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.
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., Lygate, C. A., Neubauer, S., Vendelin, M., & 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.
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.
Ramay, H. R., Liu, O. Z., & Sobie, E. A. (2011). Recovery of cardiac calcium release is controlled by sarcoplasmic reticulum refilling and ryanodine receptor sensitivity. Cardiovascular Research, 91(4), 598–605.
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.
Illaste, A., Kalda, M., Schryer, D. W., & Sepp, M. (2010). Life of mice – development of cardiac energetics. The Journal of Physiology, 588(23), 4617–4619.
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.
Beraud, N., Pelloux, S., Usson, Y., Kuznetsov, A. V., Ronot, X., Tourneur, Y., & Saks, V. (2009). Mitochondrial dynamics in heart cells: Very low amplitude high frequency fluctuations in adult cardiomyocytes and flow motion in non beating Hl-1 cells. Journal of Bioenergetics and Biomembranes, 41(2), 195–214.
Birkedal, R., Christopher, J., Thistlethwaite, A., & Shiels, H. (2009). Temperature acclimation has no effect on ryanodine receptor expression or subcellular localization in rainbow trout heart. Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology, 179(8), 961–969.
Sokolova, N., Vendelin, M., & Birkedal, R. (2009). Intracellular diffusion restrictions in isolated cardiomyocytes from rainbow trout. BMC Cell Biology, 10(1), 90.
Peterson, P. (2009). {F2PY}: a tool for connecting {Fortran} and {Python} programs. International Journal of Computational Science and Engineering, 4(4), 296–305.
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., 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.
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.

Chapters in books

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.
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.
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.
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.