Rutger Vos

All of life on earth is related, and the pattern of relatedness is shaped like a tree. Darwin realized this when he wrote in The Origin of Species:

"The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. (...)

The only illustration in Charles Darwin's seminal work The Origin of Species, published in 1859

As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications."

To reconstruct the Tree of Life - or fragments of it (e.g. Bininda-Emonds et al., 2007) - is one of the goals of the field of phylogenetics, not just because of its intrinsic beauty, but also because the phylogenetic context allows us to test hypotheses and make inferences on the origin and generation of biological diversity from the molecular level up to the biotic.

Although large numbers of phylogenies have been and are being published, they still cover only a small fraction of all the diversity of life, and each of these phylogenies usually describes the evolutionary relationship of few taxa from a relatively narrow taxonomic range. Our knowledge of 'the' tree of life is fragmented.

The challenges to overcome are wide-ranging: inferring large phylogenies poses great computational difficulties, some of which I have discussed in my dissertation. In my ongoing research I have contributed to the development of new tools, programming libraries, data standards, databases and reporting standards to integrate the ever-growing amount of comparative data from molecular, morphological and other sources in more and more detailed and comprehensive estimates of phylogeny. I also am part of various collaborations, standards bodies and recurrent meetings to develop and promote interoperability in evolutionary informatics and I organize courses and mentor students to train young scientists in the application of these technologies.

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

Lammers, Y., Peelen, T., Vos, R.A., Gravendeel, B. In review. The CITES checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data. BMC Bioinformatics.

Maryam Panahiazar, Amit P. Sheth, Ajith Ranabahu, Rutger A. Vos, Jim Leebens-Mack. In review. Advancing Data Reuse in Phyloinformatics Using an Ontology-Driven Semantic Web Approach. BMC Medical Genomics

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.

Bioinformaticist

Starting February 1st 2012 I am employed as a bioinformaticist 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.

Consultant

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

Visiting scientist

From January to August 2007 I worked as a visiting scientist at the Berlin Institute for Advanced Study (Wissenschaftskolleg zu Berlin).

Research assistant, postdoctoral fellow

Starting from January 2004 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.

Educational software developer

From June through December 2000 I worked at BioMedia, in web development and software design for life sciences education.

Educational software developer

From June through September 1999 I worked at the Amsterdam Science and Technology Education Laboratory (AMSTEL institute ) where I developed an educational CD-ROM on mitosis and meiosis visualized using 3D microscope photography.

Research assistant

From September 1998 through June 1999 I worked at the Institute for Systematics and Population Biology (ISP, now part of IBED) performing lab experiments (RAPD-PCR) tracking population divergence in laboratory strains of the Western Flower Thrips Frankliniella occidentalis.

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.

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).

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.
  

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.