Publications

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.