English speaking vacancies in Holland: VACANCY: Postdocs PhDs: Computational Analysis of NGS data

Tuesday, 3 July 2012

VACANCY: Postdocs PhDs: Computational Analysis of NGS data

06-21-2012

Vacancy number 21

PROJECT OUTLINE

Genomic alterations are major determinant of responses to (targeted) therapies in cancer. In fact, the best positive and negative predictors of responses to targeted therapies are alterations in kinases or their direct downstream effectors. To gain insight into resistance mechanisms to therapy and thus better tailor treatment, we are approaching this problem from two different angles. First we have transplanted tumors from mouse models of breast cancer and treated these tumors with a range of (targeted) therapies. Matched pre- and post treatment pairs of resistant and sensitive tumors have been full exon sequenced and are available for analysis. The goal is to detect genomic alterations associated with response to therapy. Second, we have acquired large panels of human tumors, on which we are currently performing kinase exon sequencing. More specifically, we are performing sequencing on 1) 400 samples from the NEO-ALTTO study to find alterations associated with resistance to HER2 targeted therapies; 2) at least 200 colorectal samples and 300 breast cancers (triple negatives and invasive lobular carcinomas) to detect alterations frequently occurring in these patient populations. A very strong feature of all these datasets is that matched controls are available to ensure high accuracy in variant calling. The successful candidates will work closely with the biological groups to develop computational approaches for the detection of mutations and copy number alterations associated with specific cancer subtypes as well as therapy response in human and mouse model-derived tumors.

CANDIDATE REQUIREMENTS – EDUCATION AND EXPERIENCE

We are seeking highly motivated Postdoc and PhD candidates with a degree in bioinformatics or a mathematical discipline with a strong cancer biological interest. Applicants should either have strong modeling/applied statistics skills or strong documented experience in analyzing high-throughput sequencing data. In addition, we strongly value experience in one or more of the following: sequence analysis, machine learning, applied statistics and R, computer science and expression analysis. The candidate also needs to be proficient in a programming language such as Java, Perl or Python, and be comfortable with Linux systems. Fluency in spoken and written English is a strong requirement.

LOCATION

The project will employ the complementary expertise and tools of three groups participating in the Cancer Systems Biology Center (csbc.nki.nl) at the Netherlands Cancer Institute, Amsterdam: Rene Bernards (Molecular Carcinogenesis), Jos Jonkers (Mouse Models for Breast Cancer) and Lodewyk Wessels (Computational Biology). The positions are primarily embedded within the Bioinformatics and Statistics Group (Wessels) (bioinformatics.nki.nl) at the Netherlands Cancer Institute, Amsterdam.

EMPLOYMENT CONDITIONS

The successful candidate will be employed by the Netherlands Cancer Institute. Postdocs will be appointed for a period of 3 years. The gross salary per month will be from € 3.200,- to € 4.095,- according to the FWG-function group 55 or 60, depending on proven qualities and previous experience. PhDs will be employed by the Netherlands Cancer Institute for a period of 4 years. The gross salary per month will be from € 2407,- to € 2964,- according to the PhD scales, depending on proven qualities and previous experience. The terms of employment will be in accordance with the CAO Ziekenhuizen (Collective Labour Agreement for Hospitals).

WANT MORE INFORMATION?

Please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels@nki.nl. Also see bioinformatics.nki.nl and csbc.nki.nl for further information.

INTERESTED?

Your application letter (including your resume, a list of publications and the names and addresses of at least two persons that can be approached for references) can be attached before January 15, 2012 to the application form on our website (see link below). After dispatch of the form you will receive a reaction as soon as possible.

http://www.nki.nl/Research/Career/Vacancies/Default/Postdoc_PhDs_Computational_Analysis_of_NGS_data_2011_157.htm

Looks like they made a mistake in the letter. Expiration date cant be right

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Introduction of the ‘European Blue Card’

As from 19 June 2011 the Netherlands has a new purpose of stay: the European Blue Card. The European Blue Card is a separate purpose of stay in addition to the existing National Highly Skilled Migrant Programme. The EU Blue Card Council Directive is intended for highly skilled foreign nationals who do not have EU, EEA or Swiss nationality, and who wish to work in one of the member states of the EU. The Directive is also meant to make it easier to settle in another EU member state. A residence permit will always be required in that other member state, however. To obtain this residence permit the employee must comply with the conditions applicable in that member state.

The conditions for residence in the Netherlands as an EU Blue Card holder are stricter than those for residence as a Highly Skilled Migrant. The employee must have a contract for highly qualified employment for at least one year, earning at least EUR 60,000 gross (in 2011). The employee must have completed a course of higher education lasting at least three years. The employee must prove this by having his diploma assessed by Nuffic. For a regulated profession, a competent authority will take decisions about the admission to that profession.

Advantages
One of the advantages of the EU Blue Card is that it is easier for an EU Blue Card holder and his family members to settle in another EU member state at a later date. After eighteen months foreign nationals who have an EU Blue Card are exempted from the provisional residence permit (MVV) requirement, if they want to work in another EU member State. In this second member state the employee must submit an application for a residence permit as a holder of an EU Blue Card. Each member state may implement the directive in slightly different ways. If someone holds a Blue Card in the Netherlands, this does not mean that the requirements are also met in other member states.

Another advantage is that after having stayed lawfully with the EU Blue Card holder in the Netherlands for two years, the family members may apply for a residence permit for ‘continued residence’. For other purposes of stay this is only possible after having stayed lawfully in the Netherlands for three years. The family members must have resided legally and continuously within the territory of an EU member state for at least five years, however. An employee who has stayed legally in the Netherlands as an EU Blue Card holder for two years may apply for the status of ‘long-term resident as a non-EU member country national’. He must have resided legally and continuously within EU territory for five years and must comply with the other conditions for this purpose of stay.

Highly skilled migrants from outside of the EU

A highly skilled migrant is a migrant who comes to the Netherlands to be employed, and has a gross annual income of at least €47,565, or €34,881 if he/she is under thirty. This income requirement does not apply if the employee enters service for certain functions in an educational or research institution. For information on the specific functions to which this clause applies, you can inquire at the IND office for labour and highly skilled migrants. When a foreign national has been granted residence in the Netherlands as a highly skilled migrant, the employer of the highly skilled migrant is not required to be in possession of a work permit for that foreign national.

Professional soccer players, ministers of religion, teachers of religion and prostitutes are not eligible for a residency as highly skilled migrant.

Important!
The amounts stated above will be indexed every year as of 1 January.