Berend Snel |
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| Theoretical Biology and Bioinformatics | Tel: | +31-(0)30-2538102 |
| Padualaan 8 | Fax: | +31-(0)30-2532837 |
| 3584 CH Utrecht | Email: | b.snel@uu.nl |
| the Netherlands |
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I studied biology at the university of Utrecht specializing in Theoretical Biology and Bioinformatics. I did my PhD project on comperative genome analysis and genome evolution in the
My main scientific interest is Evolutionary Genomics. e.g.:
Comparative Genome Analysis, Evolution of protein-protein interactions, evolution of protein complexes, Prediction of Protein-Protein Interactions, Pathway Evolution, Modularity in Genome Evolution, Orthology,
"Invention" of Gene Families, Distant Homology, Gene Duplication.
Stassen JH, Seidl MF, Vergeer PW, Nijman IJ, 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. Feb 1. doi: 10.1111/j.1364-3703.2011.00780.x. [Epub ahead of print]
Seidl MF, Van den Ackerveken G, Govers F, Snel B(2012) Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families. Genome Biol Evol. Jan 13. [Epub ahead of print]
Database independent proteomics analysis of the ostrich and human proteome. Altelaar AF, Navarro D, Boekhorst J, van Breukelen B, Snel B, Mohammed S, Heck AJ. (2012) Proc Natl Acad Sci U S A. 109:407-412
Mithoe SC, Boersema PJ, Berke L, Snel B, Heck AJ, Menke FL.(2012) Targeted quantitative phosphoproteomics approach for the detection of phospho-tyrosine signaling in plants. J Proteome Res. 11:438-448
van Dam TJ, Zwartkruis FJ, Bos JL, Snel B. (2011) Evolution of the TOR Pathway. J Mol Evol. 73:209-220
Boekhorst J, Boersema PJ, Tops BB, van Breukelen B, Heck AJ, Snel B. (2011) Evaluating experimental bias and completeness in comparative phosphoproteomics analysis. PLoS One 6:e23276
Prasad K, Grigg SP, Barkoulas M, Yadav RK, Sanchez-Perez GF, Pinon V, Blilou I, Hofhuis H, Dhonukshe P, Galinha C, Mähönen AP, Muller WH, Raman S, Verkleij AJ, Snel B, Reddy GV, Tsiantis M, Scheres B.(2011) Arabidopsis PLETHORA transcription factors control phyllotaxis. Curr Biol 21:1123-1128
van Dam TJ, Bos JL, Snel B. (2011) Evolution of the Ras-like small GTPases and their regulators. Small Gtpases 2:4-16.
Ding VM, Boersema PJ, Foong LY, Preisinger C, Koh G, Natarajan S, Lee DY, Boekhorst J, Snel B, Lemeer S, Heck AJ, Choo A. (2011) Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells. PLoS One 6:e17538
Seidl MF, Van Den Ackerveken G, Govers F, Snel B (2011) A domain-centric analysis of oomycete plant pathogen genomes reveals unique protein organization. Plant Physiology 155:628-644
Van Wageningen S, Kemmeren, Lijnzaad P, Margaritis T, Benschop JJ , de Castro IJ, Van Leenen D, Groot Koerkamp MJA, Ko CW, Miles AJ, Brabers N, Brok MO, Lenstra TL, Fiedler D , Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, Van de Pasch LAL, Van Hooff SR, Bakker LV,.Krogan NJ, Snel B, Holstege FCP (2010) Functional Overlap and Regulatory Links Shape Genetic Interactionsbetween Signaling Pathways. Cell 143(6):991-1004,
Bennett T, van den Toorn A, Sanchez-Perez GF, Campilho A, Willemsen V, Snel B, Scheres B (2010) SOMBRERO, BEARSKIN1, and BEARSKIN2 Regulate Root Cap Maturation in Arabidopsis Plant Cell, 22:640-654, PMID: 20197506
Fokkens L, Botelho SMC, Boekhorst J, Snel B (2010) Enrichment of homologs in insignificant BLAST hits by co-complex network alignment BMC Bioinformatics, 11:86 PMID: 20152020
Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB and Heck AJ. (2009) In depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immuno-affinity purification and stable isotope dimethyl labeling. Mol Cell Proteomics 9:84-99 PMID: 19770167
van Dam TJ, Rehmann H, Bos JL and Snel B. (2009) Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi. Cell Signal 21, 1579-1585
Fokkens L and Snel B (2009) Cohesive versus flexible evolution of functional modules in eukaryotes. PLoS Comput Biol 5, e1000276 PMID: 19180181
Szklarczyk R, Huynen MA and Snel B. (2008) Complex fate of paralogs. BMC Evol Biol 8, 337 PMID: 19094234
Boekhorst J, van Breukelen B, Heck AJ, Snel B. Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biol 2008 9, R144. PMID: 18828897
van Dam TJ and Snel B (2008) Protein complex evolution does not involve extensive network rewiring. PLoS Comput Biol.4, e1000132.
Dutilh BE, Snel B, Ettema TJ and Huynen MA (2008) Signature Genes as a Phylogenomic Tool. Mol Biol Evol 25, 1659-1667
Cordero OX, Snel B and Hogeweg P (2008) Coevolution of gene families in prokaryotes. Genome Res 18, 462-468
Boekhorst J and Snel B (2007) Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. BMC Bioinformatics 8, 356
van Noort V*, Snel B.* and Huynen MA (2007) Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions. Genome Biol 8, R197 *Contributed equally
van der Heijden RT, Snel B, van Noort V and Huynen MA. (2007) Orthology prediction at Scalable Resolution by Phylogenetic Tree analysis. BMC Bioinformatics 8, 83
Dutilh BE, van Noort V, van der Heijden RT, Boekhout T, Snel B and Huynen MA. (2007) Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics 23, 815-824
von Mering C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B. and Bork P. (2007) STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35, D358-D362
Kuramae, E.E., Robert, V., Snel, B., Weiss, M. and Boekhout, T. (2006) Phylogenomics reveal a robust fungal tree of life. FEMS Yeast Res 6,1213-1220
Kuramae, E.E., Robert, V., Snel, B. and Boekhout, T. (2006) Conflicting phylogenetic position of Schizosaccharomyces pombe. Genomics 88, 387-393
Oti, M., Snel, B., Huynen, M.A. and Brunner, H.G. (2006) Predicting disease genes using protein-protein interactions. J Med Genet 43, 691-698
Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M.W., Horn, H., Daims, H., Bartol-Mavel, D., Wincker, P., Barbe, V., Fonknechten, N., Vallenet, D., Segurens, B., Schenowitz-Truong, C., Médigue, C., Collingro, A., Snel, B., Dutilh, B.E., op den Camp, H.J.M., 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.M., Wagner, M. and Le Paslier, D. (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature, 440, 790-794
Gabaldon, T., Snel, B., van Zimmeren, F., Hemrika, W., Tabak, H. and Huynen, M. A. (2006) Origin and evolution of the peroxisomal proteome. Biol. Direct, 1, 8
Ciccarelli, F.D., Doerks, T., von Mering, C., Creevey, C.J., Snel, B. and Bork, P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science, 311, 1283-1287
Dutilh, B.E., Huynen, M.A. and Snel, B. (2006) A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. BMC Genomics, 7, 10
Notebaart, R.A., Huynen, M.A., Teusink, B., Siezen, R.J. and Snel, B. (2005) Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res., 33, 6164-6171
Snel B., Huynen, M.A. and Dutilh, B.E. (2005) Genome trees and the nature of genome evolution. Annu Rev Microbiol., 59, 191-209
Huynen, M.A., Gabaldon, T. and Snel, B. (2005) Variation and evolution of biomolecular systems: searching for functional relevance. FEBS Lett., 579, 1839-1845
Huynen, M.A., Spronk, C.A., Gabaldon, T. and Snel, B. (2005) Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin. FEBS Lett., 579, 591-596
von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. and Bork, P. (2005) STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res., 33 Database Issue:D433-437
Snel, B., van Noort, V. and Huynen, M. A.(2004) Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Nucleic Acids. Res., 32, 4725-4731
Huynen, M. A., Snel, B. and van Noort, V. (2004) Comparative genomics for reliable protein-function prediction from genomic data.Trends Genet., 20, 340-344
Dutilh, B.E., Huynen, M.A., Bruno, W.J. and Snel, B. (2004) The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise. J. Mol. Evol., 58, 527-539
Snel, B. and Huynen, M. A. (2004) Quantifying modularity in the evolution of biomolecular systems. Genome Res., 14, 391-397
van Noort, V., Snel, B. and Huynen, M. A. (2004) The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep., 5, 280-284
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. Nat. Biotechnol. , 21 790-795
van Noort, V., Snel, B. & Huynen, M. A. (2003) Predicting gene function by conserved co-expression. Trends Genet., 19, 238-242
Huynen, M. A., Snel, B., von Mering, C. & Bork, P. (2003) Function prediction and protein networks. Curr. Opin. Cell. Biol., 15, 191-198
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. Res., 31, 258-261
Huynen, M. A. & Snel, B. (2003) Exploiting the variations in the genomic associations of genes to predict pathways and reconstruct their evolution. In: Frontiers in Computational Genomics 145-166 (Editors, Galperin, M. Y. & Koonin, E. V.) Caister Academic Press
Dandekar, T., Snel, B., Schmidt, S., Lathe, W., Suyama, M., Huynen, M. & Bork, P.(2002) Comparative Genome Analysis of the Mollicutes. In: Molecular Biology and Pathogenity of Mycoplasmas 255-278 (Editors, Razin S, Herrmann R) Kluwer Academic / Plenum Publishers,
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. Proc. Natl. Acad. Sci. USA, 22, 14422-14427
Snel, B. (2002). Comparative Genome Analysis and Genome Evolution Ph. D. Thesis Utrecht University
Snel, B., Bork, P. & Huynen, M. A. (2002) Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol., 20, 410
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, 399-403
Snel, B., Bork, P. & Huynen, M. A. (2002) The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. USA, 99, 5890-5895
Korbel, J.O.+, Snel, B.+, Huynen, M. A. & Bork, P. (2002).
SHOT: a web server for the construction of genome phylogenies. Trends Genet., 18, 158-162
+ These authors contributed equally.
Snel, B., Bork, P. & Huynen, M. A. (2002) Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content Genome Res., 12, 17-25
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. Hum. Mol. Genet., 10, 2463-2468
Huynen, M. A., Snel, B., & Bork, P. (2001) Inversions and the dynamics of eukaryotic gene order. Trends Genet., 17, 304-306
Lathe III, W. C., Snel, B., & Bork, P. (2000) Gene context conservation of a higher order than operons. Trends Biochem. Sci., 25, 469-474
Bork, P., Snel, B., Lehmann, G., Suyama, M., Dandekar, T., Lathe III, W., & Huynen, M. A. (2000). Comparative genome analysis: exploiting the context of genes to infer evolution and predict function. In: Comparative Genomics, emprical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families, Computational biology series volume 1. 281-294 (Editors: Sankoff, D., & Nadeau, J. H.) Kluwer academic publishers
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 Res., 28, 3442-3444
This web-server is available at http://www.Bork.EMBL-Heidelberg.de/STRING/
Dandekar, T., Huynen, M., Regula, J. T., Ueberle, B., Zimmermann, C. U., Andrade, M. A., Doerks, T., Sanchez-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 Res., 28, 3278-3288
Huynen, M. A., Snel, B., Lathe III, W., & Bork, P. (2000) Predicting protein function by genomic context: quantative evaluation and qualitative inferences Genome Res., 10, 1204-1210
Huynen, M. A., Snel, B., Lathe III, W., & Bork, P. (2000) Exploitation of gene context. Curr. Opin. Struct. Biol., 10, 366-370
Huynen, M. A. & Snel, B. (2000) Gene and context: integrative approaches to genome analysis. Adv. Prot. Chem., 54, 345-380
Snel, B., Bork, P. & Huynen, M. A. (2000) Genome evolution: gene fusion versus gene fission. Trends Genet., 16, 9-11
Huynen, M. A., Snel, B. & Bork, P. (1999) Lateral Gene Transfer, Genome Surveys, and the Phylogeny of Prokaryotes Science, 286, 1443a (in Technical Comments)
Dandekar, T., Schuster, S., Snel, B., Huynen, M. A., & Bork, P. (1999) Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem J., 343, 115-124
Bork, P., Doerks, T., Springer, T.A. & Snel,B. (1999) Domains in plexins: links to integrins and transcription factors. Trends Biochem. Sci., 24, 261-263
Bork, P., Dandekar, T., Snel, B. & Huynen, M. A. (1999) Genome Comparsions to Monitor Molecular Evolution. In: Microbial Evolution and Infection. 80-92 (Goebel, U.B., Ruf, B.R.) Einhorn-Presse Verlag Reinbek
Snel, B., Bork, P. & Huynen, M. A. (1999) Genome phylogeny based on gene content. Nature Genet., 21, 108-110
Dandekar, T., Snel, B., Huynen, M. A. & Bork, P. (1998)
Conservation of gene order: a fingerprint of proteins that physically
interact. Trends Biochem. Sci., 23, 324-328
CMBI bioinformatics seminar series 2004: Predicting interactions between genes based on genome comparisons (
CMBI bioinformatics seminar series 2005: Predicting interactions between genes based on genome comparisons (
Masters / PhD Course Evolutionary Genomics and Protein Function Prediction
