Steffen Klaere

Research Interests:

• Combinatorial properties of phylogenetic models
  The application of Fourier transforms to models of molecular evolution provided many interesting insights into the properties and implications of these models. Extending these approaches to more complex models is challenging and exciting.
• Evaluation of the goodness of fit for statistical tests in phylogeny,
  Exploring statistical methods to develop a test for the fit between selected model and given data.
• Game theory and risk measures in ecology and economy,
  What is the deciding factor for selecting a given strategy (process with random outcome): Maximising potential of growth or minising risk of extinction? How are these statistics related?
• Quantitative measures of biodiversity
  The use of phylogenetic information in the assessment of biodiversity is limited, depending strongly on the availability and quality of genetic and/or morphological data. I want to expand my horizon beyond phylogenetics and look into the multitude of measures available for the evaluation of the three parts of biodiversity: diversity, distribution, and abundance. My goal is to find a set of measures which is the cheapest to compute while retaining as much information as possible.

Short Vita:

Education:

• 2001-2005: Ph.D. student at Ludwig-Maximilian-Universität Munich, Germany: Mathematics in Biology;
• 1995-2000: Studies at University of Jena, Germany: Mathematics in Economics;
• 1990-1994: Friedrich-Schiller-Gymnasium, Weimar, Germany;
• 1982-1990: Erich-Weinert-Gesamtschule, Legefeld, Germany.

Degrees:

• 'Dr. rer-nat.' (2005), Ludwig-Maximilian-Universität München
  Advisors: Prof. Dr. V. Liebscher, Prof. Dr. A. von Haeseler
  PhD-Thesis: Stochastic Models of Molecular Evolution: An Algebraical and Statistical Analysis
  (Accompanying files: Invariants for the Kimura 2ST model )
• 'Dipl. Math-oec.' (2000), Friedrich-Schiller-Universität Jena
  Advisors: Prof. Dr. K.-H. Fichtner, PD Dr. V. Liebscher
  Diploma-Thesis: Über eine Klasse stochastischer Differentialgleichungen ohne Adaptiertheitsforderung (in German)

Professional Experience:

• 2010-2011: Postdoctoral research fellow with Assoc. Prof. David Bryant at the Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand;
• 2009-2010: Postdoctoral research fellow with Assoc. Prof. David Bryant at the Computational Evolution Group, University of Auckland, New Zealand;
• 2005-2008: Postdoctoral research fellow with Prof. Arndt von Haeseler at the Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), Vienna, Austria;
• 2005: Postdoctoral research fellow with Prof. Arndt von Haeseler at the Institute of Bioinformatics, University of Düsseldorf, Germany;
• 2001-2005: Staff scientist at the Institute of Biomathematics and Biometry, Research Center for Environment and Health, Neuherberg, Germany

Research Grants:

• 2007: One month stay at the Programme "Phylogenetics" at the Isaac Newton Institute, Cambridge, UK
• 2003: Three month Marie-Curie grant for Programme "Mathematique, Informatique et Genomique" at the Institut Henri Poincare, Paris, France.

Publications / Conference Contributions

Paper

• Bryant, D., and Klaere S. (2011) The link between segregation and phylogenetic diversity. J. Math. Biol., (abstract);
• Nguyen, M. A., Klaere, S., and von Haeseler A. (2011) MISFITS: Highlighting alignment patterns that do not fit. Mol. Biol. Evol. 28(1), 143-152. (abstract);
• Minh, B. Q., Klaere, S., and von Haeseler, A. (2010) SDA*: A simple and unifying solution to recent bioinformatic challenges for conservation genetics. Proceedings of the 2nd International Conference on Knowledge and Systems Engineering - KSE 2010 (Hanoi, Vietnam), 33-37, IEEE Computer Society, Los Alamitos, CA, USA. (ISBN: 978-0-7695-4213-3);
• Hanada, R., Leibbrandt, A., Hanada, T., Kitaoka, S., Furuyashiki, T., Fujiwara, H., Trichereau, J., d Paolino, M., Qadri, F., Plehm, R., Klaere, S., Komnenovic, V., Mimata, H., Yoshimatsu, H., Takahashi, N., von Haeseler, A., Bader, M., Kilic, S.S., Ueta, Y., Narumiya, S., Pifl, C., and Penninger, J.M. (2009) Central control of fever and female body temperature by the osteoclast differentiation factors RANKL/RANK. Nature, 462(7272), 505-509, (abstract);
• Minh, B.Q.,Klaere, S., and von Haeseler, A. (2009) Taxon selection under split diversity. Syst. Biol., 58(6), 586-594 (abstract);
• Klaere, S., Gesell, T., and von Haeseler, A. (2008) The impact of single substitutions on multiple sequence alignments. Proc. Royal Soc. Lond. B, 363(1512), 4041-4047, (abstract);
• Kupczok, A., von Haeseler, A., and Klaere, S. (2008) An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. J. Comput. Biol., 15(6), 577-591, (abstract);
• Minh, B.Q., Pardi, F., Klaere, S., and von Haeseler, A. (2008) Budgeted Phylogenetic Diversity on Circular Split Systems. IEEE/ACM Trans. Comput. Biol. Bioinform.. 6(1), 22-29, (abstract);
• Minh, B.Q., Klaere, S, and von Haeseler, A. (2007), Phylogenetic Diversity on Split Systems, Preprint Series of the Isaac Newton Institute, (pdf);
• Minh, B.Q., Klaere, S., and von Haeseler, A. (2006), Phylogenetic Diversity within Seconds, Syst. Biol. 55(5), 769-773, (abstract).

Talks

• Some thoughts on biodiversity conservation,
  Annual New Zealand Phylogenetics Meeting, Leigh by the Sea NZ, February 2011;
• The link between segregation and phylogenetic diversity,
  Phylomania Hobart, Tasmania, Australia, November 2010;
• Phylogenetic inference in the presence of horizontal transfer,
  Adelaide Phylogenetics Conference, Port Elliot, Australia, April 2010;
• Phylogenetic inference in the presence of horizontal transfer,
  Annual New Zealand Phylogenetics Meeting, Whakapapa village NZ, February 2010;
• Inferring historic demographic changes from large SNP databases,
  Adelaide Conference on mathematical and evolutionary biology, Port Elliot, Australia, April 2009;
• Algebraic Invariants
  Annual New Zealand Phylogenetics Meeting, Kaikoura, NZ, February 2009;
• Phylogenetic Diversity and Incongruent Trees,
  Invited Talk, Institute for Computational Science, ETH Zürich, SUI, May 2008;
• Pruning Galled Trees,
  Invited Talk, School of Computing Sciences, University of East Anglia, Norwich, UK, May 2008;
• Lost in Tree Space,
  Phylogenetics Programme 2007, Cambridge, UK, October 2007;
• Some Thoughts on Phylogenetic Diversity,
  Phylogenetics Programme 2007, Cambridge, UK, October 2007;
• Phylogenetic Diversity on Split Networks,
  Evolution 2007, Christchurch, NZ, June 2007;
• Phylogenetic Diversity on Split Systems,
  Phylogroup meeting, Hinxton, GB, January 2007;
• Phylogenetische Invarianten: Aufgabenstellungen und Probleme,
  Invited Talk, Department of Mathematics, RWTH Aachen, D, September 2005;
• Markov Models on Triple Trees,
  Phylogenetic Trees and Networks II, Greifswald, D, September 2003;
• Über eine Klasse stochastischer Differentialgleichungen ohne Adaptiertheitsforderung,
  Studierendenkonferenz Mathematik, Aachen, D, September 2001;
• On a Class of Linear Stochastic Differential Equations without Adaptedness,
  QP Conference, Burg, D, March, 2001.

Conference Posters

• Phylogenetic inference in the presence of horizontal transfer: Some properties,
  presented at SMBE Annual Meeting, July 2010, Lyon France;
• Il Buono, Il Brutto, Il Cattivo,
  presented at Phyloinformatics workshop, October 2007, Edinburgh, UK;
• Phylogenetic Diversity on Split Systems,
  presented at MASAMB 2007 March 2007, Manchester, UK.
• Stochastic Models of Molecular Evolution: An Algebraic Analysis,
  presented at Conference on the Mathematics of Evolution and Phylogeny, June 2005, Paris, France.

Teaching

Lectures

• Spezielle Statistik in der Biotechnologie, WiSe 2008/2009, Veterinary University Vienna
• Spezielle Statistik in der Biotechnologie, WiSe 2007/2008, Veterinary University Vienna
• Spezielle Bioinformatik in der Biotechnologie, WiSe 2007/2008, Veterinary University Vienna
• Spezielle Statistik in der Biotechnologie, WiSe 2006/2007, Veterinary University Vienna

Tutorials

• Informatik 2, SoSe 2005, Heinrich-Heine-Universität Düsseldorf, Prof. Dr. Arndt von Haeseler
• Zeitreihenanalyse, SoSe 2004, Technical University Munich, Prof. Dr. Rupert Lasser
• Maßtheorie, WiSe 2002/2003, Technical University Munich, Prof. Dr. Rolf Wim Henrichs
• Stochastik für Wirtschaftsmathematiker, SoSe 2000, Friedrich-Schiller-Universität Jena, Prof. Dr. Karl-Heinz Fichtner
• Stochastik für Wirtschaftsmathematiker, SoSe 1999, Friedrich-Schiller-Universität Jena, Prof. Dr. Karl-Heinz Fichtner
• Informatik 1 Praktikum, WiSe 1998/1999, Friedrich-Schiller-Universität Jena, Prof. Dr. Klaus Küspert

Hobbies

• Hiking, cycling, and ornithology;
• Competitive sports like basketball, volleyball, football, badminton, or table tennis;
• Reading, watching movies, listening to music, playing computer and board games.

Addresses

S. Klaere - Last Change: July 28, 2011 .