Theoretical Biology & Bioinformatics

tree of life

PhD theses


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. Hsnson

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. Promotores: Prof.dr. P. Hogeweg and Prof.dr. F.P.M. Govers

Seidl, M.F. (2013)
Exploring Evolution and Biology of Oomycetes: Integrative and Comparative Genomics
Utrecht University. Promotor: Prof.dr. P. Hogeweg, Co-promotor: dr. B. Snel

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.