PhD on comparative metagenomics (UPM-INIA, Pozuelo de Alarcón)

PhD on comparative metagenomics (UPM-INIA, Pozuelo de Alarcón)

Job Offer: PhD project in Comparative Metagenomics
3 years, funded by the INPhiNIT international program

Computational Evolutionary Genomics group at the CBGP research centre (Madrid, Spain)

About the Institute
The Centre for Plant Genomics and Biotechnology (CBGP) is a joint (UPM-INIA) research institute
of excellence located at the Montegancedo International Campus in Pozuelo de Alarcón, Madrid.
Research activities at the CBGP are focused on plant biology and associated microorganisms.
CBGP has relevant educational and training roles for Bachelor, Master and PhD students, and
technicians, and has contributed to impulse the scientific carrier and leadership of young scientists.

The center has a main building of 7,200 m2 with state of the art laboratories and scientific
infrastructures, including metabolomics facilities, a high performance computational cluster, cell
biology platforms and a P3-level containment lab.
Project Description
We are looking for a motivated student to carry out a PhD on comparative metagenomics. The
project will be fully computational and builds upon the recent developments on functional prediction
and characterization of the unknown fraction of metagenomics data.

Although current approaches in comparative microbiome analysis have shown glimpses of
differential patterns associated to disease states and ecosystem adaptation, it is largely
acknowledged that the fraction of unknown data observed might carry crucial functional and
taxonomic information that is by default neglected.

The main goal of this project is to implement the use of such vast collection of novel data, also
known as metagenomics dark matter, into a comparative framework that enhances our ability to
find differential signatures between hosts and ecosystems. The framework will be ideally tested on
several novel metagenomic datasets from different sources, such as soil, ocean and plant
microbiomes. Novel sequences will be also used to further explore microbial biodiversity in both the
prokaryotic and eukaryotic kingdoms.

Results are expected to contribute to the global understanding of microbial communities, as well as
in developing strategies for pathogen diagnosis and bioengineering. Access to data is granted
through ongoing collaborations with research groups at ETHZ (Sunagawa lab) and EMBL (Bork
group). Additional soil metagenomics sequencing is planned in collaboration with other
experimental groups at CBGP.

– Fulfill the INPhiNIT program mobility requirements
– Degree in Biology, Biotechnology or similar disciplines
– Training in bioinformatics and data analysis (i.e. Python scripting, R analysis, Linux terminal)
– Fluent in English
Recommended additional skills:
– Knowledge in Evolutionary Biology, Microbiology or related topics
– Previous experience handling genomic or metagenomic datasets
– Experience or training working with HPC systems and big data
Contract details: 3 years with a competitive salary package via INPhiNIT program
Deadline for applications: Feb 1st, 2018
Estimated starting date: ~Sept 2018
Application process:
1. Send CV, motivation letter and, if possible, contact details of two referees to
huerta@embl.de before the official deadline
2. Submit application via the INPhiNIT website

Group info: http://compgenomics.org