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

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 (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) 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: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! (subject: DBAC Application).

Computer scientist or bioinformatician with strong computational background (Web development, data and workflow management…)

We are looking for a computer scientist or a bioinformatician with a strong computation background to join the bioinformatics unit of the IEO in Milan. The candidate will evolve in a research environment (next generation sequencing among others). The selected candidate will consolidate our team for the development and maintenance of the bioinformatics resources, and will have the opportunity to support the research groups in setting new tools and pipelines.

Place of employment and work

The candidate will be located at the Department of Experimental Oncology of the European Institute of Oncology in Milan (Italy), one of Europe’s leading research institutes in biomedical research, where he/she will also interact with one of the largest computational biology communities in Italy

Requirements:

The candidate should have good programing skills. Background in bioinformatics would be appreciated but is not mandatory. Experience with containers (docker, singularity), grid computing, web frameworks, spring boot, nextflow, continuous integrations will be appreciated.

 

For further info or to arrange an informal interview, please write to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!

PhD position - Functional Genomics and Computational Biology

A three-year Ph.D. position (65% E 13 TV-L) is immediately available at the Department of Biology (http://www.bioinfo.nat.fau.de) at the Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU).

The focus of our research group is on understanding the functional aspects of the human genome in health and disease through the analysis of the different levels of information encoded in the sequence. Some of our publications include:

Li L, Barth NKH, Hirth E, Taher L. Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units, Genome Biol Evol., 2018 (https://www.ncbi.nlm.nih.gov/pubmed/30184074).
Taher et al., Sequence signatures extracted from proximal promoters can be used to predict distal enhancers, Genome Biology, 2013 (http://www.ncbi.nlm.nih.gov/pubmed/24156763).

Eligibility:
We are looking for talented, highly motivated applicants with:
1. A master's degree or equivalent within the field of computational biology, bioinformatics or related fields.
2. Familiarity with bash scripting, Perl (or Python) and R programming.
3. Experience with the analysis of Next-Generation Sequencing data (mainly from Illumina platforms).
4. Strong written and oral communication skills in English.

How to Apply:
The position will remain open until filled. Please email applications to Leila Taher (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) with the subject "PhD Position". An application package must contain the following documents (please, send all in one PDF file):
1. A letter of interest.
2. A complete curriculum vitae.
3. A short (<10,000 characters) research proposal on the topic "regulatory functions of transposons".
4. Copies of transcripts.
5. Names and contact information for 2-3 references.

Only complete applications will be considered.