Bioinformatic/biostatistic PhD student position

Area of research:
Our research group is primarily interested in the effects of the steroid
hormone glucocorticoid (GC) that is used in the treatment of lymphoid
malignancies, specifically childhood acute lymphoblastic leukemia (ALL).
Almost all effects of GCs are mediated by their cognate receptor
(GC-receptor), a ligand activated transcription factor. Thus we study the
effects of GCs in lymphoid cells at the transcriptional level, including
transcription factor DNA interactions, DNA methylation etc employing whole
genome approaches (microarrays, hight throughput sequencing).
A 6 month ”stay abroad” during the PhD thesis, at the Fred Hutchinson
Cancer Research Center in Seattle, WA, USA, or in the group of Wolfgang
Huber at the EMBL in Heidelberg, Germany, is possible/recommended for the
PhD student.

Key words:
Transcriptional response; bioinformatic/biostatistic data analysis;
R/Bioconductor programming; leukemia research; microarray; high throughput
sequencing.

Possible research topics:
• Analysis and modeling of the transcriptional response to GCs in samples
taken from children with ALL during in vivo GC-treatment; integration of
additional, patient specific parameters into the analysis.
• Identification of in vivo binding sites of the glucocorticoid receptor
(GR) transcription factor using ChIP-seq.
• Analysis of enriched sequences from ChIP-chip or ChIP-seq experiments to
identify transcription-co-factors/enhancers.
1
• Identification of alternative transcript isoforms and alternative splice
variants using Affymetrix Exon microarrays (potentially RNA-seq).
• Identification of premature termination codons and uORFs in tran- script
sequences.
• Development/adaption/implementation of methods for the preprocess- ing of
tiling array and Exon microarray data.

Qualification/requirements/methodology:
R/Bioconductor knowledge; Perl and/or Python programming knowledge;
experience in the analysis of biological data (microarray, high throughput
sequencing data) helpful.

Contact / further informations:
http://bioinfo.i-med.ac.at
johannes.rainer@i-med.ac.at


-- 
Johannes Rainer, PhD
Bioinformatics Group,
Division Molecular Pathophysiology,
Biocenter, Medical University Innsbruck,
Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria
and
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria

Tel.:     +43 512 570485 13
Email:  johannes.rainer@i-med.ac.at
            johannes.rainer@tcri.at
URL:   http://bioinfo.i-med.ac.at

	[[alternative HTML version deleted]]

