utrecht university phd biology

Theoretical Biology & Bioinformatics

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• Bachelor program
• Master program
• PhD program
• Honours program (Qbio)
• Advanced courses
• Minor biology for math/physics students
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• Rob de Boer
• Berend Snel
• Kirsten ten Tusscher
• Paulien Hogeweg
• Monica Garcia Gomez
• Rutger Hermsen
• Michael Seidl
• Basten Snoek
• Daniel Tamarit
• Erika Tsingos
• Bram van Dijk
• Ronald Bontrop

Teaching programs

• Minor biology for math/physics students (in Dutch)

PhD program Computational Life Sciences (CLS)

The CLS PhD program is organized by the Theoretical Biology and Bioinformatics group of the Institute for Biodynamics and Biocomplexity performing interdisciplinary research that combines biology, physics, chemistry and mathematics to understand living systems at different organization levels from individual molecules, such as DNA, lipids and proteins, to cells and model organisms. Through close interaction between experimentation, theory and simulation, we aim to achieve a systems-level understanding of complex dynamic processes and their evolution. One possible route into this program is via the graduate program Quantitative Biology , which allows the best students to write their own PhD proposal.

Current expertise in the Computational Life Sciences PhD program involves a variety of biological disciplines and computational approaches. Biological areas that we cover are genome evolution, eco-evolutionary dynamics, gene regulatory networks, immunology, cell motility, development, and spatial pattern formation. This enables the PhD program to train students in Systems Biology in a variety of biological backgrounds. We cover computational approaches ranging from large scale bioinformatic data analysis, varying from genomic to gene expression data, mathematical analysis, to computational modeling, where the latter varies from the Cellular Potts model that is used to study development, evolutionary computation, to discrete-event agent based computer simulation models.

The main objective of the Computational Life Sciences PhD program is to train students to become excellent and independent researchers in Theoretical Biology and Bioinformatics, with solid expertise in modeling and bioinformatics, and a good interdisciplinary knowledge in the life sciences. Specifically, students should be able to

• critically read and judge both theoretical and experimental publications in their area of expertise,
• write scientific papers for international peer-reviewed journals, reporting their findings and interpreting these in their biological context,
• present their results on posters and presentations at international scientific conferences and workshops,
• be able to communicate with members of interdisciplinary research teams (students with a theoretical background have to understand the underlying biology, and biologists should master the innovations in computational biology),
• supervise master students, discuss scientific results with peer scientists, communicate with editors,
• formulate new exciting research questions from their own research and new findings reported by others,
• to participate in scientific discussions at an international level, and
• write competitive research proposals.

Program committee.

The Computational Life Sciences PhD program is part of the Graduate School of Life Sciences and the Life Sciences and Biocomplexity focus area of Utrecht University. The director of the program is Prof. Dr. Rob J. de Boer . All staff members of the Theoretical Biology and Bioinformatics group in this focus area will supervise PhD students, give courses, run journal clubs, and international seminars.

Admission criteria.

In the past we have attracted PhD students from all over the world and with various scientific backgrounds. The basic requirement for admission is a relevant and sufficient scientific background in Computational Life Sciences, and financial support to pay for the PhD position. Because of the interdisciplinary nature of our PhD program the admission criteria will have to be flexible and individualized. The track Theoretical Biology and Bioinformatics in the master program Biology and Biocomplexity of the Graduate School of Life Sciences provides an optimal preparation for a PhD in Computational Life Sciences. Students with a master education in mathematics or physics can also be admitted by taking additional courses in the relevant biological areas and/or modeling and bioinformatics. Similarly, students with a biological master, but an insufficient background in modeling and bioinformatics, will have to repair these computational skills to be admitted to the school. An excellent course for repairing deficiencies in background is the MSc course ``Bioinformatic Processes" that is mandatory for all MSc students in our MSc track Theoretical Biology and Bioinformatics.

Implementation.

PhD students will be supervised by at least one of the staff members of the Theoretical Biology and Bioinformatics group. We recommentd the PhD student and the supervising staff member to formulate an appropriate Course Plan together. The contents of the educational program, and the quality of the program, i.e., the scientific level of the courses the PhD student will attend, are the responsibility of the supervising staff member and the program coordinator. After the PhD has been completed, any PhD student with 20 ECTs is eligible for a Graduate School of Life Sciences certificate.

PhD students in our group attend the advanced courses that we give ourselves, and various other national and international courses. Examples of schools and courses attended by our PhD students:

• Summer school "Complexity" of the Santa Fe Institute
• Advanced immunology courses given by the Eijkmanschool
• Statistical and programming courses in R and Bioconductor
• "In Vivo Imaging - from Molecule to Organism" Optical Imaging Centre, Erasmus MC, Rotterdam.
• The EMBO Practical Workshop on Multilevel modelling of Morphogenesis given at the John Innes Centre in Norwich, UK.
• General courses on statistics, writing papers, and giving presentations.

In Holland PhD positions come with a salary. This means that the group has to have funding to hire you as a PhD student. Check our webpage Positions to check whether we have open PhD positions available. Note that we always require a solid background in Theoretical Biology and/or Bioinformatics and a genuine interest in biology. Theoretical Biology & Bioinformatics / Last modified on 20 July 2020 / Webmaster: R.J.DeBoer@uu.nl

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Environmental Biology

On this site you can find all the information of the Master's programme Environmental Biology.

The Master's programme in Environmental Biology offers you the opportunity to explore different organisational levels of life – from genes, cells, and organisms to populations and entire ecosystems. In this programme, you will study the fundamental life processes of plants, animals and microbes. The programme offers you considerable freedom to choose a specific field within Environmental Biology.

Career prospects

Environmental Biology trains you to a high academic level. You will, individually or in a team, be challenged to address fundamental and applied environmental problems. You will learn about the most modern experimental and mathematical methods and techniques and also how to apply molecular and genetic tools to a wide range of biological problems.

Our programme is directly linked to the PhD programme Environmental Biology of the Graduate School of Life Sciences.

Research and relations

The following examples illustrate typical research questions in environmental biology:.

• How does global change affect biodiversity?
• How can we manage our natural resources in a sustainable manner?
• How do plants adapt to biotic and abiotic stress?
• How do plants develop and respond to light?
• How can we learn from nature to design sustainable next-generation crops?
• What can we learn from microbes in nature and make them useful for mankind?
• How can animal behaviour be explained from an ecological and evolutionary perspective?

The following research groups at Utrecht University and external partners participate in the Master's programme Environmental Biology:

• Plant-Microbe Interactions
• Plant Stress Resilience
• Plant-Environment Signaling
• Translational Plant Biology
• Animal Behaviour and Cognition
• Ecology and Biodiversity
• Microbiology
• Palaeo-ecology  (Faculty of Geosciences)
• Energy and Resources  (Faculty of Geosciences)
• Animals in Science and Society  (Faculty of Veterinary Medicine)
• Netherlands Institute of Ecology
• The Antwerp Zoo Centre for Research and Conservation  of the Royal Zoological Society of Antwerp

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The research school Cancer Stem cells & Developmental biology (CS&D) is part of the Utrecht Graduate School of Life Sciences and combines about 100 research groups from Utrecht University, the University Medical Center Utrecht, the Hubrecht Institute for Developmental Biology and Stem Cell Research, and the Princess Maxima Center. The school offers two programmes:

• The Master's programme
• The PhD programme

Seminar Schedule

• Grant & Award News
• Research News
• Press release (in Dutch)
• Announcements
• Anna Akhmanova: Cellular Dynamics
• Lukas Kapitein: Biophysics
• Florian Berger: Theoretical Biophysics
• Agathe Chaigne: Cell division dynamics
• Ginny Farías: Neuronal Organelle Dynamics
• Martin Harterink: C. elegans neurobiology
• Casper Hoogenraad: Molecular Neuroscience
• Maarten Kole: Axonal Signalling
• Harold MacGillavry: Synapse organization
• Sabrina Oliveira: Molecular Targeted Therapies
• Ihor Smal: Image Analysis, Smart Microscopy and AI
• Frederik Verweij: Extracellular Vesicle Biology
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Home » Lab Cell Biology » Publications » PhD theses

Anna Akhmanova elected as honorary member of the UBV

Lukas Kapitein elected as EMBO Member

20.8 million euros for Gravitation project IMAGINE!

VIDI grants for Agathe Chaigne and Frederik Verweij

Commendation from the Dean for Laurens van Meeteren

Division of Cell Biology, Neurobiology and Biophysics Department of Biology Faculty of Science Utrecht University Padualaan 8, 3584 CH, Utrecht The Netherlands Tel.: +31 30 2534230 Webmaster

Utrecht University Life Sciences Science for Life Institute of Biodynamics and Biocomplexity

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UU Plants is embedded in the Institute of  Environmental Biology  in the  Department of Biology  at the Faculty of Science at Utrecht University.

Our mission is to discover novel molecular, genetic and physiological mechanisms of how plants interact with and adapt to their biotic and abiotic environments.

Our aims: Use this knowledge to address pressing societal challenges such as food security, biodiversity decline and the transition to sustainable agriculture. Train and educate the next generation of plant biologists.

Research groups

Plant Stress Resilience

“Exploring plant resilience to climatic stressors”

Plant-Microbe Interactions

“Exploring the plant’s natural immune system”

Experimental and Computational Plant Dev.

“Exploring plant development and its adaptation to environmental stresses”

Translational Plant Biology

“Exploring plant science to improve crops”

Recent articles

Fully automatic monitoring of plant growth, development and disease progression with helios.

Thanks to Helios, a new research installation that is part of the  Netherlands Plant Eco-phenotyping Centre (NPEC) , it is now possible to automatically monitor the growth and development of more than a thousand plants, while gaining insights into how microorganisms affect…

Recent news

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Grant opens door to decipher the secret sensory world of plants

Plants not only sense when they are touched, but they can also adapt to it. For example, by strengthening or defending themselves. But how do plants do this? The Green TE (Green Tissue Engineering) consortium has been granted a Gravitation grant of almost 23 million euros to investigate exactly this.

The sense of touch in plants is under scrutiny: how can they register touches? Whether it’s a fungus attempting to invade the plant, a person walking over grass, or wind blowing through leaves. The plant detects it and reacts accordingly.

Modeling and simulations for more insight

The subsidy brings together researchers from many areas of expertise. ‘In Leiden, we contribute to modeling biomechanics in plant tissues,’ says researcher Roeland Merks. ‘We will work closely with our partners, and further develop our “Virtual Leaf” simulation tool.’

For the research institutions IBL and MI, this means a significant strengthening of mathematical biology in the next ten years: a postdoc and a PhD student for the first five years, and another set in the second five-year period.

Read more on this upcoming research in WUR’s press release .

The GreenTE consortium will be led by researchers Dolf Weijers and Joris Sprakel of Wageningen University & Research. They work together with scientists of our university, and those of Utrecht University, Radboud University Nijmegen, Technical University Eindhoven, Groningen University and VU Amsterdam.

Photo header: Chang Qinq (Unsplash)

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PhD Position in Algorithmic Biology, Utrecht University, Netherlands

PhD Position in Algorithmic Biology: Join us in exploring the fascinating intersection of mathematics, computer science, and biology as a PhD candidate at Utrecht University. Delve into innovative research projects aimed at understanding biological and social systems’ evolution through mathematical and algorithmic frameworks. Work alongside Dr. Artem Kaznatcheev and contribute to groundbreaking discoveries in cancer, metascience, and beyond.

PhD Position in Mathematical and Algorithmic Biology

Location: Utrecht University, Netherlands

Eligibility/Qualification:

• Demonstrated research experience at the level of a thesis-based Master’s in Math, Computer Science, Physics, Quantitative Biology, or related fields.
• Proficiency in math and programming (Python or similar) for building and analyzing models and/or proving theorems.
• Strong interest in independent research, critical thinking, and continual learning.
• Excellent communication skills in spoken and written English.

Description: As a PhD candidate, you’ll have the autonomy to define your research problems and tools under the guidance of Dr. Kaznatcheev. Explore diverse research directions such as gene-interaction networks, computational complexity, ecological influences on evolution, game theory applications in cancer treatment, and cultural evolution dynamics. Develop skills in computational complexity, model building, data analysis, and interdisciplinary collaboration. Publish your findings in prestigious journals and conferences while engaging in teaching and mentoring activities.

How to Apply: Interested candidates should submit the following documents via the ‘Apply Now’ button:

• A concise motivation letter (under 2 pages) detailing your interests in mathematical and algorithmic biology, preferred research directions, and how your qualifications align with the position.
• Curriculum vitae highlighting education, work experience, and research outputs (papers, code, presentations, etc.).
• A writing sample, either your thesis (Bachelor’s or Master’s) or a short research proposal specific to this position (under 2 pages). Upload the writing sample under the “Master thesis” tab in the online application.

Last Date for Apply: April 23, 2024

For inquiries, please contact Dr. Artem Kaznatcheev at [email protected] . For application-related queries, email [email protected] .

Utrecht University is committed to fostering diversity and inclusivity. We encourage individuals from diverse backgrounds to apply and contribute to our collaborative research environment.

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Department of Biology

Our research is versatile and has an international level. Most parts of Biology are represented.

Research in the Department falls under the aegis of the  Institute of Environmental Biology(IEB)  and the  Intitute for Biocomplexity and Bioinformatics (IBB) .  These two institutes contain various specialized research groups, as listed below.

Research groups

• Animal Behaviour and Cognition
• Cell Biology, Neurobiology and Biophysics
• Developmental Biology
• Ecology and Biodiversity
• Experimental and Computational Plant Development
• Genome Biology and Epigenetics
• Microbiology
• Plant-Environment Signaling
• Plant-Microbe Interactions
• Plant Stress Resilience
• Theoretical Biology and Bioinformatics
• Translational Plant Biology

Prince Bernhard Centre

Prince Bernhard Centre  for International Nature Conservation. The Prince Bernhard Centre initiates, coordinates and executes international research, training and extension programmes in the field of nature conservation in partnership with countries in the southern hemisphere.

PhD Programs

The department participates in the PhD programs Environmental Biology , Computational Life Sciences , Biomembranes

Research Schools

In addition, the Department participates in the inter-university research school: 

• Experimental Plant Sciences
• Helmholtz Institute
•   PE&RC  

Utrecht University Heidelberglaan 8 3584 CS Utrecht The Netherlands Tel. +31 (0)30 253 35 50