PhD theses

Zhang, X. (2024)

The journey to the treasure: Seconday metabolite gene clusters and histone modifications in the genus Aspergillus
Utrecht University. Promotor: Prof. dr. B. Snel, Co-promotores: Dr. M.F. Seidl, Dr. J.Collemare

Van Den Herik, B.M. (2024)

Efficiently starting and preferentially filling a potato: Leveraging models to investigate the multiple roles of SP6A in source-sink dynamics
Utrecht University. Promotor: Prof. dr. K.H.W.J. ten Tusscher, Co-promotor: Dr. C.W.B. Bachem

Von Der Dunk, S.H.A. (2023)

Constructive evolution and the emergence of complex cells
Utrecht University. Promotores: Prof. dr. P. Hogeweg, Prof. dr. B. Snel

Torres Sanchez, D.E. (2023)

Plant pathogen evolution in three dimensions
Wageningen University. Promotor: Prof. dr. B.P.H.J. Thomma, Co-promotor: Dr. M.F. Seidl

Swain, A.C. (2023)

Ink Trails: Tracking the life and death of memory T cells
Utrecht University. Promotores: Prof. dr. R.J. de Boer, Prof. dr. J.A.M. Borghans

von Meijenfeldt, F.A.B. (2023)

Surprising biology in uncharted microbial sequences
Utrecht University. Promotores: Prof. dr. B. Snel, Prof. dr. P. Hogeweg, Prof. dr. B.E. Dutilh

de Greef, P.C. (2023)

Chasing the chains by testing them twice: Immunological insights from TCR repertoire analysis
Utrecht University. Promotor: Prof. dr. R.J. de Boer

Vosseberg, J. (2023)

The rise of complex life: Tracing the origins of the eukaryotic cell
Utrecht University. Promotor: Prof. dr. B. Snel

Schröter, J. (2022)

Paediatric HIV infection from a mathematical perspective: Taking care of every child
Utrecht University. Promotor: Prof. dr. R.J. de Boer

Krah, L.H.J. (2022)

Models of noise propagation in growing and regulating bacterial cells
Utrecht University. Promotor: Prof. dr. R.J. de Boer, Co-promotor: Dr. R. Hermsen

Deutekom, E.S. (2022)

Tinkering with the toolkit for comparative genomics of eukaryotes: Improving methods and concepts for eukaryotic genome evolutionary analyses
Utrecht University. Promotor: Prof. dr. B. Snel, Co-promotor: Dr. T.J.P. van Dam

Lefebvre, A.E.J.L. (2021)

Research Data Management for Open Science
Utrecht University. Promotores: Prof. dr. S. Brinkkemper, Prof. dr. B. Snel, Prof. dr. M.R. Spruit, Co-promotor: Dr. ir. B. Van Breukelen

de Jonge, P.A. (2020)

On uncovering and understanding interactions between bacteriophages and bacteria
Utrecht University. Promotor: Prof. dr. B. Snel, Co-promotores: Dr. B.E. Dutilh, Dr. S.J.J. Brouns

van Dijk, B. (2020)

Microbial Evolution on a Virtual Grain of Sand
Utrecht University. Promotor: Prof. dr. P. Hogeweg

Doekes, H.M. (2020)

Microbial Evolution at Multiple Scales
Utrecht University. Promotor: Prof. dr. R.J. de Boer, Co-promotor: Dr. R. Hermsen

Baaijens, J.A. (2019)

De novo approaches to haplotype-aware genome assembly
Utrecht University. Promotor: Prof. dr. A. Schönhuth

van Hooff, J.J.E. (2018)

Origins and divergence of the eukaryotic kinetochore
Utrecht University. Promotores: Prof. dr. G.J.P.L. Kops, Prof. dr. B. Snel

van Dorp, C.H. (2018)

Rapidly evolving pathogens in a polymorphic host population : Modeling immuno-epidemiology of HIV-1 and influenza A virus
Utrecht University. Promotor: Prof. dr. R.J. de Boer, Co-promotor: M. van Boven

Gerritsen, B. (2018)

Sequencing, analyzing, and modeling small samples from large T cell repertoires
Utrecht University. Promotor: Prof. dr. R.J. de Boer, Co-promotores: Dr. A. Pandit, Dr. A.C. Andeweg

Tromer, E.C. (2017)

Evolution of the Kinetochore Network in Eukaryotes
Utrecht University. Promotores: Prof. dr. G.J.P.L. Kops, Prof. dr. B. Snel

Vroomans, R.M.A. (2017)

Of clocks and waves, stripes and shapes : evo-devo models of sequential segmentation
Utrecht University. Promotor: Prof.dr. P. Hogeweg, Co-promotor: dr. K.H.W.J. ten Tusscher

Colizzi, E.S. (2016)

Multilevel Evolution and the Emergence of Function
Utrecht University. Promotor: Prof.dr. P. Hogeweg

Peviani, A. (2016)

Unraveling transcriptional and translational control in plant energy homeostasis : a bioinformatic approach
Utrecht University. Promotores: Prof.dr. B. Snel, Prof.dr. J.C.M Smeekens, Co-promotor: Dr. S.J. Hanson

Gadhamsetty, S. (2015)

How Do Interactions Between Cytotoxic T Cells and Targets Shape the Functional Response Describing Target Cell Death?
Utrecht University. Promotor: Prof.dr. R.J. de Boer, Co-promotor: Dr. J.B. Beltman

Carrillo Bustamante, N.P. (2015)

A license to kill : The evolution of NK cell receptors
Utrecht University. Promotor: Prof.dr. R.J. de Boer, Co-promotor: Dr. C. Kesmir

Berke, L. (2015)

Evolutionary dynamics and functional roles of regulatory systems in plants
Utrecht University. Promotores: Prof.dr. B. Snel, Prof.dr. P. Hogeweg

Van Deutekom, H.W.M. (2013)

The ongoing evolutionary battle between the immune system and viruses : MHC molecules verus HIV
Utrecht University. Promotor: Prof.dr. R.J. de Boer, Co-promotor: Dr. C. Kesmir

Fokkens, L. (2013)

The interplay between genome and network evolution in eukaryotes
Utrecht University. Promotor: Prof.dr. P. Hogeweg, Co-promotor: dr. B. Snel

Seidl, M.F. (2013)

Exploring Evolution and Biology of Oomycetes: Integrative and Comparative Genomics
Utrecht University. Promotores: Prof.dr. P. Hogeweg, Prof.dr. F.P.M. Govers, Co-promotores: dr. B. Snel, Dr. A.F.J.M. van den Ackerveken

Weise, L.D. (2012)

Spiral Wave Initiation in Reaction-Diffusion-Mechanics Systems: A Model for the Onset of Reentrant Cardiac Arrhythmia
Utrecht University. Promotores: Prof.dr. R.J. de Boer and Prof.dr. A.V. Panfilov

Calis, J.J.A. (2012)

Bound to be an epitope: determinants of the T-cell response to MHC-I presented peptides
Utrecht University. Promotor: Prof.dr. R.J. de Boer, Co-promotor: Dr. C. Kesmir

De Boer, F.K. (2012)

Coding Flexibility or : How Evolution Shapes the Structure and Complexity of Coding
Utrecht University. Promotor: Prof.dr. P. Hogeweg

Rao, X. (2012)

A detailed comparison of peptides presented by different HLA class I loci: an in silico approach
Utrecht University. Promotor: Prof.dr. R.J. de Boer, Co-promotor: Dr. C. Kesmir

Van Dam, T.J.P. (2011)

Evolution of Ras-like GTPase signaling pathways
Utrecht University. Promotor: Prof.dr. J.L. Bos, Co-promotor: Dr. B. Snel

Groot, N.G. de (2010)

A selective sweep in chimpanzees : is SIV the culprit?
Utrecht University. Promotor: Prof.dr. R.E. Bontrop

Ham, H.J. van den (2010)

A better understanding of helper T cell differentiation using mathematical models and bioinformatics
Utrecht University. Promotor: Prof.dr. R.J. de Boer

Takeuchi, N. (2010)

Evolutionary dynamics of RNA-like replicators : A bioinformatic approach to the origin of life
Utrecht University. Promotor: Prof.dr. P. Hogeweg (cum laude).

Mugwagwa, T. (2010)

Quantification of T-cell dynamics in health and disease : Mathematical modeling of experimental data
Utrecht University. Promotor: Prof.dr. R.J. de Boer, Co-promotor: Dr. J. A. M. Borghans

Althaus, C.L. (2009)

Quantifying the dynamics of viruses and the cellular immune response of the host
Utrecht University. Promotor: Prof.dr. R.J. de Boer.

Cordero Sanchez, O.X. (2009)

Macroevolutionary patterns in microbial genomes and regulomes
Utrecht University. Promotor: Prof.dr. P. Hogeweg.

Crombach, A.B.M. (2009)

Evolving the structure of genomes, networks and ecosystems
Utrecht University. Promotor: Prof.dr. P. Hogeweg.

Den Braber, A.J. (2009)

Leukocyte dynamics in mice and men
Utrecht University. Promotores: Prof.dr. R.J. de Boer and Prof.dr. F. Miedema

Grieneisen, V.A. (2009)

Dynamics of auxin patterning in plant morphogenesis - A multilevel model study
Utrecht University. Promotores: Prof.dr. P. Hogeweg and Prof.dr. B.J.G. Scheres (cum laude).

Keldermann, R.H. (2009)

Mechanisms of Ventricular Fibrillation : The role of mechano-electrical feedback and tissue heterogeneity
Utrecht University. Promotor: Prof.dr. P. Hogeweg, Co-promotor: Dr. A. V. Panfilov.

Schmid, B.V. (2009)

Limits of viral adaptation to the antigen presentation pathway
Utrecht University. Promotor: Prof.dr. R.J. de Boer

Groenenboom, M.A.C. (2008)

Spatial and temporal dynamics of the RNA silencing response.
Utrecht University. Promotor: Prof.dr. P. Hogeweg.

Van der Post, D.J. (2008)

Learning what to eat: Emerging cultural phenomena in group foragers.
Utrecht University. Promotor: Prof.dr. P. Hogeweg.

Van Hoek, M.J.A. (2008)

Evolutionary Dynamics of Metabolic Adaptation.
Utrecht University. Promotor: Prof.dr. P. Hogeweg.

Ten Tusscher, K.H.W.J. (2004)

Spiral wave dynamics and ventricular arrhythmias.
Utrecht University. Promotor: Prof.dr. P. Hogeweg, Co-promotor: Dr. A. V. Panfilov.

Snel, B. (2002)

Comparative Genome Analysis and Genome Evolution.
Utrecht University. Promotores: Prof. Dr. P. Hogeweg and Prof. Dr. M.A. Huynen.

Borghans, J.A.M. (2000)

Diversity in the Immune System.
Utrecht University. Promotor: prof. Dr. P. Hogeweg, Co-promotor: Dr. R.J. de Boer.

Marée, A.F.M. (2000)

From Pattern Formation to Morphogenesis: Multicellular Coordination in Dictyostelium discoideum.
Utrecht University. Promotor: Prof. Dr. P. Hogeweg, Co-promotor: Dr. A. V. Panfilov. (cum laude)

Van Nimwegen, E.J. (1999)

The statiscal mechanics of epochal evolution.
Utrecht University. Promotores: P. Hogeweg and J.P. Crutchfield. (cum laude)

Pagie, L.W.P. (1999)

Information integration in evolutionary processes.
Utrecht University. Promotor: Prof. Dr. P. Hogeweg

Takumi, K. (1998)

Evolutionary, Network and Cellular Memory in Immune Systems.
Utrecht University. Promotor prof. Dr. P. Hogeweg, Co-promotor Dr. R.J. de Boer.

Ek, R. (1997)

Botanical diversity in the tropical rainforest of Guyana.
Utrecht University. Promotores: Prof.dr. M.J.A. Werger and Prof.dr. P. Hogeweg.

Savill, N.J. (1997)

Eco-evolutionary consequences of spatial pattern formation.
Utrecht University. Promotor: Prof.dr. P. Hogeweg. (cum laude)

Vogt, G. (1997)

Analysis of protein function through sequence and structure comparison.
Utrecht University. Promotor: Prof.dr. P. Hogeweg, co-promotoren: Dr. P. Argos and Dr. J. Heringa.

Boerlijst, M.C. (1994)

Selfstructuring: a substrate for evolution.
Utrecht University. Promotor: Prof.dr. P. Hogeweg. (cum laude)

Van der Laan, J.D. (1994)

Spatio-temporal patterns in ecosystems: a bioinformatic approach.
Utrecht University. Promotor: Prof.dr. P. Hogeweg.

Heringa, J. (1993)

Local interactions in Protein folds: a bioinformatic approach to sequence structure relationships.
Utrecht University. Promotor: Prof.dr. P. Hogeweg. (cum laude)

Huynen, M.A. (1993)

Evolutionary dynamics and pattern generation in the sequence and secondary structure of RNA: A bioinformatic approach.
Utrecht University. Promotor: Prof.dr. P. Hogeweg.