Theoretical Biology & Bioinformatics

tree of life

PhD program Computational Life Sciences (CLS)

Biological research in the life sciences is changing rapidly and is generating vast amounts of data on exceedingly complex regulatory systems. Bioinformatics plays an essential role in making this data available in interconnected public data bases, developing computational tools for analyzing the data, and investigating the data to increase our understanding of complex biological systems. The complexity of biological systems requires a modeling approach to understand the functioning of the regulatory networks, and to go from isolated qualitative descriptions to a larger quantitative understanding. This modeling involves mathematical and computational approaches to estimate parameters, to combine different processes and different levels of organization, and to allow for large scale computer simulations. Thus, a major challenge for biological research in the next decades is to extract useful information from vast amounts of data and to develop computational models to investigate the complex dynamics of living organisms. Accomplishing these goals will depend on the use of suitable model systems and intense collaboration between experimentalists and computational biologists. This collaborative and quantitative approach of integrating biological data is nowadays called Systems Biology. Our mission with this PhD program is to train students to become computational biologists with a strong expertise in modeling and bioinformatics, and a strong footing in the life sciences.

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.

These requirements are in line with the rules for obtaining a PhD degree at Universities in the Netherlands, and the thesis is the final proof of competence. After their graduation PhD students should be ''computational biologists" capable of high-level research in biological modeling and/or bioinformatics in international research environments devoted to Systems Biology, Computational and Theoretical Biology, or Bioinformatics.

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. It is the responsibility of the supervising staff member and the program coordinator to formulate an appropriate Training and Supervision Agreement (TSA) for every individual student. 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. The TSA will be formulated together with the student such that the student is aware of the contents and the quality of his or her individual agreement. The TSA consists of general information, such as the requirement to follow courses, a work plan for research, international meetings to attend, and information about the legal position of the PhD student. The TSA specific to the PhD program Computational Life Sciences contains information regarding the structure and requirements of the Graduate School of Life Sciences.

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 19 May 2016 / Webmaster: R.J.DeBoer@uu.nl