Qualification:

• Doctoral degree (level 10 NFQ) (completed or at final stages of completion i.e. viva complete) in cellular and molecular biology or a related discipline (e.g. biochemistry, neuroscience, biomedical science, bioinformatics etc.);
• The Post Doctoral Researcher will also be an accomplished bioinformatics data scientist with experience in omics approaches to cell biology, cell culture, flow cytometry, histology, cell signalling, confocal microscopy and solid tissue preparation
• The successful applicant should have a good understanding of cancer cell signalling networks and protein-protein interactions

Candidates must be available to start on the 1st of July 2019.

The successful applicant will be part of a large multidisciplinary research team of biomedical engineers, bioscientists, clinicians and industrial partners (BD Biosciences and BD Research Centre Ireland) who are focused on the architectural characterisation of tissue. The successful applicant will have specific responsibilities and will be a senior member of a core team that is funded by Enterprise Ireland. The overall objective of this research project is focused on understanding how local tissue microenvironments can contribute to cell behaviour within colonic tumours. The specific aims of this research role are to contribute to the development a tissue-preparation technology-platform, suitable for multiparameter analysis, which can retain architectural information of tissue at near cellular level. This tissue preparation platform will be integrated for downstream multiparameter analysis using BD Biosciences single cell analysis equipment.

Key objectives of this research position

• Contribute to the development a solid tissue preparation protocol, compatible with a tissue dissection platform under development in the group that allows for the isolation of array-position-indexed single cells for downstream analysis by flow cytometry and single cell transcriptomics sequencing
• Develop a single cell sequencing bioinformatics analysis pipeline on the data generated with BD Biosciences single cell sequencing equipment
• Establish a 2D, spatially resolved single cell sequencing expression profiles of targeted markers for (a) Porcine-colonic (b) Human-patient-derived colonic tumours
• Establish a 2D, spatially resolved targeted H&E and/or immunofluorescent labelled images of serially adjacent sections of the-tissue through porcine colonic tissue and human colonic tumours
• Bioinformatically integrate, in a spatially resolved 3D-volumetric reconstruction of the original tissue-tumour, data generated through single-cell sequencing, histology image profiles, biomechanical nanoindentation and single cell immuno-labelling

Description:

Research

• Contribute to the research programme of the department under general guidance of a member of the academic staff or PI/project leader
• Define research objectives and proposals for own (or joint) research in line with research strategy
• Conduct individual and/or collaborative research projects in a variety of settings
• Determine appropriate methodologies for research, with advice and support as appropriate
• Assess research findings for the need/scope for further investigations/commercial exploitation
• Translate knowledge of advances in the subject area into research activity

Research Management

• Plan, co-ordinate and implement research project (this may include managing a small research team/co-ordinating other researcher activity)
• Manage own personal and research resources (including where required, laboratories, and specialist equipment) appropriately
• Manage own research budget, if any, and keep records as directed and in line with funder/university policy as appropriate

Income Generation/Funding

• May identify sources of funding and pursue the process of securing funds
• May work with PI to contribute to proposals for developmental purposes

Research Outputs – Write Up and Dissemination

• Write up results from own research activity
• Contribute to the research project’s dissemination, in whatever form (report, papers, chapters, book)
• Present information on research progress and outcomes e.g. to bodies supervising research; conferences, steering groups; other team members, as agreed with the PI/project leader
• Where appropriate, work with PI to register patents to protect intellectual property

Supervision

• May act as co-supervisor or be a member of a supervision panel
• May participate in limited teaching hours for own development. The extent of this must not adversely impact the primary research role
• May act as mentor to students on undergraduate placement

Essential Criteria

The successful applicant will have:

• Doctoral degree (level 10 NFQ) (completed or at final stages of completion i.e. viva complete) in cellular and molecular biology or a related discipline (e.g. biochemistry, neuroscience, biomedical science, bioinformatics etc.)
• Experience with evidence by way of publication in the at least one of the following areas:
  • ‘Omics’ approaches to cell biology
  • Handling DNA, RNA and protein
  • Cell signalling networks
  • Processing tissue
  • Molecular biology
• Evidence by way of publication, certification or conference presentation to show strong computer skills and data science background with working knowledge of Python, Matlab, R or equivalent programming languages commonly used for bioinformatics analysis and data science
• Strong publication track record with at least 1 senior authored publication in a top quartile journal
• Excellent interpersonal and communication skills
• The Post Doctoral Researcher will also be an accomplished bioinformatics data scientist with experience in omics approaches to cell biology, cell culture, flow cytometry, histology, cell signalling, confocal microscopy and solid tissue preparation
• The successful applicant should have a good understanding of cancer cell signalling networks and protein-protein interactions

Desirable Criteria

• Minimum three years’ experience in cell biology
• Experience of experimental design and characterisation with evidence of large dataset generation and analysis
• Working knowledge of (Python, Matlab, R or equivalent programming languages commonly used for bioinformatics analysis and data science)
• Working knowledge of cell culture, transfections, mutational analysis, use of siRNA/shRNA technology, flow cytometry, single cell sequencing etc.)
• Familiarity with bioinformatically analysing single cell sequencing data
• Bioinformatics experience in analysing and integrating large datasets arising from multiple analytical techniques;
• Proven ability to plan and organise experiments and projects
• Effective problem solving and decision-making skills
• Excellent teamwork skills and strong presentation skills
• Adaptability, flexibility and creativity
• Good leadership skills and the ability to think strategically in line with the requirements of the role

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