Publications

  1. Papers
  2. Book chapters and published abstracts
  3. Blogs and commentary
  4. Theses

Submitted

  • R. Dutta Roy, Christian Rosenmund, M.I. Stefan
    Cooperative Binding Mitigates the High-Dose Hook Effect.
    Submitted

  • K.S. Bonham, M.I. Stefan
    Gender disparity in computational biology research publications
    Submitted

  • Papers

    1. M.I. Stefan (2016)
      Cooperativity: A competition of definitions
      J Math Biol
      [DOI]

    2. N. Rodriguez, J.-B. Pettit, P. Dalle Pezze, L. Li, A. Henry, M.P. van Iersel, G. Jalowicki, M. Kutmon, K.N. Natarajan, D. Tolnay, M.I. Stefan, C.T Evelo, and N. Le Novère (2016)
      The Systems Biology Format Converter
      BMC Bioinformatics, 17:154.
      [DOI]

    3. M.I. Stefan, J.L. Gutlerner, R.T. Born, M. Springer (2015)
      The quantitative methods boot camp: teaching quantitative thinking and computing skills to graduate students in the life sciences.
      PLoS Comput Biol, 11(4): e1004208.
      [DOI]

    4. J. Marino, M.I. Stefan, S. Blackford (2014)
      Ten Simple Rules for Finishing Your PhD
      PLoS Comput Biol, 10(12): e1003954.
      [DOI]

    5. M.I. Stefan, T.M. Bartol, T.J. Sejnowski, M.B. Kennedy (2014)
      Multi-state Modeling of Biomolecules
      PLoS Comput Biol, 10(9): e1003844.
      [DOI]

    6. R. Dutta Roy, M.I. Stefan, C. Rosenmund (2014)
      Biophysical properties of presynaptic short-term plasticity in hippocampal neurons: insights from electrophysiology, imaging and mechanistic models
      Front Cell Neurosci, 8: 141.
      [DOI]

    7. M.I. Stefan, N. Le Novère (2013)
      Cooperative Binding
      PLoS Comput Biol, 9(6): e1003106.
      [Read more]
      [DOI]

    8. L. Li, M.I. Stefan, N. Le Novère (2012)
      Calcium Input Frequency, Duration and Amplitude Differentially Modulate the Relative Activation of Calcineurin and CaMKII
      PLoS ONE, 7(9): e43810.
      [DOI]

    9. M.I. Stefan, D.P. Marshall, N. Le Novère (2012)
      Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII
      PLoS ONE, 7(1): e29406.
      [DOI]

    10. G.M. Dall'Olio, J Marino, M. Schubert, K.L. Keys, M.I. Stefan, C.S. Gillespie, P. Poulain, K. Shameer, R. Sugar, B.M. Invergo, L.J. Jensen, J. Bertranpetit, H. Laayouni (2011)
      Ten Simple Rules for Getting Help from Online Scientific Communities
      PLoS Comput Biol, 7(9):e1002202.
      [pdf]

    11. C. Li, M. Donizelli, N. Rodriguez, H. Dharuri, L. Endler, V. Chelliah, L. Li, E. He, A. Henry, M.I. Stefan, J.L. Snoep, M. Hucka, N. Le Novère, C. Laibe (2010)
      BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
      BMC Syst Biol, 4:92.
      [pdf] [Medline]

    12. S.J. Edelstein, M.I. Stefan, N. Le Novère (2010)
      Ligand depletion in vivo modulates the dynamic range and cooperativity of signal transduction
      PLoS ONE, 5(1): e8449.
      [pdf] [Medline] [DOI]

    13. M.I. Stefan, S.J. Edelstein, N. Le Novère (2009)
      Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters
      BMC Syst Biol, 3(1):68.
      [pdf] [Medline] [DOI]

    14. M.I. Stefan, S.J. Edelstein, N. Le Novère (2008)
      An allosteric model of calmodulin explains differential activation of PP2B and CaMKII
      PNAS, 105(31):10768-73.

    15. A. Anglberger, P. Brössel, M.I. Stefan (2006)
      Rezension: Argumentation in Theorie und Praxis
      Kriterion, 20:37-41.
      [pdf]

    16. A. Anglberger, P. Brössel, N. Furlan, F. Greinecker, M. Karlegger, N. Pfeiffer, M.I. Stefan, A. Ungar (2003)
      Rezension: Was wir Karl R. Popper und seiner Philosophie verdanken
      Kriterion, 17:23-27.
      [pdf]

    Book chapters and published abstracts

    1. L. Endler, M.I. Stefan, S. Edelstein and N. Le Novère (2012)
      Using chemical kinetics to model neuronal signalling pathways
      Computational Systems Neurobiology, (N. Le Novère, ed.), Springer.

    2. M.I. Stefan, S. Pepke, S. Mihalas, T. Bartol, T. Sejnowski, M. Kennedy (2011)
      Multi-Stage Modeling of the Kinetics of Activation of CaMKII
      Front Neuroinform, Conference Abstract: 4th INCF Congress of Neuroinformatics.
      [DOI]

    3. M.I. Stefan, N. Le Novère (2007)
      Molecules for memory: modelling CaMKII
      BMC Systems Biology, 1(Suppl 1):P40.
      [pdf] [DOI]

    Blogs and commentary

    1. M.I. Stefan (since 2013)
      Wordpress

    2. M.I. Stefan (2010)
      A cv of failures
      Nature, 468, 467.
      [pdf] [DOI]

    3. M.I. Stefan (2010)
      Nature Postdoc Journal, 22 September 2010.

    4. M.I. Stefan (2010)
      Nature Postdoc Journal, 9 June 2010.

    Theses

    1. M.I. Stefan (2009)
      On the function of calcium-regulated allosteric devices in synaptic plasticity
      PhD Thesis, University of Cambridge and European Molecular Biology Laboratory.

    2. M.I. Stefan (2005)
      Morphological Characterisation and genetic mapping of the zebrafish skin mutants pusteln and dandruff
      Diploma Thesis, Max-Planck Institute for Developmental Biology and University of Salzburg.