NL
EN

PhD Position in Structural Bioinformatics/Computational Biology

  • Nieuwe Universiteitsgebouw (NU)
  • Amsterdam
  • Faculty of Science
  • PhD
  • MSc
  • Closes on
    31-07-2024
Apply
ODORWISE - Unravelling Odorant Detection Mechanisms for Biosensors in Sustainable Healthcare. If you are interested to join this exciting research in olfactory science and bioinformatics, please apply to Vrije Universiteit Amsterdam.

Your function

Despite decades of dedicated collaborative efforts, we are still missing key elements to develop the perfect electronic nose. A major obstacle is our limited understanding of how the sense of smell works, and how odorant sensors should be designed for smell detection. The project ODORWISE joins advanced computer simulation techniques together with available results from experiments to study how the proteins in our noses can detect and distinguish different chemicals. The outcome will aid the design of new biomimetic sensor units for detecting smells, which will be a significant advancement for early disease diagnosis and surveillance in non-invasive sustainable healthcare. If you are interested to join this exciting research, apply to join us at the bioinformatics group of the Vrije Universiteit Amsterdam.  
 

Your duties

Your role will be to:

  • apply computational approaches ranging from quantum chemical models to molecular dynamics and enhanced sampling techniques
  • develop data analysis methods tailored to ODORWISE  
  • formulate testable hypotheses on how to exploit biological mechanisms for the rational design of protein targets 
  • validate the models through existing experiments and in collaboration with experimental partners
  • supervise M.Sc. research projects related to ODORWISE and related to activities in the bioinformatics group  

Your profile

We are seeking a highly motivated PhD candidate to join on a 4-year research adventure to unravel the molecular mechanism underlying the olfactory sense. To join us, you should have

  • a degree in a quantitative discipline such as bioinformatics, biotechnology, physical or computational chemistry, chemical engineering, computer science, molecular physics or a related field 
  • proficiency in bioinformatics programming languages (e.g., Python, C, C++)
  • proficiency in English (oral and written), as well as good cross-disciplinary collaborative and communication skills 
  • experience in statistical mechanics, statistics, molecular dynamics, enhanced sampling techniques (is desired) 
  • experience in machine learning and computer science (is a plus)
  • experience in molecular biology and/or drug design (is a plus)

As a university, we strive for equal opportunities for all, recognising that diversity takes many forms. We believe that diversity in all its complexity is invaluable for the quality of our teaching, research and service. We are always looking for talent with diverse backgrounds and experiences. This also means that we are committed to creating an inclusive community so that we can use diversity as an asset.

We realise that each individual brings a unique set of skills, expertise and mindset. Therefore we are happy to invite anyone who recognises themselves in the profile to apply, even if you do not meet all the requirements.

What do we offer?

A challenging position in a socially engaged organisation. At VU Amsterdam, you contribute to education, research and service for a better world. And that is valuable. So in return for your efforts, we offer you:

  • a salary of € 2.770,00 (PhD) and maximum € 3.539,00 (PhD) gross per month in the fourth year, for a full-time employment
  • an employment contract of initially 18 months. If there is sufficient perspective, this will be extended to a total of 4 years. Your dissertation at the end of the fourth year forms the end of your employment contract.

We also offer you attractive fringe benefits and arrangements. Some examples:

  • A full-time 38-hour working week comes with a holiday leave entitlement of 232 hours per year. If you choose to work 40 hours, you have 96 extra holiday leave hours on an annual basis. For part-timers, this is calculated pro rata.
  • 8% holiday allowance and 8.3% end-of-year bonus
  • contribution to commuting expenses
  • optional model for designing a personalized benefits package
  • solid pension scheme (ABP)

About us

Faculty of Science
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature.

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future.

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments.

Vrije Universiteit Amsterdam
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research. Learn more about our codes of conduct

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility.  Over 6,150 staff work at the VU and over 31,000 students attend academic education.

Diversity

Diversity is the driving force of the VU. The VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding.

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

We want to develop talent and creativity by bringing together people from different backgrounds and cultures. We recruit and select based on competencies and talents. We therefore encourage anyone who recognizes themselves in a vacancy, regardless of age, gender, origin, religion, philosophy of life, orientation, disability or chronic illness, to respond. Candidates with a jobs agreement indication (“doelgroepregistratie”) will be given priority if suitable. For these candidates applies:
- A PhD candidate with a registration (“doelgroepregister”) may apply for a minimum of 0.7 fte
- An extra supervisor is available for PhD students with target group registration and their supervisors.

Interested

Are you interested in this position and do you believe that your experience will contribute to the further development of our university? In that case, we encourage you to submit your application.

Please make sure you submit the following documents:

  • CV (max 1 page)
  • Motivation letter showing why you are interested in pursuing a PhD in this field at the VU Bioinformatics in Amsterdam (max 1 page)
  • Contact details of 1-3 references (not reference letters)
  • Grades list of B.Sc. and M.Sc. studies 
     

Applications received by e-mail will not be considered.

Acquisition in response to this advertisement is not appreciated.

Your function

Despite decades of dedicated collaborative efforts, we are still missing key elements to develop the perfect electronic nose. A major obstacle is our limited understanding of how the sense of smell works, and how odorant sensors should be designed for smell detection. The project ODORWISE joins advanced computer simulation techniques together with available results from experiments to study how the proteins in our noses can detect and distinguish different chemicals. The outcome will aid the design of new biomimetic sensor units for detecting smells, which will be a significant advancement for early disease diagnosis and surveillance in non-invasive sustainable healthcare. If you are interested to join this exciting research, apply to join us at the bioinformatics group of the Vrije Universiteit Amsterdam.  
 

Your duties

Your role will be to:

  • apply computational approaches ranging from quantum chemical models to molecular dynamics and enhanced sampling techniques
  • develop data analysis methods tailored to ODORWISE  
  • formulate testable hypotheses on how to exploit biological mechanisms for the rational design of protein targets 
  • validate the models through existing experiments and in collaboration with experimental partners
  • supervise M.Sc. research projects related to ODORWISE and related to activities in the bioinformatics group  

Your profile

We are seeking a highly motivated PhD candidate to join on a 4-year research adventure to unravel the molecular mechanism underlying the olfactory sense. To join us, you should have

  • a degree in a quantitative discipline such as bioinformatics, biotechnology, physical or computational chemistry, chemical engineering, computer science, molecular physics or a related field 
  • proficiency in bioinformatics programming languages (e.g., Python, C, C++)
  • proficiency in English (oral and written), as well as good cross-disciplinary collaborative and communication skills 
  • experience in statistical mechanics, statistics, molecular dynamics, enhanced sampling techniques (is desired) 
  • experience in machine learning and computer science (is a plus)
  • experience in molecular biology and/or drug design (is a plus)

As a university, we strive for equal opportunities for all, recognising that diversity takes many forms. We believe that diversity in all its complexity is invaluable for the quality of our teaching, research and service. We are always looking for talent with diverse backgrounds and experiences. This also means that we are committed to creating an inclusive community so that we can use diversity as an asset.

We realise that each individual brings a unique set of skills, expertise and mindset. Therefore we are happy to invite anyone who recognises themselves in the profile to apply, even if you do not meet all the requirements.

What do we offer?

A challenging position in a socially engaged organisation. At VU Amsterdam, you contribute to education, research and service for a better world. And that is valuable. So in return for your efforts, we offer you:

  • a salary of € 2.770,00 (PhD) and maximum € 3.539,00 (PhD) gross per month in the fourth year, for a full-time employment
  • an employment contract of initially 18 months. If there is sufficient perspective, this will be extended to a total of 4 years. Your dissertation at the end of the fourth year forms the end of your employment contract.

We also offer you attractive fringe benefits and arrangements. Some examples:

  • A full-time 38-hour working week comes with a holiday leave entitlement of 232 hours per year. If you choose to work 40 hours, you have 96 extra holiday leave hours on an annual basis. For part-timers, this is calculated pro rata.
  • 8% holiday allowance and 8.3% end-of-year bonus
  • contribution to commuting expenses
  • optional model for designing a personalized benefits package
  • solid pension scheme (ABP)

About us

Faculty of Science
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature.

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future.

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments.

Vrije Universiteit Amsterdam
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research. Learn more about our codes of conduct

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility.  Over 6,150 staff work at the VU and over 31,000 students attend academic education.

Diversity

Diversity is the driving force of the VU. The VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding.

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

We want to develop talent and creativity by bringing together people from different backgrounds and cultures. We recruit and select based on competencies and talents. We therefore encourage anyone who recognizes themselves in a vacancy, regardless of age, gender, origin, religion, philosophy of life, orientation, disability or chronic illness, to respond. Candidates with a jobs agreement indication (“doelgroepregistratie”) will be given priority if suitable. For these candidates applies:
- A PhD candidate with a registration (“doelgroepregister”) may apply for a minimum of 0.7 fte
- An extra supervisor is available for PhD students with target group registration and their supervisors.

Questions about the vacancy?

Please contact

Halima Mouhib

Assistant Professor

Interested

Are you interested in this position and do you believe that your experience will contribute to the further development of our university? In that case, we encourage you to submit your application.

Please make sure you submit the following documents:

  • CV (max 1 page)
  • Motivation letter showing why you are interested in pursuing a PhD in this field at the VU Bioinformatics in Amsterdam (max 1 page)
  • Contact details of 1-3 references (not reference letters)
  • Grades list of B.Sc. and M.Sc. studies 
     

Applications received by e-mail will not be considered.

Acquisition in response to this advertisement is not appreciated.

Questions about the vacancy?

Please contact

Halima Mouhib

Assistant Professor

Application procedure

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