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PostDoc Researcher (m/f/d) in Evolutionary Genomics of Mammals

 

Job offer ref. #11-19012

The Senckenberg Gesellschaft für Naturforschung (SGN) is a member of the Leibniz Association and is based in Frankfurt am Main, Germany. SGN conducts natural history research with almost 800 employees and research institutions in six federal states. Within SGN, the Senckenberg Biodiversity and Climate Research Centre (BiK-F) explores the interactions between biodiversity, climate, and society.

Senckenberg BiK-F invites applications for a

 PostDoc Researcher (m/f/d)

in Evolutionary Genomics of Mammals

(100 %)

There is an exciting opportunity for a talented and motivated applicant to join the working group of Prof. Dr. Axel Janke. The applicant will be closely involved in gene flow, evolutionary-population or phylo-genetics to study speciation in mammals (bears, giraffe, kangaroos or allies) at the genomic level.

 

Your profile:

·         - PhD in Biology, Genetics, Bioinformatics or a related field

·         - strong interest and proven skills in evolutionary, population or phylo-genetics, preferentially in gene-flow analyses

· -    - experience in genome assembly, annotation and programing of scripts, R

·          - very good written and oral communication skills in English

 

Salary and benefits are according to a full time public service position in Germany (TV-H E 13, 100%). The contract should start as soon as possible and will initially be limited for two years.

The Senckenberg Research Institutes 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. #11-19012) before September 1st, 2019 by e-mail (attachment in a single pdf document) and including a cover letter describing your motivation to apply, a detailed CV, relevant credentials and certificates, two relevant publications and contact details of two potential references to:

 

Senckenberg Gesellschaft für Naturforschung

Senckenberganlage 25

60325 Frankfurt am Main

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



Links: http://www.senckenberg.de/files/content/stellenausschreibungen/ref-11-19012_postdoc_position_verlangert.pdf

Computational Biologist [Bork group]

We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

 

You will work in the Bork group, which harbours a wide range of intertwined activities in the area of computational biology. Many of these are currently applied to microbiomics, with the focus on the human gut, but increasingly also on other environments such as ocean or soil.  Metagenome-wide association studies are coupled with targeted approaches and also, in the context of local collaborations, with experimental analysis of synthetic and ex-vivo microbial communities.

 

Your role

 

The post holder will analyse and integrate new and existing datasets to study the microbiome of hosts and their global environments and the implications these have for human health. Particular focus areas will include high-resolution analyses of microbial communities (e.g. at sub-species or strain-level) as well as the infant microbiome, where questions such as microbial transmission and the effect of probiotics on microbiome and human development will be explored. The required tasks will involve developing and applying bioinformatics methods to mine large multi-‘omics datasets from various biological systems. The work will comprise technical as well as discovery aspects and will be carried out both independently and with internal and external collaborators. The post holder will also mentor trainees, provide hands-on guidance in their research, and teach technical and analytical skills.

 

You have

 

You should have a PhD in a field related to Computational Biology as well as a solid training in Microbial Ecology, Computer Science, and Microbiomics. At least 1.5 years of postdoctoral and practical experience analysing metagenomic datasets is required and you should at least have experience in 16S rRNA and shotgun metagenomics profiling.

 

Strong motivation, excellent scientific skills as well as willingness to work in a multicultural & interdisciplinary environment are essential. As part of the work involves international collaborations, project management, communication and presentation skills as well as the ability to work in a team are also required. You should be familiar with the UNIX environment and have advanced experience in programming. Excellent data analysis skills in R or python are also required.

 

For more information and to submit your application, please visit our website: https://www.embl.de/jobs/searchjobs/index.php?ref=HD01593&newlang=1&srch_trm=HD01593. Closing date: 1 Sep 2019.

Bio-IT Computational Support & Training

EMBL is Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome. 

 

Applications are invited for the above post to join the Gibson Team. The Gibson team develops and applies biological software tools in the analysis of protein data. An important activity of the group is to interface with experimental research groups at EMBL. The post-holder will be the focal point in providing bioinformatics support to the experimental researchers at EMBL. In this context, it is expected that the post-holder will organise a minimum of 4 bioinformatics/computational training courses per year.

 

Your role

 

The position is part of the EMBL Bio-IT project, a community-driven initiative to support the development and technical capacity of the diverse bio-computational community at EMBL. As one of the key members of this project, the post-holder will work closely with other members of Bio-IT to develop and/or organise various bioinformatics training courses, community-oriented outreach activities, community assessment tasks, and consulting. Through active communication and collaboration with many bioinformatics service experts at EMBL Heidelberg (e.g. the Computational Centres covering statistics, networks, image analysis, and systems models), the post-holder will help expand and maintain a lively network of bioinformaticians throughout the institute.

In addition, EMBL is a partner in the de.NBI (German Network for Bioinformatics Infrastructure) consortium which constitutes the ELIXIR Germany node. The post-holder will interact with individuals from de.NBI/ELIXIR to collaborate and jointly organise training and outreach activities. The post-holder will also have opportunities to attend and present at relevant conferences and events.

This is a highly collaborative role that provides diverse opportunities to engage with and support the scientific community while developing your own leadership skills. As well as being able to communicate and work well within a team, initiative, flexibility and willingness to learn will complete your profile.

 

You have

·         Ph.D. in Bioinformatics, Computational Biology, or related fields, or equivalent experience

·         Knowledge of a range of bioinformatics tools to provide support and training

·         Familiarity with one or multiple programming/scripting languages such as Bash, Python, R

·         Excellent communication and interpersonal skills

·         Experience of working at the interface between biology and computation

·         Experience in organising and teaching scientific/technical workshops

·         Interest in learning from other research communities of practices

 

Find more information and apply through our website.

Postdoc position “Modeling microbial communities of the Southern Ocean”

We are looking for a Post-Doc to work for 3 years in the research team of dr. Julia Engelmann in the department of Marine Microbiology and Biogeochemistry at the Royal Netherlands Institute of Sea Research on Texel (The Netherlands). The team applies bioinformatic and network biology approaches to marine marker gene, metagenomic and transcriptomic data. On top of describing microbial communities, we are interested in how the individual species interact with each other. We use modern sequencing approaches and network modeling techniques to infer these interactions.

THE DEPARTMENT

The Department of Marine Microbiology and Biogeochemistry on Texel performs detailed studies on microbial communities in the marine environment. We study the diversity, physiology and activity of phytoplankton, prokaryotes (archaea and bacteria) and viruses in diverse marine environmental settings by a variety of techniques, including modern genomic techniques.

THE PROJECT

At the base of the marine food web, microbes act both as primary producers and degraders of organic material. The organic matter they provide feeds the oceans and life on land. While we have seen a tremendous increase in knowledge about the diversity, genome composition and metabolic capabilities of microbial species living in the ocean, we still lack insights about how these communities work at a systems level. Because of the high complexity of many natural communities, inter-species interactions are difficult to study. 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 providing nutrients or energy substrates to another species, competing for nutrients or responding to signaling molecules. The Post-Doc will focus on elucidating marine microbial inter-species interactions in the Southern Ocean (close to Rothera, Antarctica) and perform sampling, high-throughput sequencing, network modeling and validation experiments in the laboratory. Part of the project will address the question of how climate change will impact microbial species abundance and especially their inter-species interactions in the Southern Ocean.

THE CANDIDATE

The candidate must hold a PhD degree in Bioinformatics, Computational Biology, Microbiology, Molecular Ecology, Microbial Ecology, Computer Science, (Bio-)Statistics, Physics or related fields and be highly organized and motivated. The position requires both strong computational as well as experimental skills. Candidates with a theoretical background should have at least some experience with microbiology and/or molecular microbial ecology techniques, and candidates with an experimental background need to have proof of computational skills, including excellent command of at least one programming language such as R or python. Experience with Unix/Linux systems is mandatory. The ideal candidate has experience in the analysis of high throughput genomic data. Due to the international character of the research group, excellent command of the English language is expected.

CONDITIONS OF EMPLOYMENT

We are offering a fulltime 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 (Research Scientist).

Additional information about the procedure can be obtained from Alexandra Noppeney (Sr HR Advisor).


APPLY ONLINE:

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

 

Interviews will be held on Texel, 25 September 2019. 

Postdoctoral Fellow in Computational Biology [Rome, Italy]

 

Location:

Rome, Italy

Staff Category:

Postdoctoral Fellow

Contract Duration:

2 years (renewable)

Grading:

Postdoc Stipend

Closing Date:

1 October 2019

Reference Number:

RM00084

The Boulard and Gross Groups are seeking to recruit a Postdoctoral Fellow with experience in computational biology to lead a project at the interface of epigenetics and neuroscience. The project combines the expertise of the Boulard and Gross groups in chromatin biology and neural circuits, respectively, to explore the cell-type specific interplay between transcription factors and the brain epigenome. The successful applicant will be part of a collaborative team of molecular biologists, biochemists, and neuroscientists that are working together on the large-scale exploration of previously uncharacterized transcription factors in mammalian brains.

Your role

The successful applicant will devise and carry out computational analyses of large-scale epigenomic and transcriptomic datasets internally generated, including:

·       developing methods and pipelines to analyze CutnRun and DAP-seq data sets, and

·       integrating, comparing, mining, and visualizing omic data sets.

You have

·       PhD degree in Bioinformatics, Computer Science, Mathematics, or related fields.

·       Solid skillset and experience in bioinformatics:

o   Excellent knowledge of R and biostatistics

o   Experience and proven track record in handling NGS datasets and developing analysis pipelines

·       Outstanding interpersonal and communication skills are essential

 

You might also have

 

·       Experience with Unix-based environment and high-performance computing cluster environment is not required, but would be considered an advantage.

·       Experience in motif discovery is not required, but would be considered an advantage.

   

Why join us

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organization. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits. Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.  

What else you need to know

EMBL is one of the highest ranked scientific research organizations in the world. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome. The Neurobiology and Epigenetics Unit at EMBL Rome studies mammalian physiology from the molecular to the systems level using the laboratory mouse as a model system. We take advantage of a full range of core facilities, including bioinformatics services and a high-performance computing cluster. For more information, please see our website at www.embl.it To apply please submit a cover letter clearly stating your motivation and future research interests/plans and a CV with at least two referees through our online system at www.embl.it/jobs. Applications are welcome from all nationalities, appointment will be based on merit alone.

 

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

University professorship - Bioinformatics - (Salary level W2 )

The University Medical Center Göttingen (UMG) pursues the consistent development of its profile-forming research foci neurosciences, cardiovascular medicine and oncology with translational and
systems-medical approaches and is closely networked on the Göttingen campus with the natural and bioscientific facilities of the university as well as the non-university facilities at the location.

At the UMG there is a

University professorship
Bioinformatics
(Salary level W2 )


to fill at the earliest possible date. The appointment of the professorship will initially be effected for a period of 5 years with the option for tenure track.

The professorship is associated with the establishment and management of a working group at the Institute of Medical Bioinformatics (Director: Prof. Dr. Tim Beißbarth). The professorship will build a
bridge from Medical Bioinformatics to the Center for Applied Computer Science, the Center for Statistics and the Data Science activities currently under development in Göttingen. An outstanding
doctorate in bioinformatics, computer science, statistics, natural sciences or a related subject with a
strong component in the quantitative analysis of biomedical data is required as well as experience in independent scientific research in the field of bioinformatics or data science after the doctorate, which is documented by relevant publications and/or third-party funding.

The successful candidate will work on the methodical development of analytical methods for biomedical high-throughput data, e.g. methods of machine learning and integrative data analysis.
Experience with Omics data or image data in biomedicine is desirable. In addition, an interest in
collaborations and applications within research alliances in the main research areas of the UMG is
expected. Methodical research in bioinformatics forms the basis for modern Systems Medicine. The
professorship should support the applications of bioinformatics in Systems Medicine through appropriate methodological research.

A positively evaluated junior professorship, habilitation or equivalent academic achievements as well
as commitment to teaching are assumed, as is the willingness to participate in academic self-administration.

Further expected are:

  • a high level of commitment to teaching
  • the readiness for interdisciplinary scientific work
  • the willingness and ability to competitively solicit third-party funded research projects


The further prerequisites for the recruitment of professors are set out in § 25 Lower Saxony
Higher Education Act (NHG) in the currently valid version. Applicants who have completed
their doctorate at the University of Göttingen can generally only be considered if they have
worked outside the UMG for at least two years after completing their doctorate. UMG has the right of appeal.

Applications from scientists from abroad are expressly welcome. The UMG aims to increase the proportion of women and therefore expressly invites qualified women to apply. Severely handicapped persons will be given preferential treatment if they are suitable.

Please submit your application documents until August 25th 2019 online via the following link:
http://www.med.uni-goettingen.de/de/content/ueberuns/berufungen_onlinebewerbung.html

If you have any questions, please do not hesitate to contact us at This email address is being protected from spambots. You need JavaScript enabled to view it..

1 Postdoc in Bioinformatics, 1 Bioinformatician / Computational Scientist, 1 Scientific Software Developer [DKFZ, Heidelberg]

Three open positions in the Bioinformatics and Omics Data Analytics Group at the DKFZ in Heidelberg.   

The new Collaborative Research Centre “Understanding and Targeting Resistance in Glioblastoma” (UNITEGLIOBLASTOMA, SFB1389) is focused on decoding and combating resistance in glioblastoma, a serious and usually fatal brain tumor in children and adults. The goal of the research consortium is to understand the molecular mechanisms of resistance against current therapies and to develop new types of treatment. At the heart of the CRC is the “Core Collection”, for which uniform, integrated data sets from multiple omics analyses, preclinical models, imaging, and clinical data are being generated.

We invite applications of enthusiastic and motivated Bioinformaticians / Computational Scientists / Scientific Software Developers to join the UNITE core work package “Data integration, bioinformatics analysis, and data exploration for precision neurooncology”.

The complete announcements, contact details and information how to apply can be found here:

 



Research Associate (m/w/d) in Bioinformatics (TV-H E13 100%) [Gießen]

The Professorship for Algorithmic Bioinformatics at Justus Liebig University Giessen invites applications for the full-time position of a Research Assistant.

Duties:

·        -  Own scientific training; Scientific services in research and teaching according to § 65 HHG; university didactic qualification

·         - Taking on teaching duties according to the teaching obligation ordinance of the state of Hesse

·        -  development of bioinformatic algorithms and sustainable engineering of their implementations in fields like phylogenetics and annotation recruitment in close collaboration with other team members as well as statistical analyses of microbiome big data. 

Qualifications:

·         Completed academic studies in a natural science subject as well as teaching experience in the field of bioinformatics / genome research / sequence analysis

·         strong practical skills in genomics, especially in automated microbial genome annotation•fluency in Python would be ideal

·         experiences with high performance computing, grid clusters or clouds as well as routine use of collaborative software engineering tools are highly preferred

 

 

Link to complete job description: http://www.inst.uni-giessen.de/stellenmarkt/pdf/stelle0012055.pdf

Post-doc in Biomedical Data Science (TB) (E13 TV-L, 100%) [Tübingen]

The Chair for Methods in Medical Informatics (Prof. Dr. Nico Pfeifer), Department of Computer Science at Eberhard Karls University Tübingen, one of eleven German universities distinguished as excellent under the German government’s initiative, is currently looking for a

 

Post-doc in Biomedical Data Science (TB) (E13 TV-L, 100%)

 

starting as soon as possible. The initial fixed-term contract will have an end date of 31st December 2020 with possible extension.

According to WHO there were 558,000 cases of drug-resistant tuberculosis (TB) infections world-wide in 2017 of which 82% were multidrug-resistant. In this project, which is funded through a Horizon 2020 grant by the European Commission, the successful candidate will build a prediction engine that is able to provide treatment decision support for TB-infected patients by applying and extending state-of-the-art machine learning methods. This will be in close collaboration with our Western and Eastern European partners, with a focus on multidrug-resistant strains from Eastern Europe.

The group has extensive knowledge at the interface between statistical machine learning, digital medicine, and computational biology. Nico is a PI in the excellence cluster “Machine Learning: New Perspectives for Science” starting in January 2019. We are developing methods that allow answering new biomedical questions (Speicher and Pfeifer 2015, Proceedings of ISMB/ECCB 2015) and optimize them in close contact with our excellent national and international biomedical partners (Carlson et al. 2016, Nature Medicine, Schoofs et al. 2016, Science, Döring et al. 2016, Retrovirology, Mendoza et al. 2018, Nature).

Prerequisites

The ideal candidate will have a Ph.D. or equivalent in Biomedical Data Science, Biometry, Biostatistics, Machine Learning, Bioinformatics, Medical Informatics, Computer Science, Computational Biology or a related life science discipline. Applicants should have an interest in interdisciplinary work. Proven experience in data science and machine learning as well as strong programming/scripting skills (C/C++, R, Matlab, Python, JavaScript, Java) are desirable. Other relevant qualifications include:

·       Background in Statistics

·       Proficiency in Russian language (communication with Eastern European partners)

·       Knowledge of the adaptive immune system (especially humoral immune response)

·       Experience with medical data (clinical data, molecular data, …)

·       Experience with high-throughput data (next-generation sequencing)

·       Databases (MySQL, NoSQL)

In case of equal qualification and experience, physically challenged applicants are given preference. The University of Tübingen aims at increasing the share of women in science and encourages female scientists to apply. Candidates will be officially employed by the administration of the University of Tübingen. 

Please send your application (including motivation letter, curriculum vitae, transcripts and certificates, and contact details of two academic references) via e-mail to
This email address is being protected from spambots. You need JavaScript enabled to view it. with the subject: Post-Doc application Biomedical Data Science (TB).

Application deadline: 4th August 2019.

Candidates are encouraged to send their application material early since we will start reviewing applications already before the deadline.