Berend Snel

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
 

Background / CV

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 group of Peer Bork at EMBL (Heidelberg, Germany). Subsequently I worked first as a normal post-doc and then as a VENI post-doc in Martijn Huynen's Comparative Genomics (COMICS) group at the CMBI / NCMLS in Nijmegen, Holland. In 2006 I moved to the Utrecht University as associate professor. In Utrecht I head my own Evolutionary Genomics and Integrative Bioinformatics group as part of Theoretical biology and Bioinformatics in the Department of Biology at Utrecht University. As of June 2014 I am appointed as professor in bioinformatics and chair of the executive board of the Utrecht Bioinformatics Center.
 

Scientific Interests

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.

Publications

2015

Koster MJ, Snel B Timmers HT. (2015) Genesis of Chromatin and Transcription Dynamics in the Origin of Species. Cell. 161:724-736.

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 Evol Biol. 15:44.

Putker M, Vos HR, van Dorenmalen K, de Ruiter H, Duran AG, Snel B, Burgering BM, Vermeulen M, Dansen TB. (2015) Evolutionary Acquisition of Cysteines Determines FOXO Paralog-Specific Redox Signaling. Antioxid Redox Signal 22:15-28.

Zeilmaker T, Ludwig NR, Elberse J, Seidl MF, Berke L, Van Doorn A, Schuurink RC, 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 J 81:210-222.

2014

Gamm M, Peviani A, Honsel A, Snel B, Smeekens S, Hanson J. (2014) Increased sucrose levels mediate selective mRNA translation in Arabidopsis BMC Plant Biol 14:306.

Kemmeren P, Sameith K, van de Pasch LA, Benschop JJ, Lenstra TL, Margaritis T, O'Duibhir E, Apweiler E, van Wageningen S, Ko CW, van Heesch S, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ, Bouwmeester D, van Hooff SR, van Bakel H, Sluiters E, Bakker LV, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Holstege FC. (2014) Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors. Cell 157:740-752

van Hooff JJ, Snel B, Seidl MF. (2014) Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication. Genome Biol Evol. 6:1079-1085

Resjö S, Ali A, Meijer HJ, Seidl MF, 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. J Proteome Res 4:1848-1859

Berke L, Snel B.(2014) The Histone Modification H3K27me3 Is Retained after Gene Duplication and Correlates with Conserved Noncoding Sequences in Arabidopsis. Genome Biol Evol. 6:572-579

Gruhn N, Halawa M, Snel B, Seidl MF, Heyl A. (2014) A new subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants. Plant Physiol 165:227-237

2013

Vleugel M, Tromer E, Omerzu M, Groenewold V, Nijenhuis W, Snel B, Kops GJ. (2013) Arrayed BUB recruitment modules in the kinetochore scaffold KNL1 promote accurate chromosome segregation. J Cell Biol. 203:943-955

Schneider A, Seidl MF, Snel B.(2013) Shared protein complex subunits contribute to explaining disrupted co-occurrence. PLoS Comput Biol. 9:e1003124

Jiang RH, de Bruijn I, Haas BJ, Belmonte R, Löbach L, Christie J, van den Ackerveken G, Bottin A, Bulone V, Díaz-Moreno SM, Dumas B, Fan L, Gaulin E, Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJ, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JH, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, van West P. (2013) Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica. PLoS Genet. 9:e1003272

Nijenhuis W, von Castelmur E, Littler D, De Marco V, Tromer E, Vleugel M, van Osch MH, Snel B, Perrakis A, Kops GJ. (2013) A TPR domain-containing N-terminal module of MPS1 is required for its kinetochore localization by Aurora B. J Cell Biol. 201:217-231.

Wind JJ, Peviani A, Snel B, Hanson J, Smeekens SC. (2013) ABI4: versatile activator and repressor. Trends Plant Sci. 18:125-132

2012

Seidl MF, Wang RP, 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:e51295.

Berke L, Sanchez-Perez GF, Snel B. (2012) Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis. Genome Biol. 13:R94.

Vleugel M, Hoogendoorn E, Snel B*, Kops GJ*. (2012) Evolution and function of the mitotic checkpoint. Dev Cell. 23:239-250. *Contributed equally

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

Suijkerbuijk SJ, van Dam TJ, Karagöz GE, von Castelmur E, Hubner NC, Duarte AM, Vleugel M, Perrakis A, Rüdiger SG, Snel B, Kops GJ. (2012) The Vertebrate Mitotic Checkpoint Protein BUBR1 Is an Unusual Pseudokinase. Dev Cell. 2012 22:1321-1329

de Lau WB, Snel B, Clevers HC. (2012) The R-spondin protein family. Genome Biol. 2012 13:242

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. 13:719-731

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. 4:199-211

Altelaar AF, Navarro D, Boekhorst J, van Breukelen B, Snel B, Mohammed S, Heck AJ. (2012) Database independent proteomics analysis of the ostrich and human proteome. 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

2011

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

2010

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

2009

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

2008

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

2007

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

2006

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

2005

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

2004

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

2003

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

2002

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

2001

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

2000

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

1999

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

1998

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
 

Lectures

CMBI bioinformatics seminar series 2004: Predicting interactions between genes based on genome comparisons ( ppt )

CMBI bioinformatics seminar series 2005: Predicting interactions between genes based on genome comparisons ( ppt )

Masters / PhD Course Evolutionary Genomics and Protein Function Prediction