Prof. Dr. Mareike Fischer

Kontakt

Prof. Dr. Mareike Fischer

Universität Greifswald
Institut für Mathematik und Informatik
Walther-Rathenau-Straße 47 
17489 Greifswald

Telefon +49 3834 420 4643
mareike.fischeruni-greifswaldde

siehe auch Professur für Biomathematik und Stochastik

Short CV
Professional Experience
  • Since April 2016: Professor for Biomathematics and Stochastics at the University of Greifswald, Germany

    • Special commitments

      •  head of the biomathematics examination board

      • study advisor for biomathematics

      • Erasmus exchange coordinator

      • Internship coordinator

      • organizer and coordinator of an international student exchange wit New Zealand

  • 2012-2016: Junior Professor for Discrete Biomathematics at the University of Greifswald, Germany (tenure track);
  • 2009-2012: Postdoctoral researcher at the Center for Integrative Bioinformatics Vienna (CIBIV)
Teaching Experience
  • 2022 Winter term: No teaching (research sabbatical)
  • 2022 Summer term: Lecturer for "Discrete Modelling in Biology" and "Discrete Structures in Biology"
  • 2021/2022 Winter term: Lecturer for "Graph theory", tutor for "Graph theory", seminar "Tree Balance"
  • 2021 Summer term: Lecturer for "Stochastic Models in Biology", "Combinatorics" and "Discrete Structures in Biology"
  • 2020/2021 Winter term: Lecturer for "Discrete Modelling in Biology" and "Game theory" as well as tutor for "Game theory"
  • 2019/2020 Winter term and 2020 Summer term: no teaching (parental leave)
  • 2019 Summer term: Lecturer for "Discrete Structures in Biology" and "Game theory"
  • Winter term 2018/2019: No teaching (research sabbatical)
  • 2018 Summer term: Lecturer for "Discrete Structures in Biology" and "Discrete Modelling in Biology"
  • 2017/2018 Winter term: Lecturer for "Coding Theory", seminar "Phylogenetic networks"
  • 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"
  • 2014 Summer term: no teaching (parental leave)
  • 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

  • 2022: Excellent teaching award at the University of Greifswald in the special category: best student advisor
  • 2015: Excellent teaching award at the University of 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

Jederzeit 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, Möglichkeiten eines Auslandsaufenthalts oder eines Praktikums etc.), dann nehme ich mir unabhängig von einer fixen Sprechstunde Zeit dafür! Sie können einfach einen Termin mit mir vereinbaren, am besten per E-Mail.

Zum Ersti-Programm "Auf Darwins Spuren" - Alles über die Darwineumsexkursion, die Dozentenvorträge und die Absolventenvorträge!

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 in writing 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.

Teaching

Publications

Published

(Bio-)Mathematics:

 

  • Wicke, K., Fischer, M. and Kubatko, L. (2023) Effects of discordance between species and gene trees on phylogenetic diversity conservation, J. Math. Biol. 86, 13, Online First: doi.org/10.1007/s00285-022-01845-w (preliminary version: Arxiv: 2112.10717)
  • Fischer, M., Francis, A. and Wicke, K. (2022) Phylogenetic diversity rankings in the face of extinctions: the robustness of the Fair Proportion index. Systematic Biology, Online First: DOI: 10.1093/sysbio/syac030 (preliminary version: Arxiv: 2107.00748)
  • Fischer, M., Galla, M. and Wicke, K. (2022) Non-binary universal tree-based networks. Journal of Graph Algorithms and Applications (JGAA), 26(1): 81-90, DOI: 10.7155/jgaa.00583) (preliminary version: Arxiv: 2001.06093)
  • Kersting, J. and Fischer, M. (2021) Measuring tree balance using symmetry nodes - A new balance index and its extremal properties. Mathematical Biosciences, 341, DOI: 10.1016/j.mbs.2021.108690 (preliminary version: Arxiv: 2105.00719) 
  • Collienne, L., Elmes, K., Fischer, M., Bryant, D. and Gavryushkin, A. (2021) Discrete Coalescent Trees. Journal of Mathematical Biology, Volume 83 (60), DOI: 10.1007/s00285-021-01685-0 (preliminary version: Arxiv: 2101.02751)
  • Bouckaert, R., Fischer, M. and Wicke, K. (2021)Combinatorial perspectives on Dollo-k characters in phylogenetics. Advances in Applied Mathematics, 131, DOI: 10.1016/j.aam.2021.102252 (preliminary version: Arxiv: 2011.13479)
  • Fischer, M., Galla, M., Herbst, L. Long, Y. and Wicke, K. (2021) Unrooted non-binary tree-based phylogenetic networks. Discrete Applied Mathematics, 283: 10-30, DOI: 10.1016/j.dam.2021.01.005 (preliminary version: Arxiv: 1810.06853)
  • Fischer, M. (2021) Extremal values of the Sackin tree balance index. Annals of Combinatorics, 25: 515–541. DOI: 10.1007/s00026-021-00539-2 (preliminary version: Arxiv: 1801.10418)
  • Fischer, M. and Liebscher, V. (2021)On the balance of unrooted trees. Journal of Graph Algorithms and Applications, 25: 133-150, DOI: 10.7155/jgaa.00553.  (preliminary version: Arxiv: 1510.07882)
  • Fischer, M. and Francis, A. (2020) The space of tree-based networks. Bulletin of Mathematical Biology, 82: 70, DOI: 10.1007/s11538-020-00744-9. (preliminary version: Arxiv: 1910.05679)
  • Fischer, M., Galla, M., Herbst, L., Long, Y. and Wicke, K. (2020)Classes of tree-based networks.Journal of Visual Computing for Industry, Biomedicine, and Art; Special Issue “Applications of Graph Theory in Bioinformatics”. 3: 12, DOI: 10.1186/s42492-020-00043-z. (preliminary version: Arxiv: 1810.06844)
  • Fischer, M. and Francis, A. (2020)How tree-based is my network? Proximity measures for unrooted phylogenetic networks. Discrete Applied Mathematics. 283: 98-114. ISSN 0166-218X, DOI: 10.1016/j.dam.2019.12.019. (preliminary version: Arxiv: 1906.06163)
  • Wicke, K. and Fischer, M. (2020)Combinatorial views on persistent characters in phylogenetics. Advances in Applied Mathematics, 119: 102046, ISSN 0196-8858, DOI: 10.1016/j.aam.2020.102046. (preliminary version: Arxiv: 1802.02520)
  • Coronado, T., Fischer, M., Herbst, L., Rosselló, F. and Wicke, K. (2020) On the minimum value of the Colless index and the bifurcating trees that achieve it. Journal of Mathematical Biology, 80(7): 1993-2054. DOI: 10.1007/s00285-020-01488-9 (preliminary version: Arxiv: 1907.05064 )
  • Fischer, M., Galla, M., Herbst, L., Long, Y. and Wicke, K. (2020)Classes of tree-based networks.Journal of Visual Computing for Industry, Biomedicine, and Art; Special Issue “Applications of Graph Theory in Bioinformatics”. 3: 12, DOI: 10.1186/s42492-020-00043-z. (preliminary version: Arxiv: 1810.06844)
  • Fischer, M. (2019) On the uniqueness of the maximum parsimony tree for data with up to two substitutions: an extension of the classic Buneman theorem in phylogenetics. Molecular Phylogenetics and Evolution, 137: 127-137.DOI: 10.1016/j.ympev.2019.03.013. (preliminary version: Arxiv: 1808.07098)
  • Galla, M., Wicke, K. and Fischer, M. (2019) On the statistical inconsistency of Maximum Parsimony for k-tuple-site data. Bulletin of Mathematical Biology. DOI: 10.1007/s11538-018-00552-2, (preliminary version: Arxiv: 1706.05568)
  • Wicke, K. and Fischer, M. (2018) Phylogenetic diversity and biodiversity indices on phylogenetic networks. Mathematical Biosciences. DOI: 10.1016/j.mbs.2018.02.005, (preliminary version: Arxiv: 1706.05279)
  • Herbst, L. and Fischer, M. (2018) On the accuracy of ancestral sequence reconstruction for ultrametric trees with parsimony. Bulletin of Mathematical Biology, DOI: 10.1007/s11538-018-0407-5,(preliminary version: Arxiv: 1706.06085)
  • Wicke, K. and Fischer, M. (2018) On the Shapley value of unrooted phylogenetic trees. Bulletin of Mathematical Biology, Special Issue: Algebraic Methods in Phylogenetics, DOI: 10.1007/s11538-018-0392-8, (preliminary version: Arxiv: 1707.09908)
  • Herbst, L. and Fischer, M. (2017) Ancestral sequence reconstruction with parsimony. Bulletin of Mathematical Biology,79: 2865, DOI: 10.1007/s11538-017-0354-6, (preliminary version: Arxiv: 1702.01436)
  • Bordewich, M., Deutschmann, I., Fischer, M., Kasbohm, E., Semple, C. and Steel, M. (2017) On the information content of discrete phylogenetic characters. Journal of Mathematical Biology, DOI: 10.1007/s00285-017-1198-2, (preliminary version: Arxiv: 1703.04734)
  • Kelk, S. and Fischer, M.  (2017) On the complexity of computing MP distance between binary phylogenetic trees. Annals of Combinatorics, 21:4, 573-604, (preliminary version: Arxiv: 1412.4076), DOI: 10.1007/s00026-017-0361-1
  • Wicke, K. and Fischer, M. (2017) 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.  (2016) Reduction rules for the maximum parsimony distance on phylogenetic trees. Theoretical Computer Sciences, 646:1-15, DOI: http://doi.org/10.1016/j.tcs.2016.07.010, (preliminary version: Arxiv: 1512.07459)
  • Boes, O., Fischer, M. and Kelk, S. (2016) A linear bound on the number of states in optimal convex characters for maximum parsimony distance. IEEE Transactions on Computational Biology and Bioinformatics, DOI: 10.1109/TCBB.2016.2543727, (preliminary version: Arxiv: 1506.06404 )
  • Fischer, M. and Kelk, S. (2016) On the Maximum Parsimony distance between phylogenetic trees. Annals of Combinatorics, 20: 87-113. (preliminary version: Arxiv: 1402.1553)
  • Fischer, M., van Iersel, L., Kelk, S., Scornavacca, C. (2015) 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., Galla, M., Herbst, L., Steel, M. (2014) The most parsimonious tree for random data. Molecular Phylogenetics and Evolution, 80, 165 - 168, DOI: 10.1016/j.ympev.2014.07.010, (preliminary version: Arxiv: 1406.0217)
  • Fischer, M. (2013) Mathematical aspects of phylogenetic groves. Annals of Combinatorics, DOI 10.1007/s00026-013-0179-4 (preliminary version: Arxiv: 1104.2562)
  • Fischer, M. (2012) Non-hereditary maximum parsimony trees. Journal of Mathematical Biology, 65:2, 293-308, DOI: 10.1007/s00285-011-0458-9, (preliminary version: Arxiv: 1007.3964)
  • Fischer, M., Klaere, S., Nguyen M.A., von Haeseler, A. (2012) On the group theoretical background of assigning stepwise mutations onto phylogenies. Algorithms for Molecular Biology, 7:36, DOI:10.1186/1748-7188-7-36 (preliminary version: Arxiv: 1110.3943)
  • Fischer, M., Thatte, B.D. (2010) 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. (2009) 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. (2009) 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., Steel, M. (2009) 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. (2008) Perfectly misleading distances from ternary characters. Systematic Biology, 57: 4, 540 - 543. (DOI: 10.1080/10635150802203880)
  • Fischer, M., Steel, M. (2008) Expected anomalies in the fossil record. Evolutionary Bioinformatics Online, 4, 61 - 67. (PMID: 19204808)

 

Other scientific areas:

 

  • Schütz, A., Krause, E.T., Fischer, M., Müller, T., Freuling, C., Conraths, F., Homeier-Bachmann, T. and Lentz, H. (2022) Computer vision for detection of body posture and behavior of red foxes. Animals, 12, 3, DOI:  10.3390/ani12030233 
  • Schütz, A., Schöler, V., Krause, E.T., Fischer, M., Müller, T., Freuling, C., Conraths, F., Stanke, M., Homeier-Bachmann, T. and Lentz, H. (2021)Application of YOLOv4 for detection and motion monitoring of red foxes. Animals, Volume 11(6), DOI: 10.3390/ani11061723.
  • Brzoska, L., Fischer, M. and Lentz, H. (2020) Hierarchical structures in livestock trade networks - a stochastic block model of the German cattle trade network. Frontiers in Veterinary Science. DOI: 10.3389/fvets.2020.00281
  • Belka, A., Fischer, M., Pohlmann, A., Höper, D., Beer, M. (2018) LVQ-KNN: Composition-based DNA/RNA classification of short nucleotide sequences utilizing a prototype-based k-nearest neighbor approach. Virus Research, 258: 55-63. DOI: 10.1016/j.virusres.2018.10.002
  • Koeppel, L., Siems, T., Fischer, M., Lentz, H. (2018) Automatic classification of farms and traders in the pig production chain. Preventive Veterinary Medicine, 150, 86-92. DOI: h10.1016/j.prevetmed.2017.12.003
  • Fischer, S., Freuling, C.M., Müller, T., Pfaff, F., Bodenhofer, U., Höper, D., Fischer, M., Marston, D., Fooks, A.R., Mettenleiter, T.C., Conraths, F.J., Homeier-Bachmann, T. (2018) Defining objective clusters for rabies virus sequences using affinity propagation clustering. PLOS Neglected Tropical Diseases, 12:1, 2018,DOI: 10.1371/journal.pntd.0006182
Submitted

    (Bio-)Mathematics:

     Submitted:

     

    • Fischer, M. and Hendriksen, M. Refinement-stable consensus methods. (preliminary version: Arxiv: 2102.04502) 
    • Fischer, M. Defining binary phylogenetic trees using parsimony. (preliminary version: Arxiv: 2111.04385)
    • Fischer, M., Herbst, L. Kersting, S., Kühn, L. and Wicke, K. Tree balance indices: A comprehensive survey. (preliminary version: Arxiv: 2109.12281)
    • Fischer, M. and Kreidl, M. Non-hereditary Minimum Deep Coalescence trees. Submitted. (preliminary version: Arxiv: 1507.07209 )

     

     

    Preprints

    Software