Rutger Vos

  • PhD
  • Computational Biologist
  • Naturalis National Museum of Natural History

Research Interests

phyloinformatics phylogenomics interoperability data standards software engineering bioinformatics computational biology

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About

I am a computational biologist at Naturalis Biodiversity Center, a contributor to various open source software projects and I keep myself busy thinking about computational biology, phylogenetics and evolution.

Publications

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

Katayama T, Wilkinson M, Aoki-Kinoshita K, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim J, 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, Buttigieg P, Campbell M, Chen Y, Chiba H, Cock P, Cohen K, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall M, 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, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin S, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel P, Yamada I, Yamasaki C, Yamashita R, York W, Zmasek C, Kawamoto S, Takagi T

Journal of biomedical semantics (2014)

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Enriched biodiversity data as a resource and service.

Vos R, Biserkov J, Balech B, Beard N, Blissett M, Brenninkmeijer C, van Dooren T, Eades D, Gosline G, Groom Q, Hamann T, Hettling H, Hoehndorf R, Holleman A, Hovenkamp P, Kelbert P, King D, Kirkup D, Lammers Y, DeMeulemeester T, Mietchen D, Miller J, Mounce R, Nicolson N, Page R, Pawlik A, Pereira S, Penev L, Richards K, Sautter G, Shorthouse D, Tähtinen M, Weiland C, Williams A, Sierra S

Biodiversity data journal (2014)

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Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek C, Vaidya G, Pontelli E, Cranston K, Vos R, Webb C, Harmon L, Pirrung M, O'Meara B, Pennell M, Mirarab S, Rosenberg M, Balhoff J, Bik H, Heath T, Midford P, Brown J, McTavish E, Sukumaran J, Westneat M, Alfaro M, Steele A, Jordan G

BMC bioinformatics (2013)

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SUPERSMART: Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages and Relationships of Taxa

Antonelli A, Töpel M, Vos R, Nilsson K, Nylander J, Oxelman B, Sjökvist E, Nilsson H, Silvestro D, Sanderson M

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The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Katayama T, Wilkinson M, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun H, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal R, 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, Kinjo A, Konishi F, Kwon K, Labarga A, Lamprecht A, 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, Prins P, Saito T, Samwald M, Satagopam V, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos R, Withers D, Yamasaki C, Zmasek C, Kawamoto S, Okubo K, Asai K, Takagi T

Journal of biomedical semantics (2013)

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Biogem: an effective tool based approach for scaling up open source software development in bioinformatics

Bonnal R, Aerts J, Githinji G, Goto N, MacLean D, Miller C, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom T, Woodcroft B, Katayama T, Prins P

Bioinformatics (2012)

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NeXML: rich, extensible, and verifiable representation of comparative data and metadata

Vos R, Balhoff J, Caravas J, Holder M, Lapp H, Maddison W, Midford P, Priyam A, Sukumaran J, Xia X, Stoltzfus A

Systematic Biology (2012)

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BIO::Phylo-phyloinformatic analysis using perl.

Vos R, Caravas J, Hartmann K, Jensen M, Miller C

BMC bioinformatics (2011)

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The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

Katayama T, Wilkinson M, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun H, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita K, Arakawa K, Aranda B, Bonnal R, Fernández J, Fujisawa T, Gordon P, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim Y, Kinjo A, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park K, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T

Journal of biomedical semantics (2011)

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Evolution of embryonic developmental period in the marine bird families Alcidae and Spheniscidae: roles for nutrition and predation?

Hipfner J, Gorman K, Vos R, Joy J

BMC Evolutionary Biology (2010)

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The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita K, Yamamoto Y, Yamaguchi A, Kawashima S, Chun H, Aerts J, Aranda B, Barboza L, Bonnal R, Bruskiewich R, Bryne J, Fernández J, Funahashi A, Gordon P, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas E, Kerhornou A, Kibukawa E, Kinjo A, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn T, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley D, Sugawara H, Tashiro T, Trelles O, Vos R, Wilkinson M, York W, Zmasek C, Asai K, Takagi T

Journal of biomedical semantics (2010)

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TreeBASE2: Rise of the Machines

Vos R, Lapp H, Piel W, Tannen V

Nature Precedings (2010)

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Evolutionary Data Leaping to Web 3.0: Some Highlights From NESCent's Third Hackathon

Lapp H, Stoltzfus A, Vision T, Vos R

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TreeBASE v. 2: A Database of Phylogenetic Knowledge

Piel W, Chan L, Dominus M, Ruan J, Vos R, Tannen V

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Data standards in phylogenetics: the NeXML project

Vos R

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The 2006 NESCent Phyloinformatics Hackathon: A Field Report

Lapp H, Bala S, Balhoff J, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katayama T, Lewis P, Mackey A, Osborne B, Piel W, Pond S, Poon A, Qiu W, Stajich J, Stoltzfus A, Thierer T, Vilella A, Vos R, Zmasek C, Zwickl D, Vision T

Evolutionary Bioinformatics (2007)

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The delayed rise of present-day mammals

Bininda-Emonds O, Cardillo M, Jones K, MacPhee R, Beck R, Grenyer R, Price S, Vos R, Gittleman J, Purvis A

Nature (2007)

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Bio::CDAT - An Object for Evolutionary Analysis of Data

Stoltzfus A, Vos R, Reese J, Qiu W

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Estimating the relative order of speciation or coalescence events on a given phylogeny.

Gernhard T, Ford D, Vos R, Steel M

Evolutionary bioinformatics online (2006)

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Inferring Large Phylogenies: The Big Tree Problem

Vos R

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Western flower thrips (Thysanoptera: Thripidae) preference for thrips-damaged leaves over fresh leaves enables uptake of symbiotic gut bacteria

de Vries E, Vos R, Jacobs G, Breeuwer H

European Journal of Entomology (2006)

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The Shapes of Phylogenies

Mooers A, Vos R

Mathematics of Evolution and Phylogeny (2005)

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Reconstructing divergence times for supertrees: a molecular approach.

Vos R, Mooers A

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Accelerated likelihood surface exploration: the likelihood ratchet.

Vos R

Systematic Biology (2003)

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Supertree for the Geomyoids (Mammalia: Rodentia, Geomyoidea)

Wong D, Vos R, Mooers A

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Hybridization without guilt: gene flow and the biological species concept

Rundle H, Breden F, Griswold C, Mooers A, Vos R, Whitton J

Journal of Evolutionary Biology (2001)

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A Dated MRP Supertree for the Order Primates

Vos R, Mooers A

Systematic Biology

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EvoIO: Community-driven standards for sustainable interoperability

Stoltzfus A, Cranston K, Lapp H, McKay S, Pontelli E, Vos R, Cellinese N

Nature Precedings

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Professional experience

Computational Biologist

Naturalis National Museum of Natural History

February 2012 - Present

Education history

Simon Fraser University Department of Biological Sciences

PhD

January 2001 - May 2006 (5 years 4 months)

Biology, University of Amsterdam

MSc

December 1994 - June 2000 (5 years 6 months)