Publications: Theoretical Biology / Bioinformatics Group, Utrecht University 2006

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Publications: 2006

Theoretical Biology / Bioinformatics Group, Utrecht University

Boekhorst J., Helmer Q., Kleerebezem M. & Siezen R.J. ( 2006a).: Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria.
Microbiology., 152: 273-280. MEDLINE. DownLoad PDF.
Boekhorst J., Wels M., Kleerebezem M. & Siezen R.J. ( 2006b).: The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment.
Microbiology., 152: 3175-3183. MEDLINE. DownLoad PDF.
Ciccarelli F.D., Doerks T., Von Mering C., Creevey C.J., Snel B. & Bork P. (2006).: Toward automatic reconstruction of a highly resolved tree of life.
Science, 311: 1283-1287. MEDLINE. DownLoad PDF.
Clayton R.H., Zhuchkova E.A. & Panfilov A.V. (2006).: Phase singularities and filaments: simplifying complexity in computational models of ventricular fibrillation.
Prog. Biophys. Mol. Biol., 90: 378-398. MEDLINE. DownLoad PDF.
Cordero O.X. & Hogeweg P. (2006).: Feed-forward loop circuits as a side effect of genome evolution.
Mol. Biol. Evol., 23: 1931-1936. MEDLINE. DownLoad PDF.
De Boer R.J. (2006).: Estimating the role of thymic output in hiv infection.
Curr. Opin. HIV AIDS, 1: 16-21.
De Boer R.J., Ganusov V.V., Milutinovic D., Hodgkin P.D. & Perelson A.S. (2006).: Estimating lymphocyte division and death rates from CFSE data.
Bull. Math. Biol., 68: 1011-1031. MEDLINE. DownLoad PDF.
Dutilh B.E., Huynen M.A. & Snel B. (2006).: A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.
BMC. Genomics., 7: 10. MEDLINE. DownLoad PDF.
Franke L., Bakel H., Fokkens L., De Jong E.D., Egmont-Petersen M. & Wijmenga C. (2006).: Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes.
Am. J. Hum. Genet., 78: 1011-1025. MEDLINE. DownLoad PDF.
Gabaldon T., Snel B., Van Zimmeren F., Hemrika W., Tabak H. & Huynen M.A. (2006).: Origin and evolution of the peroxisomal proteome.
Biol. Direct., 1: 8. MEDLINE. DownLoad PDF.
Ganusov V.V. & Antia R. (2006).: Imperfect vaccines and the evolution of pathogens causing acute infections in vertebrates.
Evolution. Int. J. Org. Evolution., 60: 957-969. MEDLINE. DownLoad PDF.
Ganusov V.V. & De Boer R.J. (2006).: Estimating Costs and Benefits of CTL Escape Mutations in SIV/HIV Infection.
PLoS. Comput. Biol., 2: e24. MEDLINE. DownLoad PDF.
Ganusov V.V., Pilyugin S.S., Ahmed R. & Antia R. (2006).: How does cross-reactive stimulation affect the longevity of CD8+ T cell memory?
PLoS. Comput. Biol., 2: e55. MEDLINE. DownLoad PDF.
Kafer J., Hogeweg P. & Maree A.F. (2006).: Moving forward moving backward: directional sorting of chemotactic cells due to size and adhesion differences.
PLoS. Comput. Biol., 2: e56. MEDLINE. DownLoad PDF.
Korthals Altes H., De Boer R. & Boerlijst M. (2006).: Role of avidity and breadth of the CD4 T cell response in progression to AIDS.
Proc. Biol. Sci., 273: 1697-1704. MEDLINE. DownLoad PDF.
Kuramae E.E., Robert V., Snel B. & Boekhout T. ( 2006a).: Conflicting phylogenetic position of Schizosaccharomyces pombe.
Genomics., 88: 387-393. MEDLINE. DownLoad PDF.
Kuramae E.E., Robert V., Snel B., Weiss M. & Boekhout T. ( 2006b).: Phylogenomics reveal a robust fungal tree of life.
FEMS. Yeast. Res., 6: 1213-1220. MEDLINE.
Maree A.F., Jilkine A., Dawes A., Grieneisen V.A. & Edelstein-Keshet L. (2006a).: Polarization and movement of keratocytes: a multiscale modelling approach.
Bull. Math. Biol., 68: 1169-1211. MEDLINE. DownLoad PDF.
Maree A.F., Kublik R., Finegood D.T. & Edelstein-Keshet L. ( 2006b).: Modelling the onset of Type 1 diabetes: can impaired macrophage phagocytosis make the difference between health and disease?
Philos. Transact. A. Math. Phys. Eng. Sci., 364: 1267-1282. MEDLINE. DownLoad PDF.
Maree A.F., Santamaria P. & Edelstein-Keshet L. ( 2006c).: Modeling competition among autoreactive CD8+ T cells in autoimmune diabetes: implications for antigen-specific therapy.
Int. Immunol., 18: 1067-1077. MEDLINE. DownLoad PDF.
Merks R.M., Hoekstra A.G., Kaandorp J., Sloot P.M.A. & Hogeweg P. ( 2006).: Problem-solving environments for biological morphogenesis.
Computing in Science and Engineering, 8: 61-72.
Muller V. & De Boer R.J. (2006).: The integration hypothesis: an evolutionary pathway to benign SIV infection.
PLoS. Pathog., 2: e15. MEDLINE. DownLoad PDF.
Oti M., Snel B., Huynen M.A. & Brunner H.G. (2006).: Predicting disease genes using protein-protein interactions.
J. Med. Genet., 43: 691-698. MEDLINE. DownLoad PDF.
Panfilov A.V. (2006).: Is heart size a factor in ventricular fibrillation? Or how close are rabbit and human hearts?
Heart. Rhythm., 3: 862-864. MEDLINE. DownLoad PDF.
Rapin N., Kesmir C., Frakild S., Nielsen M., Lundegaard C., Brunak S. & Lund O. (2006).: Modelling the human immune system by combining bioinformatics and systems biology approaches.
J. Biol.Phys., 32: 335-353. DownLoad PDF.
Siezen R., Boekhorst J., Muscariello L., Molenaar D., Renckens B. & Kleerebezem M. (2006).: Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria.
BMC. Genomics., 7: 126. MEDLINE. DownLoad PDF.
Strous M., Pelletier E., Mangenot S., Rattei T., Lehner A., Taylor M.W., Horn M., Daims H., Bartol-Mavel D., Wincker P., Barbe V., Fonknechten N., Vallenet D., Segurens B., Schenowitz-Truong C., Medigue C., Collingro A., Snel B., Dutilh B.E., Op den Camp H.J., Van der Drift C., Cirpus I., Van de Pas-Schoonen K.T., Harhangi H.R., Van Niftrik L., Schmid M., Keltjens J., Van de Vossenberg J., Kartal B., Meier H., Frishman D., Huynen M.A., Mewes H.W., Weissenbach J., Jetten M.S., Wagner M. & Le Paslier D. (2006).: Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
Nature, 440: 790-794. MEDLINE. DownLoad PDF.
Ten Tusscher K.H., Bernus O., Hren R. & Panfilov A.V. (2006).: Comparison of electrophysiological models for human ventricular cells and tissues.
Prog. Biophys. Mol. Biol., 90: 326-345. MEDLINE. DownLoad PDF.
Ten Tusscher K.H. & Panfilov A.V. (2006a).: Alternans and spiral breakup in a human ventricular tissue model.
Am. J. Physiol. Heart. Circ. Physiol., 291: H1088-H1100. MEDLINE. DownLoad PDF.
Ten Tusscher K.H. & Panfilov A.V. (2006b).: Cell model for efficient simulation of wave propagation in human ventricular tissue under normal and pathological conditions.
Phys. Med. Biol., 51: 6141-6156. MEDLINE. DownLoad PDF.
Van den Dool C. & De Boer R.J. (2006).: The effects of age, thymectomy, and HIV Infection on alpha and beta TCR excision circles in naive T cells.
J. Immunol., 177: 4391-4401. MEDLINE. DownLoad PDF.
Van Der Post D.J. & Hogeweg P. (2006).: Resource distributions and diet development by trial-and-error learning.
Behav. Ecol. Sociobiol., 61: 65-80. DownLoad PDF.
Van Hoek M.J. & Hogeweg P. (2006).: In silico evolved lac operons exhibit bistability for artificial inducers, but not for lactose.
Biophys. J., 91: 2833-2843. MEDLINE. DownLoad PDF.