Marko Vendelin

I am the head of Laboratory of Systems Biology. I have defended by PhD in 2001 (Institute of Cybernetics at Tallinn University of Technology). After continuing my research in the Institute of Cybernetics (2002), I was a post-doctoral fellow at Université J. Fourier (2003-2004, Laboratory of Fundamental and Applied Bioenergetics, INSERM E0221) and Université Paris-Sud (2005, Faculté de Pharmacie, INSERM U446). After the post-doctorall studies, I returned to the Institute of Cybernetics and, with the help of Wellcome Trust International Senior Research Fellowship, started Laboratory of Systems Biology (2007).

Research Interests

My general research interests are linked with the physiology of the heart. I am interested in regulation of bioenergetics, its link to mechanics and electrophysiology. As a part of studies of regulation of intracellular processes in the heart, I am studying molecular movements and how intracellular communication is influenced by local environment as well as different diffusion obstacles in the heart muscle cells. For specific aims and interests, see the general homepage of Laboratory of Systems Biology.




Laboratory of Systems Biology
Institute of Cybernetics, Tallinn University of Technology
Akadeemia 21,
12618 Tallinn

fax: (+372) 620 4151
phone: (+372) 620 4169

Last Publications

Karro, N., Laasmaa, M., Vendelin, M., & Birkedal, R. (2019). Respiration of permeabilized cardiomyocytes from mice: no sex differences, but substrate-dependent changes in the apparent ADP-affinity. Scientific Reports, 9(1), 1–11.
Laasmaa, M., Karro, N., Birkedal, R., & Vendelin, M. (2019). IOCBIO Sparks detection and analysis software. PeerJ, 7, e6652.
Laasmaa, M., Birkedal, R., & Vendelin, M. (2016). Revealing calcium fluxes by analyzing inhibition dynamics in action potential clamp. Journal of Molecular and Cellular Cardiology, 100, 93–108.
Karro, N., Sepp, M., Jugai, S., Laasmaa, M., Vendelin, M., & Birkedal, R. (2016). Metabolic compartmentation in rainbow trout cardiomyocytes: coupling of hexokinase but not creatine kinase to mitochondrial respiration. Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology.
Simson, P., Jepihhina, N., Laasmaa, M., Peterson, P., Birkedal, R., & Vendelin, M. (2016). Restricted ADP movement in cardiomyocytes: Cytosolic diffusion obstacles are complemented with a small number of open mitochondrial voltage-dependent anion channels. Journal of Molecular and Cellular Cardiology, 97, 197–203.
Kalda, M., Peterson, P., & Vendelin, M. (2015). Cross-Bridge Group Ensembles Describing Cooperativity in Thermodynamically Consistent Way. PLoS ONE, 10(9), e0137438.
Sepp, M., Sokolova, N., Jugai, S., Mandel, M., Peterson, P., & Vendelin, M. (2014). Tight Coupling of Na+/K+-ATPase with Glycolysis Demonstrated in Permeabilized Rat Cardiomyocytes. PLoS ONE, 9(6), e99413.
Birkedal, R., Laasmaa, M., & Vendelin, M. (2014). The location of energetic compartments affects energetic communication in cardiomyocytes. Frontiers in Physiology, 5, 376.
Sokolova, N., Pan, S., Provazza, S., Beutner, G., Vendelin, M., Birkedal, R., & Sheu, S.-S. (2013). ADP Protects Cardiac Mitochondria under Severe Oxidative Stress. PLoS ONE, 8(12), e83214.
Branovets, J., Sepp, M., Kotlyarova, S., Jepihhina, N., Sokolova, N., Aksentijevic, D., … Birkedal, R. (2013). Unchanged mitochondrial organization and compartmentation of high-energy phosphates in creatine deficient GAMT-/- mouse heart. American Journal of Physiology - Heart and Circulatory Physiology.
Peterson, P., Kalda, M., & Vendelin, M. (2013). Real-time determination of sarcomere length of a single cardiomyocyte during contraction. American Journal of Physiology - Cell Physiology, 304(6), C519–C531.
Kalda, M., Peterson, P., Engelbrecht, J., & Vendelin, M. (2013). A Cross-Bridge Model Describing the Mechanoenergetics of Actomyosin Interaction. In G. A. Holzapfel & E. Kuhl (Eds.), Computer Models in Biomechanics (pp. 91–102). Springer Netherlands. Retrieved from
Schryer, D. W., Peterson, P., Illaste, A., & Vendelin, M. (2012). Sensitivity Analysis of Flux Determination in Heart by H218O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways. PLoS Comput Biol, 8(12), e1002795.
Karo, J., Peterson, P., & Vendelin, M. (2012). Molecular Dynamics Simulations of Creatine Kinase and Adenine Nucleotide Translocase in Mitochondrial Membrane Patch. Journal of Biological Chemistry, 287(10), 7467–7476.
Illaste, A., Laasmaa, M., Peterson, P., & Vendelin, M. (2012). Analysis of Molecular Movement Reveals Latticelike Obstructions to Diffusion in Heart Muscle Cells. Biophysical Journal, 102(4), 739–748.
Jepihhina, N., Beraud, N., Sepp, M., Birkedal, R., & Vendelin, M. (2011). Permeabilized rat cardiomyocyte response demonstrates intracellular origin of diffusion obstacles. Biophysical Journal, 101(9), 2112–2121.
Laasmaa, M., Vendelin, M., & Peterson, P. (2011). Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images. Journal of Microscopy, 243(2), 124–140.
Schryer, D., Vendelin, M., & Peterson, P. (2011). Symbolic flux analysis for genome-scale metabolic networks. BMC Systems Biology, 5(1), 81.
Vendelin, M., Mateo, P., Soboll, S., Gillet, B., Mazet, J.-L., & Hoerter, J. A. (2010). Response to Aliev et al.: PCr and ATP Export Both Participate in Energy Transfer from Mitochondria in Normoxic Heart. Journal of Biological Chemistry, 285(52), le22.
Vendelin, M., Hoerter, J. A., Mateo, P., Soboll, S., Gillet, B., & Mazet, J.-L. (2010). Modulation of Energy Transfer Pathways between Mitochondria and Myofibrils by Changes in Performance of Perfused Heart. Journal of Biological Chemistry, 285(48), 37240–37250.
Sepp, M., Vendelin, M., Vija, H., & Birkedal, R. (2010). ADP Compartmentation Analysis Reveals Coupling between Pyruvate Kinase and ATPases in Heart Muscle. Biophysical Journal, 98, 2785–2793.
Ramay, H. R., & Vendelin, M. (2009). Diffusion Restrictions Surrounding Mitochondria: A Mathematical Model of Heart Muscle Fibers. Biophysical Journal, 97(2), 443–452.
Schryer, D. W., Peterson, P., Paalme, T., & Vendelin, M. (2009). Bidirectionality and Compartmentation of Metabolic Fluxes Are Revealed in the Dynamics of Isotopomer Networks. International Journal of Molecular Sciences, 10, 1697–1718.
Sokolova, N., Vendelin, M., & Birkedal, R. (2009). Intracellular diffusion restrictions in isolated cardiomyocytes from rainbow trout. BMC Cell Biology, 10(1), 90.
Monge, C., Beraud, N., Kuznetsov, A. V., Rostovtseva, T., Sackett, D., Schlattner, U., … Saks, V. A. (2008). Regulation of respiration in brain mitochondria and synaptosomes: restrictions of ADP diffusion in situ, roles of tubulin, and mitochondrial creatine kinase. Molecular and Cellular Biochemistry, 318(1–2), 147–165.
Vendelin, M., & Birkedal, R. (2008). Anisotropic Diffusion of Fluorescently Labeled ATP in Rat Cardiomyocytes Determined by Raster Image Correlation Spectroscopy. American Journal of Physiology - Cell Physiology, 295(5), C1302–C1315.
Saks, V. A., Vendelin, M., Aliev, M. K., Kekelidze, T., & Engelbrecht, J. (2007). 8.1 Mechanisms and Modeling of Energy Transfer Between Intracellular Compartments. In A. Lajtha, G. E. Gibson, & G. A. Dienel (Eds.), Handbook of Neurochemistry and Molecular Neurobiology (pp. 815–860). Springer US. Retrieved from
Saks, V., Kaambre, T., Guzun, R., Anmann, T., Sikk, P., Schlattner, U., … Vendelin, M. (2007). The creatine kinase phosphotransfer network: thermodynamic and kinetic considerations, the impact of the mitochondrial outer membrane and modelling approaches. Sub-Cellular Biochemistry, 46, 27–65.
Saks, V., Dzeja, P. P., Guzun, R., Aliev, M. K., Vendelin, M., Terzic, A., & Wallimann, T. (2007). System Analysis of Cardiac Energetics–Excitation–Contraction Coupling: Integration of Mitochondrial Respiration, Phosphotransfer Pathways, Metabolic Pacing, and Substrate Supply in the Heart. In V. Saks (Ed.), Molecular System Bioenergetics (pp. 367–405). Wiley-VCH Verlag GmbH & Co. KGaA. Retrieved from
Beard, D. A., & Vendelin, M. (2006). Systems Biology of the Mitochondrion. American Journal of Physiology - Cell Physiology, 291(6), C1101–C1103.
Birkedal, R., Shiels, H. A., & Vendelin, M. (2006). Three-Dimensional Mitochondrial Arrangement in Ventricular Myocytes: From Chaos to Order. American Journal of Physiology - Cell Physiology, 291(6), C1148–C1158.
Saks, V., Dzeja, P., Schlattner, U., Vendelin, M., Terzic, A., & Wallimann, T. (2006). Cardiac System Bioenergetics: Metabolic Basis of the Frank-Starling Law. The Journal of Physiology, 571(2), 253–273.
Engelbrecht, J., & Vendelin, M. (2006). Mathematical Modelling of Cardiac Mechanoenergetics. In P. G. A. Holzapfel & P. R. W. Ogden (Eds.), Mechanics of Biological Tissue (pp. 369–378). Springer Berlin Heidelberg. Retrieved from
Guerrero, K., Wuyam, B., Mezin, P., Vivodtzev, I., Vendelin, M., Borel, J.-C., … Pison, C. (2005). Functional Coupling of Adenine Nucleotide Translocase and Mitochondrial Creatine Kinase Is Enhanced After Exercise Training in Lung Transplant Skeletal Muscle. American Journal of Physiology - Regulatory, Integrative and Comparative Physiology, 289(4), R1144–R1154.
Anmann, T., Eimre, M., Kuznetsov, A. V., Andrienko, T., Kaambre, T., Sikk, P., … Saks, V. A. (2005). Calcium‐induced contraction of sarcomeres changes the regulation of mitochondrial respiration in permeabilized cardiac cells. FEBS Journal, 272(12), 3145–3161.
Vendelin, M., Béraud, N., Guerrero, K., Andrienko, T., Kuznetsov, A. V., Olivares, J., … Saks, V. A. (2005). Mitochondrial Regular Arrangement in Muscle Cells: A “crystal-Like” Pattern. American Journal of Physiology - Cell Physiology, 288(3), C757–C767.
Vendelin, M., Lemba, M., & Saks, V. A. (2004). Analysis of Functional Coupling: Mitochondrial Creatine Kinase and Adenine Nucleotide Translocase. Biophysical Journal, 87(1), 696–713.
Vendelin, M., Eimre, M., Seppet, E., Peet, N., Andrienko, T., Lemba, M., … Saks, V. A. (2004). Intracellular diffusion of adenosine phosphates is locally restricted in cardiac muscle. Molecular and Cellular Biochemistry, 256/257(1/2), 229–241.
Saks, V. A., Kuznetsov, A. V., Vendelin, M., Guerrero, K., Kay, L., & Seppet, E. K. (2004). Functional coupling as a basic mechanism of feedback regulation of cardiac energy metabolism. Molecular and Cellular Biochemistry, 256257(1), 185–199.
Andrienko, T., Kuznetsov, A. V., Kaambre, T., Usson, Y., Orosco, A., Appaix, F., … Saks, V. A. (2003). Metabolic Consequences of Functional Complexes of Mitochondria, Myofibrils and Sarcoplasmic Reticulum in Muscle Cells. Journal of Experimental Biology, 206(12), 2059–2072.
Saks, V., Kuznetsov, A., Andrienko, T., Usson, Y., Appaix, F., Guerrero, K., … Vendelin, M. (2003). Heterogeneity of ADP Diffusion and Regulation of Respiration in Cardiac Cells. Biophysical Journal, 84(5), 3436–3456.
Vendelin, M., Bovendeerd, P. H. M., Saks, V., Engelbrecht, J., & Arts, T. (2003). Simulating Cardiac Mechanoenergetics in the Left Ventricle. In I. E. Magnin, J. Montagnat, P. Clarysse, J. Nenonen, & T. Katila (Eds.), Functional Imaging and Modeling of the Heart (pp. 72–80). Springer Berlin Heidelberg. Retrieved from
Vendelin, M., Bovendeerd, P. H. M., Engelbrecht, J., & Arts, T. (2002). Optimizing Ventricular Fibers: Uniform Strain or Stress, but Not ATP Consumption, Leads to High Efficiency. American Journal of Physiology - Heart and Circulatory Physiology, 283(3), H1072–H1081.
Vendelin, M., Kongas, O., & Saks, V. (2000). Regulation of mitochondrial respiration in heart cells analyzed by reaction-diffusion model of energy transfer. American Journal of Physiology - Cell Physiology, 278(4), C747–C764. Retrieved from
Saks, V. A., Kongas, O., Vendelin, M., & Kay, L. (2000). Role of the creatine/phosphocreatine system in the regulation of mitochondrial respiration. Acta Physiologica Scandinavica, 168(4), 635–641.
Vendelin, M., Bovendeerd, P. H. M., Arts, T., Engelbrecht, J., & van Campen, D. H. (2000). Cardiac Mechanoenergetics Replicated by Cross-Bridge Model. Annals of Biomedical Engineering, 28(6), 629–640.
Engelbrecht, J., Vendelin, M., & Maugin, G. A. (2000). Hierarchical internal variables reflecting microstructural properties: Application to cardiac muscle contraction. Journal of Non-Equilibrium Thermodynamics, 25(2), 119–130.

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