PhD Candidate Digital Strategies for (2D-)LC-MS Data

University of Amsterdam
June 30, 2023
Offerd Salary:€ 2,541
Working address:N/A
Contract Type:Other
Working Time:Full time
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PhD Candidate Digital Strategies for (2D-)LC-MS Data

Faculty/Services: Faculty of Science

Educational level: Master

Function type: PhD position

Closing date: 30.06.2023

Vacancy number: 11644

Oligonucleotide-based (ON) drugs offer great promise as revolutionary therapies for hitherto untreatable diseases. However, by their synthetic nature and inherent instability, ON therapeutics are chemically complex. Nevertheless, to understand their function and activity, and guarantee quality and safety, full characterization of ON drugs is mandatory. In the Innovative Analytics for Therapeutic Oligonucleotide Research (InnovATOR) project, a consortium of academic and industrial researchers collaborates to develop the required analytical strategies for ON therapeutics.

In this PhD-project, you will build algorithms and models to quantify the coverage of chemical space associated with the method and use that information for the method development. This incorporates the use of analysis of (2D-)LC-HRMS data and the application of machine learning to connect the chemical structure of analytes to the concept of chemical space. The developed algorithms will be used to enhance the separation and detection technology that is developed by the other two InnovATOR PhD-projects and will allow unique insights in molecular structures of chemical forms of ON therapeutics will be obtained.

This PhD position is embedded in the labs of the Analytical Chemistry Group at University of Amsterdam (UvA) both the Division of BioAnalytical Chemistry at VU, where you will be supervised by dr. Bob Pirok and dr. Saer Samanipour. You will work closely with the project partners at UvA and VU, and at the companies AstraZeneca, Novartis, GSK, MS Vision and Tosoh. Together with the team, you will present the obtained research results at national and international scientific conferences, and in relevant journals.

What are you going to do?

You are expected to:

  • Participate in the fundamental and applied research of our analytical- chemistry group.
  • Take ownership of your research project and independently tackle scientific challenges.
  • Collaborate intensively with a large user group of public and private organisations.
  • Publish and present your work within the project and on (inter-)national scientific platforms.
  • Contribute to the teaching activities of the department.
  • What do we require?

  • A recent MSc degree in a field relevant to the project.
  • Programming skills with at least one higher programming language (e.g. MATLAB, R, Python, Julia, etc.).
  • Demonstrated affinity with data analysis.
  • Ability to function in an international research team.
  • Motivation to take ownership and independently tackle solutions to scientific challenges.
  • Willingness to collaborate with PhD candidates and postdoctoral researchers in related research projects and with other research groups within and outside the Netherlands.
  • Good communication skills in oral and written English.
  • Our offer

    A temporary contract for 38 hours per week, preferably starting on September 1, 2023 for the duration of four years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended to a total duration of four years). This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and Masters students.

    Based on a full-time contract (38 hours per week) the gross monthly salary will range from € 2,541.- in the first year to € 3,247.- (scale P) in the last year. This is exclusive 8% holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling', may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable.

    Besides the salary and a vibrant and challenging environment at Science Park we offer you multiple fringe benefits:

  • 232 holiday hours per year (based on fulltime) and extra holidays between Christmas and 1 January;
  • multiple courses to follow from our Teaching and Learning Centre;
  • a complete educational program for PhD students;
  • multiple courses on topics such as leadership for academic staff;
  • multiple courses on topics such as time management, handling stress and an online learning platform with 100+ different courses;
  • 7 weeks birth leave (partner leave) with 100% salary;
  • partly paid parental leave;
  • the possibility to set up a workplace at home;
  • a pension at ABP for which UvA pays two third part of the contribution;
  • the possibility to follow courses to learn Dutch;
  • help with housing for a studio or small apartment when you're moving from abroad.
  • Are you curious to read more about our extensive package of secondary employment benefits, take a look here.

    The UvA offers excellent possibilities for further professional development and education.

    Any questions?

    Do you have questions about this vacancy? Or do you want to know more about our organisation? Please contact:

  • Bob Pirok, Assistant Professor, tel. + 31 (0)20 525 6531, email [email protected] or
  • Saer Samanipour, Assistant Professor, email [email protected].
  • About us

    The University of Amsterdam is the Netherlands' largest university, offering the widest range of academic programmes. At the UvA, 30,000 students, 6,000 staff members and 3,000 PhD candidates study and work in a diverse range of fields, connected by a culture of curiosity.

    The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.

    The Van't Hoff Institute for Molecular Sciences (HIMS) is one of eight institutes of the University of Amsterdam (UvA) Faculty of Science. HIMS performs internationally recognized chemistry and molecular research, curiosity driven as well as application driven. This is done in close cooperation with the chemical, flavour & food, medical and high-tech industries. Research is organised into four themes: Synthesis & Catalysis, Analytical Chemistry, Computational Chemistry and Molecular Photonics.

    The Analytical-chemistry group collaborates intensively with colleagues at the Vrije Universiteit Amsterdam. Candidates for the present positions may be appointed at either university, but may work at both locations with the objective of obtaining a joint PhD degree between the two universities.

    Job application

    Do you recognize yourself in the job profile? Then we look forward to receiving your application by 30 June 2023. You can apply online by using the link below.

    Applications should include:

  • a detailed curriculum vitae;
  • a motivation letter (max 1 page) that explains why you choose to apply for this position, including a statement of your research experience and interest;
  • a list of scientific publications
  • the name and email address of at least two references, who will be asked for their recommendation letters when you are shortlisted.
  • Applications without the motivation letter will not be taken into consideration.

    The UvA is an equal-opportunity employer. We prioritize diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.

    No agencies please.


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