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Applications are solicited for a PhD program in Computational Biology in Milan, Italy:
Epigenome evolution in tumor models (Amati group, IIT & IEO)
Cancer originates from a complex combination of alterations at the level of the genome as well as of the epigenome. We are using next-generation DNA sequencing technology to create a multi-layered set of genome-wide profiles that will globally address genome and epigenome evolution during cancer progression. To this aim, we will analyze both cultured cells and tumors developing in vivo in genetically modified mice. The profiles to be determined include: quantitative mapping of the RNA transcriptome (RNAseq for coding, non-coding and small RNAs); protein-DNA interactions (ChIPseq); epigenome (histone modifications and DNA methylation using ChIPseq and RRBS, respectively); long-range DNA interactions and 3D-folding of the genome (ChIA-PET); mutational analysis (exome sequencing).
The Student will have the uncommon opportunity of gaining experience on the analysis of genomics data from a comprehensive set of high-throughput methodologies. Data are generated with the cutting edge technologies, such Illumina HiSEQ, and ad hoc computing resources are available on campus for the data analysis. The final challenge and opportunity is a better comprehension of the combinatorial nature of the analyzed marks and their contribution in driving the tumor development.
Any of these would be advantageous, but not compulsory:
- familiarity with the Linux environment
- some programming experience, especially in R
- previous experience in genomics
An extensive background in biology is not required for this position.
The Student will work in the Amati group under the direct supervision of Dr. Mattia Pelizzola, Team Leader in computational biology at the Center for Genomic Science of IIT@SEMM.
Applications due by 25 September 2011
Epigenome evolution in tumor models (Amati group, IIT & IEO)
Cancer originates from a complex combination of alterations at the level of the genome as well as of the epigenome. We are using next-generation DNA sequencing technology to create a multi-layered set of genome-wide profiles that will globally address genome and epigenome evolution during cancer progression. To this aim, we will analyze both cultured cells and tumors developing in vivo in genetically modified mice. The profiles to be determined include: quantitative mapping of the RNA transcriptome (RNAseq for coding, non-coding and small RNAs); protein-DNA interactions (ChIPseq); epigenome (histone modifications and DNA methylation using ChIPseq and RRBS, respectively); long-range DNA interactions and 3D-folding of the genome (ChIA-PET); mutational analysis (exome sequencing).
The Student will have the uncommon opportunity of gaining experience on the analysis of genomics data from a comprehensive set of high-throughput methodologies. Data are generated with the cutting edge technologies, such Illumina HiSEQ, and ad hoc computing resources are available on campus for the data analysis. The final challenge and opportunity is a better comprehension of the combinatorial nature of the analyzed marks and their contribution in driving the tumor development.
Any of these would be advantageous, but not compulsory:
- familiarity with the Linux environment
- some programming experience, especially in R
- previous experience in genomics
An extensive background in biology is not required for this position.
The Student will work in the Amati group under the direct supervision of Dr. Mattia Pelizzola, Team Leader in computational biology at the Center for Genomic Science of IIT@SEMM.
Applications due by 25 September 2011
