Prof. Dr. Mareike Fischer

The trees will teach you things that no man will tell you. (Bernhard von Clairvaux)
Nothing in biology makes sense except in the light of evolution. (Theodosius Dobzhansky)

Kontakt

Prof. Dr. Mareike Fischer

Institut für Mathematik und Informatik
Walther-Rathenau-Straße 47 (Office 3.15)
17489 Greifswald

Telefon +49 3834 420 4643
email(at)mareikefischer(dot)de

siehe auch Professur für Biomathematik und Stochastik

Short CV
Professional Experience
  • Since April 2016: Associate Professor (W2) for Biomathematics and Stochastics at the Ernst-Moritz-Arndt-University in Greifswald, Germany
  • 2012-2016: Junior Professor for Discrete Biomathematics at the Ernst-Moritz-Arndt-University in Greifswald, Germany (tenure track);
  • 2009-2012: Postdoctoral researcher at the Center for Integrative Bioinformatics Vienna (CIBIV)
Teaching Experience
  • 2017 Summer term: Lecturer for "Combinatorics" and "Discrete Structures in Biology"
  • 2016/2017: Winter term: Lecturer for "Stochastic Models in Biology", "Molecular Evolution" and "Game Theory"
  • 2016: Summer term: Lecturer for "Discrete Structures in Biology" and "Discrete Modelling in Biology"
  • 2015/2016 Winter term: Lecturer for "Coding Theory" and lecturer and tutor for "Molecular Evolution"
  • 2015 Summer term: Lecturer for "Discrete Structures in Biology" and "Stochastic Models in Biology"
  • 2014/2015 Winter term: Lecturer and tutor for "Molecular Evolution"
  • 2013/2014 Winter term: Lecturer for "Molecular Evolution" and seminar "Applied Phylogenetics" at the University of Greifswald
  • 2013: Summer term: Lecturer for "Discrete Structures and Processes" at the University of Greifswald
  • 2012/2013 Winter term: Lecturer for "Stochastic Models in Biology" and "Molecular Evolution" at the University of Greifswald
  • 2012: Summer term: Lecturer for "Discrete Structures and Processes" at the University of Greifswald
  • 2009-2012: Lecturer for "Stats for VetMed students" and parts of the lecture series "Introduction to Bioinformatics, both at the Center for Integrative Bioinformatics Vienna, Austria
  • 2007-2009:
    • Tutor for Stats111 and Stats112 at the University of Canterbury, Christchurch, New Zealand
    • Tutor for physically challenged tertiary students, e.g. for Coding Theory, at the Disability Support Service, University of Canterbury, Christchurch, New Zealand
Education
  • 2006 - 2009: PhD studies at the University of Canterbury, New Zealand. Supervisor: Prof. Mike Steel
  • 2007 - 2012: Studies of Economics at the Distance University in Hagen, Germany
  • 1999 - 2005: Studies of Mathematics, Computer Science and Philosophy at the University of Kaiserslautern, Germany
  • 1990 - 1999: Mary Ward School in Mainz, Germany
Degrees
  • 2012: Diplom-Wirtschaftsmathematikerin (German Masters degree in Economics based on the existing mathematical Masters degree), Distance University of Hagen, Germany;
  • 2009: Doctor of Philosophy in Mathematics (PhD) at the University of Canterbury, New Zealand;
    Thesis: Novel Mathematical Aspects of Phylogenetic Estimation.
  • 2005: Diplom-Mathematikerin (German Masters degree in Mathematics) at the University of Kaiserslautern, Germany
  • 1999: Abitur (German A-Levels) at the Mary Ward School in Mainz, Germany
Awards

Awards

  • 2015: Preis für exzellente Lehre (excellent teaching award) an der Universität Greifswald
  • 2014: Admission as a fellow to the "Young ZIF" (Center for Interdisciplinary Research, University of Bielefeld)
  • 2012: Penny Ante Prize awarded at the Annual New Zealand Phylogenetics Meeting for the solution of the taxon coverage conjecture by M. Steel and M. Sanderson
  • 2009: Dean's List Award at the University of Canterbury
  • 2008: Aitken Prize awarded by the New Zealand Mathematical Society
  • 2008: Award for the best talk at the New Zealand Mathematics and Statistics Postgraduate Conference
  • 2007: Runner-up award in the scientific reportage competition of the University of Kaiserslautern, Germany
  • 2006: Admission as a scholarship holder of the Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand
  • 2005: Runner-up award in the scientific reportage competition of the University of Kaiserslautern, Germany
  • 2000: Admission as a scholarship holder of the Studienstiftung des deutschen Volkes (German National Academic Foundation)
  • 1999: Award for the best school report of the graduation class

Prüfungsausschussvorsitzende

für B.Sc. und M.Sc. Biomathematik

Fachstudienberaterin

für B.Sc. und M.Sc. Biomathematik

und Koordinatorin

von ERASMUS- und anderen Auslandsaufenthalten

Sprechstunde

In den Semesterferien nur nach Vereinbarung.

Anmerkung: Meine Sprechstunde ist grundsätzlich flexibel und richtet sich danach, wann jemand mit mir sprechen möchte - wenn Sie mit mir sprechen möchten (über eine Vorlesung, über Studienprobleme, über eine Entscheidung bezüglich des Studiengangs, über Informationen bezüglich Biomathematik, etc.), dann nehme ich mir auch außerhalb der Sprechstunde Zeit dafür! Sie können einfach einen Termin mit mir vereinbaren, am besten per E-Mail.

Research interests

  • Biomathematics, in particular Phylogenetics and Population Genetics
  • Discrete Mathematics
  • Combinatorics
  • Probability Theory
  • Graph Theory
  • Group Theory

Wenn Sie Interesse haben, in einem dieser Gebiete eine Abschlussarbeit zu schreiben (Bachelor, Master, Promotion), so zögern Sie nicht, sich an mich zu wenden.

If you are interested to write a thesis (Bachelor, Master or PhD) in any of the topics mentioned above (or a combination thereof), please do not hesitate to contact me!

Possible research topics for students in my working group can vary according to the applicant's own interests between purely theoretical and applied - the latter either in the sense of programming or in the sense of data analysis (or both). Collaborations with biologists or computer scientists are possible.

Publications

In press
  • Kelk, S. and Fischer, M.  On the complexity of computing MP distance between binary phylogenetic trees. In press at Annals of Combinatorics. (preliminary version: Arxiv: 1412.4076), Online First version (open access), DOI: 10.1007/s00026-017-0361-1
Published
  • Wicke, K. and Fischer, M. Comparing the rankings obtained from two biodiversity indices: the Fair Proportion Index and the Shapley Value. Journal of Theoretical Biology, Volume 430, 207-214, DOI: 10.1016/j.tbi.2017.07.010, (preliminary version: Arxiv: 1507.08620), Software: Perl program: FairShapley.zip (right-click the link and select "save file", then extract the zip folder in order to use the .pl file), Readme file: FairShapleyREADME.txt
  • Bryant, C., Fischer, M., Linz, S. and Semple, C. (2017) On the quirks of maximum parsimony on phylogenetic networks, Journal of Theoretical Biology, Volume 417:21, 100–108, DOI 10.1016/j.jtbi.2017.01.013.
  • Kelk, S., Fischer, M., Moulton, V. and Wu, T. Reduction rules for the maximum parsimony distance on phylogenetic trees. Theoretical Computer Sciences, 646:1-15, 2016, DOI: http://doi.org/10.1016/j.tcs.2016.07.010, (preliminary version: Arxiv: 1512.07459)
  • Boes, O., Fischer, M. and Kelk, S. A linear bound on the number of states in optimal convex characters for maximum parsimony distance. IEEE Transactions on Computational Biology and Bioinformatics, 2016, DOI: 10.1109/TCBB.2016.2543727, (preliminary version: Arxiv: 1506.06404 )
  • Fischer, M., Galla, M., Herbst, L., Steel, M. The most parsimonious tree for random data. Molecular Phylogenetics and Evolution, 80, 165 - 168, 2014, DOI: 10.1016/j.ympev.2014.07.010, (preliminary version: Arxiv: 1406.0217)
  • Fischer, M. and Kelk, S. On the Maximum Parsimony distance between phylogenetic trees. In press at Annals of Combinatorics. (preliminary version: Arxiv: 1402.1553)
  • Fischer, M., van Iersel, L., Kelk, S., Scornavacca, C. On computing the Maximum Parsimony score of a phylogenetic network. SIAM J. Discrete Math (SIDMA), 29 (1), 559 - 585, DOI: 10.1137/140959948  (preliminary version: Arxiv: 1302.2430)
  • Fischer, M. Non-hereditary maximum parsimony trees. Journal of Mathematical Biology, 65:2, 293-308, 2012, DOI: 10.1007/s00285-011-0458-9, (preliminary version: Arxiv: 1007.3964)
  • Fischer, M., Klaere, S., Nguyen M.A., von Haeseler, A. On the group theoretical background of assigning stepwise mutations onto phylogenies. Algorithms for Molecular Biology 2012, 7:36, DOI:10.1186/1748-7188-7-36 (preliminary version: Arxiv: 1110.3943)
  • Fischer, M. Mathematical aspects of phylogenetic groves. Annals of Combinatorics, DOI 10.1007/s00026-013-0179-4 (preliminary version: Arxiv: 1104.2562)
  • Fischer, M. Novel Mathematical Aspects of Phylogenetic Estimation. PhD thesis in partial fulfillment of the requirements for the degree Doctor of Philosophy (PhD) in Mathematics at the University of Canterbury. (University of Canterbury Research Repository).
  • Fischer, M., Thatte, B.D. Revisiting an equivalence between maximum parsimony and maximum likelihood methods in phylogenetics. Journal of Mathematical Biology, 72: 1, 208 - 220. (final version: DOI: 10.1007/s11538-009-9446-2, preliminary version: Arxiv: 0808.3609).
  • Fischer, M., Thatte, B.D. Maximum parsimony on subsets of taxa. Journal of Theoretical Biology, 260: 290 - 293. (final version: DOI: 10.1016/j.jtbi.2009.06.010, preliminary version: Arxiv: 0809.3653).
  • Fischer, M., Steel, M. Sequence length bounds for resolving a deep phylogenetic divergence. Journal of Theoretical Biology, 256: 247 - 252. (final version: DOI: 10.1016/j.jtbi.2008.09.031, preliminary version: Arxiv: 0806.2500)
  • Bandelt, H.-J., Fischer, M. Perfectly misleading distances from ternary characters. Systematic Biology, 57: 4, 540 - 543. (DOI: 10.1080/10635150802203880)
  • Fischer, M., Steel, M. Expected anomalies in the fossil record. Evolutionary Bioinformatics Online, 4, 61 - 67. (PMID: 19204808)
Submitted

    Mathematical phylogenetics:

    Accepted:

    • Herbst, L. and Fischer, M. Ancestral sequence reconstruction with parsimony. Accepted at Bulletin of Mathematical Biology. (preliminary version: Arxiv: 1702.01436)
    • Bordewich, M., Deutschmann, I., Fischer, M., Kasbohm, E., Semple, C. and Steel, M. On the information content of discrete phylogenetic characters. Accepted subject to revisions at Journal of Mathematical Biology. (preliminary version: Arxiv: 1703.04734)

     Submitted:

    • Cleary, S., Fischer, M., Griffiths, R. and Sainudiin, R. Some distributions on finite rooted binary trees. Submitted. (preliminary version: Arxiv: 1708.06130)
    • Wicke, K. and Fischer, M. On the Shapley value of unrooted phylogenetic trees. Submitted. (preliminary version: Arxiv: 1707.09908)
    • Wicke, K. and Fischer, M. Phylogenetic diversity and biodiversity indices on phylogenetic networks. Submitted. (preliminary version: Arxiv: 1706.05279)
    • Galla, M., Wicke, K. and Fischer, M. On the statistical inconsistency of Maximum Parsimony for k-tuple-site data. Submitted. (preliminary version: Arxiv: 1706.05568)
    • Herbst, L. and Fischer, M. On the accuracy of ancestral sequence reconstruction for ultrametric trees with parsimony. Submitted. (preliminary version: Arxiv: 1706.06085)
    • Fischer, M. and Kreidl, M. Non-hereditary Minimum Deep Coalescence trees. Submitted. (preliminary version: Arxiv: 1507.07209 
    • Fischer, M. Perfect taxon sampling and phylogenetically decisive taxon coverage.  Submitted. (preliminary version: Arxiv: 1206.3472), Software: Mathematica package (.m file)Mathematica Notebook (.nb file)
    • Fischer, M. and Liebscher, V. On the balance of unrooted trees. Submitted. (preliminary version: Arxiv: 1510.07882)
    • Fischer, M. Perfect taxon sampling and phylogenetically decisive taxon coverage. Submitted.

     

    Other topics:

    Submitted:

    • Müller, T.F., Fischer, S., Freuling, C.M., Pfaff, F., Bodenhofer, U., Höper, D., Fischer, M., Denise, M., Fooks, A.R., Mettenleiter, T.C., Conraths, F.J., Homeier-Bachmann, T.  Defining objective clusters for rabies virus sequences using affinity propagation clustering. Submitted to PLOS Neglected Tropical Diseases.
    • Koeppel, L., Siems, T., Fischer, M., Lentz, H. Classification of farms and traders in the pig production chain. Submitted to Preventive Veterinary Medicine.
      • Belka, A., Fischer, M., Pohlmann, A., Höper, D., Beer, M.: LVQ-KNN: Composition-based DNA/RNA classification of short nucleotide sequences utilizing a prototype-based k-nearest neighbor approach. Submitted to Bioinformatics (Oxford).
      Preprints

      Software