Curriculum vitae


Research experience

2013 – present Plymouth Marine Laboratory. Senior scientist developing marine ecosystem models, with emphasis on representation of biodiveristy.
2009 – 2013 University of Oxford, Junior Research Fellow, St. John's College/Department of Earth Sciences. Supported by Rubicon grant from the Netherlands Organisation for Scientific Research (NWO) from 2009 till 2011.
2003 Wageningen University and Research Centre, Department of Bioinformatics, the Netherlands. Junior scientist working on development of text mining algorithms for scientific literature.

Education

2004 – 2009 Ph.D. Theoretical Biology, Vrije Universiteit Amsterdam, the Netherlands. Dissertation: “Succession in plankton communities: a trait-based perspective”. Supervisor: Prof. Dr. S.A.L.M. Kooijman.
1997 – 2003 M.Sc. Biology, Vrije Universiteit Amsterdam, the Netherlands. Specialization: theoretical biology.
1991 – 1997 Gymnasium, Christelijk College Nassau-Veluwe, Harderwijk, the Netherlands.

Work experience

2006 – present Bolding & Burchard ApS, Asperup, Denmark. Development of GOTM and GETM hydrodynamic models and their coupling to biogeochemistry.
2006 – 2008 Kluwer B.V., the Netherlands. Freelance software application trainer for yearly Excel Experience Day.
2005 Research School for Socio-Economic and Natural Sciences of the Environment (SENSE), the Netherlands. Website development.
2001 – 2002 The Urban Wildlands Group, Los Angeles, USA. Freelance scientific software development.

Output

Articles

in prep. Bruggeman, J., A. Merico, U. Gaedke, S.A.L.M. Kooijman, and K.W. Wirtz. Environment-driven seasonal and interannual variability of phytoplankton community structure: a size-based perspective.
  Bruggeman, J., A. Oschlies, and S.A.L.M. Kooijman. Global patterns of plankton diversity from a self-assembling model
  Bruggeman, J., and S.A.L.M. Kooijman. Live fast, die young: evolutionary trade-offs in phytoplankton.
  Bruggeman, J., B.W. Kooi, and S.A.L.M. Kooijman. Succession in a water column: an adapting ecosystem manoeuvring between autotrophy and heterotrophy.
in press Terseleer, N., J. Bruggeman, C. Lancelot, N. Gypens. Trait-based representation of diatom functional diversity in a Plankton Functional Type model of the eutrophied Southern North Sea. Limnology and Oceanography
  Bruggeman, J., K. Bolding. A general framework for aquatic biogeochemical models. Environmental Modelling & Software
2013 Young, J. N., J. Bruggeman, R.E.M. Rickaby, J. Erez, M. Conte. Evidence for changes in carbon isotopic fractionation by phytoplankton between 1960 and 2010. Global Biogeochemical Cycles 27: 505–515
  Riek, A., Bruggeman, J. Estimating field metabolic rates for Australian marsupials using phylogeny. Comparative Biochemistry and Physiology - Part A 164 (4): 598–604
2012 Trolle, D., Hamilton, D. P., Hipsey, M. R., Bolding, K., Bruggeman, J., Mooij, W. M., Janse, J. H., Nielsen, A., Jeppesen, E., Elliott, A., Makler-Pick, V., Petzoldt, T., Rinke, K., Flindt, M. R., Arhonditsis, G. B., Gal, G., Bjerring, R., Tominaga, K., 't Hoen, J., Downing, A. S., Marques, D. M., Fragoso, C. R. J., Søndergaard, M. & Hanson, P. C. A community-based framework for aquatic ecosystem models. Hydrobiologia 683 (1): 25-34
2011 Bruggeman, J. A phylogenetic approach to the estimation of phytoplankton traits. Journal of Phycology 47(1): 52-65
2010 Saba, V.S., M.A.M. Friedrichs, M.-E. Carr, D. Antoine, R.A. Armstrong, I. Asanuma, O. Aumont, N.R. Bates, M.J. Behrenfeld, V. Bennington, L. Bopp, J. Bruggeman, E.T. Buitenhuis, M.J. Church, A.M. Ciotti, S.C. Doney, M. Dowell, J. Dunne, S. Dutkiewicz, W. Gregg, N. Hoepffner, K.J.W. Hyde, J. Ishizaka, T. Kameda, D.M. Karl, I. Lima, M.W. Lomas, J. Marra, G.A. McKinley, F. Mélin, J.K. Moore, A. Morel, B. Salihoglu, M. Scardi, T.J. Smyth, S. Tang, J. Tjiputra, J. Uitz, M. Vichi, K. Waters, T.K. Westberry, and A. Yool. Challenges of modeling depth-integrated marine primary productivity over multiple decades: A case study at BATS and HOT. Global Biogeochemical Cycles 24, GB3020
2009 Bruggeman, J., J. Heringa, and B.W. Brandt. PhyloPars: estimation of missing parameters values using phylogeny. Nucleic Acids Research 37(Web Server issue): W179-W184.
  Merico, A., Bruggeman, J., and K.W. Wirtz. A trait-based approach for downscaling complexity in plankton ecosystem models. Ecological Modelling 220(21): 3001-3010
  Eijsackers, H., J. Bruggeman, J. Harmsen, Th. de Kort, and A.H. Schakel. Colonization of PAH-contaminated dredged sediment by earthworms. Applied Soil Ecology 43: 216–225.
  Omta, A.W., Bruggeman, J., Kooijman, S.A.L.M., and H. Dijkstra. The organic carbon pump in the Atlantic. Journal of Sea Research 62: 179–187.
2008 Broekhuizen, N., G. J. Rickard, J. Bruggeman, and A. Meister. An improved and generalized second order, unconditionally positive, mass conserving integration scheme for biochemical systems. Applied Numerical Mathematics 58: 319–340.
2007 Bruggeman, J., and S.A.L.M. Kooijman. A biodiversity-inspired approach to aquatic ecosystem modeling. Limnology and Oceanography 52: 1533-1544.
  Bruggeman, J., H. Burchard, B.W. Kooi, and B. Sommeijer. A second-order, unconditionally positive, mass-conserving integration scheme for biochemical systems. Applied Numerical Mathematics 57: 36-58.
2006 Omta, A.-W., J. Bruggeman, S.A.L.M. Kooijman, and H. A. Dijkstra. Biological carbon pump revisited: Feedback mechanisms between climate and the Redfield ratio. Geophysical Research Letters 33: L14613.
2006 Van Driel, M.A., J. Bruggeman, G. Vriend, H.G. Brunner, and J.A. Leunissen. A text-mining analysis of the human phenome. European Journal of Human Genetics 14: 535-542.
2003 Longcore, T., R. Mattoni, C. Zonneveld, and J. Bruggeman. Insect Count Analyzer: A Tool to Assess Responses of Butterflies to Habitat Restoration. Ecological Restoration 21:60-61.

Other

2011 Bruggeman, J., Framework for Aquatic Biogeochemical Models (FABM). Technical report, European Commission Seventh Framework Program "Marine Ecosystem Evolution in a Changing Environment".
2009 Bruggeman, J., Succession in plankton communities: a trait-based perspective. PhD thesis, Vrije Universiteit Amsterdam.

Software applications

name description platform tools
PhyloPars Estimates species traits from incomplete observations and phylogeny web server Python
PyNcView NetCDF viewer Windows, Linux, Mac OS X Python, Qt4
GOTM-GUI Graphical User Interface to the General Ocean Turbulence Model Windows, Linux, Mac OS X Python, Qt4, FORTRAN, C++
PlotReader Plot digitizer Windows C#, .NET
INCA: INsect Count Analyzer Model-based analysis of transect count data Windows C++, MFC, HTML, VBScript

Professional activities

Presentations at conferences, workshops, symposia

2011 Resource Allocation workshop, University of Exeter, UK; 5 December 2011. “The hunt for trade-offs: linking mechanistic theory and observations”
  FABM-Workshop: A new framework for aquatic biogeochemical models, Center for Marine and Atmospheric Sciences (ZMAW), Hamburg, Germany; 14 November 2011. “The Framework for Aquatic Biogeochemical Models”
  Advances in Marine Ecosystem Modelling Research symposium, Plymouth, UK; 27 June 2011. Member of steering committee, keynote lecture: “Diversity and ecosystem function: An excursion into the world of adaptive models”
  MEECE Model Parameterisation and Coupling Workshop, Copenhagen, Denmark; 25 January 2011. “The Framework for Aquatic Biogeochemical Models (FABM): a demonstration of current capabilities”
2010 Advanced school in Complexity, adaptation and emergence in marine ecosystems, Abdus Salam International Centre for Theoretical Physics, Trieste, Italy; 19 October 2010. “Trait-based models in plankton succession”
  KNAW Colloquium “Predictability of Plankton communities in an unpredictable world”, Amsterdam, The Netherlands; 6 April 2010. Poster: “Environment-driven variability of phytoplankton community structure: a size-based perspective”
  Workshop “Modelling evolutionary and ecological processes in biogeochemical cycles”, University of East Anglia, Norwich, UK, 15 February 2010. “The plankton community as an evolving distribution of functional traits”
  MEECE 18 month Science Meeting, Heraklion, Crete, 4 February 2010. “A generic framework for biogeochemical models”
2008 Green Ocean Workshop, Villefranche-sur-Mer, France, 23 October 2008. “Biodiversity in ecosystem models: an adapting model manoeuvring between autotrophy and heterotrophy in global setting”
  Deutsche Gesellschaft für Limnologie annual meeting, Konstanz, Germany, 24 September 2008. “Environment-driven seasonal and interannual variability of phytoplankton community structure: a size-based perspective”
  Advances in Marine Ecosystem Modelling Research symposium, Plymouth, UK, 24 June 2008. “Biodiversity in ecosystem models: an adapting model manoeuvring between autotrophy and heterotrophy in global setting”
2007 6th European Conference on Ecological Modelling, Trieste, Italy, 29 November 2007. “An adapting, trait-based ecosystem model for phytoplankton succession”
  German Advances in Marine Ecosystem Modelling symposium, Hamburg, Germany, 13 November 2007. “Trait distributions as basis for ecosystem models: origins, strengths & caveats”
  Dutch Society for Theoretical Biology annual symposium, Schoorl, The Netherlands, 10 May 2007. “Succession in a water column: an adapting ecosystem manoeuvring between autotrophy and heterotrophy”
  ICES Workgroup for the Modeling of Physical-Biological Interactions annual meeting, Bergen–Bodø, Norway, 26 March 2007. “From species to traits: biodiversity-inspired ecosystem models”
2006 ICES Workgroup for the Modelling of Physical-Biological Interactions annual meeting, Nantes, France, 6 April 2006. “A biodiversity-inspired approach to marine ecosystem modelling”
2005 Advances in Marine Ecosystem Modelling Research symposium, Plymouth, UK, 28 June 2005. Poster: “Trait-based models to capture biodiversity: the phytoplankton test case”
  ICES Workgroup for the Modelling of Physical-Biological Interactions annual meeting, Hamburg, Germany, 6 April 2005. “Integration schemes for biochemical systems: unconditional positivity and mass conservation”
  Dutch Society for Theoretical Biology annual symposium, Schoorl, The Netherlands, 4 March 2005. “Trait-based models for functional groups”
  Netherlands Organisation for Scientific Research (NWO), Computational Life Sciences (CLS) program meeting, Utrecht, The Netherlands, 25 February 2005. Poster: “Modelling the biological carbon pump”

Invited seminars

2012 Université Libre de Bruxelles, Belgium; 16 February 2012. “Biodiversity in a moving world: Simple ways to model complex plankton communities”
  Danish Technical Institute – National Institute of Aquatic Resources (DTU Aqua), Copenhagen, Denmark; 1 February 2012. “Size-based phytoplankton: How complex communities can be captured with simple models”
2011 Institute for Hydrobiology and Fisheries Science, University of Hamburg, Germany; 17 November 2011. “Introducing biodiversity in biogeochemical models: Explorations with size-based phytoplankton”
  National Oceanography Centre, Southampton, UK; 11 November 2011. “Size-based phytoplankton: How complex communities can be captured with simple models”
  Geophysical Fluid Dynamics Laboratory, Princeton, NJ, USA; 7 October 2011. “Resolving biodiversity and adaptation with minimal model complexity: a trait-based approach”
  Princeton University, NJ, USA; 2 October 2011. “The mixotroph: a template for adapting plankton communities in the world ocean”
2010 University of Liverpool, UK; 7 October 2010. “Modelling global plankton communities: How diversity and evolution make life easier”
  Massachusetts Institute of Technology, Cambridge, MA, USA; 5 May 2010. “Nature made simple: Simple adaptive models for complex plankton communities”
2008 Massachusetts Institute of Technology, Cambridge, MA, USA, 2 December 2008, “Succession in plankton communities: a trait-based perspective”
  Universität Potsdam, Ökologie/Ökosystemmodellierung, Potsdam, Germany, 2 June 2008. “Size-driven succession in phytoplankton in Lake Constance: an adaptive model built upon laboratory and field observations”
  GKSS Institute of Coastal Research, Operational Systems, Helgoland, Germany, 23 April 2008. “Cell size as driving factor in plankton succession: results from Lake Constance”
  Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands, 6 March 2008 “Embracing biodiversity to build simpler models: the marine ecosystem as adapting mixotrophic community”
2007 Leibniz Institute of Marine Science (IFM-GEOMAR), Marine Biogeochemistry – Biogeochemical Modelling, Kiel, Germany, 5 November 2007. “Adapting ecosystem models for aquatic systems”
2006 GKSS Institute of Coastal Research, Operational Systems, Geesthacht, Germany, 17 October 2006. “A biodiversity-inspired approach to marine ecosystem modelling”
  Leibniz Institute of Marine Science (IFM-GEOMAR), Marine Biogeochemistry – Biogeochemical Modelling, Kiel, Germany, 4 September 2006. “A biodiversity-inspired approach to marine ecosystem modelling”
  Danish Institute for Fisheries Research (DIFRES), Copenhagen, Denmark, 31 May 2006. “A biodiversity-inspired approach to marine ecosystem modelling”
2005 GKSS Institute of Coastal Research, Operational Systems, Geesthacht, Germany, 26 September 2005. “Accounting for biodiversity in marine ecosystem models”.
  Universität Kassel, Fachbereich für Mathematik, Germany, 22 March 2005. “Integration schemes for biochemical systems: unconditional positivity and mass conservation”
2004 Leibniz Institute for Baltic Sea Research, Warnemünde, Germany, 8 December 2004. “Quantifying the organic carbon pump”

Events co-organized

2008 International Council for Exploration of the Sea (ICES) Annual Science Conference, Halifax, Canada, 22-23 September 2008. Session “Size is almost everything! Size and trait based processes and models in ecosystems and management”.
2007 ICES Workgroup for the Modelling of Physical-Biological Interactions, annual meeting, Bergen-Bodø, Norway, 26 March 2007. Session “Alternative approaches to ecosystem modelling”.

Memberships

Centre for Ocean Life, Copenhagen, Denmark. Member of international advisory board.

Teaching experience

2010 – present supervision of 4th year research projects (phytoplankton size from ocean optics, global biogeochemical models and iron limitation), Department of Earth Sciences, University of Oxford.
2012 instructor at 4th year course "Topics in Oceanography", Department of Earth Sciences, University of Oxford.
2006 – 2008 instructor for Kluwer B.V., yearly Excel Experience Day, session “Statistical methods and models for forecasts”
2004 – 2008 occasional assistance to Dr. Bob Kooi, courses mathematics for first-year biology students, population ecology, biomathematics
2007 instructor for Bolding & Burchard, training course for the General Ocean Turbulence Model, with Prof.Dr. Hans Burchard and Dr. Karsten Bolding, Leibniz Institute for Baltic Sea Research Warnemünde, Germany
1999 – 2001 teaching assistant to Dr. Bob Kooi, yearly mathematics course for first-year biology students, Vrije Universiteit Amsterdam

Other activities

2005 – 2008 treasurer Dutch Society for Theoretical Biology
2002 – 2003 member student council biology, Vrije Universiteit Amsterdam

Spoken languages

Dutch native language
English fluent
French good
German, Arabic basic

Computer skills

platforms Windows, Linux
languages FORTRAN, C++, C#, Perl, Python, PHP, SQL, HTML, VBscript, JavaScript, LaTeX
programming frameworks MFC, .NET, Qt4
website development ASP, CGI
applications Word, Excel, PowerPoint, MATLAB, Mathematica, Maple, R