1. Papers
  2. Book chapters and conference proceedings
  3. Editorials, blogs and commentary
  4. Theses


S. Roman Garcia, C. Welsh, N.H. Di Cara, D. Sterratt, N. Romano, M.I. Stefan.
Data Hazards as an ethical toolkit for neuroscience.
OSF 11 Mar 2024

Y. Xie, M. Kazmierczyk, B.P. Graham , M.B. Dutia, and M.I. Stefan
A multi-scale model reveals cellular and physiological mechanisms underlying hyperpolarisation-gated synaptic plasticity.
bioRxiv 418228


C. Lee, D. Bremner, C. Clerkin, M.I. Daw, S. Hussain, P. McDonald, J. Menzies, J.C. Meyer, J. Ponciano, S. Shan, M. Shipston, S. Welburn, H. Yang, M.I. Stefan (2023)
Evaluating the Student Experience at UK-China Joint Institutes
Front. Educ. 9:1330984

S. Gaillard, T. van Viegen, M. Veldsman, M.I. Stefan, V. Cheplygina (2022)
Ten simple rules for failing successfully in academia.
PLoS Comput. Biol., 18(12):e1010538.

R. Fitzpatrick and M.I. Stefan (2022)
Validation Through Collaboration: Encouraging Team Efforts to Ensure Internal and External Validity of Computational Models of Biochemical Pathways.
Neuroinform., 20:277-284.

T. Feng, S. Leptihn, K. Dong, B. Loh, Y. Zhang, M.I. Stefan, M. Li, X. Guo, Z. Cui (2021)
JD419, a Staphylococcus aureus phage with a unique morphology and broad host range
Front. Microbiol., 12:840.

Y. Liu, A. Béliveau, H. Besche, A.D. Wu, X. Zhang, M.I. Stefan, J. Gutlerner, C, Kim (2021)
Bayesian Mixed Effects Model and Data Visualization for Understanding Item Response Time and Response Order in Open Online Assessment
Front. Educ., 5:607260.

Q. Li, D.-C. Marcu, O. Palazzo, F. Turner, D. King, T.L. Spires-Jones, M.I. Stefan, K.E. Busch. (2020)
High neural activity accelerates the decline of cognitive plasticity with age in Caenorhabditis elegans
eLife, 9:e59711 .

S.M. Keating, D. Waltemath, M. König, F. Zhang, A. Dräger, C. Chaouiya, F.T. Bergmann, A. Finney, C.S. Gillespie, T. Helikar, S. Hoops, R.S. Malik-Sheriff, S.L. Moodie, I.I. Moraru, C.J. Myers, A. Naldi, B.G. Olivier, S. Sahle, J.C. Schaff, L.P. Smith, M.J. Swat, D. Thieffry, L. Watanabe, D.J. Wilkinson, M.L. Blinov, K. Begley, J.R. Faeder, H.F. Gómez, T.M. Hamm, Y. Inagaki, W. Liebermeister, A.L. Lister, D. Lucio, E. Mjolsness, C.J. Proctor, K. Raman, N. Rodriguez, C.A. Shaffer, B.E. Shapiro, J. Stelling, N. Swainston, N. Tanimura, J. Wagner, M. Meier-Schellersheim, H.M. Sauro, B. Palsson, H. Bolouri, H. Kitano, A. Funahashi, H. Hermjakob, J.C. Doyle, M. Hucka, R.R. Adams, N.A. Allen, B.R. Angermann, M. Antoniotti, G.D. Bader, J. Červený, M. Courtot, C.D. Cox, P. Dalle Pezze, E. Demir, W.S. Denney, H. Dharuri, J. Dorier, D. Drasdo, A. Ebrahim, J. Eichner, J. Elf, L. Endler, C.T. Evelo, C. Flamm, R.M.T. Fleming, M. Fröhlich, M. Glont, E. Gonçalves, M. Golebiewski, H. Grabski, A. Gutteridge, D. Hachmeister, L.A. Harris, B.D. Heavner, R. Henkel, W.S. Hlavacek, B. Hu, D.R. Hyduke, H. de Jong, N. Juty, P.D. Karp, J.R. Karr, D.B. Kell, R. Keller, I. Kiselev, S. Klamt, E. Klipp, C. Knüpfer, F. Kolpakov, F. Krause, M. Kutmon, C. Laibe, C. Lawless, L. Li, L.M. Loew, R. Machne, Y. Matsuoka, P. Mendes, H. Mi, F. Mittag, P.T. Monteiro, K. Nath Natarajan, P.M.F. Nielsen, T. Nguyen, A. Palmisano, J.-B. Pettit, T. Pfau, R.D. Phair, T. Radivoyevitch, J.M. Rohwer, O.A. Ruebenacker, J. Saez-Rodriguez, M. Scharm, H. Schmidt, F. Schreiber, M. Schubert, R. Schulte, S.C. Sealfon, K. Smallbone, S. Soliman, M.I. Stefan, D.P. Sullivan, K. Takahashi, B. Teusink, D. Tolnay, I. Vazirabad, A. von Kamp, U. Wittig, C. Wrzodek, F. Wrzodek, I. Xenarios, A. Zhukova, J. Zucker. (2020)
SBML Level 3: an extensible format for the exchange and reuse of biological models
Molecular Systems Biology, 16(8):e9110.

D. Waltemath, M. Golebiewski, M.L. Blinov, P. Gleeson, H. Hermjakob, M. Hucka, E.T. Inau, S.M. Keating, M. König, O. Krebs, R.S. Malik-Sheriff, D. Nickerson, E. Oberortner, H.M. Sauro, F. Schreiber, L. Smith, M.I. Stefan, U. Wittig, C.J. Myers (2020).
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
J Integr. Bioinform., 17:2-3.

M.C. Pharris, N.M. Patel, T.G. VanDyk, T.M. Bartol, T.J. Sejnowski, M.B. Kennedy, M.I. Stefan, T.L. Kinzer-Ursem (2019)
A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation.
PLoS Comput. Biol., 15:12.

N.A. Viswan, G.V. HarshaRani, M.I. Stefan, U.S. Bhalla (2018)
FindSim: a Framework for Integrating Neuronal Data and Signaling Models.
Front Neuroinform, 12:38.

K.S. Bonham, M.I. Stefan (2017)
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.

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

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

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.

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.

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

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

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.

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

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.

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.

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.
[DOI] [pdf]

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.
[DOI] [pdf] [Medline]

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]

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]

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.

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

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.

Book chapters and conference proceedings

D. Linkevicius, A. Chadwick, M.I. Stefan, D.C. Sterratt (2021)
Modeling the dynamics of partially known systems via the integration of a system of ordinary differential equations into a recurrent neural network
30th Annual Computational Neuroscience Meeting: CNS*2021, J Comput. Neurosci 49, Suppl 1: S175-S176
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).
[pdf] [E-Book]

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.

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.

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

Editorials, blogs and commentary

N. Bielczyk, M. Veldsman, A. Ando, C. Caldinelli, M.M. Makary, A. Nikolaidis, M.A. Scelsi, M.I. Stefan, OHBM Student and Postdoc Special Interest Group, A. Badhwar. (2018)
Establishing online mentorship for early career researchers: Lessons from the Organization for Human Brain Mapping International Mentoring Programme
European Journal of Neuroscience

WikiJSci Editorial Board. (2018)
The aims and scope of WikiJournal of Science
WikiJournal of Science 1 (1): 1.

S. Bekker, O.H. Ahmed, U. Bakare, T.A. Blake, A.M. Brooks, T.E. Davenport, L. De Michelis Mendonca, L.V. Fortington, M. Himawan, J. L. Kemp, K. Litzy, R.F. Loh, J. MacDonald, C.D. McKay, A.B Mosler, M. Mountjoy, A. Pederson, M.I. Stefan, E. Stokes, A.J. Vassallo, J.L. Whittaker. (2018)
We need to talk about manels: the problem of implicit gender bias in sport and exercise medicine
Br J Sports Med, published online first: 17 March 2018

M.I. Stefan (2018)
APA Science

M.I. Stefan (since 2013)

M.I. Stefan (2010)
A cv of failures
Nature, 468, 467.

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

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


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.

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.