PhD Position on Evolution of Stress Response Networks across the Plant Kingdom

Do you want to be part of the development of resilient cropsthat require far fewer inputs thatnegatively impact our planet, andcontribute to healthy life? Then you could be the ideal candidate to join our new, interdisciplinary

research institute CropXR With a budget of 96 million Euro over the next decade, CropXR focuses on creating eXtra Resilient (XR), sustainable, and climate-adaptive crops. By combining plant biology, simulation modelling, and artificial intelligence we aim to develop ‘smart breeding and cultivation’ methods to speed up breeding for complex resilience traits in different growing systems for several crops. This collaborative effort involves four universities, numerous companies, and encompasses scientific research, data collection and sharing, education, and practical applications in agriculture and plant breeding. This PhD position is part of a project within the CropXRs core research programme. The project will study the evolution of the regulatory responses of plants to abiotic stresses such as temperature and drought. These networks will be investigated both in model plants and crop species, using bioinformatics and comparative genomics on genomic and transcriptomic datasets. This knowledge can be directly used in breeding for more resilient crops. Research will help to answer question such as: How are the genes underlying the stress response network evolving? Is the expression of the genes underlying the stress response network conserved in important crop species? Can we predict which genes conserve their function in stress responses using machine learning? What is the role of duplicated genes in stress response networks? The collected data and methods developed to answer these questions will be utilized by other researchers in CropXR to develop complex mechanistic models of stress response in crop species. As a PhD candidate, you will co-execute the research project “Unravelling the evolution of stress response networks across the plant kingdom”. This involves: performing large scale orthology and detailed phylogenetics of stress response genes; integrating transcriptomic data with comparative genomics data; collecting genomic and proteomic features to train machine learning models to predict expression of key genes in crop organisms; interacting with academic and company colleagues working in related CropXR projects. Next to that, you will support in teaching BSc and MSc students who participate in the project. You will also interact withother PhD candidates and researchers involved in experimental research, bioinformatics and/or modelling at Utrecht University, Wageningen University and Research, University of Amsterdam, and TU Delft, as well as with experts from breeding and green genomics companies who are partners to CropXR. We highly encourage candidates from diverse backgrounds and nationalities to apply. We strive to create an open, diverse, and inclusive work environment for everyone. People of any gender identity, ethnicity and sexual orientation are welcome. We are looking for a highly motivated and creative PhD candidate to join us in CropXR. You are: a team player motivated to help CropXR in working towards its mission; skilled in bioinformatics work in the areas of comparative genomics and/or transcriptomics; interested in collaborating with colleagues in academia and industry. You have: a strong interest in regulatory networks, genome evolution, and bioinformatics; a MSc in Bioinformatics, Computational Biology, or another relevant field; demonstrable experience with comparative genomics and ideally transcriptomics; experience with the Unix command line and Python; demonstrable communication and organisation skills and the ability to contribute to a friendly and collaborative working environment in an international and cross-disciplinary scientific research team; an excellent command of written and spoken English. Our offer

We offer: a gross monthly salary ranging between€2,770 in the first year to €3,539 in the fourth yearin the case of full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU)); 8% holiday pay and 8.3% year-end bonus; a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU. Do you want to be part of the development of resilient cropsthat require far fewer inputs thatnegatively impact our planet, andcontribute to healthy life? Then you could be the ideal candidate to join our new, interdisciplinary

research institute CropXR external link

! Your job

With a budget of 96 million Euro over the next decade, CropXR focuses on creating eXtra Resilient (XR), sustainable, and climate-adaptive crops. By combining plant biology, simulation modelling, and artificial intelligence we aim to develop ‘smart breeding and cultivation’ methods to speed up breeding for complex resilience traits in different growing systems for several crops. This collaborative effort involves four universities, numerous companies, and encompasses scientific research, data collection and sharing, education, and practical applications in agriculture and plant breeding. This PhD position is part of a project within the CropXRs core research programme. The project will study the evolution of the regulatory responses of plants to abiotic stresses such as temperature and drought. These networks will be investigated both in model plants and crop species, using bioinformatics and comparative genomics on genomic and transcriptomic datasets. This knowledge can be directly used in breeding for more resilient crops. Research will help to answer question such as: How are the genes underlying the stress response network evolving? Is the expression of the genes underlying the stress response network conserved in important crop species? Can we predict which genes conserve their function in stress responses using machine learning? What is the role of duplicated genes in stress response networks? The collected data and methods developed to answer these questions will be utilized by other researchers in CropXR to develop complex mechanistic models of stress response in crop species. As a PhD candidate, you will co-execute the research project “Unravelling the evolution of stress response networks across the plant kingdom”. This involves: performing large scale orthology and detailed phylogenetics of stress response genes; integrating transcriptomic data with comparative genomics data; collecting genomic and proteomic features to train machine learning models to predict expression of key genes in crop organisms; interacting with academic and company colleagues working in related CropXR projects. Next to that, you will support in teaching BSc and MSc students who participate in the project. You will also interact withother PhD candidates and researchers involved in experimental research, bioinformatics and/or modelling at Utrecht University, Wageningen University and Research, University of Amsterdam, and TU Delft, as well as with experts from breeding and green genomics companies who are partners to CropXR. You receive co-supervision from

Wageningen University & Research external link

(WUR) (Professor Dick de Ridder) and

Genetwister

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(Dr Lidija Berke). We highly encourage candidates from diverse backgrounds and nationalities to apply. We strive to create an open, diverse, and inclusive work environment for everyone. People of any gender identity, ethnicity and sexual orientation are welcome. Your qualities

We are looking for a highly motivated and creative PhD candidate to join us in CropXR. You are: a team player motivated to help CropXR in working towards its mission; skilled in bioinformatics work in the areas of comparative genomics and/or transcriptomics; interested in collaborating with colleagues in academia and industry. You have: a strong interest in regulatory networks, genome evolution, and bioinformatics; a MSc in Bioinformatics, Computational Biology, or another relevant field; demonstrable experience with comparative genomics and ideally transcriptomics; experience with the Unix command line and Python; demonstrable communication and organisation skills and the ability to contribute to a friendly and collaborative working environment in an international and cross-disciplinary scientific research team; an excellent command of written and spoken English. Our offer

We offer: a position for fouryears (1.0 FTE); a gross monthly salary ranging between€2,770 in the first year to €3,539 in the fourth yearin the case of full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU)); 8% holiday pay and 8.3% year-end bonus; a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU. In addition to the terms of employment external link

laid down in the CAO NU, Utrecht University has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development

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, leave schemes and schemes for sports and cultural activities

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, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. For more information, please visit Working at Utrecht University

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. About us

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University external link

, the various disciplines collaborate intensively towards major strategic themes

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. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Pathways to Sustainability. Sharing science, shaping tomorrow

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. At the Faculty of Science external link

there are 6 departments to make a fundamental connection with: Biology, Chemistry, Information and Computing Sciences, Mathematics, Pharmaceutical Sciences and Physics. Each of these is made up of distinct institutes that work together to focus on answering some of humanity’s most pressing challenges. More fundamental still are the individual research groups – the building blocks of our ambitious scientific projects. The

Bioinformatics chair group external link

at Utrecht University develops and implements state-of-the art bioinformatics methods to provide fundamental understanding of the functions and evolution of genomes and their encoded regulatory networks. The group has strong lines of research on comparative genomics of eukaryotes, metagenomics, phylogenomics, genetics of traits and multi modal single cell genomics. The Bioinformatics group has tight links to the Theoretical Biology group: the groups function together within the Biology department, sharing offices, their computer cluster, teaching, and group talks.

CropXR external link

was launched in 2023 to help make agricultural production less vulnerable to climate change and less dependent on artificial fertilizers and chemical pesticides. The institute is a joint venture of the universities of Amsterdam, Delft, Wageningen and Utrecht in partnership with Plantum, the Dutch plant breeding sector association. CropXR brings together efforts from different academic disciplines (such as plant sciences, computational and data sciences, and social sciences) and private industry to help bring about sustainable change. It receives support from

NWO

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, the

Dutch National Growth Fund

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, and the

Foundation for Food & Agricultural Research

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. More information

For more information, please contact

Professor Berend Snel external link

atb.snel@uu.nl or

Dr Basten Snoek

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atl.b.snoek@uu.nl . Candidates for this vacancy will be recruited by Utrecht University. Apply now

As Utrecht University, we want to be a home external link

for everyone. We value staff with diverse backgrounds, perspectives and identities, including cultural, religious or ethnic background, gender, sexual orientation, disability or age. We strive to create a safe and inclusive environment in which everyone can flourish and contribute. If you are enthusiastic about this position, just apply via the 'Apply now' button. Please enclose: your motivation letter; your curriculum vitae; reference letters (optional but appreciated). If this specific opportunity isn’t for you, but you know someone else who may be interested, please forward this vacancy to them. The application deadline is 3 July 2024.

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