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Postdoctoral Researcher (f/m) in Genome Sequencing
Friedrich-Schiller-Universität Jena / Friedrich Schiller University Jena / German Centre for Integrative Biodiversity Research (iDiv)
The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig is one of four National Research Centres funded by the German Research Foundation (DFG). Its central mission is to promote theory-driven synthesis and data-driven theory in this emerging field. The concept of iDiv encompasses the detection of biodiversity, understanding its emergence, exploring its consequences for ecosystem functions and services, and developing strategies to safeguard biodiversity under global change. It is located in the city of Leipzig and it‘s a central institution of the University Leipzig, jointly hosted by the Martin-Luther-University Halle-Wittenberg, the Friedrich Schiller University Jena and the Helmholtz Centre for Environmental Research (UFZ). Furthermore, it gains support by the Max Planck Society, the Leibniz Association and the Free State of Saxony. More information about iDiv: www.idiv.de
The Friedrich Schiller University Jena offers the following position at the next possible date, latest September 2018, at iDiv in Leipzig:
in Genome Sequencing in the group of Prof. Dr. Manja Marz at the
Friedrich Schiller University Jena (limited to 2 years
in full-time, salary: Entgeltgruppe 13 TV-L)
Severely disabled persons are encouraged to apply and will be given preference in the case of equal suitability.
To record biological diversity is fundamental but faces many challenges. A modern way to achieve this goal on a molecular level is genome or transcriptome sequencing by third generation sequencing methods. To analyse genomes and transcriptomes from all organisms e.g. in soil or gut of insects, we usually use different (wet-lab) extraction protocols:
(i) for bacteria, we use a metagenomic approach and sequence the sample; (ii) for fungi from the same samples, we typically use a different protocol for cell disruption before sequencing; (iii) for (DNA)viruses, size filtration is needed before sequencing; (iv) for RNA viruses, we need combined protocols of size fragmentation and RNA extraction before sequencing. Sometimes, (v) a common host needs also to be sequenced and (vi) analysing transcriptome and genomes becomes more important. Instead of sequencing about 10 times the same sample (from different extraction protocols) to obtain the complete biodiversity, the aim of the researcher will be to develop a method to multiplex organisms from different kingdoms into one sequencing approach. We will use different spike-ins as quantitative controls.
Coordination and design of various DNA and RNA extraction methods
Design and calculation of various HTS sequencing approaches
De novo assembly of viruses, bacteria and higher organisms
Development of a de novo multispecies assembly tool
PhD degree in Bioinformatics, Computational Biology or a related area
Deeper knowledge in statistics
Knowledge in handling with large data sets (up to 500 terrabyte)
Experience in programming in a script language (Python) and an object-oriented language and Linux on command line
Experience with Illumina sequencing data and MinIon data is desirable
High motivation and the ability to work both independently and in a team
Applications with reference file number 162/2018 are accepted until 19 th July, 2018.
All applications should include:
A one-page cover letter (in English) describing motivation, research interests & relevant experience
Two contact details of former PIs for recommendation
Kindly use our application portal under https://apply.idiv.de/#/login. Hard copy applications can be sent to German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Dr. Hanna Weise; Deutscher Platz 5e, 04103 Leipzig. For queries on the application process, please contact Dr. Hanna Weise (firstname.lastname@example.org); for research project questions, please contact Prof. Dr. Manja Marz (email@example.com).