and understand complex biological and medical data.

 

Main activities at the DKFZ involving big data:

•             Development and application of computa­tional methods for the integrative analysis of genomic, epigenomic, transcriptomic, proteomic, meta­bolomic and radiomic data

•             Development of methods for modeling and simulation of biological and medical processes

•             DNA mutation analysis by next-generation DNA sequencing of individual human cancer genomes

•             Application of state-of-the-art technologies in automated live-cell imaging and image analysis

•             Computer-assisted radiology and surgery

•             Biostatistical evaluation of experimental and clinical data

•             Integration and development of new methods for systems biology and systems medicine

 

More information at https://www.dkfz.de/datascience

 

Full funding is provided for the duration of the PhD.

 

If you are interested in doing your PhD in the field of computational cancer research, why not join the International PhD Program at the DKFZ with more than 500 PhD students?

More information about the program at https://www.dkfz.de/en/phd-program/index.html?campaign=phd/bioinf

 

Application deadline: 31st May 2019

 

 

Leiterin / Leiter (m/w/d) Computational Core Unit (Bioinformatik) (Vollzeit TV-L EG 13, unbefristet)

Zur Unterstützung von Forschungsprojekten in den Fakultäten für Biologie und Vorklinische Medizin, Medizin und Physik suchen wir eine/n wissenschaftliche/n Mitarbeiter/in für den Aufbau und die Leitung einer Core Unit zur Analyse von OMICS Daten, insbesondere von Hochdurchsatz-Sequenzierungs-Daten (NGS).

Bewerbungen bitte bis 15. Mai 2019 per E-Mail an This email address is being protected from spambots. You need JavaScript enabled to view it. senden.

 

Links: https://www.uni-regensburg.de/universitaet/stellenausschreibungen/lehre-forschung/index.html

Ph.D. candidate in Computational Biology

At the Department of Gynaecology (Charité Medical University Berlin, Campus Virchow Clinic) we are looking for a Ph.D. candidate in Computational Biology or Bioinformatics in a project to redefine our understanding of principal drivers of molecular subtypes in ovarian cancer. Our centre has a unique environment, with regards to equipment, facilities and access to clinical samples with a strong track record in translational research. We have collected molecular samples and molecular data for the largest cohort of ovarian cancer. In collaboration with Prof. Nils Blüthgen, (Institute of Pathology, Charité Medical University, Berlin, Germany), we will now develop and use computational methods to our large collection of diverse omics data with the goal to acquire a functional understanding of signaling networks and their deregulation in ovarian cancer. The bioinformatics researcher will be part of one of the world's leading laboratories, with specialization and years of experience in implementing complex, bioinformatics methods for the interpretation of signal transduction pathways. The group leverages existing tools and develops novel algorithm for pathway modeling to study drug effects, hence efficacy of pharmacological inhibitors and to understand resistance mechanisms.
 
Requirements
The candidate for this Computational Biologist position must be computer literate, competent using programming/scripting languages that are used in computational biology (such as R). She/he ideally has experience in dealing with gene expression as well as proteomics data. The candidate will identify, use and develop suitable techniques for an integrative analysis of the large cohorts.

 •     Research scientist require a MSc degree in bioinformatics, biophysics or any other field with relevance to biology/computational biology
 •     Proficiency in basic programming fundamentals for data analysis (preferably in R)
 •     Ability to collaborate and communicate complex technical concepts
 •     Understanding of basic cancer molecular biology principles
 

Einstellungstermin
ab sofort

Beschäftigungsdauer
36 Monate
 
Arbeitszeit
39 Wochenstunden
 
Vergütung
E13 TVöD (65%) Die Eingruppierung erfolgt unter Berücksichtigung der Qualifikation und der persönlichen Voraussetzungen.

 
Kontakt:

 

 


Dr Hagen Kulbe

 

Senior Scientist / Department of Gynaecology

 

Charité Comprehensive Cancer Centre

Charité Medical University Berlin, Campus Virchow Clinic

Augustenburger Platz 1

13353 Berlin

Germany

 

Tel: +49 (0)30 450 564 476

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

PhD Position in Homology-Based Genome Annotation

Apply until April 3rd for the three-year PhD position (65% E 13 TV-L) that is available immediately and
funded by the US National Institutes of Health as part of the project ‘Addressing Open Challenges of Computational Genome Annotation’.

The candidate shall perform research in the area of bioinformatics tool development for genome annotation. In particular, the plan is to develop a new functionality of the AUGUSTUS program for homology-based gene prediction.

The candidate should be familiar with hidden Markov models, current genomics tools and C++ programming and
have practical experience in handling large amounts of data.

Links: Official Job Announcement

Postdoctoral Researcher position in Bioinformatics [Dortmund]

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

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

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

 

Job description

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

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

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

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

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

[2] https://cellprofiler.org/

 

Requirements

The successful candidate has:

·         a PhD in Bioinformatics

·         expert knowledge in Statistics

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

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

Payment

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

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

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

 

Application

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

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

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

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

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

Links: https://www.mpi-dortmund.mpg.de/ ; https://www.mpg.de/de

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

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

More details can be found here.

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

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

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

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

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

The position's requirements are:

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

·        Preferably a PhD in one of the fields

·         Proven qualifications in programming and bioinformatics

·         Experience with next generation sequencing data and DNA-Barcoding

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

·         Language skills: English (written and spoken)

 

Application documents:

·         Letter of motivation

·         Curriculum vitae

·         Transcripts of studies

·         Two letters of recommendation

 

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

 

The University of Bonn is an equal opportunities employer.

 

 

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

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