Publications
2021
Scholarly publications
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. [e106536]. https://doi.org/10.15252/embj.2020106536
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. [bbaa206]. https://doi.org/10.1093/bib/bbaa206
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. https://doi.org/10.1038/s41559-020-01320-z
2020
Scholarly publications
van Wijk, L. M., & Snel, B. (2020, Jan 31). The first eukaryotic kinome tree illuminates the dynamic history of present-day kinases. bioRxiv. https://doi.org/10.1101/2020.01.27.920793
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. https://doi.org/10.1016/j.cub.2020.02.021
Von Der Dunk, S. H. A., & Snel, B. (2020). Recurrent sequence evolution after independent gene duplication. BMC Evolutionary Biology, 20(1), [98]. https://doi.org/10.1186/s12862-020-01660-1
2019
Scholarly publications
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. https://doi.org/10.1007/s00412-019-00700-0
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. https://doi.org/10.1101/gad.300475.117
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), [e1007301]. https://doi.org/10.1371/journal.pcbi.1007301
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. https://doi.org/10.1073/pnas.1821945116
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), [1900006]. https://doi.org/10.1002/bies.201900006
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. https://doi.org/10.1261/rna.067983.118
2018
Scholarly publications
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(Pt A), 36-49. https://doi.org/10.1016/j.pbi.2018.05.001
2017
Scholarly publications
Vosseberg, J., & Snel, B. (2017). Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery. Biology Direct, 12, [30]. https://doi.org/10.1186/s13062-017-0201-6
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. https://doi.org/10.1093/gbe/evx088
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), 1473-1671. https://doi.org/10.15252/embr.201744102
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. https://doi.org/10.1111/nph.14355
2016
Scholarly publications
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, [160315]. https://doi.org/10.1098/rsob.160315
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. https://doi.org/10.1105/tpc.16.00656
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, [30444]. https://doi.org/10.1038/srep30444
2015
Scholarly publications
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). https://doi.org/10.1186/s12915-015-0222-5
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. https://doi.org/10.1021/acs.jproteome.5b00370
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. https://doi.org/10.1093/gbe/evv140
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). https://doi.org/10.1186/s12862-015-0319-z
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. https://doi.org/10.1016/j.cell.2015.04.033
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), 210-22. https://doi.org/10.1111/tpj.12719
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. https://doi.org/10.1089/ars.2014.6056
2014
Scholarly publications
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). https://doi.org/10.1186/s12870-014-0306-3
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. https://doi.org/10.1021/pr4009095
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. https://doi.org/10.1104/pp.113.228080
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. https://doi.org/10.1093/gbe/evu081
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. https://doi.org/10.1093/gbe/evu040
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. https://doi.org/10.1016/j.cell.2014.02.054
2013
Scholarly publications
de Bruijn, I., de 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., Morris, P., ... West, P. (2013). Distinctive expansions of the potential virulence genes in the genome of the oomycete fish pathogen. PLoS Genetics, 9 (6).
https://dspace.library.uu.nl/bitstream/handle/1874/287058/Jiang2013.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/287058/Jiang2013.pdf?sequence=1
Jiang, R. H. I., de Bruijn, I., de Haas, B., 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 expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica. PLoS Genetics, 9(6), e1003272. https://doi.org/10.1371/journal.pgen.1003272
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. https://doi.org/10.1186/1471-2164-14-483
Schneider, A., Seidl, M. F., & Snel, B. (2013). Shared protein complex subunits contribute to explaining disrupted co-occurrence. PLoS Computational Biology, 9(7), e1003124. https://doi.org/10.1371/journal.pcbi.1003124
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. https://doi.org/10.1083/jcb.2/01307016
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. https://doi.org/10.1083/jcb.201210033
2012
Scholarly publications
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). https://doi.org/10.1371/journal.pone.0051295
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, 719-731.
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. https://doi.org/10.1021/pr200893k
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. https://doi.org/10.1016/j.devcel.2012.03.009
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.
https://dspace.library.uu.nl/bitstream/handle/1874/257246/Reconstruction%2520of%2520oomycete%2520genome%2520evolution%2520identifies%2520differences%2520in.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/257246/Reconstruction%2520of%2520oomycete%2520genome%2520evolution%2520identifies%2520differences%2520in.pdf?sequence=1
Other output
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
Scholarly publications
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. https://doi.org/10.1104/pp.110.167841
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
Scholarly publications
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.
Other output
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
Scholarly publications
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
Scholarly publications
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
Scholarly publications
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.
https://dspace.library.uu.nl/bitstream/handle/1874/27120/Von%2520Mering%2520et%2520al.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/27120/Von%2520Mering%2520et%2520al.pdf?sequence=1
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
Scholarly publications
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.
https://dspace.library.uu.nl/bitstream/handle/1874/19483/51%2520Tabak%2520Biol%2520Direct%252006.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/19483/51%2520Tabak%2520Biol%2520Direct%252006.pdf?sequence=1
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
Scholarly publications
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. https://doi.org/10.1093/nar/gki913
Huynen, M. A., Gabaldón, T., & Snel, B. (2005). Variation and evolution of biomolecular systems: Searching for functional relevance. FEBS Letters, 579(8), 1839-1845. https://doi.org/10.1016/j.febslet.2005.02.004
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. https://doi.org/10.1016/j.febslet.2004.11.111
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. https://doi.org/10.1093/nar/gki005
Snel, B., Huynen, M. A., & Dutilh, B. E. (2005). Genome trees and the nature of genome evolution. Annual Review of Microbiology, 59, 191-209. https://doi.org/10.1146/annurev.micro.59.030804.121233
2004
Scholarly publications
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. https://doi.org/10.1007/s00239-003-2575-6
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. https://doi.org/10.1093/nar/gkh815
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. https://doi.org/10.1016/j.tig.2004.06.003
Snel, B., & Huynen, M. A. (2004). Quantifying modularity in the evolution of biomolecular systems. Genome Research, 14(3), 391-397. https://doi.org/10.1101/gr.1969504
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. https://doi.org/10.1038/sj.embor.7400090
2003
Scholarly publications
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. https://doi.org/10.1038/nbt834
Van Noort, V., Snel, B., & Huynen, M. A. (2003). Predicting gene function by conserved co-expression. Trends in Genetics, 19(5), 238-242. https://doi.org/10.1016/S0168-9525(03)00056-8
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. https://doi.org/10.1016/S0955-0674(03)00009-7
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. https://doi.org/10.1093/nar/gkg034
2002
Scholarly publications
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. https://doi.org/10.1073/pnas.212527599
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. https://doi.org/10.1073/pnas.092632599
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. https://doi.org/10.1101/gr.176501
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. https://doi.org/10.1016/S0168-9525(01)02597-5
Snel, B. (2002). Comparative genome analysis and genome evolution. Universiteit Utrecht.
2001
Scholarly publications
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. https://doi.org/10.1016/S0168-9525(01)02302-2
2000
Scholarly publications
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. https://doi.org/10.1101/gr.10.8.1204
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. https://doi.org/10.1016/S0968-0004(00)01663-7
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. https://doi.org/10.1016/S0959-440X(00)00098-1
Snel, B., Bork, P., & Huynen, M. (2000). Genome evolutiongene fusion versus gene fission. Trends in Genetics, 16(1), 9-11. https://doi.org/10.1016/S0168-9525(99)01924-1
Other output
Huynen, M. A., & Snel, B. (2000, Oct 13). Gene and context: Integrative approaches to genome analysis. Academic Press Inc.
1999
Scholarly publications
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. https://doi.org/10.1016/S0968-0004(99)01416-4
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
Scholarly publications
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. https://doi.org/10.1016/S0968-0004(98)01274-2