Rutger Vos

Introduction

2009-03-04T03:31:00.000-08:00

My parents are both physical geographers, which meant on family trips they always pointed out the scars of an old earth weathered over large timescales. They showed my brothers and me the basalt pillars that turned into the black, sandy beaches, toe-searingly hot in the sun, of the crater lake where we swam every summer; the huge grooves carved into the rock faces of the Alps by glaciers that long ago filled the valleys where we went hiking; the Rhine river depositing the clay once used by the brickworks in our hometown. And in the rocks that my father collected, sometimes a fossil of an animal or a plant.

I don’t remember ever not having the vague notion that, over large time scales, species become other species, or go extinct and become fossils. This is what evolution is to most people: a story of things appearing and disappearing, from trilobites to cavemen, all very long ago and neatly organized into eras that you’re supposed to memorize. Only as an undergraduate student, near graduation, did I come to realize that evolution is not actually a story: it's a process, which creates the patterns we see around us in nature.

In my research at the time I was trying to show how primates had evolved to fill up different ecological niches to various levels of specialization, thinking that there might be simple rules that underlie this. My adviser taught me to look at this diversity as the outcome of a repeated natural experiment: from a common ancestor, primate lineages had to come up with different, evolved solutions under different pressures. Or, sometimes, the same solution independently arrived at multiple times, under the same pressures. By drawing the right comparisons across combinations of solutions, the rules that led to them should reveal themselves.

Because all living and extinct species are related to one another we have to be careful with drawing comparisons among them: not every pattern that we see in nature is the result of solutions repeatedly arrived at by evolution. At least some similarities across species are the result of a solution arrived at just once, in a common ancestor, whose characteristics simply stuck around in its descendants. Where we might think there is a general rule, there’s actually just a single event that happened before the tree of life branched out further into new species.

The methods that are used to reconstruct the shape of the tree of life and to place evolutionary changes on this tree are my main scientific interest. To pursue this interest in the way that I want I have had to pick up the nerd skills that broadly have to do with how we digitally represent, describe, combine and analyze observations we make - at the level of DNA all the way to that of individuals and groups. I have so far been able to apply these techniques to interesting questions about evolution in life forms as diverse as primates, pitcher plants, snakes, tomatoes, birds, orchids, and numerous insects.

Recent funding sources

2009-03-03T21:34:00.000-08:00

Funding for my research comes from a disparate number of sources. In the last years, these included:

HIP: Hackathons, Interoperability, Phylogenies: from 2011-2013, the National Evolutionary Synthesis Center has awarded Arlin Stoltzfus, Enrico Pontelli and me funding and support to organize hackathons on interoperability in evolutionary informatics.
Marie Curie fellowship from 2009-2011, the Community Research and Development Information Service for Science, Research and Development of the European Commission has awarded me a fellowship for comparative genomics research at the University of Reading.
Google Summer of Code grants to hire student developers, 2007, 2008 and 2010
NESCent working group from 2007-2009, the National Evolutionary Synthesis Center awarded Arlin Stoltzfus and me funding to organize four meetings of a working group on evolutionary informatics.
UBC Postdoctoral fellowship, 2006-2009
President’s Research Stipend, 2005
SSB Systematic Biology Graduate Research Award, 2003
SFU Travel Award, 2003
SFU Graduate Fellowships, 2002, 2003

Publications

2007-10-11T08:23:00.000-07:00

Mutanen, M., Kivelä, S.M., Vos, R.A., Doorenweerd, C., Ratnasingham, S., Hausmann, A., Huemer, P., Dincă, V., van Nieukerken, E.J., Lopez-Vaamonde, C., Vila, R., Aarvik, L., Decaëns, T., Efetov, K.A., Hebert, P.D.N., Johnsen, A., Karsholt, O., Pentinsaari, M., Rougerie, R., Segerer, A., Tarmann, G., Zahiri, R., Godfray, H.C.J. 2016. Species-Level Para-and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera. Systematic Biology [10.1093/sysbio/syw044]

Pentinsaari, M., Vos, R.A., Mutanen, M. 2016. Algorithmic single-locus species delimitation: effects of sampling effort, variation and non-monophyly in four methods and 1870 species of beetles. Molecular Ecology Resources [10.1111/1755-0998.12557]

R.A. Vos. 2016. Ten simple rules for managing high-throughput nucleotide sequencing data. bioRxiv [10.1101/049338]

Schilthuizen, M., Pimenta, L., Lammers, Y., Steenbergen, P., Flohil, M., Beveridge, N., van Duijn, P., Meulblok, M., Sosef, N., van de Ven, R., Werring, R., Beentjes, K., Meijer, K., Vos, R., Vrieling, K., Gravendeel, B., Choi, Y., Verpoorte, R., Smit, C., L. Beukeboom. 2016. Incorporation of an Invasive Plant Into a Native Insect Herbivore Food Web. PeerJ [10.7717/peerj.1954]

Koureas, D., Hardisty, A., Vos, R.A., Agosti, D., Arvanitidis, C., Bogatencov, P., Buttigieg, P.L., De Jong, Y., Horvath, F., Gkoutos, G., Groom, Q.J., Kliment, T., Kõljalg, U., Manakos, I., Marcer, A., Marhold, K., Morse, D., Mergen, P., Penev, L., Pettersson, L.B., Svenning, J.-C., Van de Putte, A., Smith, V.S. 2016. Unifying European Biodiversity Informatics (BioUnify). Research Ideas and Outcomes 2: e7787 [10.3897/rio.2.e7787]

Miller, J.A., Agosti, D., Penev, L., Sautter, G., Georgiev, T., Catapano, T., Patterson, D., King, D., Pereira, S., Vos, R.A., Sierra, S. 2015. Integrating and visualizing primary data from prospective and legacy taxonomic literature. Biodiversity Data Journal 3: e5063 [10.3897/BDJ.3.e5063]

Boettiger, C., Lapp, L., Chamberlain, S., Vos, R. 2015. RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R. Methods in Ecology and Evolution [10.1111/2041-210X.12469]

Schwallier, R., Raes, N., de Boer, H., Vos, R., van Vugt, R., and B. Gravendeel. 2015. Phylogenetic analysis of niche divergence reveals distinct evolutionary histories and climate change implications for tropical carnivorous plants. Diversity and Distributions [10.1111/ddi.12382]

Bochove, K., Bakker, F., Beentjes, K., Vos, R., and B. Gravendeel. In review. Low pH and presence of organic matter reduce amount of detectable environmental DNA in freshwater. Molecular Ecology Resources

Antonelli, A., Condamine, F.L., Hettling, H., Nilsson, K.S., Nilsson, R.H., Oxelman, B., Sanderson, M.J., Sauquet, H., Scharn, R., Silvestro, D., Töpel, M., and R.A. Vos. 2014. SUPERSMART: Ecology and Evolution in the Era of Big Data. PeerJ Preprints 2:e501v1 [10.7287/peerj.preprints.501v1]

Gravendeel, B., Finkers, R., Lammers, Y., Nieman, A., Sanchez-Perez, G.F., Schijlen, E., Smets, E. and R.A. Vos. In review. Reconstruction of the breeding history of tomato (Solanum lycopersicum var. lycopersicum) by whole-genome sequencing of historical collections. The Plant Journal

Vos, R.A., Biserkov, J.V., Balech, B., Beard, N., Blissett, M., Brenninkmeijer, C., van Dooren, T., Eades, D., Gosline, G., Groom, Q.J., Hamann, T.D., Hettling, H., Hoehndorf, R., Holleman, A., Hovenkamp, P., Kelbert, P., King, D., Kirkup, D., Lammers, Y., DeMeulemeester, T., Mietchen, D., Miller, J.A., Mounce, R., Nicolson, N., Page, R.D.M., Pawlik, A., Pereira, S., Penev, L., Richards, K., Sautter, G., Shorthouse, D.P., Tähtinen, M., Weiland, C., Williams, A.R. and S. Sierra. 2014. Enriched biodiversity data as a resource and service. Biodiversity Data Journal 2:e1125 [10.3897/BDJ.2.e1125]

Aflitos, S., Schijlen, E., Finkers, R., Smit, S., Wang, J., Zhang, G., Li, N., Mao, L., de Jong, H., Bakker, F., Gravendeel, B., Breit, T., Dirks, R., Huits, H., Struss, D., Swanson-Wagner, R., van Leeuwen, H., van Ham, R.C.H.J., Fito, L., Guignier, L., Sevilla, M., Ellul, P., Ganko, E., Kapur, A., Reclus, E., de Geus, B., van de Geest, H., te Lintel Hekkert, B., van Haarst, J., Smits, L., Koops, A., Sanchez-Perez, G., van Heusden, A.W., Visser, R., Quan, Z., Min, J., Liao, L., Wang, X., Wang, G., Yue, Z., Yang, X., Xu, N., Schranz, E., Smets, E., Vos, R.A., Rauwerda, J., Ursem, R., Schuit, C., Kerns, M., van den Berg, J., Vriezen, W., Janssen, A., Jahrmann, T., Moquet, F., Bonnet, J., Peters, S. 2014. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. The Plant Journal. [10.1111/tpj.12616]

van Geel, B., Protopopov, A., Bull, I., Duijm, E., Gill, F., Nieman, A., Rudaya, N., Tikhonov, A., Trofimova, S., van Reenen, G., Vos, R.A., Zhilich, S., Gravendeel, B. 2014. Multiproxy study of the last meal of a mid-Holocene Oyogos Yar horse, Sakha Republic, Russia. The Holocene: 1-9 [10.1177/0959683614540953]

van Geel, B., Protopopov, A., Bull, I., Duijm, E., Gill, F., Nieman, A., Rudaya, N., Trofimova, S., Tikhonov, A., Vos, R.A., Zhilich, S., Gravendeel, B. 2014. Multiproxy diet analysis of the last meal of an early Holocene Yakutian Bison. Journal of Quarternary Science. 3:261-268 [10.1002/jqs.2698]

Lammers, Y., Peelen, T., Vos, R.A., Gravendeel, B. 2014. The CITES checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data. BMC Bioinformatics. 15:44 [10.1186/1471-2105-15-44]

T. Katayama, M.D. Wilkinson, K.F. Aoki-Kinoshita, S. Kawashima, Y. Yamamoto, A. Yamaguchi, S. Okamoto, S. Kawano, J.-D. Kim, Y. Wang, H. Wu, Y. Kano, H. Ono, H. Bono, S. Kocbek, J. Aerts, Y. Akune, E. Antezana, K. Arakawa, B. Aranda, J. Baran, J. Bolleman, R. JP Bonnal, P. L. Buttigieg, M. P Campbell, Yi-. Chen, H. Chiba, P. JA Cock, K. B Cohen, A. Constantin, G. Duck, M. Dumontier, T. Fujisawa, T. Fujiwara, N. Goto, R. Hoehndorf, Y. Igarashi, H. Itaya, M. Ito, W. Iwasaki, M. Kalas, T. Katoda, T. Kim, A. Kokubu, Y. Komiyama, M. Kotera, C. Laibe, H. Lapp, T. Lütteke, M.S. Marshall, T. Mori, H. Mori, M. Morita, K. Murakami, M. Nakao, H. Narimatsu, H. Nishide, Y. Nishimura, J. Nystrom-Persson, S. Ogishima, Y. Okamura, S. Okuda, K. Oshita, N. H Packer, P. Prins, R. Ranzinger, P. Rocca-Serra, S. Sansone, H. Sawaki, S.-H. Shin, A. Splendiani, F. Strozzi, S. Tadaka, P. Toukach, I. Uchiyama, M. Umezaki, R. Vos, P.L. Whetzel, I. Yamada, C. Yamasaki, R. Yamashita, W.S. York, C.M. Zmasek, S. Kawamoto, T. Takagi. 2014. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics. 5:5. [10.1186/2041-1480-5-5]

Vonk, F.J., Casewell, N.R., Henkel, C.V., Heimberg, A., Jansen, H.J., McCleary, R.J., Kerkkamp, H., Vos, R.A., , Guerreiro, I., Calvette, J., Wuster, W., Woods, A.E., Logan, J., Harrison, R.A., Castoe, T.A., de Koning, A.J., Pollock, D.D., Yandell, M., Calderon, D., Renjifo, C., Currier, R.B., Salgado, D., Pla, D., Sanz, L., Hyder, A.S., Ribeiro, J.M.C., Arntzen, J.W., van den Thillart, G.E.E.J.M., Boetzer, M., Pirovano, W., Dirks, R., Spaink, H.P., Duboule, D., McGlinn, E., Kini, R.M., Richardson, M.K. 2013. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. PNAS. [10.1073/pnas.1314702110]

Maryam Panahiazar, Amit P. Sheth, Ajith Ranabahu, Rutger A. Vos, Jim Leebens-Mack. 2013. Advancing Data Reuse in Phyloinformatics Using an Ontology-Driven Semantic Web Approach. BMC Medical Genomics 6(Suppl 3):S5 [10.1186/1755-8794-6-S3-S5]

Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon, Megan Pirrung, Brian O'Meara, Matthew W Pennell, Siavash Mirarab, Michael S Rosenberg, James P Balhoff, Holly M Bik, Tracy Heath, Peter Midford, Joseph W Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E Alfaro and Aaron Steele. 2013. Phylotastic! Making Tree-of-Life Knowledge Accessible, Re-usable and Convenient. BMC Bioinformatics 14:158 [10.1186/1471-2105-14-158]

T. Katayama, M. D. Wilkinson, G. Micklem, S. Kawashima, A. Yamaguchi, M. Nakao, Y. Yamamoto, S. Okamoto, K. Oouchida, H.-W. Chun, J. Aerts, H. Afzal, E. Antezana, K. Arakawa, B. Aranda, F. Belleau, J. Bolleman, R. J. Bonnal, B. Chapman, P. Cock, T. Eriksson, P. Gordon, N. Goto, K. Hayashi, H. Horn, R. Ishiwata, E. Kaminuma, A. Kasprzyk, H. Kawaji, N. Kido, Y. J. Kim, A. R. Kinjo, F. Konishi, K.-H. Kwon, A. Labarga, A.-L. Lamprecht, Y. Lin, P. Lindenbaum, L. McCarthy, H. Morita, K. Murakami, K. Nagao, K. Nishida, K. Nishimura, T. Nishizawa, S. Ogishima, K. Ono, K. Oshita, K.-J. Park, P. Prins, T. L. Saito, M. Samwald, V. P. Satagopam, Y. Shigemoto, R. Smith, A. Splendiani, H. Sugawara, J. Taylor, R. Vos, D. Withers, C. Yamasaki, C. M. Zmasek, S. Kawamoto, K. Okubo, K. Asai, T. Takagi. 2013. The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies. Journal of Biomedical Semantics 4:6 [10.1186/2041-1480-4-6]

A. Stoltzfus, B. O'Meara, J. Whitacre, R. Mounce, E. L. Gillespie, S. Kumar, D. F. Rosauer, and R. A. Vos. 2012. Sharing and Re-use of Phylogenetic Trees (and associated data) to Facilitate Synthesis. BMC Research Notes 5:574 [10.1186/1756-0500-5-574]

R. J. P. Bonnal, J. Aerts, G. Githinji, N. Goto, D. MacLean, C. Miller, H. Mishima, M. Pagani, R. Ramirez-Gonzalez, G. Smant, F. Strozzi, R. Syme, R. A. Vos, T. J. Wennblom, B. J. Woodcroft, T. Katayama and P. Prins. 2012. Ruby Biogems: pluggable software modules for the next generation. Bioinformatics 28(7):1035-1037. [10.1093/bioinformatics/bts080]

Rutger A. Vos, J. P. Balhoff, J. A. Caravas, M. T. Holder, H. Lapp, W. P. Maddison, P. E. Midford, A. Priyam, J. Sukumaran, X. Xia, and A. Stoltzfus. 2012. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology. 61(4): 675-689 [10.1093/sysbio/sys025]

T. Katayama, M. D. Wilkinson, R. A. Vos, T. Kawashima, S. Kawashima, M. Nakao, Y. Yamamoto, H.-W. Chun, A. Yamaguchi, S. Kawano, J. Aerts, K. F. Aoki-Kinoshita, K. Arakawa, B. Aranda, R. J. P. Bonnal, J. M. Fernández, T. Fujisawa, P. M. K. Gordon, N. Goto, S. Haider, T. Harris, T. Hatakeyama, I. Ho, M. Itoh, A. Kasprzyk, N. Kido, Y. J. Kim, A. R. Kinjo, F. Konishi, Y. Kovarskaya, G. von Kuster, A. Labarga, V. Limviphuvadh, L. McCarthy, Y. Nakamura, Y. Nam, K. Nishida, K. Nishimura, T. Nishizawa, S. Ogishima, T. Oinn, S. Okamoto, S. Okuda, K. Ono, K. Oshita, K.-J. Park, N. Putnam, M. Senger, J. Severin, Y. Shigemoto, H. Sugawara, J. Taylor, O. Trelles, C. Yamasaki, R. Yamashita, N. Satoh and T. Takagi. 2011. The 2nd DBCLS BioHackathon: interoperable bioinformatics web services for integrated applications. Journal of Biomedical Semantics: 2:4 [10.1186/2041-1480-2-4]

B. O'Meara, J. Whitacre, R. Mounce, D. Rosauer, R. A. Vos, A. Stoltzfus. 2011. Publishing Re-usable Phylogenetic Trees, in Theory and Practice. Nature Precedings, peer-reviewed for iEvoBio. [10.1038/npre.2011.6048.1]

R. A. Vos, J. Caravas, K. Hartmann, M. A. Jensen, C. Miller. 2011. Bio::Phylo - Phyloinformatic Analysis Using Perl. BMC Bioinformatics.: 12:63 [10.1186/1471-2105-12-63]

T. Katayama, K. Arakawa, M. Nakao, K. Ono, K. F. Aoki-Kinoshita, Y. Yamamoto, J. Aerts, B. Aranda, L. H. Barboza, R. J. P. Bonnal, R. Bruskiewich, J. C. Bryne, H.-W. Chun, J. M. Fernendez, A. Funahashi, P. M. K. Gordon, N. Goto, A. Groscurth, A. Gutteridge, R. Holland, Y. Kano, E. A. Kawas, S. Kawashima, A. Kerhornou, E. Kibukawa, A. R. Kinjo, M. Kuhn, H. Lapp, H. Lehvaslaiho, H. Nakamura, Y. Nakamura, T. Nishizawa, C. Nobata, T. Noguchi, T. M. Oinn, S. Okamoto, S. Owen, E. Pafilis, M. Pocock, P. Prins, R. Ranzinger, F. Reisinger, L. Salwinski, M. Schreiber, M. Senger, Y. Shigemoto, D. M. Standley, H. Sugawara, T. Tashiro, O. Trelles, R. A. Vos, M. D. Wilkinson, A. Yamaguchi, W. York, C. M. Zmasek, K. Aasai and T. Takagi. 2010. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. Journal of Biomedical Semantics: 1:8 [10.1186/2041-1480-1-8]

Vos, R.A., H. Lapp, W. Piel, and V. Tannen. 2010. TreeBASE2: Rise of the Machines. Nature Precedings, peer-reviewed for iEvoBio. [10101/npre.2010.4600.1]

Vos, R.A.. 2010. Bio::Phylo – Phyloinformatic Analysis Using Perl. Nature Precedings, peer-reviewed for iEvoBio. [10.1038/npre.2010.4601.1]

A. Stoltzfus, K. Cranston, H. Lapp, S. McKay, E. Pontelli, R. A. Vos and N. Cellinese. 2010. EvoIO: Community-driven standards for sustainable interoperability. Nature Precedings, peer-reviewed for iEvoBio. [10101/npre.2010.4588.1]

M. A. Miller, L. Chan, M. T. Holder, P. Hoover, T. Leibowitz, P. Midford, R. A. Vos and T. Warnow. In review. The CIPRES Portal for Inference of Phylogenetic Trees. Bioinformatics

J. M. Hipfner, K. B. Gorman, J. B. Joy and R. A. Vos, 2010. Evolution of embryonic developmental period in the marine bird families Alcidae and Spheniscidae: roles for nutrition and predation? BMC Evolutionary Biology: 10:179 [10.1186/1471-2148-10-179]

Vos, R. A., accepted. Accelerated Metropolis-Hastings coupled Markov chain Monte Carlo burn-in by iterative jackknifing. Systematic Biology

Vos, R. A. and A. Ø. Mooers, in revision. A dated MRP supertree for the order Primates. Systematic Biology

William H. Piel, Lucie Chan, Mark J. Dominus, Jin Ruan, Rutger A. Vos, Val Tannen. 2009. TreeBASE Version 2: A Database Of Phylogenetic Knowledge. e-Biosphere 09 International Conference on Biodiversity Informatics

Rutger A. Vos. 2008. Data standards in phylogenetics: the NeXML project. Proceedings of TDWG [abstract]

H. Lapp, S. Bala, J. P. Balhoff, A. Bouck, N. Goto, M. Holder, R. Holland, A. Holloway, T. Katayama, P. O. Lewis, A. Mackey, B. I. Osborne, W. H. Piel, S. L. Kosakovsky Pond, A. Poon, W.-G. Qiu, J. E. Stajich, A. Stoltzfus, T. Thierer, A. J. Vilella, R. A. Vos, C. M. Zmasek, D. Zwickl and Todd J. Vision. 2007. The 2006 NESCent Phyloinformatics Hackathon: A field report. Evolutionary Bioinformatics Online3: 357-366. [abstract]

O. R. P. Bininda-Emonds, M. Cardillo, K. E. Jones, R. D. E. MacPhee, R. M. D. Beck, R. Grenyer, S. A. Price, R. A. Vos, J. L. Gittleman and A. Purvis, 2007. The delayed rise of present-day mammals. Nature 446: 507-512. [doi:10.1038/nature05634]

E. J. de Vries, R. A. Vos, G. Jacobs, and J. A. J. Breeuwer, 2006. Western flower thrips (Thysanoptera: Thripidae) preference for thrips-damaged leaves over fresh leaves enables uptake of symbiotic gut bacteria. European Journal of Entomology 103: 779-786. [abstract]

T. Gernhard, D. Ford, R. A. Vos and M. Steel, 2006. Estimating the relative order of speciation or coalescence events on a given phylogeny. Evolutionary Bioinformatics Online 2: 309-317. [abstract]

A. Ø. Mooers and Vos, R. A., 2005. The Shapes of Phylogenies. Mathematics of Evolution and Phylogeny Conference. [abstract]

Vos, R. A. and A. Ø. Mooers, 2004. Reconstructing divergence times for supertrees: a molecular approach. In: O. R. P. Bininda-Emonds (Ed.), Phylogenetic supertrees: Combining information to reveal the Tree of Life. pp 281-299. Kluwer Academic Publishers, Dordrecht.

Vos, R. A. 2003. Accelerated likelihood surface exploration: The likelihood ratchet. Systematic Biology 52: 368-373. [doi:10.1080/10635150390196993]

Rundle, H. D., F. Breden, C. Griswold, A. Ø. Mooers, R. A. Vos, and J. Whitton. 2001. Hybridization without Guilt: Gene Flow and the Biological Species Concept. Journal of Evolutionary Biology 14: 868-869. [doi:10.1046/j.1420-9101.2001.00338.x]

Vos, R.A., 2000. The generalist-to-specialist hypothesis in primate evolution. MSc Thesis, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam.

Employment history

2007-10-11T06:51:00.000-07:00

Lecturer

Onwards from 2017 I coordinate the MSc course "Methods in Biodiversity Analysis" at the Institute of Biology, Leiden University.

Researcher, bioinformaticist

Starting February 1st 2012 I am employed as a researcher in bioinformatics at NCB Naturalis.

Marie Curie Research Fellow

Starting from Fall 2009 to Fall 2011, I was employed as a research fellow at the University of Reading as a member of the Reading Evolutionary Biology Group working with Mark Pagel on natural selection in Primates, developing a comparative framework integrating molecules and natural history.

Bioinformatics consultant

Starting from Fall 2008 till November 2010, I have worked on the TreeBASE project as an outside consultant for the University of Pennsylvania.

Postdoctoral fellow

Starting from 2006 till Fall 2009, I have worked at the University of British Columbia, as an international collaborator on the CIPRES project, contributing to architecture and database design.

Research assistant

From January 2001 through August 2006 I have worked intermittently as a research assistant at Simon Fraser University on a number of projects involving phylogenetic inference.

Software

2007-10-11T06:32:00.000-07:00

I am an active contributor of open source bioinformatics software. In the past, I have developed educational software (web-based, for BioMedia, the Zoological Museum of Amsterdam, Simon Fraser University; and CD-ROM based for the AMSTEL institute). The projects listed below – for which I am the primary author – are current and ongoing. Their combined worth is estimated by an independent open source code analysis group at nearly $9 million. My programming skills include Java (Spring, Hibernate), Perl, C, web standards (XML/XSLT/XSD/HTML/CSS), ontologies (OWL, protege), databases (MySQL, PostgreSQL, dbxml, DB2), collaborative development best practices (svn, test-driven development) and design patterns.

TreeBASE

TreeBASE is a relational database of phylogenetic information hosted by the San Diego Supercomputing Center. In the Fall of 2008 I joined the development project to redesign TreeBASE from the ground up. I presently volunteer some of my time as the developer of the web service API.

Bio::Phylo

Bio::Phylo is a collection of modules for phylogenetic analysis and biodiversity assessments. Primary author: Rutger Vos, with contributions from Aki Mimoto, Klaas Hartmann, Jason Caravas and Mark Jensen.

NeXML

NeXML is an emerging data exchange standard for phylogenetics and bioinformatics.

CIPRES

The CyberInfrastructure for Phylogenetic Research is an NSF-sponsored 5 year project to develop an architecture for data exchange and distributed analysis. I am the designer of the perl5 branch of the infrastructure.

COPE

An implementation of OMG-compliant CORBA ORB and related architecture, COPE was originally conceived by Bart Schuller, I am the current maintainer.

Exception::Class::TCF

A port of Java/C++ style exception handling.

Teaching

2007-10-11T05:55:00.000-07:00

I enjoy teaching. In addition to the longer courses below I have given guest lectures for Shad Valley, taught seminars on bioinformatics at Simon Fraser University and given various conference talks at the SSE Evolution Conference and the Pacific Ecology Conference. In my classes I seek to combine new media with my lectures. I consistently receive positive student evaluations. Recently, I have also mentored two graduate students (Klaas Hartmann and Jason Caravas) for the NeXML project, and one student (Anurag Priyam) for the NeXML project, both with funding by Google.

Invited speaker, lecturer

In 2007, 2008, 2009 and 2010 I have taught a course on computational phyloinformatics hosted the first two years at the National Evolutionary Synthesis Center in the US, in 2009 at the Gulbenkian Institute in Lisbon, Portugal and in 2010 at the Beijing Genomics Institute in Shenzhen, China.

Teaching assistant

For various courses at Simon Fraser University I have given lectures and organized seminars, notably for a 4th level Biodiversity course (Fall semesters 2001 and 2004), a 1st level Introduction to Biology course (Fall semester 2001) and a 4th level Evolution course (Spring semester 2002).

For an international master course on phylogenetics I developed and taught a web-based lab on the systematics of lemurs at the Zoological Museum of Amsterdam (Fall semester 1999).

Services to the scientific community

2007-10-11T05:40:00.000-07:00

Below are some of the things I've volunteered to do over the last few years:

Review Editor of Frontiers in Bioinformatics and Computational Biology
Programme committee member IEEE e-Science 2011 Workshop on Interoperability in Scientific Computing, Stockholm, 5th December 2011
Board member of the Phyloinformatics Research Foundation.
Co-PI (with Arlin Stoltzfus and Enrico Pontelli) of the NESCent Hackathons, Interoperability, Phylogenetics working group and conference series (2010-2012)
Co-PI (with Arlin Stoltzfus) of the NESCent Evolutionary Informatics working group and conference series (2007-2009)
Co-organizer (with Mark Holder, Arlin Stoltzfus, Jason Stajich, Aaron Mackey, Hilmar Lapp and Todd Vision) of the 1st NESCent Phyloinformatics Hackathon (2006).
Co-chair (with Patrik Nosil), organizing committee for the 24th Annual Pacific Ecology and Evolution Conference (2003).
Webmaster for Scientists For Species, which successfully lobbied for a strengthened Species At Risk Act (SARA; passed by Canadian Senate December 16th, 2002).
Guest speaker for Shad Valley on Human Evolution and on Phylogenetics.
Member of the Doctoral Students Advisory Group for Burnaby Mountain College.
Co-organizer departmental seminar series, Simon Fraser University.
Organizer of SFU seminar series on Perl programming for biologists.
Reviewer for Phylogenetic supertrees: Combining information to reveal the Tree of Life, The American Naturalist, Systematic Biology, Evolution, Bioinformatics, iEvoBio, BMC Bioinformatics, Molecular Phylogenetics and Evolution, Evolutionary Genomics: statistical and computational methods and the Journal of Biomedical Semantics.

My affiliations

2007-10-11T05:23:00.000-07:00

Through my work I am affiliated in one form or another with various research projects and research institutes. Among these are currently:

The PhyloInformatics Research Foundation a Connecticut non-stock corporation founded in 2010 to promote phyloinformatics research and provide governance and direction for TreeBASE and the Tree of Life Web Project.
The TreeBASE project, a relational database for phylogenetic data. I am the lead developer for the latest version of this important community resource.
The TDWG Interest Group on Phylogenetics Standards.
The Data Integration working group of iPlant Collaborative.
BioHackathon, an annually held meeting to promote interoperability in the life sciences, organized by the Database Center for Life Science in Tokyo.
The National Evolutionary Synthesis Center (NESCent), a research institute devoted to evolutionary biology. I visit NESCent regularly in the context of several conference series I help organize. I've also given some lectures there.

Past affiliations include:

Reading Evolutionary Biology Group, Mark Pagel's lab at the University of Reading, where I have done my Marie Curie Fellowship.
The CyberInfrastructure for Phylogenetic Research (CIPRES), a research project dedicated to developing - among other things - a distributed architecture for phylogenetic inference. I contributed to this project by developing a client side and server side API to communicate through the architecture in perl.
The FAB* lab, a collective of labs at Simon Fraser University whose joint focus is on organic evolution. FAB* stands for Felix Breden, Arne Mooers, Bernie Crespi and Mike Hart, the main labs involved. I did my doctoral research in the FAB* lab - Arne Mooers was my thesis adviser.
Interdisciplinary Research in the Mathematical and Computational Sciences (IRMACS), a research school at Simon Fraser University. IRMACS is where I defended my dissertation - it has great videoconferencing facilities. Most of Arne Mooers's graduate students now hold office there.