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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

Postdoctoral Fellow Position in Machine Learning for Drug Discovery at the Western Norway University of Applied Sciences

A postdoc position is available at the Western Norway University of Applied Sciences in the research group of Alexander Selvikvåg Lundervold (This email address is being protected from spambots. You need JavaScript enabled to view it.).
 
The position is associated with the RESPOND3 project “Towards better computational approaches and responsible innovation strategies in early drug discovery: application to antibiotics and COPD”. RESPOND3 is part of the Centre for Digital Live Norway (https://digitallifenorway.org ) and 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 Computer Science, Electrical Engineering and Mathematical Sciences 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.
 
The RESPOND3 research team will eventually consist of four postdocs, three PhD students and five principle investigators, covering medicinal chemistry, computational chemistry and biology, structural biology, computer science, mathematics, and law. In addition to working with the RESPOND3 team, the postdoctoral fellow will be part of the vibrant research community at the recently established Mohn Medical Imaging and Visualization Center (MMIV, https://mmiv.no ), Haukeland University Hospital, with access to world-class computing infrastructure and to top expertise in life sciences, machine learning and computation. The researcher will also be associated with the ICT-oriented strategic research programme in computer science at HVL (http://ict.hvl.no) which spans the areas of software engineering, sensor networks, machine learning, and engineering computing.
 
The announced postdoc position will focus on applications of machine learning in drug discovery and development. The exact direction of research will depend on the background and interests of the successful candidate. Potential research areas and directions include
  • 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 potential for machine learning methods in de novo structure generation (e.g. using variants of generative adversarial networks)
 
In addition, the successful candidate will
  • Assist in the supervision of MSc students and PhD candidates.
  • Contribute to the development of joint project applications for external funding in collaboration with permanent research staff members at HVL, MMIV and UiB
 

 

More details about this position and information on how to apply can be found here: https://www.jobbnorge.no/en/available-jobs/job/177135/postdoctoral-fellow-position-in-machine-learning-for-drug-discovery. Deadline November 24th 2019.

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

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

PhD student position 1
:

o    Topic: Development of novel modulators for the nicotinic acetylcholine receptor for the treatment of nerve agent poisoning

o    Availability: The position is available as of now.

PhD student position 2:

o    Topic: Enzymatic halogenation: enzyme identification, characterization, application

o    Availability: The position is available as of 01.12.2019.

Please find more detailed information regarding the respective topic under: https://cpclab.uni-duesseldorf.de/index.php/Openings

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 modelling.

 

Application process
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
This email address is being protected from spambots. You need JavaScript enabled to view it. . Please provide all documents as one PDF file and specify for which position you are applying.