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]]

Bioinformatic/biostatistic PhD student position available in the Applied Bioinformatics Group, Division of Molecular Pathophysiology, Biocenter, Medical University Innsbruck, Austria. 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, next generation sequencing). A "stay abroad" for 6 months during the period of the 3 year PhD position is possible/recommended. Options are: Fred Hutchinson Cancer Research Center in Seattle, WA, USA, or the group of Wolfgang Huber at the EMBL in Heidelberg, Germany. Key words: Transcriptional response; bioinformatic/biostatistic data analysis; R/Bioconductor programming; leukemia research; microarrays; next generation sequencing. Conact/further informations: http://bioinfo.i-med.ac.at johannes.rainer at 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 at i-med.ac.at ? ? ? ? ? ? johannes.rainer at tcri.at URL:?? http://bioinfo.i-med.ac.at