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Postdoc position “Modeling microbial communities of the Southern Ocean” [Royal NIOZ, Texel, the Netherlands]

We are looking for an enthusiastic early career scientist to work as a Post Doc in the research team of dr. Julia Engelmann (department of Marine Microbiology and Biogeochemistry, Royal NIOZ, Texel, the Netherlands). The team’s overarching interest is to understand how marine microbes interact with each other and form communities. The team applies bioinformatic and network biology approaches to marine marker gene, metagenomic and transcriptomic sequencing data to infer these interactions.

LOCATION: NIOZ TEXEL

VACANCY NR.: 2019 – 65

CLOSING DATE: 05-01-2020

THE PROJECT

At the base of the marine food web, microbes act both as primary producers and degraders of organic material. This organic matter fuels life in the oceans. While recent years have seen a tremendous increase in knowledge about diversity, genome composition and metabolic capabilities of microbes living in the ocean, we are still lack insights about how these communities interact and work at the systems level. 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 for example the provision of nutrients or energy substrates, competition for nutrients or response to signaling molecules. The Post-Doc will focus on elucidating marine microbial inter-species interactions in the Southern Ocean (Rothera, Antarctica; a 2 month expedition in 2021 is planned) and will perform sampling, high-throughput sequencing, network modeling and validation experiments both in the laboratories at Rothera and the NIOZ. One question we aim at answering is how climate change impacts microbial communities and especially their inter-species interactions in the Southern Ocean.

THE CANDIDATE

Do you have a PhD degree in Bioinformatics, Computational Biology, Microbiology, Molecular Ecology, Microbial Ecology, (Bio-)Statistics, or related fields? Are you organized and motivated to work in a vibrant research environment? Do you have computational and experimental (laboratory, field work) skills? Do you have good command of at least one programming language such as R or python and experience with Unix/Linux systems? Then apply for this post! Ideally, you also have experience in the analysis of high throughput genomic data. Due to the international character of the research group and institute, an excellent command of the English language is expected.

CONDITIONS OF EMPLOYMENT

We are offering a full-time 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.

FURTHER INFORMATION

Additional information about the vacancy can be obtained from: Dr. Julia Engelmann (This email address is being protected from spambots. You need JavaScript enabled to view it., Research Scientist).

Additional information about the procedure can be obtained from Alexandra Noppeney (This email address is being protected from spambots. You need JavaScript enabled to view it., Sr HR Advisor).

Interviews will be held Jan 16, 2020.

APPLY ONLINE

https://www.workingatnioz.com/job-application.html?id=7486

 

Application deadline: Jan 5, 2020

PhD position (m/f/d) in Computational Neuroimaging at Goethe-University Frankfurt / University Hospital Frankfurt

The laboratory for neuroimaging / the research group of Professor Christine Ecker at University Hospital Frankfurt is looking for a highly motivated and skilled PhD-candidate with a Master’s degree in neuroinformatics, bioinformatics, physics, or a related field.

You will be part of the “Transcranial brain stimulation as innovative therapy for chronic paediatric neuropsychiatric disorders” project (STIPED, https://cordis.europa.eu/project/rcn/207203/factsheet/en) and your tasks will include:

-	Acquisition of neuroimaging data (sMRI, DTI, and rsfMRI)
-	Pre-processing of neuroimaging data using standard neuroimaging software packages and custom pipelines 
-	Reproducible analysis of neuroimaging data using statistical methods and machine learning approaches in Matlab, Python and R
-	Writing research papers and other publications

For more information on the laboratory for neuroimaging, please visit https://www.kgu.de/einrichtungen/kliniken/zentrum-fuer-psychische-gesundheit/psychiatrie-psychosomatik-und-psychotherapie-des-kindes-und-jugendalters/forschungsbereiche/laboratory-of-neuroimaging

The contract is limited to 36 months. Salary and benefits are in accordance with a public service position in Germany (collective agreement TV-G-U E13, 70%). Working language is English or German.

If you have any questions left, please contact Dr. Tim Schäfer (tim.schaefer[at]kgu.de). To apply, send your application (a short letter of motivation, a current CV, and contact data of up to three references) by email to Prof. Christine Ecker (christine.ecker[at]kgu.de). Please provide all documents as a single PDF file.


PhD Position (m/f/d) - Functional Comparative Genomics of Oomycetes

Job offer Ref. # 12-19013

 

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

 

PhD position (m/f/d)

Functional Comparative Genomics of Oomycetes

(TV-H E13, half time position)

 

 

Your tasks

 

·         Library preparation and genome sequencing using latest technologies (including oxford nanopore sequencing)

·         Genome assemblies and annotation

·         Comparative genomics focusing on functional aspects, such as pathogenicity genes and regulatory networks

·         Pattern analyses using standard algorithms and deep learning approaches

 

Your profile

 

·         Master or equivalent Diploma in biology, bioinformatics or related subjects

·         Experience with handling large amounts of sequence data

·         Experience and exceptional interest in comparative genomics and evolutionary biology research

·         Ability to effectively communicate and organize workflows, to closely collaborate in interdisciplinary teams

·         Proficient use of the English language (C1 or native)

 

What is awaiting you?

 

·         An interesting task in a dynamic team of researchers in an international research group

·         Exposure to an additional 20 research groups in the LOEWE excellence centre

·         A workplace close to the city center of Frankfurt, a lively and diverse city with high life quality

·         Flexible working hours –company pension scheme – Senckenberg badge for free entry in museums in Frankfurt a family-conscious personnel policy

 

 

Salary and benefits are in accordance with a public service position in Germany (collective agreement TV-H E13, 50%). The contract shall start as soon as possible and will be limited to 36 months. Equally qualified handicapped applicants will be given preference. The place of work is in Frankfurt am Main at the Senckenberg Biodiversity and Climate Research Centre (SBiK-F). The employer is the Senckenberg Gesellschaft für Naturforschung.

 

We look forward to your application!

 

Please send your application, mentioning the reference of this job offer (ref. #12-19013) by January 15th, 2020 (deadline) by e-mail (attachment in a single pdf document) and including

- 
a cover letter describing your suitability and motivation

a detailed CV

your credentials and certificates

-  and contact details of two potential references to:

  

Senckenberg Gesellschaft für Naturforschung                                                                        

Senckenberganlage 25

60325 Frankfurt

 

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

  

 

For scientific enquiries please get in contact with Prof. Dr. Marco Thines (This email address is being protected from spambots. You need JavaScript enabled to view it.).

PhD-Position in Nutritional Medicine & Bioinformatics at University of Kiel

The Research Group for Nutriinformatics at the University of Kiel is seeking a PhD-candidate with a Masters degree in bioinformatics, biostatistics, biotechnology or another study program with a strong focus on quantitative methods in molecular life sciences.

The candidate will apply bioinformatic and systems biology approaches in the field of nutritional medicine. The PhD-Project will be carried out in close collaboration with experimental research labs in Kiel and the University Hospital Schleswig-Holstein. The candidate will have access to large data sets and state-of-the-art experimental and computational facilities to investigate the interplay between human and microbial metabolism and the impact of nutrition.

Together with other world-renowned research institutes in Kiel (e.g. Max-Plank-Institute for Evolutionary Biology and the GEOMAR - Helmholtz Centre for Ocean Research ), Kiel University has become a hot-spot for Microbiome Research. Therefore, Kiel is an ideal location for scientific communication and to further develop essential skill for a career in science and information technology.

Kiel is located in northern Germany directly at the coast of the Baltic sea and offers plenty of opportunities for outdoor activities.

How to apply:
Please refer to the application procedure details in the job announcement (https://www.uni-kiel.de/personal/de/stellen/extern/wiss/dateien-extern-wiss/ausschreibungstext-promotion.pdf). For questions regarding the position please contact Jun.-Prof. Silvio Waschina (This email address is being protected from spambots. You need JavaScript enabled to view it.).


Links:

Detailed job offer: https://www.uni-kiel.de/personal/de/stellen/extern/wiss/dateien-extern-wiss/ausschreibungstext-promotion.pdf

PhD or Postdoc Position in Network Analysis Algorithms at University of Konstanz

I would like to point out a PhD / Postdoc position (E13-TVL, 100% ) at the University of Konstanz. 
The research is part of “Centre for the Advanced Study of Collective Behaviour” with focus on network analysis algorithms to investigate interactions within collectives, in particular for the exploration of animal collective behaviour in immersive environments.  

More information can be found at https://stellen.uni-konstanz.de/jobposting/38b757311f4ee62f0221fe6a369d630680e0d11c0

Postdoc position in computational cancer biology in Milan, Italy

The computational cancer biology lab of Martin Schaefer at the European Institute of Oncoglogy (IEO) in Milan, Italy, is seeking a highly motivated and talented postdoctoral researcher. The postdoc will develop and apply network-based methods to identify cancer driver events from genomic and epigenomic data.

Cancer is driven by alterations on all molecular levels. However, while our knowledge about the contribution of point mutations to the phenotypic hallmarks of cancer has advanced substantially over the last decade, we still need to solve the puzzle of how the numerous quantitative changes (eg epigenetic or transcriptional) and copy number alterations of larger genomic regions are related to cancer initiation and progression.

Candidates should hold a PhD (in a relevant area), have expertise in statistics, programming, and the analysis of cancer omics data. Interest in network biology and knowledge of data science techniques such as machine learning and being familiar with concepts of tumor evolution are a plus.

The IEO is one of Europe’s leading cancer research institutes. The lab is in the Department of Experimental Oncology (DEO), which is located on the IFOM-IEO campus in a central location of Milan. The IEO hosts an international and vibrant research community (with a growing computational component). It is strong in genomics analyses, clinical aspects and mechanistic understanding of cancer. The IEO has an excellent HPC infrastructure and core facilities.

A competitive salary will be paid based on the qualification of the applicant.

More details on the position and our lab can be found on our homepage: schaeferlab.org

For informal inquiries or to send an application (which should include a CV, cover letter, a list of publications and contact details of 2 - 3 referees) please contact: This email address is being protected from spambots. You need JavaScript enabled to view it.. The position is available immediately but the starting date can be negotiated.

 

Scientific Associate for cloud-based benchmarking platform for cellular deconvolution

The University Heidelberg is involved through the Health Data Science Unit (www.hdsu.org) in an international project funded by the European EIT Health program.

The goal of the COMETH project is to set up a benchmarking platform to perform cellular deconvolution i.e. determine cellular composition of patient samples from expression data (RNA-seq) or DNA methylation data. Within this project, we want to
(1) Provide an easy-to-use and flexible online platform offering several state-of-the-art methods for cellular deconvolution; (2) Test datasets with controlled cellular composition to allow benchmarking of the data.

This benchmarking platform will be based on the codalab system (https://codalab.org/) which has already been successfully used for several competitions and benchmarking efforts.

The partner from University Heidelberg will be in charge of implementing this platform on the de.NBI cloud environment, in order to provide a flexible and stable benchmarking framework for data analysists and interested clinicians. The tasks will involve

(1) Implementing the codalab framework in the de.NBI cloud environment
(2) Packaging the deconvolution tools using Docker containers
(3) Providing test datasets for the benchmarking

Besides these technical tasks, the candidate might also contribute to methodological development such as the multi-omics deconvolution task incorporating expression and methylation data. This would be done in collaboration with other groups.

What we look for:
We are looking for a candidate holding an M.Sc. or Ph.D in computer science or computational biology with experience in the implementation of bioinformatics tools and workflows in a cloud environment and interest in the processing of omics datasets. First experience with Docker containers would be appreciated. Collaborative skills are required.

What we offer:
This is a one-year position paid according to german TV-L 13.

 
Contacts
Please send your application to Carl Herrmann (This email address is being protected from spambots. You need JavaScript enabled to view it.) with CV and contacts for references.
 

Bioinformatician in Microbiome Research [Sunagawa Lab, ETH Zurich]

We are seeking a highly motivated, skilled and organized bioinformatician to join our research group. We are interested in studying ecological and evolutionary factors that determine the structure, function and diversity of microbial communities – with a focus on the ocean ecosystem and the gastrointestinal tract of animals and humans. Embedded in the Institute of Microbiology at the Department of Biology, we develop and combine computational and experimental approaches to integrate quantitative ‘meta-omics’ readouts with contextual information, with the goal to better understand and predict the role of environmental microorganisms and the underlying mechanisms of host-microbial homeostasis.
The postholder is able to develop, implement and maintain state-of-the-art methodology and infrastructure for microbiome data analysis (databases for original and derived data, workflows/pipelines for omics-data, etc.) and analyze meta-omics data from environmental and host-associated microbiome studies. Her/his motivation is to provide cutting-edge support for ongoing research projects in the group and to showcase the potential of her/his developments in the context of a research project in the area of microbiome research.
 
Essential qualifications include:
• MSc or PhD degree in Bioinformatics, Computer Science, or a related field
• development of bioinformatic analysis workflows
• strong expertise in Python/R programming
• work experience in Linux environment
• familiarity with HPC systems
• strong communication and teamwork skills
 
The following additional qualifications will be advantageous: 
• experience in (meta)genomic data analysis
• background in (environmental/host-associated) genomics
• background in (environmental/host-associated) ecology, evolution
• experience in web/database development (HTML, SQL)
 
Applications and informal inquiries should be directed by email to Prof. Dr. Shinichi Sunagawa (This email address is being protected from spambots. You need JavaScript enabled to view it.).
 
Contact:
 
Prof. Dr. Shinichi Sunagawa
 
ETH Zürich
Institute of Microbiology, Department of Biology
Vladimir-Prelog-Weg 4; HCI F 423
8093 Zürich, Switzerland
This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +41 (0) 44 633 61 55 

 

 

PhD position in Biomedical Data Science/Computational Genomics

The group “Biomedical Data Science”, which will be founded in January 2020
(Principal Investigator: Alexander Schönhuth), is seeking a motivated PhD
student. By rank, the position is classified as a German Scientific Assistant,
with salaries being determined based on prior experience and qualifications
(‘E13-TVL’).  Working language is English or German, depending on personal
preference.

The corresponding research activities will relate to topics from areas such as
“Artifical Intelligence in Biomedicine/Computational Personalized
Medicine/Algorithmic Bioinformatics/Computational (Single Cell/Pan-) Genomics”.

Particular examples of potential research are:

    - Deep Learning for understanding/diagnosis/therapy selection of so far
      insufficiently understood diseases, such as cancer, amyotrophic lateral
      sclerosis, and further neuropathological disorders, in particular when
      relating to the microbiome

    - the creation and implementation of programming frameworks that support
      the analysis of the genetic diversity of diseases

    - the evaluation of single cell genomics experiments, as a precision tool
      to support the finegrained understanding of cancer heterogeneity

and cancer in general, and developmental processes that, for example,
characterize the shaping of the immune system, possibly in interaction with the
two points from above.

    - the creation and analysis of novel algorithmic/mathematical structures
      and indexes that support the mapping of the genetic diversity of entire
      populations (“Computational Pan-Genomics”)

Research and publication activities will cover 75 % of worktime, assistance and
guidance of teaching activities 20 % and participation in academic management
5%.

The exact choice of topic can be determined in personal discussions, according
to personal preferences and strengths.

For more information, in particular the application procedure, see https://www.uni-bielefeld.de/Universitaet/Aktuelles/Stellenausschreibungen/Anzeigen/Wiss/wiss19232_englisch.pdf

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