Koch, D., Nandan, A.P., Ramesan, G., and Koseska, A. (2023). Beyond fixed points: transient quasi-stable dynamics emerging from ghost channels and ghost cycles. arXiv, 2309.17201 
Nandan, A.P., and Koseska, A. (2023). Non-asymptotic transients away from steady states determine cellular responsiveness to dynamic spatial-temporal signals. PLoS Comput. Biol. 19, e1011388.
Stanoev, A., and Koseska, A. (2022). Robust cell identity specifications through transitions in the collective state of growing developmental systems. Curr Opin Syst Biol 31, 100437.
Nandan, A., Das, A., Lott, R., and Koseska, A. (2022). Cells use molecular working memory to navigate inchanging chemoattractant fields. eLife 76825.
Raina, D., Bahadori, A., Stanoev, A., Protzek, M., Koseska, A., and Schröter, C. (2021). Cell-cell communication through FGF4 generates and maintains robust proportions of differentiated cell types in embryonic stem cells. Development 48, dev199926.
Gavriljuk, K., Scocozza, B., Ghasemalizadeh, F., Seidel, H., Nandan, A.P., Campos-Medina, M., Schmick, M., Koseska, A., and Bastiaens, P.I.H. (2021). A self-organized synthetic morphogenic liposome responds with shape changes to local light cues. Nat Commun 12, 1548.
Stanoev, A., Schröter, C., Koseska, A. (2021). Robustness and timing of cellular differentiation through population-based symmetry breaking. Development 148, dev197608.
Koseska, A., and Bastiaens, P.I.H. (2020). Processing temporal growth factor patterns by an epidermal growth factor receptor network dynamically established in space. Annu Rev Cell Dev Biol 36, 359-383.
Stanoev, A., Nandan, A.P., and Koseska, A. (2020). Organization at criticality enables processing of time-varying signals by receptor networks. Mol Syst Biol 16, e8870.
Stankevich, N. and Koseska, A. (2020). Cooperative maintenance of cellular identity in systems with intercellular communication defects. Chaos 30, 013144.
Stankevich, N., Mosekilde, E., and Koseska, A. (2018). Stochastic switching in systems with rare and hidden attractors. Eur Phys J Spec Top 227, 747–756.
Stanoev, A., Mhamane, A., Schuermann, K.C., Grecco, H.E., Stallaert, W., Baumdick, M., Brüggemann, Y., Joshi, M.S., Roda-Navarro, P., Fengler, S., Stockert, R., Roßmannek, L., Luig, J., Koseska, A., and Bastiaens, P.I.H. (2018). Interdependence between EGFR and phosphatases spatially established by vesicular dynamics generates a growth factor sensing and responding network. Cell Syst 7, 295-309.
Koseska, A. and Bastiaens, P.I.H. (2017). Cell signaling as a cognitive process. EMBO J 36, 568-582.
Zou, W., Senthilkumar, D.V., Nagao, R., Kiss, I.Z., Tang, Y., Koseska, A., Duan, J., and Kurths, J. (2015). Restoration of rhythmicity in diffusively coupled dynamical networks. Nat Commun 6, 7709.
Trpevski, I., Stanoev, A., Koseska, A., and Kocarev, L.J. (2014). Discrete-time distributed consensus algorithm on multiplex networks. New J Phys 16, 113063.
Koseska, A., Volkov, E., and Kurths, J. (2013). Oscillation quenching mechanisms: amplitude vs. oscillation death. Phys Rep 531, 173-199.
Koseska, A., Volkov, E., and Kurths, J. (2013). Transition from amplitude to oscillation death via Turing bifurcation. Phys Rev Lett 111, 024103.
Zakharova, A., Nikoloski, Z., and Koseska, A. (2013). Dimensionality reduction of bistable biological systems. Bull Math Biol 75, 373-392.
Zakharova, A., Schneider, I., Kyrychko, Y.N., Blyuss, K.B., Koseska, A., Fiedler, B., and Schöll, E. (2013). Time delay control of symmetry-breaking primary and secondary oscillation death. Europhys Lett 104, 50004.
Zou, W., Senthilkumar, D.V., Koseska, A., and Kurths, J. (2013). Generalizing the transition from amplitude to oscillation death in coupled oscillators. Phys Rev E Stat Nonlin Soft Matter Phys 88, 050901.
Winck, F.V., Arvidsson, S., Riaño-Pachón, D.M., Hempel, S., Koseska, A., Nikoloski, Z., Urbina Gomez, D.A., Rupprecht, J., and Mueller-Roeber, B. (2013). Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation. PLoS One 8, e79909.
Hempel, S., Koseska, A., and Nikoloski, Z. (2013). Data-driven reconstruction of directed networks. Eur Phys J B 86, 250.
Ullner, E., Ares, S., Morelli, L.G., Oates, A.S., Jülicher, F., Nicola, E., Heussen, R., Whitmore, D., Blyuss, K., Fryett, M., Zakharova, A., Koseska, A., Nene, N.R., and Zaikin, A. (2012). Noise and oscillations in biological systems: multidisciplinary approach between experimental biology, theoretical modelling and synthetic biology. Int J Mod Phys B 26, 1246009.
Zakharova, A., Kurths, J., Vadivasova, T., and Koseska, A. (2011). Analysing dynamical behavior of cellular networks via stochastic bifurcations. PLoS One 6, e19696.
Koseska, A., Volkov, E., and Kurths, J. (2011). Synthetic multicellular oscillatory systems: controlling protein dynamics with genetic circuits. Phys Scr 84, 045007.
Hempel, S., Koseska, A., Kurths, J., and Nikoloski, Z. (2011). Inner composition alignment for inferring directed networks from short time series. Phys Rev Lett 107, 054101.
Hempel, S., Koseska, A., Nikoloski, Z., and Kurths, J. (2011). Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study. BMC Bioinformatics 12, 292.
Grimbs, S., Arnold, A., Koseska, A., Kurths, J., Selbig, J., and Nikoloski, Z. (2011). Spatiotemporal dynamics of the Calvin cycle: multistationarity and symmetry breaking instabilities. Biosystems 103, 212-23.
Koseska, A. and Kurths, J. (2010). Topological structures enhance the presence of dynamical regimes in synthetic networks. Chaos 20, 045111.
Koseska, A., Volkov, E., and Kurths, J. (2010). Parameter mismatches and oscillation death in coupled oscillators. Chaos 20, 023132.
Koseska, A., Ullner, E., Volkov, E., Kurths, J., and GarcÃa-Ojalvo, J. (2010). Cooperative differentiation through clustering in multicellular populations. J Theor Biol 263, 189-202.
Zakharova, A., Vadivasova, T., Anishchenko, V., Koseska, A., and Kurths, J. (2010). Stochastic bifurcations and coherencelike resonance in a self-sustained bistable noisy oscillator. Phys Rev E Stat Nonlin Soft Matter Phys 81, 011106.
Koseska, A., Volkov, E., and Kurths, J. (2009). Detuning-dependent dominance of oscillation death in globally coupled synthetic genetic oscillators. Europhys Lett 85, 28002.
Koseska, A., Zaikin, A., Kurths, J., GarcÃa-Ojalvo, J. (2009). Timing cellular decision making under noise via cell-cell communication. PLoS One 4, e4872.
Ullner, E., Koseska, A., Kurths, J., Volkov, E., Kantz, H., GarcÃa-Ojalvo, J. (2008). Multistability of synthetic genetic networks with repressive cell-to-cell communication. Phys Rev E Stat Nonlin Soft Matter Phys 78, 031904.
Koseska, A., Volkov, E., Zaikin, A., and Kurths, J. (2007). Quantized cycling time in artificial gene networks induced by noise and intercell communication. Phys Rev E Stat Nonlin Soft Matter Phys 76, 020901.
Koseska, A., Volkov, E., Zaikin, A., and Kurths, J. (2007). Inherent multistability in arrays of autoinducer coupled genetic oscillators. Phys Rev E Stat Nonlin Soft Matter Phys 75, 031916.
Koseska, A., Zaikin, A., Garcia-Ojalvo, J., and Kurths, J. (2007). Stochastic suppression of gene expression oscillators under intercell coupling. Phys Rev E Stat Nonlin Soft Matter Phys 75, 031917.