Publications

Papers
Book chapters and conference proceedings
Editorials, blogs and commentary
Theses

Preprints

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

[DOI]

Papers

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

[DOI]

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.

[DOI]

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.

[DOI]

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.

[DOI]

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.

[DOI]

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 .

[DOI]

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.

[DOI]

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.

[DOI]

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.

[DOI]

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.

[DOI]

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.

[DOI]

[Read more on Kevin Bonham's blog]

R. Dutta Roy, C. Rosenmund, M.I. Stefan (2017)

Cooperative Binding Mitigates the High-Dose Hook Effect.

BMC Systems Biology, 11:74.

[DOI] [Preprint on bioRxiv]

M.I. Stefan (2017)

Cooperativity: A competition of definitions

J Math Biol, 74(7): 1679.

[DOI]

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]

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]

J. Marino, M.I. Stefan, S. Blackford (2014)

Ten Simple Rules for Finishing Your PhD

PLoS Comput Biol, 10(12): e1003954.

[DOI]

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]

[Wikipedia]

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]

M.I. Stefan, N. Le Novère (2013)

Cooperative Binding

PLoS Comput Biol, 9(6): e1003106.

[Read more]

[DOI]

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]

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]

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.

[Read more]

[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.

[pdf]

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

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.

[DOI] [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.

[DOI]

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

[DOI]

WikiJSci Editorial Board. (2018)

The aims and scope of WikiJournal of Science

WikiJournal of Science 1 (1): 1.

[DOI]

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

[DOI]

M.I. Stefan (2018)

Wie Enten im Teich: Sprechen wir über das Scheitern in der wissenschaftlichen Karriere

APA Science

M.I. Stefan (since 2013)

Life and Learning

Wordpress

M.I. Stefan (2010)

A cv of failures

Nature, 468, 467.

[DOI]

M.I. Stefan (2010)

Culture Shocks

Nature Postdoc Journal, 22 September 2010.

M.I. Stefan (2010)

The postdoc bumps

Nature Postdoc Journal, 9 June 2010.

Theses

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.