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A PhD position is available in the Computational Biology group of the Technical University of Munich (Prof. Julien Gagneur) starting as soon as possible.

Your role
You will develop computational methods and analyse multi-omics datasets (genome, transcriptome, proteome, metabolome) to unravel the genetic and molecular basis of genetic disorders. Your research topics include: Detection of aberrant molecular events in multi-omics dataset, generalizing our software OUTRIDER for RNA-seq to multiple omics data modalities [1]; development of genetic variant and gene prioritization algorithms by integrating multi-omics data together with deep learning models of regulatory variants, leveraging the model repository of machine learning models for genomics Kipoi (https://kipoi.org, [2]); Integration of multi-omics with wearable sensor data in the context of a new research network with Stanford (Lars Steinmetz lab). You will work directly on patient data, in tight collaboration with two close collaborators: Dr. Holger Prokisch, who is coordinating the European consortium for mitochondrial disorder GENOMIT (example collaboration [3]), and Prof. Christoph Klein, head of the Children’s Hospital of the University of Munich (example collaboration [4]).

You are
Applicants must hold a master in bioinformatics, or in physics, statistics, or applied mathematics with a genuine interest in applications to genomics. We expect know-how in machine learning or statistical modeling and demonstrated programming experience with R or python.  (S)he should have excellent communications skills and be able to articulate clearly the scientific and technical needs, set clear goals and work within an interdisciplinary setting (biologists and geneticists).

We are
The Gagneur lab is a lively, international, and interdisciplinary computational biology group with a research focus on the genetic basis of gene regulation and its implication in diseases. Our group is located in the informatics department of the Technical University of Munich, one of the top ranked European universities. Our lab has strong links to other local scientists and institutions in biology and medicine. Munich offers an outstanding, dynamic, interactive and internationally oriented research environment. Munich, the 2018 “most livable city in the world” according to the urban magazine Monocle, and the proximity of the Alps provide an excellent quality of life.

Apply
The position is funded from core funding with a salary according to the TV-L (German academic salary scale). We encourage joining the graduate school QBM (Quantitative Bioscience Munich). 

Applications including a cover letter, CV, and references must be sent to Julien Gagneur (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, cc: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) until Nov 30th 2018 referring to “PhD-rare18” in the title.

More
https://www.gagneurlab.in.tum.de
https://kipoi.org
https://qbm.genzentrum.lmu.de
1. Brechtmann et al., OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data, AJHG, in press and bioRxiv
2. Avsec et al., Kipoi: accelerating the community exchange and reuse of predictive models for genomics, bioRxiv, 2018
3. Kremer et al., Genetic diagnosis of Mendelian disorders via RNA sequencing. Nature communs, 2017
4. Witzel et al., Chromatin remodelling factor SMARCD2 regulates transcriptional networks controlling early and late differentiation of neutrophil granulocytes, Nature Genetics, 2017