Royal College of Surgeons in Ireland Coláiste Ríoga na Máinleá in Éirinn

FUNDED PhD: Dr Darran O’Connor and Prof. Jochen Prehn - Cancer Systems Biology/Bioinformatics

The aim of this project is to develop a novel decision support tool for Her2+ breast cancer.

Project description

The development of trastuzumab transformed the outlook for breast cancer patients with Her2+ disease. Since then, a wide variety of Her2-targeted agents have become available, from additional monoclonal antibodies (e.g. pertuzumab), to small molecule inhibitors (e.g. lapatinib).

The current standard of care for patients with Her2+ disease is dictated by the results of recent clinical trials, patient disease state, co-morbidities and previous treatment history. Internationally, the gold standard involves coadministration of trastuzumab and pertuzumab together with cytotoxic chemotherapy. However, equally robust responses can be achieved in some patients with trastuzumab alone, or indeed the combination of trastuzumab with a small molecule inhibitor. Which class of Her2-tageted agent is most suitable for which Her2+ patient is currently unknown.

The clinical use of decision support systems is predicated on the availability of choice. Given the proliferation of Her2-targeted agents available to clinicians, there is a pressing need to develop tools to allow tailoring of Her2-targeted therapy in a personalised manner.

We are currently seeking a talented PhD candidate to develop a novel decision support tool for Her2+ breast cancer. Funded by Science Foundation Ireland, you will develop mathematical models of Her2+ breast cancer and response to different Her2-targeted treatment regimes, integrating next-generation sequencing data (exome-Seq, RNA-Seq, methyl-Seq) with digital pathology data and clinico-pathological data.

Our research groups at the Department of Molecular & Cellular Therapeutics and at the Department of Physiology & Medical Physics/RCSI Centre for Systems Medicine provide cross-disciplinary support for both bioinformatic analysis and systems modelling.

  • Department: Molecular & Cellular Therapeutics/Centre for Systems Medicine
  • Tenure: Four years
  • Salary: €18,000 per year (plus fees)

Specific duties include:
  • Multiscale mathematical modelling of ‘omic’ and clinico-pathological data
  • To publish research findings To attend conferences and disseminate research


The successful candidate should be able to demonstrate the following: 


  • BSc (grade 2.1 or above) in mathematics, applied mathematics, statistics or related subject with substantial quantitative component, e.g. physics, engineering, computer science
  • Excellent computational skills including experience of using statistical software packages, e.g. R, STATA or SAS
  • Extensive experience working in a Unix environment
  • Interest in applying mathematics to problems in health-related fields
  • Scientifically competent
  • Effective communication style – excellent English (for candidates who do not speak English as their first language: an IELTS (academic) score of 6.5 or above)
  • Strong organisational and administrative skills
  • Ability to make decisions and meet deadlines
  • Ability to work on one’s own initiative as well as in a multidisciplinary, team environment


  • MSc in systems biology or bioinformatics (or other relevant discipline)
  • Experience of programming in R, STATA, SAS, Python or C/C++
  • Experience with molecular networks in biology and their modelling

Please note: this job description may be subject to change to reflect the evolving requirements of the Department and RCSI in developing healthcare leaders who make a difference worldwide. 

Application process

Please apply here with the following:

  • An up-to-date CV
  • A completed application form (available from the application portal
  • A 500-word cover letter outlining your interest in and suitability for the position
  • Scanned transcripts (preferred), or detailed degree grade breakdown
  • Contact details of two referees

Applications will be accepted on a rolling basis until the position is filled. 

Mentors Dr Darran O’Connor and Prof. Jochen Prehn