--- title: "Marko Vendelin's Publications" url: 'https://sysbio.taltech.ee/people/marko-vendelin/publications' markdown: 'https://sysbio.taltech.ee/people/marko-vendelin/publications.md' date: '2026-08-15' description: 'Publications by Marko Vendelin Karimi, H., Gustavson, O., Česnokova, I., Branovets, J., Birkedal, R., Laasmaa, M., & Vendelin, M. (2026). A Unified Platform for FCS and RICS Analysis with Advanced Statistical Inference. ACS Omega, 11(12), 19201–19219. https://doi.org/10.1021/acs…' --- # Publications by Marko Vendelin Karimi, H., Gustavson, O., Česnokova, I., Branovets, J., Birkedal, R., Laasmaa, M., & Vendelin, M. (2026). A Unified Platform for FCS and RICS Analysis with Advanced Statistical Inference. *ACS Omega*, *11*(12), 19201–19219. Branovets, J., Laasmaa, M., Stolova, J., Shen, X., Rätsepso, T., Bernasconi, R., Soodla, K., Balodis, M. J., Grahv, C., Hendrikson, E., Louch, W. E., Birkedal, R., & Vendelin, M. (2025). Lifelong creatine deficiency leads to augmented sarcoplasmic reticulum calcium release but not heart failure. *American Journal of Physiology-Heart and Circulatory Physiology*, *329*(2), H471–H489. Karimi, H., Laasmaa, M., Pihlak, M., & Vendelin, M. (2025). Statistical analysis of fluorescence intensity transients with Bayesian methods. *Science Advances*, *11*(16), eads4609. Bernasconi, R., Soodla, K., Sirp, A., Zovo, K., Kuhtinskaja, M., Lukk, T., Vendelin, M., & Birkedal, R. (2025). Higher AMPK activation in mouse oxidative compared with glycolytic muscle does not correlate with LKB1 or CaMKKβ expression. *American Journal of Physiology-Endocrinology and Metabolism*, *328*(1), E21–E33. Suut-Tuule, E., Jarg, T., Tikker, P., Lootus, K.-M., Martõnova, J., Reitalu, R., Ustrnul, L., Ward, J. S., Rjabovs, V., Shubin, K., Nallaparaju, J. V., Vendelin, M., Preis, S., Öeren, M., Rissanen, K., Kananovich, D., & Aav, R. (2024). Mechanochemically driven covalent self-assembly of a chiral mono-biotinylated hemicucurbit[8]uril. *Cell Reports Physical Science*, *5*(9), 102161. Jaska, L., Birkedal, R., Laasmaa, M., & Vendelin, M. (2024). Simple Analysis of Gel Images With IOCBIO Gel Software. *Bio-Protocol*, *14*(16), e5053. Birkedal, R., Branovets, J., & Vendelin, M. (2024). Compartmentalization in cardiomyocytes modulates creatine kinase and adenylate kinase activities. *FEBS Letters*, *598*(21), 2623–2640. Branovets, J., Soodla, K., Vendelin, M., & Birkedal, R. (2023). Rat and mouse cardiomyocytes show subtle differences in creatine kinase expression and compartmentalization. *PLOS ONE*, *18*(11), e0294718. Kütt, J., Margus, G., Kask, L., Rätsepso, T., Soodla, K., Bernasconi, R., Birkedal, R., Järv, P., Laasmaa, M., & Vendelin, M. (2023). Simple analysis of gel images with IOCBIO Gel. *BMC Biology*, *21*(1), 225. Risti, R., Gunn, K. H., Hiis-Hommuk, K., Seeba, N.-N., Karimi, H., Villo, L., Vendelin, M., Neher, S. B., & Lõokene, A. (2023). Combined action of albumin and heparin regulates lipoprotein lipase oligomerization, stability, and ligand interactions. *PLOS ONE*, *18*(4), e0283358. Laasmaa, M., Branovets, J., Stolova, J., Shen, X., Rätsepso, T., Balodis, M. J., Grahv, C., Hendrikson, E., Louch, W. E., Birkedal, R., & Vendelin, M. (2023). Cardiomyocytes from female compared to male mice have larger ryanodine receptor clusters and higher calcium spark frequency. *The Journal of Physiology*, *601*(18), 4033–4052. Birkedal, R., Laasmaa, M., Branovets, J., & Vendelin, M. (2022). Ontogeny of cardiomyocytes: ultrastructure optimization to meet the demand for tight communication in excitation–contraction coupling and energy transfer. *Philosophical Transactions of the Royal Society B: Biological Sciences*, *377*(1864), 20210321. Branovets, J., Karro, N., Barsunova, K., Laasmaa, M., Lygate, C. A., Vendelin, M., & Birkedal, R. (2021). Cardiac expression and location of hexokinase changes in a mouse model of pure creatine deficiency. *American Journal of Physiology-Heart and Circulatory Physiology*, *320*(2), H613–H629. Laasmaa, M., Branovets, J., Barsunova, K., Karro, N., Lygate, C. A., Birkedal, R., & Vendelin, M. (2021). Altered calcium handling in cardiomyocytes from arginine-glycine amidinotransferase-knockout mice is rescued by creatine. *American Journal of Physiology-Heart and Circulatory Physiology*, *320*(2), H805–H825. Vendelin, M., Laasmaa, M., Kalda, M., Branovets, J., Karro, N., Barsunova, K., & Birkedal, R. (2020). IOCBIO Kinetics: An open-source software solution for analysis of data traces. *PLOS Computational Biology*, *16*(12), e1008475. Barsunova, K., Vendelin, M., & Birkedal, R. (2020). Marker enzyme activities in hindleg from creatine-deficient AGAT and GAMT KO mice – differences between models, muscles, and sexes. *Scientific Reports*, *10*(1), 1–9. Kalda, M., & Vendelin, M. (2020). Cardiac muscle regulatory units are predicted to interact stronger than neighboring cross-bridges. *Scientific Reports*, *10*(1), 1–13. Bartkova, S., Vendelin, M., Sanka, I., Pata, P., & Scheler, O. (2020). Droplet image analysis with user-friendly freeware CellProfiler. *Analytical Methods*. Lu, P., Veletić, M., Laasmaa, M., Vendelin, M., Louch, W. E., Halvorsen, P. S., Bergsland, J., & Balasingham, I. (2019). Multi-nodal nano-actuator pacemaker for energy-efficient stimulation of cardiomyocytes. *Nano Communication Networks*, *22*, 100270. Laasmaa, M., Lu, P., Veletić, M., Louch, W. E., Bergsland, J., Balasingham, I., & Vendelin, M. (2019). Energy-efficiency of Cardiomyocyte Stimulation with Rectangular Pulses. *Scientific Reports*, *9*(1), 1–9. 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. Karro, N., Sepp, M., Jugai, S., Laasmaa, M., Vendelin, M., & Birkedal, R. (2017). Metabolic compartmentation in rainbow trout cardiomyocytes: coupling of hexokinase but not creatine kinase to mitochondrial respiration. *Journal of Comparative Physiology B*, *187*(1), 103–116. 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. 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., Lygate, C. A., Neubauer, S., Vendelin, M., & Birkedal, R. (2013). Unchanged mitochondrial organization and compartmentation of high-energy phosphates in creatine-deficient GAMT−/− mouse hearts. *American Journal of Physiology-Heart and Circulatory Physiology*, *305*(4), H506–H520. 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. [http://link.springer.com/chapter/10.1007/978-94-007-5464-5\_7](http://link.springer.com/chapter/10.1007/978-94-007-5464-5_7) 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., Vendelin, M., & 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. [http://link.springer.com/referenceworkentry/10.1007/978-0-387-30411-3\_30](http://link.springer.com/referenceworkentry/10.1007/978-0-387-30411-3_30) 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. Saks, V., Kaambre, T., Guzun, R., Anmann, T., Sikk, P., Schlattner, U., Wallimann, T., Aliev, M., & 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. 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. [http://link.springer.com/chapter/10.1007/3-540-31184-X\_26](http://link.springer.com/chapter/10.1007/3-540-31184-X_26) Guerrero, K., Wuyam, B., Mezin, P., Vivodtzev, I., Vendelin, M., Borel, J.-C., Hacini, R., Chavanon, O., Imbeaud, S., Saks, V., & 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., Seppet, E., Tiivel, T., Vendelin, M., Seppet, E., & 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., Kay, L., & 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., Engelbrecht, J., Seppet, E. K., & 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*, *256–257*(1), 185–199. Andrienko, T., Kuznetsov, A. V., Kaambre, T., Usson, Y., Orosco, A., Appaix, F., Tiivel, T., Sikk, P., Vendelin, M., Margreiter, R., & 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., Kaambre, T., Sikk, P., Lemba, M., & 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. [http://link.springer.com/chapter/10.1007/3-540-44883-7\_8](http://link.springer.com/chapter/10.1007/3-540-44883-7_8) 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. 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. 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. 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. --- ## Navigation - Parent: [Marko Vendelin](https://sysbio.taltech.ee/people/marko-vendelin.md) - Previous: [Online Supplements](https://sysbio.taltech.ee/people/marko-vendelin/online-supplements.md)