PhD candidate in Bioinformatics/Biosystems data analysis

Faculty of Science – Swammerdam Institute for Life Sciences

The Swammerdam Institute for Life Sciences (SILS) of the University of Amsterdam is one of the loargest institutes of the Faculty of Science. Its approximately 250 scientists and staff members work in 15 research groups that perform excellent research centered on three themes:

1. Cell & Sytems Biology;
2.  Neurosciences, and
3. Molecular Life Sciences.

3 PhD candidate positions in Cell, Computational/Systems Biology and Bioinformatics are available in the research groups of Dr Pernette Verschure (Project Coordinator), Prof. Hans Westerhoff and Prof. Antoine van Kampen at UvA, Faculty of Science, SILS.

The PhD projects are embedded in a prestigious Marie Skłodowska Curie Innovative Training Network entitled 'Epigenetic regulation of endocrine therapy resistance in breast cancer: A systems medicine approach to predict treatment outcome' Acronym: EpiPredict. The research and training network consists of 15 European organisations - academic institutes and companies - from 8 different countries. The EpiPredict training network offers a unique, timely, and multidisciplinary training and research program for 12 outstanding young researchers. The multidisciplinary group of PhD candidates will master and apply urgently needed new approaches to address complex diseases taking personalized patient aspects and systems medicine into consideration being equipped to succeed in their careers. Strong involvement of the private sector ensures exploitation of EpiPredict achievements and exposure to an entrepreneurial mind-set.

Project description

The early-stage researchers (ESRs) will focus on a narrowly defined case, epigenetic regulation of Tamoxifen-induced resistance in Estrogen Receptor positive (ER+) breast cancer, considering five interacting resistance pathways. The EpiPredict intersectorial training programme employs a systems medicine approach combining next-generation systematic epigenetic, gene/protein/metabolite profiling with innovative gene-specific epigenetic interference technologies and computational approaches. Together the ESRs will identify key epigenetic changes underlying Tamoxifen induced resistance providing an important step towards diagnostic markers/tools to predict treatment outcome and response monitoring.

EpiPredict PhD candidate position 2, Marie Skłodowska Curie PhD Fellowship in Bioinformatics/Biosystems data analysis, in the research group of Prof. Antoine van Kampen. 

Project title: 'Development of knowledge base and integrative bioinformatics analysis of epigenetic regulation in endocrine resistance' 

Supervisors: PI: Prof. Antoine van Kampen, Prof. Age Smilde, Dr Perry Moerland (Swammerdam Institute for Life Sciences / Academic Medical Center, University of Amsterdam, the Netherlands), Dr Pernette Verschure (SILS, UvA); EpiPredict co-PI: Dr Alex Michie (ClinicaGeno, UK)

PhD programme: Swammerdam Institute for Life Sciences (SILS), UvA, Netherlands Bioinformatics and Systems Biology Research School.

Brief overview of this project’s objectives and expected results
Objectives

• To build a Tamoxifen-Resistance knowledge base (TRkb) from literature/expert knowledge as input for downstream computational approaches;
• to develop bioinformatics tools that use prior knowledge from TRkb in bioinformatics analysis to refine/elucidate Tamoxifen resistance pathways;
• to determine disease signatures (multivariate biomarkers) to subclassify patient's resistance outcome;
• to analyse and/or reconstruct resistance pathways.

Expected Results

• Tamoxifen-Resistance knowledge base (TRkb);

• bioinformatics methods that incorporate prior knowledge from TRkb in bioinformatics analyses;
• bioinformatics methods for pathway reconstruction/analysis;
• predictive disease signatures (multivariate biomarkers).

Requirements

• MSc degree in Bioinformatics, Computational Biology, Informatics, Statistics, or another relevant discipline;
• strong experience with bioinformatics methods, the R statistical package, programming, databases, Unix;
• background/expertise in omics data analysis, statistics, informatics;
• strong knowledge and interest in molecular/cell biology;
• the ability to work in a multidisciplinary team and independently;
• highly motivated to pursue a career in science;
• excellent mastery of the English language;
• enthusiasm to attend the full EpiPredict training program as offered in the project and to actively contribute to the project aims and objectives;
• enthusiasm to contribute to the dissemination of results and outreach to both specialists and the public at large;
• enthusiasm to visit one or multiple other EpiPredict organisations for a number of months for secondments (internships);
• enthusiasm to be trained by supervisors from different institutes, disciplines and sectors.

In accordance with the Marie Skłodowska Curie ITN eligibility criteria:

• candidates did not reside or carry out their main activity (work, studies, etc.) in the Netherlands for more than 12 months during the 3 years immediately prior to the appointment date;
• candidates are in the first four years (full-time equivalent research experience) of their research careers and have not been awarded a doctoral degree, and
• candidates hold an MSc degree in Bioinformatics, Computational Biology, Informatics, Statistics, or another elevant discipline.

Further information

More information can be obtained from:

• Prof. Antoine van Kampen
  T: +31 (0)20 5667096
• EpiPredict

Appointment

Based on a full-time appointment, the duration of the appointment as a Marie Curie ITN fellow will be for a maximum period of 3 years and will, in line with the duration of a PhD study in the Netherlands, be extended another year according to the employment rules of the University of Amsterdam. The appointment will be 18 months plus a further 30 months after a positive evaluation and should lead to a dissertation (PhD thesis). A personal Career Development Plan will be drafted that includes the attendance of EpiPredict courses and (international) meetings. The PhD candidate will become member of the Netherlands BioSB graduate School, to present her/his work annually, attend the BioSB conferences and follow the BioSB training program.

The gross monthly salary will be according to the salary scales for PhD candidates in the host country. It includes the Marie Curie Living Allowance and Mobility Allowance. The Collective Labour Agreement for Dutch Universities is applicable. Besides the salary, the PhD candidate will obtain a mobility allowance for the duration of the 3 years of the Marie Curie ITN project. For the one-year extension of the appointment after the Marie Curie project, the gross monthly salary will be according to the salary scales of the University of Amsterdam. Positions are aimed at being full-time, but by exception, if needed for family reasons, part-time appointments are possible.

Selection

After the application deadline the relevant EpiPredict Principal Investigators (PIs) will file a shortlist with eligible candidates to the project coordinator based on the initial written applications.

Selected candidates will be invited for a first round of interviews with the PI and co-PI through teleconference. In a second round the selected candidates are asked to present their previous (master) research, the personal interviews will be held at the premises of the host institution with the PI and additional video conference can take place with the co-PI and other members of the EpiPredict supervisory board. The recruitment criteria are listed under the general and research project specific requirements. Each applicant’s overall researcher’s potential is judged together with their creativity and level of independence. Travel expenses for the candidate will be covered by the host institution.

Job application

Applications can be sent to application-science@uva.nl, bearing vacancy number 15-123 and the position you are applying for in the subject line. Please combine all documents in one single attachment.

Outstanding and highly motivated candidates are asked to provide the required information:

• CV (EU format; ), specifying: 

   - doctoral study entrance qualification;

   - TOEFL scores;

   - list of internships (subject, name supervisor, grade, etc);

   - publications (if applicable);

   - scientific interest, complementary qualifications, achievements;
   - other relevant informatio.

• Grades (with explanation on the grading system);
• Two letters of recommendation and contact information of two referees.

No agencies please