Publications

  1. Papers
  2. Book chapters and conference proceedings
  3. Blogs and commentary
  4. Theses

Papers

  1. K.S. Bonham, M.I. Stefan
    Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology
    PLoS Comput Biol, 13(10): e1005134.
    [DOI]

  2. R. Dutta Roy, Christian Rosenmund, M.I. Stefan (2017)
    Cooperative Binding Mitigates the High-Dose Hook Effect.
    BMC Systems Biology, 11:74.

  3. M.I. Stefan (2017)
    Cooperativity: A competition of definitions
    J Math Biol, 74(7): 1679.
    [DOI]

  4. 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]

  5. 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]

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

  7. 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]

  8. 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]

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

  10. 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]

  11. 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]

  12. 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]

  13. 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]

  14. 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]

  15. 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]

  16. 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.

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

  18. 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 conference proceedings

  1. K. Pajo and M.I. Stefan (2017)
    Methods for simulating actin filament dynamics in MCell
    V International Conference on Particle-based Methods - Fundamentals and Applications: PARTICLES 2017 (P. Wriggers and M. Bischoff and E. Oñate and D.R.J. Owen and T. Zohdi, eds.), International Center for Numerical Methods in Engineering (CIMNE).

  2. 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.

  3. 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]

  4. 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.