RCSI Funded PhD in Cancer Systems Biology/Bioinformatics

Royal College of Surgeons in Ireland
July 17 2017
Position Type
Full Time
Organization Type

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 personalized 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 (http://pi.rcsi.ie/pi/darranoconnor/) and at the Dept. of Physiology & Medical Physics/RCSI Centre for Systems Medicine (http://www.systemsmedicineireland.ie/home/investigators/jochen-prehn/) provide cross-disciplinary support for both bioinformatic analysis and systems modelling.


Examples of recent relevant publications by the RCSI teams and their collaborators:

  • Kelly D, Das S, Moran B, Han K, Mulligan N, Barrett C, Buckley PG, Mc Mahon P, Mc Caffrey J, Van Essen HF, Connor K, Ylstra B, Lambrechts D, Gallagher WM, O'Connor DP*, Kelly CM*. Post-mortem examination of an aggressive case of medullary thyroid carcinoma characterized by catastrophic genomic abnormalities. JCO - Precision Oncology 2017 (in press) *Shared Senior Authorship

  • Li B, Ni Chonghaile T, Fan Y, Madden S, Klinger R, O'Connor AE, O'Hurley G, Mallya G, Joseph J, Tarrant F, Conroy E, Gaber A, Chin SF, Bardwell HA, Provenzano E, Dubois T, Linn S, Jirstrom K, Caldas C, O'Connor DP* & Gallagher WM*. Therapeutic rationale to target highly expressed CDK7 conferring poor outcomes in triple-negative breast cancer. Cancer Res 2017 (in press) *Shared Senior Authorship

  • Salvucci M, Würstle ML, Morgan C, Curry S, Cremona M, Lindner AU, Bacon O, Resler AJ, Murphy ÁC, O'Byrne R, Flanagan L, Dasgupta S, Rice N, Pilati C, Zink E, Schöller LM, Toomey S, Lawler M, Johnston PG, Wilson R, Camilleri-Broët S, Salto-Tellez M, McNamara DA, Kay EW, Laurent-Puig P, Van Schaeybroeck S, Hennessy BT, Longley DB, Rehm M, Prehn JH. A Stepwise Integrated Approach to Personalized Risk Predictions in Stage III Colorectal Cancer. Clin Cancer Res. 2017 Mar 1;23(5):1200-1212. 

  • Lindner AU, Salvucci M, Morgan C, Monsefi N, Resler AJ, Cremona M, Curry S, Toomey S, O'Byrne R, Bacon O, Stühler M, Flanagan L, Wilson R, Johnston PG, Salto-Tellez M, Camilleri-Broët S, McNamara DA, Kay EW, Hennessy BT, Laurent-Puig P, Van Schaeybroeck S, Prehn JH. BCL-2 system analysis identifies high-risk colorectal cancer patients. Gut. 2016 Sep 23. pii: gutjnl-2016-312287.



Person Specification

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 

Application process

Please upload the following by Friday 18th August, 2017 at 5 p.m.

  • an up-to-date CV

  • Contact details of two academic referees (included in CV)

  • Cover letter (500 words) outlining your interest in and suitability for the position

  • Scanned transcripts (preferred), or detailed degree grade breakdown

Interviews: End August/ Early September 2017

RCSI is an equal opportunities employer


For informal enquiries please email: darranoconnor@rcsi.ie

This job comes from a partnership with Science Magazine and Euraxess

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