Genomic predictors and oncogenic drivers in hepatocellular carcinoma

Job summary

1. A postdoctoral position is available in Professor Llovet’s laboratory. The position involves working wit a team of scientists studying the molecular pathogenesis of hepatocellular carcinoma (HCC). The programme is a continuation of work recently published in different journals including: New England Journal of Medicine (Hoshida et al. 2008), Nature Biotech (Keng et al. 2009), Cancer Research (Chiang et al. 2008; Hoshida et al. 2009), Gastroenterology (Villanueva et al. 2008), Journal of Hepatology (Newell P et al. 2009, Tovar et al. 2010), which has provided a molecular classification of HCC based on integrative genomic analysis of a large cohort of human samples with prognostic implication. Briefly, Prof Llovet leads an international consortium co-participated by H. Clinic – IDIBAPS (Barcelona), Mt Sinai (New York), Istituto Nazionale dei Tumori (Milan) and Broad Institute – Harvard/MIT (Boston) focused on the study of HCC genomics. This consortium has conducted several translational research initiatives focused on the study of the molecular pathogensis of this cancer, including molecular classification, description of novel oncogenes, activation of signaling pathways and evaluation of novel therapeutic molecular targets in experimental models of HCC.

The purpose of this programme of work will be to develop a prognostic model based on integrative genomic analysis of HCC samples in conjunction with clinical data. In addition, due to the comprehensive database that will be generated, we envision to identify novel oncogenic drivers that will be subsequently validated in experimental models of HCC.

2. The project is likely to involve some or all of the following techniques:

• Generation of data from DNA sequencing (Solexa), mRNA expression (Affymetrix and Illumina), DNA copy number changes (Affymetrix) and methylation changes (Illumina).
• Bioinformatic analysis of high-throughput data: gene expression profiling, methylation data, next-generation sequencing
• Generation of prognostic models, molecular classification and gene signatures with impact in patient decision-making and management.

Main Duties

To conduct research focused on sophisticated analysis of genomic data (including gene expression, epigenetics and sequencing) from human samples generated in high-throughput platforms.

Duties and Responsabilities

• To contribute to the design and planning of experiments in relation to this project
• To develop a thorough understanding of the research field and be involved in the intellectual decision making process required for successful completion of the project
• To set up and run experiments in consultation with the Principal Investigator
• To record, analyse and write up the results of experiments and ensure that laboratory notebooks are kept fully up to date as a formal record of the research
• To prepare and present findings of research to the Principal Investigator and other members of the centre
• To prepare progress reports on research
• The post holder may be required to perform some limited teaching and/or supervision of other members of staff and/or students, under the guidance of the Principal Investigator
• Responsible for ensuring that designated equipment is safe and maintained in good working order
• As duties and responsibilities change, the job description will be reviewed and amended in consultation with the post holder
• The post holder will carry out any other duties that are within the scope, spirit and purpose of the job, as requested by the Principal Investigator

Person specification

Knowledge and Qualifications

Essential:

• Undergraduate degree in a life science discipline
• PhD in an appropriate life science discipline (preferably in the bioinformatic/biostatistics sphere)

Desirable:

• Interest in translational research and oncogenomics
• Basic knowledge of bioinformatics, biostatistics and computational biology.
• Publications in high impact factor peer reviewed journals

Skills

Essential:

• Ability to develop ideas logically and design experiments to test hypotheses
• Ability to modify and apply new methods to advance a project
• Ability to analyse and write up data for presentations and publications
• Ability to present complex information effectively to a range of audiences
• Effective written and verbal communication skills
• Ability to meet deadlines
• Record of delivering high quality research

Desirable:

• Research skills in sophisticated data mining and programming. Management of high-throughput data, pre-processing, background correction and normalization. Expertise in clustering, class discovery/prediction, regression, association rule learning, scientific modelling and systems biology.
• Ability to direct junior members of the laboratory in simple analytical procedures

Experience

Essential:

Experience of working in a research environment

Desirable:

Experience of multi-disciplinary working

Personal Qualities

Essential:

• Commitment to high quality research
• Ability to work effectively as part of the team
• Ability to work independently and to use own initiative when required

(Read eligibility criteria)