Publicaties
2025
Wetenschappelijke publicaties
2024
Wetenschappelijke publicaties
Almeida, A. C., Rocha, H., Raas, M. W. D., Witte, H., Sommer, R. J., Snel, B., Kops, G. J. P. L., Gassmann, R., & Maiato, H. (2024). An evolutionary perspective on the relationship between kinetochore size and CENP-E dependence for chromosome alignment. Journal of Cell Science, 137(24), Article jcs263466. [DOI] [Portal]
Richards, T. A., Eme, L., Archibald, J. M., Leonard, G., Coelho, S. M., de Mendoza, A., Dessimoz, C., Dolezal, P., Fritz-Laylin, L. K., Gabaldón, T., Hampl, V., Kops, G. J. P. L., Leger, M. M., Lopez-Garcia, P., McInerney, J. O., Moreira, D., Muñoz-Gómez, S. A., Richter, D. J., Ruiz-Trillo, I., ... Wideman, J. G. (2024). Reconstructing the last common ancestor of all eukaryotes. PLoS Biology, 22(11), Article e3002917. [DOI] [Portal]
von der Dunk, S. H. A., Hogeweg, P., & Snel, B. (2024). Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis. PLoS Computational Biology, 20(2), 1-18. Article e1011860. [DOI] [Repository]
Norppa, AJ., Chowdhury, I., van Rooijen, LE., Ravantti, JJ., Snel, B., Varjosalo, M., & Frilander, MJ. (2024). Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome. Nucleic Acids Research, 52(7), 4037-4052. Article gkae070. [DOI] [Repository]
Wu, J., Raas, M. W. D., Alcaraz, P. S., Vos, H. R., Tromer, E. C., Snel, B., & Kops, G. J. P. L. (2024). A farnesyl-dependent structural role for CENP-E in expansion of the fibrous corona. The Journal of cell biology, 223(1), 1-27. Article e202303007. [DOI] [Repository]
2023
Wetenschappelijke publicaties
von der Dunk, S. H. A., Hogeweg, P., & Snel, B. (2023). Obligate endosymbiosis enables genome expansion during eukaryogenesis. Communications Biology, 6(1), 1-10. Article 777. [DOI] [Repository]
van Rooijen, L. E., Tromer, E. C., van Hooff, J. J. E., Kops, G. J. P. L., & Snel, B. (2023). Increased Sampling and Intracomplex Homologies Favor Vertical Over Horizontal Inheritance of the Dam1 Complex. Genome Biology and Evolution, 15(3), 1-11. Article evad017. [DOI] [Repository]
Vosseberg, J., Stolker, D., Von Der Dunk, S. H. A., & Snel, B. (2023). Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome. Molecular Biology and Evolution, 40(1), 1-15. Article msad011. [DOI] [Repository]
Broeils, L. A., Ruiz-Orera, J., Snel, B., Hubner, N., & van Heesch, S. (2023). Evolution and implications of de novo genes in humans. Nature Ecology and Evolution, 7(6), 804-815. [DOI] [Repository]
de Potter, B., Raas, M. W. D., Seidl, M. F., Verrijzer, C. P., & Snel, B. (2023). Uncoupled evolution of the Polycomb system and deep origin of non-canonical PRC1. Communications Biology, 6(1), Article 1144. [DOI] [Repository]
2022
Wetenschappelijke publicaties
Li, J., Chroumpi, T., Garrigues, S., Kun, R. S., Meng, J., Salazar-Cerezo, S., Aguilar-Pontes, M. V., Zhang, Y., Tejomurthula, S., Lipzen, A., Ng, V., Clendinen, C. S., Tolić, N., Grigoriev, I. V., Tsang, A., Mäkelä, M. R., Snel, B., Peng, M., & de Vries, R. P. (2022). The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum. Journal of fungi (Basel, Switzerland), 8(12), Article 1315. [DOI] [Repository]
Deutekom, E. S., van Dam, T. J. P., & Snel, B. (2022). Phylogenetic profiling in eukaryotes: The effect of species, orthologous group, and interactome selection on protein interaction prediction. PLoS One, 17(4 April), Article e0251833. [DOI] [Repository]
He, L., van Beem, L., Snel, B., Hoogenraad, C. C., & Harterink, M. (2022). PTRN-1 (CAMSAP) and NOCA-2 (NINEIN) are required for microtubule polarity in Caenorhabditis elegans dendrites. PLoS Biology, 20(11), Article e3001855. [DOI] [Repository]
von der Dunk, S. H. A., Snel, B., & Hogeweg, P. (2022). Evolution of Complex Regulation for Cell-Cycle Control. Genome Biology and Evolution, 14(5), Article evac056. [DOI] [Repository]
Snel, B., van den Heuvel, S., & Seidl, M. F. (2022). Caenorhabditis elegans MES-3 is a highly divergent ortholog of the canonical PRC2 component SUZ12. iScience, 25(7), 1-10. Article 104633. [DOI] [Repository]
Vosseberg, J., Schinkel, M., Gremmen, S., & Snel, B. (2022). The spread of the first introns in proto-eukaryotic paralogs. Communications Biology, 5(1), 1-9. Article 476. [DOI] [Repository]
2021
Wetenschappelijke publicaties
de Wolf, B., Oghabian, A., Akinyi, M. V., Hanks, S., Tromer, E. C., van Hooff, J. J. E., van Voorthuijsen, L., van Rooijen, L. E., Verbeeren, J., Uijttewaal, E. C. H., Baltissen, M. P. A., Yost, S., Piloquet, P., Vermeulen, M., Snel, B., Isidor, B., Rahman, N., Frilander, M. J., & Kops, G. J. P. L. (2021). Chromosomal instability by mutations in the novel minor spliceosome component CENATAC. EMBO Journal, 40(14), 1-18. Article e106536. [DOI] [Repository]
Deutekom, E. S., Snel, B., & van Dam, T. J. P. (2021). Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes. Briefings in Bioinformatics, 22(3), 1-9. Article bbaa206. [DOI] [Repository]
Vosseberg, J., van Hooff, J. J. E., Marcet-Houben, M., van Vlimmeren, A., van Wijk, L. M., Gabaldón, T., & Snel, B. (2021). Timing the origin of eukaryotic cellular complexity with ancient duplications. Nature Ecology and Evolution, 5(1), 92-100. [DOI] [Repository]
2020
Wetenschappelijke publicaties
van Wijk, L. M., & Snel, B. (2020, Jan 31). The first eukaryotic kinome tree illuminates the dynamic history of present-day kinases. bioRxiv. [DOI] [Repository]
Kops, G. J. P. L., Snel, B., & Tromer, E. C. (2020). Evolutionary Dynamics of the Spindle Assembly Checkpoint in Eukaryotes. Current Biology, 30(10), R589-R602. [DOI] [Repository]
Von Der Dunk, S. H. A., & Snel, B. (2020). Recurrent sequence evolution after independent gene duplication. BMC Evolutionary Biology, 20(1), Article 98. [DOI] [Repository]
2019
Wetenschappelijke publicaties
Plowman, R., Singh, N., Tromer, E. C., Payan, A., Duro, E., Spanos, C., Rappsilber, J., Snel, B., Kops, G. J. P. L., Corbett, K. D., & Marston, A. L. (2019). The molecular basis of monopolin recruitment to the kinetochore. Chromosoma, 128(3), 331-354. [DOI] [Repository]
Antonova, S. V., Boeren, J., Timmers, H. T. M., & Snel, B. (2019). Epigenetics and transcription regulation during eukaryotic diversification: the saga of TFIID. Genes and Development, 33(15-16), 888-902. [DOI] [Repository]
Deutekom, E. S., Vosseberg, J., van Dam, T. J. P., & Snel, B. (2019). Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences. PLoS Computational Biology, 15(8), Article e1007301. [DOI] [Repository]
Tromer, E. C., van Hooff, J. J. E., Kops, G. J. P. L., & Snel, B. (2019). Mosaic origin of the eukaryotic kinetochore. Proceedings of the National Academy of Sciences of the United States of America, 116(26), 12873-12882. [DOI] [Repository]
van Hooff, J. J. E., Tromer, E. C., van Dam, T. J. P., Kops, G. J. P. L., & Snel, B. (2019). Inferring the Evolutionary History of Your Favorite Protein: A Guide for Molecular Biologists. BioEssays, 41(5), Article 1900006. [DOI] [Repository]
van der Horst, S., Snel, B., Hanson, J., & Smeekens, S. (2019). Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in Arabidopsis thaliana. RNA, 25, 292-304. [DOI] [Repository]
2018
Wetenschappelijke publicaties
Dröge-Laser, W., Snoek, B. L., Snel, B., & Weiste, C. (2018). The Arabidopsis bZIP transcription factor family: an update. Current Opinion in Plant Biology, 45(Part A), 36-49. [DOI] [Repository]
2017
Wetenschappelijke publicaties
Vosseberg, J., & Snel, B. (2017). Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery. Biology Direct, 12, Article 30. [DOI] [Repository]
van Hooff, J. J. E., Snel, B., & Kops, G. J. P. L. (2017). Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1. Genome Biology and Evolution, 9(5), 1295-1303. [DOI] [Repository]
van Hooff, J. J., Tromer, E., van Wijk, L., Snel, B., & Kops, G. J. (2017). Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics. EMBO Reports, 18(9), 1559-1571. [DOI] [Repository]
Bai, B., Peviani, A., van der Horst, S., Gamm, M., Snel, B., Bentsink, L., & Hanson, J. (2017). Extensive translational regulation during seed germination revealed by polysomal profiling. New Phytologist, 214(1), 233-244. [DOI] [Repository]
2016
Wetenschappelijke publicaties
Tromer, E., Bade, D., Snel, B., & Kops, G. J. P. L. (2016). Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint. Biology Open, 6, Article 160315. [DOI] [Repository]
Santuari, L., Sanchez-Perez, G. F., Luijten, M., Rutjens, B., Terpstra, I., Berke, L., Gorte, M., Prasad, K., Bao, D., Timmermans-Hereijgers, J. L. P. M., Maeo, K., Nakamura, K., Shimotohno, A., Pencik, A., Novak, O., Ljung, K., van Heesch, S., de Bruijn, E., Cuppen, E., ... Heidstra, R. (2016). The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots. Plant Cell, 28(12), 2937-2951. [DOI] [Repository]
Peviani, A., Lastdrager, J., Hanson, J., & Snel, B. (2016). The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. Scientific Reports, 6, Article 30444. [DOI] [Repository]
2015
Wetenschappelijke publicaties
Sameith, K., Amini, S., Groot Koerkamp, M. J. A., van Leenen, D., Brok, M., Brabers, N., Lijnzaad, P., van Hooff, S. R., Benschop, J. J., Lenstra, T. L., Apweiler, E., van Wageningen, S., Snel, B., Holstege, F. C. P., & Kemmeren, P. (2015). A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions. BMC Biology, 13(112). [DOI] [Repository]
Peng, M., Aye, T. T., Snel, B., Van Breukelen, B., Scholten, A., & Heck, A. J. R. (2015). Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution. Journal of Proteome Research, 14(7), 2976-2987. [DOI] [Repository]
Tromer, E., Snel, B., & Kops, G. J. P. L. (2015). Widespread Recurrent Patterns of Rapid Repeat Evolution in the Kinetochore Scaffold KNL1. Genome Biology and Evolution, 7(8), 2383-93. [DOI] [Repository]
Berke, L., & Snel, B. (2015). The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history. BMC Evolutionary Biology, 15(1). [DOI] [Repository]
Koster, M. J. E., Snel, B., & Timmers, H. T. M. (2015). Genesis of chromatin and transcription dynamics in the origin of species. Cell, 161(4), 724-736. [DOI] [Repository]
Zeilmaker, T., Ludwig, N. R., Elberse, J., Seidl, M. F., Berke, L., Van Doorn, A., Schuurink, R. C., Snel, B., & Van den Ackerveken, G. (2015). DOWNY MILDEW RESISTANT 6 and DMR6-LIKE OXYGENASE 1 are partially redundant but distinct suppressors of immunity in Arabidopsis. Plant Journal, 81(2), 210-222. [DOI] [Repository]
Putker, M., Vos, H., van Dorenmalen, K., de Ruiter, H., Duran, A. G., Snel, B., Burgering, B. M., Vermeulen, M., & Dansen, T. B. (2015). Evolutionary Acquisition of Cysteines determines FOXO Paralog-Specific Redox Signaling. Antioxidants & redox signaling, 22(1), 15-28. [DOI] [Repository]
2014
Wetenschappelijke publicaties
Gamm, M., Peviani, A., Honsel, A., Snel, B., Smeekens, S., & Hanson, J. (2014). Increased sucrose levels mediate selective mRNA translation in Arabidopsis. BMC Plant Biology, 14(306). [DOI] [Repository]
Resjö, S., Ali, A., Meijer, H. J. G., Seidl, M. F., Snel, B., Sandin, M., Levander, F., Govers, F., & Andreasson, E. (2014). Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family. Journal of Proteome Research, 13(4), 1848-1859. [DOI]
Gruhn, N., Halawa, M., Snel, B., Seidl, M. F., & Heyl, A. (2014). A subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants. Plant Physiology, 165(1), 227-37. [DOI] [Repository]
Van Hooff, J. J. E., Snel, B., & Seidl, M. F. (2014). Small homologous blocks in phytophthora genomes do not oint to an ancient whole-genome duplication. Genome Biology and Evolution, 6(5), 1079-1085. [DOI] [Repository]
Berke, L., & Snel, B. (2014). The histone modification H3K27me3 is retained after gene duplication and correlates with conserved noncoding sequences in Arabidopsis. Genome Biology and Evolution, 6(3), 572-579. [DOI] [Repository]
Kemmeren, P. P. C. W., Sameith, K., van de Pasch, L. A. L., Benschop, J. J., Lenstra, T. L., Margaritis, A., O'Duibhir, E., Apweiler, E., van Wageningen, S., Ko, C. W., van Heesch, S. A. A. C., Kashani, M. M., Ampatziadis-Michailidis, G., Brok, M. O., Brabers, N. A. C. H., Miles, A. J., Bouwmeester, D., van Hooff, S. R., van Bakel, H. H. M. J., ... Holstege, F. C. P. (2014). Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors. Cell, 157, 740-752. [DOI]
2013
Wetenschappelijke publicaties
Jiang, R. H. I., de Bruijn, I., Haas, B. J., Belmonte, R., Löbach, L., Christie, J., van den Ackerveken, A. F. J. M., Bottin, A., Bulone, V., Diaz-Moreno, S. M., Dumas, B., Fan, L., Gaulin, E., Govers, F., Grenville-Briggs, L. J., Horner, N. R., Levin, J. Z., Mammella, M., Meijer, H. J., ... West, P. (2013). Distinctive expansions of the potential virulence genes in the genome of the oomycete fish pathogen. PLoS Genetics, 9(6), Article e1003272. [DOI] [Repository]
Seidl, M. F., Schneider, A., Govers, F., & Snel, B. (2013). A predicted functional gene network for the plant pathogen Phytophthora infestans as a framwork for genomic biology. BMC Genomics, 14, 483. [DOI]
Schneider, A., Seidl, M. F., & Snel, B. (2013). Shared protein complex subunits contribute to explaining disrupted co-occurrence. PLoS Computational Biology, 9(7), e1003124. [DOI]
Vleugel, A., Tromer, E. C., Omerzu, M., Groenewold, V., Nijenhuis, W., Snel, B., & Kops, G. J. P. L. (2013). Arrayed BUB recruitment modules in the kinetochore scaffold KNL1 promote accurate chromosome segregation. Journal of Cell Biology, 203(6), 943-955. [DOI]
Wind, J. J., Peviani, A., Snel, B., Hanson, S. J., & Smeekens, J. C. M. (2013). ABI4: versatile activator and repressor. Trends in Plant Science, 18, 125-132.
Nijenhuis, W. A. J., von Castelmur, E., Littler, D. R., de Marco, V., Tromer, E. C., Vleugel, M., van Osch, M. H. J., Snel, B., Perrakis, A., & Kops, G. J. P. L. (2013). A TPR domain-containing N-terminal module of MPS1 is required for its kinechore localization. Journal of Cell Biology, 201(2), 217-231. [DOI]
2012
Wetenschappelijke publicaties
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 Biology, 13(10), Article R94. [DOI] [Repository]
Seidl, M. F., Wang, R.-P., Van den Ackerveken, G., Govers, F., & Snel, B. (2012). Bioinformatic Inference of Specific and General Transcription Factor Binding Sites in the Plant Pathogen Phytophthora infestans. PLoS One, 7(12). [DOI]
Stassen, J. H. M., Seidl, M. F., Vergeer, P. W. J., Nijman, I. J., Snel, B., Cuppen, E., & van den Ackerveken, A. F. J. M. (2012). Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing. Molecular Plant Pathology, 13(7), 719-731. [DOI] [Repository]
Seidl, M. F., van den Ackerveken, A. F. J. M., Govers, F., & Snel, B. (2012). Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day larte gene families. Genome Biology and Evolution, 4, 199-211.
Mithoe, S. C., Boersema, P. J., Berke, L., Snel, B., Heck, A. J. R., & Menke, F. L. H. (2012). Targeted quantitative phosphoproteomics approach for the detection of phospho-tyrosine signaling in plants. Journal of Proteome Research, 11, 438-448. [DOI]
Vleugel, M., Hoogendoorn, E., Snel, B., & Kops, G. J. P. L. (2012). Evolution and function of the mitotic checkpoint. Developmental Cell, 23, 239-250. http://www.ncbi.nlm.nih.gov/pubmed/22898774
Seidl, M. F., Wang, R. P., van den Ackerveken, A. F. J. M., Govers, F., & Snel, B. (2012). Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen phytophtora infestans. PLoS One, 7, e51295.
Suijkerbuijk, S. J. E., van Dam, J., Karagoz, E., von Castelmur, E., Hubner, N. C., dos santos Duarte, A., Vleugel, M., Perrakis, A., Rüdiger, S. G. D., Snel, B., & Kops, G. J. P. L. (2012). The Vertebrate Mitotic Checkpoint Protein BUBR1 Is an Unusual Pseudokinase. Developmental Cell, 22(6), 1321-1329. [DOI]
Berke, L., Sanchez-Perez, G. F., & Snel, B. (2012). Contribution of teh epigenetic mark H3k27me3 to functional divergence after whole genome duplication in Arabidopsis. Genome Biology, 13, R94.
Fokkens, L., Hogeweg, P., & Snel, B. (2012). Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age. BMC Evolutionary Biology, 12, 99.
Altelaar, A. F. M., Navarro, D., Boekhorst, J., van Breukelen, B., Snel, B., Mohammed, S., & Heck, A. J. R. (2012). Database independent proteomics analysis of the ostrich and human proteome. Proceedings of the National Academy of Sciences of the United States of America, 109, 407-412.
de Lau, W. B. M., Snel, B., & Clevers, H. C. (2012). The R-spondin protein family. Genome Biology, 13, 242.
Seidl, M. F., van den Ackerveken, A. F. J. M., Govers, F., & Snel, B. (2012). Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day largegene families. Genome Biology and Evolution, 4(3), 199–211. [DOI] [Repository]
Overige resultaten
Zeilmaker, T., Elberse, J. H. M., Seidl, M. F., Berke, L., Snel, B., & van den Ackerveken, A. F. J. M. (2012). DMR6 and DM6-like lxygenase 1 have overlapping but distinct activities as negative regulators of immunity in Arabidopsis. Paper presented at 23rd International Conference on Arabidopsis Research, Vienna, Austria.
Zeilmaker, T., Elberse, J. H. M., Cabral, A., Yatusevich, R., Parker, J., Seidl, M. F., Berke, L., Snel, B., & van den Ackerveken, A. F. J. M. (2012). Suppression of plant immunity. Paper presented at Plant Biology Congress, Freiburg, Germany.
2011
Wetenschappelijke publicaties
Prasad, K., Grigg, S. P., Barkoulas, M., Yadav, R. K., Sanchez-Perez, G. F., Pinon, V. N., Blilou, I., Hofhuis, H. F., Dhonukshe, P. B., Galinha, C., Mahonen, A. P., Muller, W. H., Raman, S., Verkleij, A. J., Snel, B., Reddy, G. V., Tsiantis, M., & Scheres, B. J. G. (2011). Arabidopsis PLETHORA transcription factors control phyllotaxis. Current Biology, 21, 1123-1128.
van Dam, J., Zwartkruis, F. J., Bos, J. L., & Snel, B. (2011). Evolution of the TOR Pathway. Journal of Molecular Evolution, 73(3-4), 209-220. http://www.ncbi.nlm.nih.gov/pubmed/22057117
Seidl, M. F., van den Ackerveken, A. F. J. M., Govers, F., & Snel, B. (2011). A domain-centric analysis of oomycete plant pathogen genomes reveals unique protein organization. Plant Physiology, 155, 628-644. [DOI]
van Dam, J., Bos, J. L., & Snel, B. (2011). Evolution of the Ras-like small GTPases and their regulators. Small GTPases, 2, 4-16. http://10.4161/sgtp.2.1.15113
Boekhorst, J., Boersema, P. J., Tops, B. B. J., van Breukelen, B., Heck, A. J. R., & Snel, B. (2011). Evaluating experimental bias and completeness in comparative phosphoproteomics analysis. PLoS One, 6(8), 23276.
Ding, V. M., Boersema, P. J., Foong, L. Y., Preisinger, C., Koh, G., Natarajan, S., Lee, D. Y., Boekhorst, J., Snel, B., Lemeer, S. M., Heck, A. J. R., & Choo, A. (2011). Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells. PLoS One, 6(3), 17538.
2010
Wetenschappelijke publicaties
Fokkens, L., Botelho, S. M. C., Boekhorst, J., & Snel, B. (2010). Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. BMC Bioinformatics, 11, Article 86. [DOI] [Repository]
van Wageningen, S., Kemmeren, P. P. C. W., Lijnzaad, P., Margaritis, A., Benschop, J. J., de Castro, I. J., van Leenen, D., Groot Koerkamp, M. J. A., Ko, C., Miles, A. J., Brabers, N. A. C. H., Brok, M. O., Lenstra, T. L., Fiedler, D., Fokkens, L., Aldecoa, R., Apweiler, E., Taliadouros, V., Sameith, K., ... Holstege, F. C. P. (2010). Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell, 143(6), 991-1004. http://www.ncbi.nlm.nih.gov/pubmed/21145464
Boersema, P. J., Foong, L. Y., Ding, V. M., Lemeer, S., van Breukelen, B., Philp, R., Boekhorst, J., Snel, B., den Hertog, J., Choo, A. B., & Heck, A. J. (2010). In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Molecular & Cellular Proteomics, 9(1), 84-99. http://www.ncbi.nlm.nih.gov/pubmed/19770167
Bennett, T. A., van den Toorn, A. J., Sanchez-Perez, G. F., Campilho, A. M., Willemsen, V. A., Snel, B., & Scheres, B. J. G. (2010). SOMBRERO, BEARSKINI1 and BEARSKIN2 regulate root cap maturation in Arabidopsis. The Plant Cell, 22, 640-654.
Overige resultaten
Bennett, T. A., van den Toorn, A. J., Sanchez-Perez, G. F., Campilho, A. M., Willemsen, V. A., Snel, B., & Scheres, B. J. G. (2010). SOMRERO, BEARSKIN1, and BEARSKIN2 regulate root cap maturation in arabidopsis. 640-654. Abstract from Unknown event.
Fokkens, L., Botelho, T. R., Boekhorst, J., & Snel, B. (2010). Enrichment of homologs in significant BLAST hits by co-complex network alignment. BMC Bioinformatics, 11(DOI. MEDLINE. DownLoad PDF.), 86.
2009
Wetenschappelijke publicaties
Fokkens, L., & Snel, B. (2009). Cohesive versus flexible evolution of functional modules in eukaryotes. PLoS Computational Biology, 5.
van Dam, J., Rehmann, H., Bos, J. L., & Snel, B. (2009). Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi. Cellular Signalling, 21(11), 1579-1585. http://www.ncbi.nlm.nih.gov/pubmed/19567266?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1
2008
Wetenschappelijke publicaties
Boekhorst, J., van Breukelen, B., Heck, A. J. R., & Snel, B. (2008). Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biology, 9, R144.1-R144.9.
Szklarczyk, R., Huynen, M. A., & Snel, B. (2008). Complex fate of paralogs. BMC Evolutionary Biology, 8, 337-DOI> MEDLINE.
van Dam, J., & Snel, B. (2008). Protein complex evolution does not involve extensive network rewiring. PLoS Computational Biology, 4(7), e1000132. http://10.1371/journal.pcbi.1000132
Dutilh, B. E., Snel, B., Ettema, T. J., & Huynen, M. A. (2008). Signature genes as a phylogenomic tool. Molecular Biology and Evolution, 25, 1659-1667.
Cordero Sanchez, O. X., Snel, B., & Hogeweg, P. (2008). Coevolutions of gene families in prokaryotes. Cytogenetic and Genome Research, 18, MEDLINE.
2007
Wetenschappelijke publicaties
Boekhorst, J., & Snel, B. (2007). Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. BMC Bioinformatics, 8, 356.
van der Heijden, R. T., Snel, B., van Noort, V., & Huynen, M. A. (2007). Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics, 8, 83-83.
von Mering, C., Jensen, L. J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B., & Bork, P. (2007). String 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Research, 35, D358-D362. [Repository]
van Noort, V., Snel, B., & Huynen, M. A. (2007). Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions. Genome Biology, 8, R197-R197.
Dutilh, B. E., van Noort, V., van der Heijden, R. T., Boekhout, T., Snel, B., & Huynen, M. A. (2007). Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics, 23(7), 815-824.
2006
Wetenschappelijke publicaties
Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M. W., Horn, H., Daims, H., Bartol-Malvel, D., Wincker, P., Barbe, V., Fonknechten, N., Vallenet, D., Segurens, B., Schenowitz-Truong, C., Medigue, C., Collingro, A., Snel, B., Dutilh, B. E., ... Le Paslier, D. (2006). Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature, 440, 790-794.
Oti, M., Snel, B., Huynen, M. A., & Brunner, H. G. (2006). Predicting disease genes using protein-protein interactions. Journal of Medical Genetics, 43, 691-698.
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.
Kuramae, E. E., Robert, V., Snel, B., & Boekhout, T. (2006). Conflicting phylogenetic position of Schizosaccharomyces pombe. Genomics, 88, 387-393.
Gabaldón, T., Snel, B., van Zimmeren, F., Hemrika, W., Tabak, H. F., & Huynen, M. A. (2006). Origin and evolution of the peroxisomal proteome. Biology Direct, 1(8), 1-14. [Repository]
Kuramae, E. E., Robert, V., Snel, B., Weiss, M., & Boekhout, T. (2006). Phylogenomics reveal a robust fungal tree of life. FEMS Yeast Research, 6, 1213-1220.
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, 1-10.
2005
Wetenschappelijke publicaties
Notebaart, R. A., Huynen, M. A., Teusink, B., Siezen, R. J., & Snel, B. (2005). Erratum: Correlation between sequence conservation and the genomic context after gene duplication (Nucleic Acids Research (2005) vol. 33 (6164-6171)). Nucleic Acids Research, 33(22), 7176. [DOI]
Schell, M. A., Karmirantzou, M., Snel, B., Vilanova, D., Berger, B., Pessi, G., Zwahlen, M. C., Desiere, F., Bork, P., Dellev, M., Pridmore, R. D., & Arisoni, F. (2005). Erratum: The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract (Proceedings of the National Academy of Sciences of the United States of America (October 29, 2002) 99, 22 (14422-14427)). Proceedings of the National Academy of Sciences of the United States of America, 102(26), 9430. [DOI]
Notebaart, R. A., Huynen, M. A., Teusink, B., Siezen, R. J., & Snel, B. (2005). Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Research, 33(19), 6164-6171. [DOI]
Huynen, M. A., Gabaldón, T., & Snel, B. (2005). Variation and evolution of biomolecular systems: Searching for functional relevance. FEBS Letters, 579(8), 1839-1845. [DOI]
Huynen, M. A., Spronk, C. A. E. M., Gabaldón, T., & Snel, B. (2005). Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin. FEBS Letters, 579(3), 591-596. [DOI]
von Mering, C., Jensen, L. J., Snel, B., Hooper, S. D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M. A., & Bork, P. (2005). STRING: Known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research, 33(SUPPL. 1), D433-D437. [DOI]
Snel, B., Huynen, M. A., & Dutilh, B. E. (2005). Genome trees and the nature of genome evolution. Annual Review of Microbiology, 59, 191-209. [DOI]
2004
Wetenschappelijke publicaties
Dutilh, B. E., Huynen, M. A., Bruno, W. J., & Snel, B. (2004). The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. Journal of Molecular Evolution, 58(5), 527-539. [DOI]
Snel, B., van Noort, V., & Huynen, M. A. (2004). Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Nucleic Acids Research, 32(16), 4725-4731. [DOI]
Huynen, M. A., Snel, B., & Van Noort, V. (2004). Comparative genomics for reliable protein-function prediction from genomic data. Trends in Genetics, 20(8), 340-344. [DOI]
Snel, B., & Huynen, M. A. (2004). Quantifying modularity in the evolution of biomolecular systems. Genome Research, 14(3), 391-397. [DOI]
van Noort, V., Snel, B., & Huynen, M. A. (2004). The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Reports, 5(3), 280-284. [DOI]
2003
Wetenschappelijke publicaties
Morett, E., Korbel, J. O., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Schmidt, S., Snel, B., & Bork, P. (2003). Systematic discovery of analogous enzymes in thiamin biosynthesis. Nature Biotechnology, 21(7), 790-795. [DOI]
Van Noort, V., Snel, B., & Huynen, M. A. (2003). Predicting gene function by conserved co-expression. Trends in Genetics, 19(5), 238-242. [DOI]
Huynen, M. A., Snel, B., Von Mering, C., & Bork, P. (2003). Function prediction and protein networks. Current Opinion in Cell Biology, 15(2), 191-198. [DOI]
von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., & Snel, B. (2003). STRING: A database of predicted functional associations between proteins. Nucleic Acids Research, 31(1), 258-261. [DOI]
2002
Wetenschappelijke publicaties
Schell, M. A., Karmirantzou, M., Snel, B., Vilanova, D., Berger, B., Pessi, G., Zwahlen, M.-C., Desiere, F., Bork, P., Delley, M., Pridmore, R. D., & Arigoni, F. (2002). The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proceedings of the National Academy of Sciences of the United States of America, 99(22), 14422-14427. [DOI]
Von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S., & Bork, P. (2002). Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417(6887), 399-403.
Snel, B., Bork, P., & Huynen, M. A. (2002). The identification of functional modules from the genomic association of genes. Proceedings of the National Academy of Sciences of the United States of America, 99(9), 5890-5895. [DOI]
Snel, B., Bork, P., & Huynen, M. A. (2002). Genomes in flux: The evolution of Archaeal and Proteobacterial gene content. Genome Research, 12(1), 17-25. [DOI]
Korbel, J. O., Snel, B., Huynen, M. A., & Bork, P. (2002). SHOT: A web server for the construction of genome phylogenies. Trends in Genetics, 18(3), 158-162. [DOI]
Snel, B. (2002). Comparative genome analysis and genome evolution. [Doctoral thesis 1 (Research UU / Graduation UU), Universiteit Utrecht]. Universiteit Utrecht.
2001
Wetenschappelijke publicaties
Huynen, M. A., Snel, B., Bork, P., & Gibson, T. J. (2001). The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly. Human Molecular Genetics, 10(21), 2463-2468.
Huynen, M. A., Snel, B., & Bork, P. (2001). Inversions and the dynamics of eukaryotic gene order. Trends in Genetics, 17(6), 304-306. [DOI]
2000
Wetenschappelijke publicaties
Huynen, M., Snel, B., Lathe III, W., & Bork, P. (2000). Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Research, 10(8), 1204-1210. [DOI]
Lathe III, W. C., Snel, B., & Bork, P. (2000). Gene context conservation of a higher order than operons. Trends in Biochemical Sciences, 25(10), 474-479. [DOI]
Snel, B., Lehmann, G., Bork, P., & Huynen, M. A. (2000). String: A web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Research, 28(18), 3442-3444.
Dandekar, T., Huynen, M., Regula, J. T., Ueberle, B., Zimmermann, C. U., Andrade, M. A., Doerks, T., Sánchez-Pulido, L., Snel, B., Suyama, M., Yuan, Y. P., Herrmann, R., & Bork, P. (2000). Re-annotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames. Nucleic Acids Research, 28(17), 3278-3288.
Huynen, M., Snel, B., Lathe III, W., & Bork, P. (2000). Exploitation of gene context. Current Opinion in Structural Biology, 10(3), 366-370. [DOI]
Snel, B., Bork, P., & Huynen, M. (2000). Genome evolutiongene fusion versus gene fission. Trends in Genetics, 16(1), 9-11. [DOI]
Overige resultaten
Huynen, M. A., & Snel, B. (2000, Oct 13). Gene and context: Integrative approaches to genome analysis. Academic Press.
1999
Wetenschappelijke publicaties
Bork, P., Doerks, T., Springer, T. A., & Snel, B. (1999). Domains in plexins: Links to integrins and transcription factors. Trends in Biochemical Sciences, 24(7), 261-263. [DOI]
Dandekar, T., Schuster, S., Snel, B., Huynen, M. A., & Bork, P. (1999). Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochemical Journal, 343, 115-124.
Snel, B., Bork, P., & Huynen, M. A. (1999). Genome phylogeny based on gene content. Nature Genetics, 21(1), 108-110.
1998
Wetenschappelijke publicaties
Dandekar, T., Snel, B., Huynen, M., & Bork, P. (1998). Conservation of gene order: A fingerprint of proteins that physically interact. Trends in Biochemical Sciences, 23(9), 324-328. [DOI]