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Rutger Vos

Dr. R.A. (Rutger) Vos, Research Fellow - Endless forms

Contact

Email: rutger.vos@naturalis.nl
Phone: +31 (0)06 27 08 5806
Room number: 3.xx, Darwinweg 4
“I study biodiversity using intense computation.”

I want to help understand where biodiversity comes from and where it might be going in a changing world. I think that a good way to do this is by comparing the characteristics and histories of many different species, so that we can tease the commonalities in how they change through space and time apart from what makes them distinct. In some sense we can view the history of life on earth as a repeated natural experiment in evolutionary response to change. To understand the outcomes of this experiment in the broad scale we have to represent it in silico, and develop the data sets, tools, algorithms, hypotheses and tests to make sense of it all. I contribute to this by developing open data and open source software and by discussing these in open access publications.

Career

At Naturalis Biodiversity Center I hold a position as research fellow.  I am also a member of the board of the Phyloinformatics Research Foundation, the governing body of TreeBASE and the Tree of Life Web Project. I obtained my PhD in large-scale phylogenetic inference at Simon Fraser University, Canada. After a postdoctoral fellowship at the University of British Columbia (Canada) and the Berlin Institute for Advanced Studies (Germany) I secured a Marie Curie postdoctoral fellowship to do research at the University of Reading (UK). In my current role at Naturalis I lead a small team of researcher/developers who develop analytical software tools to advance internal and extramural research programmes.

Research

Research interest

My main research interest is to understand the processes that generate patterns of biodiversity in space and time across large groups of species. I seek to use open data integration, phylogenetic inference, divergence data estimation, and the comparative analysis of complex data to characterize the patterns of diversity and test hypotheses of the underlying processes. I do this in collaborative settings where I contribute my expertise in open source scientific software development, algorithm development, and high performance computing.

Keywords

comparative genomics, big data, computational biology, open source, emergent characters, phyloinformatics, comparative analysis

Current research topics

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Collaborations

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Teaching

Courses

Available student projects

Publications

2017

Journals SCI, peer-reviewed

Pentinsaari M., Vos R., Mutanen M. 2017. Algorithmic single-locus species delimitation: effects of sampling effort, variation and non-monophyly in four methods and 1870 species of beetles. Molecular Ecology Resources 17: 393-404.
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Antonelli A., Hettling H., Condamine F.L., Vos K., Nilsson R.H., Sanderson M.J., Sauquet H., Scharn R., Silvestro D., Töpel M., Bacon C.D., Oxelman B., Vos R.A. 2017. Towards a self-updating platform for estimating rates of speciation and migration, ages, and relationships of taxa (SUPERSMART). Systematic Biology 66: 152-166.
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Dirks-Mulder A., Butot R., Schaik P. van, Wijnands J.W.P.M., Berg R. van den, Krol L., Doebar S., Kooperen K. van, Boer H. de, Kramer E.M., Smets E.F., Vos R.A., Vrijdaghs A., Gravendeel B. 2017. Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system. BMC Evolutionary Biology 17: 89.
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Stoltzfus A., Rosenberg M., Lapp H., Budd A., Cranston K., Pontelli E., Oliver S., Vos R.A. 2017. Community and Code: Nine Lessons from Nine NESCent Hackathons . F1000Research 6: 786-805.
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Essens T., Langevelde F. van, Vos R.A., Swaay C.A.M. van, Vries M.F.W. de 2017. Ecological determinants of butterfly vulnerability across the European continent . Journal of Insect Conservation 21: 439-450.
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2016

Journals SCI, peer-reviewed

Boettiger C., Chamberlain S., Vos R., Lapp H. 2016. RNeXML: a package for reading and writing richly annotated phylogenetic, character and trait data in r. Methods in Ecology and Evolution 7: 352–357.
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Schwallier R., Raes N., de Boer H.J., Vos R.A., van Vugt R., Gravendeel B. 2016. Phylogenetic analysis of niche divergence reveals distinct evolutionary histories and climate change implications for tropical carnivorous pitcher plants . Diversity and Distributions 22: 97-110.
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Mutanen M., Kivelä S.M., Vos R.A., Doorenweerd C., Ratnasingham S., Hausmann A., Huemer P., Dincă V., Nieukerken E.J. van, 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 C.J. 2016. Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera. Systematic Biology 65: 1024-1040.
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Lens F., Vos R., Charrier G., Niet T. van der, Merckx V., Baas P., Aguirre Gutierrez J., Jacobs B., Chacon Doria L., Smets E., Delzon S., Janssens S. 2016. Scalariform-to-simple transition in vessel perforation plates triggered by differences in climate during the evolution of Adoxaceae. Annals of Botany 118: 1043-1056.
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Hoehndorf R., Alshahrani M., Gkoutos G., Gosline G., Groom Q., Hamann T., Kattge J., Mota de Oliveira S., Schmidt M., Sierra S., Smets E., Vos R.. Weiland C. 2016. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. Journal of Biomedical Semantics 7: 65.
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Hardisty A.R., Bacall F., Beard N., Balcázar-Vargas M.-P., Balech B., Barcza Z., Bourlat S.J., Giovanni R. De, Jong Y. de, Leo F. De, Dobor L., Donvito G., Fellows D., Fernandez Guerra A., Ferreira N., Fetyukova Y., Fosso B., Giddy J., Goble C., Güntsch A., Haines R., Ernst V.H., Hettling H., Hidy D., Horváth F., Ittzés D., Ittzés P., Jones A., Kottmann R., Kulawik R., Leidenberger S., Lyytikäinen-Saarenmaa P., Mathew C., Morrison N., Nenadic A., Nieva de la Hidalga A., Obst M., Oostermeijer G., Paymal E., Pesole G., Pinto S., Poigné A., Quevedo Fernandez F., Santamaria M., Saarenmaa H., Sipos G., Sylla K.-H., Tähtinen M., Vicario S., Vos R.A., Williams A.R., Yilmaz P. 2016. BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology. BMC Ecology 16: 49.
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Schilthuizen M., Santos Pimenta L.P., Lammers Y., Steenbergen P.J., Flohil M., Beveridge N.G.P., Duijn, P.T. van, Meulblok M.M., Sosef N., Ven R. van de, Werring R., Beentjes K.K., Meijer K., Vos R.A., Vrieling K., Gravendeel B., Choi Y., Verpoorte R., Smit C., Beukeboom L.B. 2016. Incorporation of an invasive plant into a native insect herbivore food web. PeerJ 4: e1954.
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2015

Journals SCI, peer-reviewed

Thessen A.E., Bunker D.E., Buttigieg P.L., Cooper L.D., Dahdul W.M., Domisch S., Franz N.M., Jaiswal P., Lawrence-Dill C.J., Midford P.E., Mungall C.J., Ramírez M.J., Specht C.D., Vogt L., Vos R.A., Walls R.L., White J.W., Zhang G., Deans A.R., Huala E., Lewis S.E., Mabee P.M. 2015. Emerging semantics to link phenotype and environment. PeerJ 3: e1470.
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Journals non-SCI, peer-reviewed

Miller J.M., 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.
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2014

Journals SCI, peer-reviewed

Katayama T., Wilkinson M.D., Aoki-Kinoshita K.F., Kawashima S., Yamamoto Y., Yamaguchi A., Okamoto S., Kawano S., Kim J.-D., Wang Y., Wu H., Kano Y., Ono H., Bono H., Kocbek S., Aerts J., Akune Y., Antezana E., Arakawa K., Aranda B., Baran J., Bolleman J., Bonnal R.J.P., Buttigieg P.L., Campbell M.P., Chen Y., Chiba H., Cock P.J.A., Cohen K.B., Constantin A., Duck G., Dumontier M., Fujisawa T., Fujiwara T., Goto N., Hoehndorf R., Igarashi Y., Itaya H., Ito M., Iwasaki W., Kalas M., Katoda T., Kim T., Kokubu A., Komiyama Y., Kotera M., Laibe C., Lapp H., Lütteke T., Marshall M.S., Mori T., Mori H., Morita M., Murakami K., Nakao M., Narimatsu H., Nishide H., Nishimura Y., Nystrom-Persson J., Ogishima S., Okamura Y., Okuda S., Oshita K., Packer N.H., Prins P., Ranzinger R., Rocca-Serra P., Sansone S., Sawaki H., Shin S.-H., Splendiani A., Strozzi F., Tadaka S., Toukach P., Uchiyama I., Umezaki M., Vos R., Whetzel P.L., Yamada I., Yamasaki C., Yamashita R., York W.S., Zmasek C.M., Kawamoto S., Takagi T. 2014. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics 5: 5.
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Lammers Y., Peelen T., Vos R.A., Gravendeel B. 2014. The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data. BMC Bioinformatics 15: 44.
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Geel B. van, 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 Quaternary Science 29: 261-268.
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Aflitos S., Schijlen E., Finkers R., Smit S., Wang J., Zhang G., Li N., Mao L., Jong H. de, Bakker F., Gravendeel B., Breit T., Dirks R., Huits H., Struss D., Swanson-Wagner R., Leeuwen H. van, Ham R.C.H.J. van, Fito L., Guignier L., Sevilla M., Ellul P., Ganko E., Kapur A., Reclus E., Geus B. de, Geest H. van de, Lintel Hekkert B. te, Haarst J. van, Smits L., Koops A., Sanchez-Perez G., Heusden A.W. van, 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., Berg J. van den, 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. Plant Journal 80: 136-148.
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Gravendeel B., Protopopov A., Bull I., Duijm E., Gill F., Nieman A., Rudaya N., Tikhonov A.N., Trofimova S., Reenen G.B.A. van, Vos R., Zhilich., Geel B. van 2014. Multiproxy study of the last meal of a mid-Holocene Oyogos Yar horse, Sakha Republic, Russia. Holocene 24: 1-9.
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Journals non-SCI, peer-reviewed

Vos R.A., Biserkov J.V., Balech B., Beard N., Blissett M., Brenninkmeijer C., Dooren T. van, 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., Pawlik A., Pereira S., Penev L., Richards K., Sautter G., Shorthouse D.P., Tähtinen M., Weiland C., Williams A.R., Sierra S. 2014. Enriched biodiversity data as a resource and service. Biodiversity Data Journal 2: 1-15.
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2013

Journals SCI, peer-reviewed

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., Koning A.J. de, 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., Thillart G.E.E.J.M. van den, 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. Proceedings of the National Academy of Sciences of the United States of America 110: 20651-20656.
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Maryam P., Sheth A.P., Ranabahu A., Vos R.A., Leebens-Mack J. 2013. Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach. BMC Medical Genomics 6: S5.
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Stoltzfus A., Lapp H., Matasci N., Deus H., Sidlauskas B., Zmasek C.M., Vaidya G., Pontelli E., Cranston K., Vos R., Webb C.O., Harmon L.J., Pirrung M., O'Meara B., Pennell M.W., Mirarab S., Rosenberg M.S., Balhoff J.P., Bik H.M., Heath T., Midford P., Brown J.W., McTavish E.J., Sukumaran J., Westneat M., Alfaro M.E., Steele A. 2013. Phylotastic! Making Tree-of-Life knowledge accessible, re-usable and convenient. BMC Bioinformatics 14: 158.
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Katayama T., Wilkinson M.D., Micklem G., Kawashima S., Yamaguchi A., Nakao M., Yamamoto Y., Okamoto S., Oouchida K., Chun H.-W., Aerts J., Afzal H., Antezana E., Arakawa K., Aranda B., Belleau F., Bolleman J., Bonnal R.J., Chapman B., Cock P., Eriksson T., Gordon P., Goto N., Hayashi K., Horn H., Ishiwata R., Kaminuma E., Kasprzyk A., Kawaji H., Kido N., Kim Y.J., Kinjo A.R., Konishi F., Kwon K.-H., Labarga A., LamprechtA.-L., Lin Y., Lindenbaum P., McCarthy L., Morita H., Murakami K., Nagao K., Nishida K., Nishimura K., Nishizawa T., Ogishima S., Ono K., Oshita K., Park K.-J., Prins P., Saito T.L., Samwald M., Satagopam V.P., Shigemoto Y., Smith R., Splendiani A., Sugawara H., Taylor J., Vos R., Withers D., Yamasaki C., Zmasek C.M., Kawamoto S., Okubo K., Asai K., Takagi T. 2013. The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies. Journal of Biomedical Semantics 4: 6.
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2012

Journals SCI, peer-reviewed

Bonnal R.J.P., Aerts J., Githinji G., Goto N., MacLean D, Miller C.A., Mishima H., Pagani M., Ramirez-Gonzalez R., Smant G., Strozzi F., Syme R., Vos R., Wennblom T.J., Woodcroft B.J., Katayama T., Prins P. 2012. Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics 28: 1035-1037.
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Vos R.A., Balhoff J.P., Caravas J.A., Holder M.T., Lapp H., Maddison W.P., Midford P.E., Priyam A., Sukumaran J., Xia X., Stoltzfus A. 2012. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology 61: 675-689.
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2011

Journals SCI, peer-reviewed

Vos R.A., Caravas J., Hartmann K., Jensen M.A., Miller C. 2011. BIO::Phylo-phyloinformatic analysis using perl. BMC Bioinformatics 12: 63.
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2010

Journals SCI, peer-reviewed

Hipfner J.M., Gorman K.B., Vos R.A., Joy J.B. 2010. Evolution of embryonic developmental period in the marine bird families Alcidae and Spheniscidae: roles for nutrition and predation?. BMC Evolutionary Biology 10: 179.
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2008

Journals SCI, peer-reviewed

Bininda-Emonds O.R.P., Cardillo M., Jones K.E., MacPhee R.D.E., Beck R.M.D., Grenyer R., Price S.A., Vos R.A., Gittleman J.L., Purvis A. 2008. The delayed rise of present-day mammals (vol 446, pg 507, 2007). Nature 456: 274-274.
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2007

Journals SCI, peer-reviewed

Lapp H., Bala S., Balhoff J.P., Bouck A., Goto N., Holder M., Holland R., Holloway A., Katayama T., Lewis P.O., Mackey A.J., Osborne B.I., Piel W.H., Kosakovsky Pond S.L., Poon A.F.Y., Qiu W.-G., Stajich J.E., Stoltzfus A., Thierer T., Vilella A.J., Vos R.A., Zmasek C.M., Zwickl D.J., Vision T.J. 2007. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics 3: 287-296.

2006

Journals SCI, peer-reviewed

Gernhard T., Ford D., Vos R., Steel M. 2006. Estimating the relative order of speciation or coalescence events on a given phylogeny. Evolutionary Bioinformatics 2: 285-293.
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Vries E.J. de, Vos R.A., Jacobs G., Breeuwer H.A.J. 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.
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2004

Chapters in books

Vos R.A., Mooers A. 2004. Reconstructing divergence times for supertrees: a molecular approach. 281--299: Kluwer Academic Publishers, Dordrecht.

2003

Journals SCI, peer-reviewed

Vos R.A. 2003. Accelerated likelihood surface exploration: The likelihood ratchet. Systematic Biology 52: 368-373.
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2001

Journals SCI, peer-reviewed

Rundle H.D., Breden F., Griswold C., Mooers A., Vos R.A., Whitton J. 2001. Hybridization without guilt: gene flow and the biological species concept - Commentary. Journal of Evolutionary Biology 14: 868-869.
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