2 postdoc positions

Organization
European Institute of Oncology
Job Location
Via Adamello 16
20139 Milan MI
Italy
Salary
to be negotiated
Job Description

Two postdoctoral positions (bioinformatics) available in the group of Prof PG Pelicci at the Department of Experimental Oncology, IEO, MilanPosition 1: molecular mechanisms of obesity-associated leukemia.

Obesity has emerged as a socially prominent risk factor for cancer-related death, but a clear understanding of the underlying molecular mechanisms is lacking.

We and others have demonstrated that a specific type of leukemia, Acute Promyelocytic Leukemia (APL), is heavily influenced by the systemic metabolic state (Breccia et al Blood 2012 and unpublished data). APL is well modeled in the mouse, and we have devised experimental setups that very well reproduce the effect of systemic metabolic alterations (high fat diet and caloric restriction) on the natural history of APL. We are now using this experimental setting to delve more deeply into the mechanism. Two main bioinformatics-intensive projects are ongoing:

-using whole genome sequencing of cellular genomes to measure single-cell mutational history. We wish to evaluate intra-individual mutational variability to understand if diet can modulate the rate of mutation acquisition

-using ChIP-seq, RNAseq and metabolomics on mouse APL samples to identify epigenetic changes associated with metabolic adaptation to diet modification, a process that we have seen is highly susceptible to pharmacological targeting.

The candidate is expected to implement comprehensive bioinformatics analysis and to also integrate with other ongoing research projects in the group.

The candidate shall operate within the IFOM-IEO-IIT campus, within a large and expanding bioinformatics community. State-of-the-art facilities for sequencing are available (Illumina and ION Torrent instruments). The institute has also recently gained access to the Oxford Nanopore MinIon Access Program for single-molecule nanopore sequencing, providing a rare opportunity to develop methodologies for a platform that is not yet commercially available.

The ideal candidate for this position should have experience in the analysis of large genomic and epigenomic datasets. The applicant must have excellent analytical skills, a strong statistical background, ability to work independently and as part of a team, very good oral/written communication and interpersonal skills to efficiently interact with the experimental collaborators and write and/or contribute to production of research reports and publications for peer reviewed journals. In particular, the applicant should have:

Experience in software and algorithm development

Strong programming skills in at least one of the following languages: Python, Perl, Java, C++

Experience of statistical analysis softwares (R, Matlab)

Proficiency in Unix/Linux operating systems

PhD degrees in Computer Science, Engineering, Mathematics, Statistics or Physics are preferred.

 

 

Position 2: establishment of a clinical bioinformatics pipeline for precision medicine in oncology

The Institute has recently launched a Clinical Genomics program with the intention to establish itself as a reference center in Italy for Precision Medicine in Oncology. The aim is to routinely obtain high-throughput genomic characterization of individual cancer genomes, so as to match each patient with the best available treatment. The program benefits from close collaboration with all the institutional clinical programs and the Division of Early Clinical Trials (headed by Dr G Curigliano), which ensures rapid allocation of patients to clinical trials with experimental drugs in early development.

Several projects within the Clinical Genomics Program have been launched, including participation to nation-wide and Europe-wide Cancer Genomics molecular screening programs (Alleanza Contro il Cancro, AURORA and others) and a recently funded phase II clinical trial in which metastatic breast cancer patients will be systematically subjected to cancer sequencing by NGS methods and randomized to receive conventional or genomics-based treatment. The trial will be the first of this sort in Italy and one of the first in the world.

The candidate will be responsible for establishing the bioinformatics pipeline for the program. He/she will develop dedicated methods of analyzing, storing, annotating and encrypting data generated by next generation sequencing of patients' samples. The clinical setting and the sensitive nature of the data will require particular care in the development of the appropriate data protection methodologies.

He/She will be based both at the IFOM-IEO-IIT campus and at the IEO hospital campus, within a large and expanding bioinformatics community. State-of-the-art facilities for sequencing are available (the whole range of Illumina and ION Torrent instruments). The institute has also recently gained access to the Oxford Nanopore MinIon Access Program for single-molecule nanopore sequencing, providing a rare opportunity to develop methodologies for a platform that is not yet commercially available.

The ideal candidate for this position should have experience in the construction of complex informatics infrastructures. The applicant must have excellent analytical skills, a strong statistical background, ability to work independently and as part of a team, very good oral/written communication and interpersonal skills to efficiently interact with the experimental collaborators and write and/or contribute to production of research reports and publications for peer reviewed journals. In particular, the applicant should have:

Experience in software and algorithm development

Strong programming skills in at least one of the following languages: Python, Perl, Java, C++

Experience of statistical analysis softwares (R, Matlab)

Proficiency in Unix/Linux operating systems

PhD degrees in Computer Science, Engineering, Mathematics, Statistics or Physics are preferred.

 

 

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