Publications: Theoretical Biology / Bioinformatics Group, Utrecht University 2012

previous year

next year

Publications: 2012

Theoretical Biology / Bioinformatics Group, Utrecht University

Altelaar A.F., Navarro D., Boekhorst J., Van Breukelen B., Snel B., Mohammed S. & Heck A.J. (2012).: Database independent proteomics analysis of the ostrich and human proteome.
Proc. Natl. Acad. Sci. U.S.A., 109: 407-412. DOI. MEDLINE. DownLoad PDF.
Althaus C.L. & De Boer R.J. (2012).: Impaired immune evasion in HIV through intracellular delays and multiple infection of cells.
Proc. Biol. Sci., 279: 3003-3010. DOI. MEDLINE. DownLoad PDF.
Ariotti S., Beltman J.B., Chodaczek G., Hoekstra M.E., Van Beek A.E., Gomez-Eerland R., Ritsma L., Van Rheenen J., Maree A.F., Zal T., De Boer R.J., Haanen J.B. & Schumacher T.N. (2012).: Tissue-resident memory CD8+ T cells continuously patrol skin epithelia to quickly recognize local antigen.
Proc. Natl. Acad. Sci. U.S.A., 109: 19739-19744. DOI. MEDLINE. DownLoad PDF.
Auton A., Fledel-Alon A., Pfeifer S., Venn O., Segurel L., Street T., Leffler E.M., Bowden R., Aneas I., Broxholme J., Humburg P., Iqbal Z., Lunter G., Maller J., Hernandez R.D., Melton C., Venkat A., Nobrega M.A., Bontrop R., Myers S., Donnelly P., Przeworski M. & McVean G. (2012).: A fine-scale chimpanzee genetic map from population sequencing.
Science, 336: 193-198. DOI. MEDLINE. DownLoad PDF.
Baltcheva I., Veel E., Volman T., Koning D., Brouwer A., Le Boudec J.Y., Tesselaar K., De Boer R.J. & Borghans J.A. (2012).: A generalized mathematical model to estimate T- and B-cell receptor diversities using AmpliCot.
Biophys. J., 103: 999-1010. DOI. MEDLINE. DownLoad PDF.
Berke L., Sanchez-Perez G.F. & Snel B. (2012).: Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis.
Genome Biol., 13: R94. DOI. MEDLINE. DownLoad PDF.
Bowden R., MacFie T.S., Myers S., Hellenthal G., Nerrienet E., Bontrop R.E., Freeman C., Donnelly P. & Mundy N.I. (2012).: Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population.
PLoS. Genet., 8: e1002504. DOI. MEDLINE. DownLoad PDF.
Calis J.J., De Boer R.J. & Kesmir C. (2012).: Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire.
PLoS. Comput. Biol., 8: e1002412. DOI. MEDLINE. DownLoad PDF.
Cuypers T.D. & Hogeweg P. (2012).: Virtual genomes in flux: an interplay of neutrality and adaptability explains genome expansion and streamlining.
Genome Biol. Evol., 4: 212-229. DOI. MEDLINE. DownLoad PDF.
De Boer F.K. & Hogeweg P. (2012).: Less can be more: RNA-adapters may enhance coding capacity of replicators.
PLoS. One., 7: e29952. DOI. MEDLINE. DownLoad PDF.
De Boer R.J. (2012).: Which of our modeling predictions are robust?
PLoS. Comput. Biol., 8: e1002593. DOI. MEDLINE. DownLoad PDF.
De Boer R.J., Perelson A.S. & Ribeiro R.M. (2012).: Modelling deuterium labelling of lymphocytes with temporal and/or kinetic heterogeneity.
J. R. Soc. Interface, 9: 2191-2200. DOI. MEDLINE. DownLoad PDF.
De Groot N.G., Otting N., Robinson J., Blancher A., Lafont B.A., Marsh S.G., O'Connor D.H., Shiina T., Walter L., Watkins D.I. & Bontrop R.E. (2012).: Nomenclature report on the major histocompatibility complex genes and alleles of Great Ape, Old and New World monkey species.
Immunogenetics., 64: 615-631. DOI. MEDLINE.
De Lau W.B., Snel B. & Clevers H.C. (2012).: The R-spondin protein family.
Genome Biol., 13: 242. DOI. MEDLINE.
Den Braber I., Mugwagwa T., Vrisekoop N., Westera L., Mogling R., De Boer A.B., Willems N., Schrijver E.H., Spierenburg G., Gaiser K., Mul E., Otto S.A., Ruiter A.F., Ackermans M.T., Miedema F., Borghans J.A., De Boer R.J. & Tesselaar K. (2012).: Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans.
Immunity, 36: 288-297. DOI. MEDLINE.
Doxiadis G.G., De Vos-Rouweler A.J., De Groot N., Otting N. & Bontrop R.E. (2012a).: DR haplotype diversity of the cynomolgus macaque as defined by its transcriptome.
Immunogenetics., 64: 31-37. DOI. MEDLINE.
Doxiadis G.G., Hoof I., De Groot N. & Bontrop R.E. ( 2012b).: Evolution of HLA-DRB Genes.
Mol. Biol. Evol., 29: 3843-3853. DOI. MEDLINE.
Fokkens L., Hogeweg P. & Snel B. (2012).: Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age.
BMC. Evol. Biol., 12: 99. DOI. MEDLINE.
Friesema I.H., Meijer A., Van Gageldonk-Lafeber A.B., Van der Lubben M., Van Beek J., Donker G.A., Prins J.M., De Jong M.D., Boskamp S., Isken L.D., Koopmans M.P., Van der Sande M.A. & Dutch ZonMw Influenza A(H1N1) 2009 consortium . (2012).: Course of pandemic influenza A(H1N1) 2009 virus infection in Dutch patients.
Influenza. Other. Respi. Viruses., 6: e16-e20. DOI. MEDLINE.
Ganusov V.V. & De Boer R.J. (2012).: A mechanistic model for bromodeoxyuridine dilution naturally explains labelling data of self-renewing T cell populations.
J R Soc Interface, 0: O. DOI. MEDLINE.
Grieneisen V.A., Scheres B., Hogeweg P. & M Maree A.F. (2012).: Morphogengineering roots: comparing mechanisms of morphogen gradient formation.
BMC. Syst. Biol., 6: 37. DOI. MEDLINE.
Groenenboom M.A. & Hogeweg P. (2012).: Modelling the dynamics of viral suppressors of RNA silencing.
J. R. Soc. Interface, 9: 436-447. DOI. MEDLINE.
Hogeweg P. (2012).: Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability.
Adv. Exp. Med. Biol., 751: 195-224. DOI. MEDLINE.
Hoof I., Van Baarle D., Hildebrand W.H. & Kesmir C. (2012).: Proteome sampling by the HLA class I antigen processing pathway.
PLoS. Comput. Biol., 8: e1002517. DOI. MEDLINE.
Iwami S., Sato K., De Boer R.J., Aihara K., Miura T. & Koyanagi Y. ( 2012).: Identifying viral parameters from in vitro cell cultures.
Front. Microbiol., 3: 319. DOI. MEDLINE.
Mithoe S.C., Boersema P.J., Berke L., Snel B., Heck A.J. & Menke F.L. (2012).: Targeted quantitative phosphoproteomics approach for the detection of phospho-tyrosine signaling in plants.
J. Proteome. Res., 11: 438-448. DOI. MEDLINE.
Mostowy R., Kouyos R.D., Hoof I., Hinkley T., Haddad M., Whitcomb J.M., Petropoulos C.J., Kesmir C. & Bonhoeffer S. (2012).: Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase.
PLoS. Comput. Biol., 8: e1002525. DOI. MEDLINE.
Otten H.G., Calis J.J., Kesmir C., Van Zuilen A.D. & Spierings E. ( 2012).: Predicted Indirectly Recognizable HLA epitopes presented by HLA-DR correlate with the de novo development of donor-specific HLA IgG antibodies after kidney transplantation.
Hum Immunol., 0: O. DOI. MEDLINE.
Otting N., De Groot N., De Vos-Rouweler A.J., Louwerse A., Doxiadis G.G. & Bontrop R.E. (2012).: Multilocus definition of MHC haplotypes in pedigreed cynomolgus macaques (Macaca fascicularis).
Immunogenetics., 64: 755-765. DOI. MEDLINE.
Persengiev S., Kondova I. & Bontrop R.E. (2012a).: Functional Annotation of Small Noncoding RNAs Target Genes Provides Evidence for a Deregulated Ubiquitin-Proteasome Pathway in Spinocerebellar Ataxia Type 1.
J. Nucleic. Acids., 2012: 672536. DOI. MEDLINE.
Persengiev S.P., Kondova I.I. & Bontrop R.E. (2012b).: The Impact of MicroRNAs on Brain Aging and Neurodegeneration.
Curr. Gerontol. Geriatr. Res., 2012: 359369. DOI. MEDLINE.
Schipper H.S., Nuboer R., Prop S., Van den Ham H.J., De Boer F.K., Kesmir C., Mombers I.M., Van Bekkum K.A., Woudstra J., Kieft J.H., Hoefer I.E., De Jager W., Prakken B., Van Summeren M. & Kalkhoven E. (2012).: Systemic inflammation in childhood obesity: circulating inflammatory mediators and activated CD14++ monocytes.
Diabetologia, 55: 2800-2810. DOI. MEDLINE.
Schluepmann H., Berke L. & Sanchez-Perez G.F. (2012).: Metabolism control over growth: a case for trehalose-6-phosphate in plants.
J. Exp. Bot., 63: 3379-3390. DOI. MEDLINE.
Schneider E., Mayer S., El Hajj N., Jensen L.R., Kuss A.W., Zischler H., Kondova I., Bontrop R.E., Navarro B., Fuchs E., Zechner U. & Haaf T. ( 2012).: Methylation and expression analyses of the 7q autism susceptibility locus genes MEST , COPG2, and TSGA14 in human and anthropoid primate cortices.
Cytogenet. Genome Res., 136: 278-287. DOI. MEDLINE.
Seidl M.F., Van den Ackerveken G., Govers F. & Snel B. ( 2012a).: Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families.
Genome Biol. Evol., 4: 199-211. DOI. MEDLINE.
Seidl M.F., Wang R.P., Van den Ackerveken G., Govers F. & Snel B. ( 2012b).: Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen phytophthora infestans.
Plos One, 7: e51295. DOI.
Stassen J.H., Seidl M.F., Vergeer P.W., Nijman I.J., Snel B., Cuppen E. & Van den Ackerveken G. (2012).: Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing.
Mol. Plant Pathol., 13: 719-731. DOI. MEDLINE.
Suijkerbuijk S.J., Van Dam T.J., Karagoz G.E., Von Castelmur E., Hubner N.C., Duarte A.M., Vleugel M., Perrakis A., Rudiger S.G., Snel B. & Kops G.J. (2012).: The vertebrate mitotic checkpoint protein BUBR1 is an unusual pseudokinase.
Dev. Cell, 22: 1321-1329. DOI. MEDLINE.
Takeuchi N. & Hogeweg P. (2012a).: Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life.
Phys. Life Rev., 9: 219-263. DOI. MEDLINE. DownLoad PDF.
Takeuchi N. & Hogeweg P. (2012b).: Reply to the commentaries on ''Evolutionary dynamics of rna-like replicator systems: A bioinformatic approach to the origin of life''.
Phys. Life Rev., 9: 279 - 284. DOI. DownLoad PDF.
Van den Ham H.J. & De Boer R.J. (2012).: Cell division curtails helper phenotype plasticity and expedites helper T-cell differentiation.
Immunol. Cell Biol., 90: 860-868. DOI. MEDLINE.
Verstrepen B.E., De Groot N.G., Groothuismink Z.M., Verschoor E.J., De Groen R.A., Bogers W.M., Janssen H.L., Mooij P., Bontrop R.E., Koopman G. & Boonstra A. (2012).: Evaluation of IL-28B Polymorphisms and Serum IP-10 in Hepatitis C Infected Chimpanzees.
PLoS. One., 7: e46645. DOI. MEDLINE.
Vleugel M., Hoogendoorn E., Snel B. & Kops G.J. (2012).: Evolution and function of the mitotic checkpoint.
Dev. Cell, 23: 239-250. DOI. MEDLINE.
Vroomans R.M., Maree A.F., De Boer R.J. & Beltman J.B. (2012).: Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens.
PLoS. Comput. Biol., 8: e1002763. DOI. MEDLINE.
Weise L.D. & Panfilov A.V. (2012).: Emergence of spiral wave activity in a mechanically heterogeneous reaction-diffusion-mechanics system.
Phys. Rev. Lett., 108: 228104. DOI. MEDLINE. DownLoad PDF.
Wind J.J., Peviani A., Snel B., Hanson J. & Smeekens S.C. (2012).: ABI4: versatile activator and repressor.
Trends Plant Sci., 0: O. DOI. MEDLINE.