List of Publications
Mathematical Models of Death Signaling Networks
Srinivasan, M., R. Clarke, P. Kraikivski. (2022). Entropy 24(10), 1402.
A continuous-time stochastic Boolean model provides a quantitative description of the budding yeast cell cycle.
Laomettachit, T., P. Kraikivski, and J.J. Tyson. Scientific Reports (2022). (under review, preprint https://doi.org/10.21203/rs.3.rs-1800192/v1).
A Dynamic Mechanistic Model of Perceptual Binding
Kraikivski, P. Mathematics (2022), 10(7), 1135; https://doi.org/10.3390/math10071135
Crosstalk between Plk1, p53, Cell Cycle, and G2/M DNA Damage Checkpoint Regulation in Cancer: Computational Modeling and Analysis.
Y. Jung, P. Kraikivski, S. Shafiekhani, S. S. Terhune and R.K. Dash. Nature Partner Journal, Systems Biology and Applications 7:46. (2021). https://doi.org/10.1038/s41540-021-00203-8
Modeling and analysis of the macronutrient signaling network in budding yeast.
A. Jalihal, P. Kraikivski, T.M. Murali and J.J. Tyson. Mol. Biol. Cell (2021). https://doi.org/10.1091/mbc.E20-02-0117
Implications of Noise on Neural Correlates of Consciousness: A Computational Analysis of Stochastic Systems of Mutually Connected Processes
Kraikivski, P. Entropy (2021), 23(5), 583; https://doi.org/10.3390/e23050583
Dynamical analysis of the fission yeast cell cycle via Markov chain
S. Shafiekhani, P. Kraikivski, N. Gheibi, M. Ahmadian, A. H. Jafari . Current Genetics 67:785-797. (2021). https://doi.org/10.1007/s00294-020-01146-z
A systems biology approach to discovering pathway signaling dysregulation in metastasis
R. Clarke, P. Kraikivski, B. C. Jones, C. M. Sevigny, S. Sengupta & Y. Wang . Cancer and Metastasis Reviews (2020) https://doi.org/10.1007/s10555-020-09921-7 To view article: https://rdcu.be/b6bOS
Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants
J. E. Gallegos, N.R. Adames, M. F. Rogers, P. Kraikivski, A. Ibele, K. Nurzynski-Loth, E. Kudlow, T. M. Murali, J. J. Tyson & J. Peccoud. Nature Partner Journal, Systems Biology and Applications 6:11 (2020), https://doi.org/10.1038/s41540-020-0134-z
Systems of Oscillators Designed for a Specific Conscious Percept
P. Kraikivski. New Mathematics and Natural Computation (2020), Volume 16(1), pp. 73-88. https://doi.org/10.1142/S1793005720500052
Modeling the dynamic behavior of biochemical regulatory networks
J. J Tyson, T. Laomettachit and P. Kraikivski. Journal of Theoretical Biology (2019), Volume 462, pp. 514-527.
CrossPlan: systematic planning of genetic crosses to validate mathematical models
Pratapa A., N. Adames, P. Kraikivski, N. Franzese, J. J Tyson, J. Peccoud, T M Murali. Bioinformatics (2018), bty072, https://doi.org/10.1093/bioinformatics/bty072
Building Systems Capable of Consciousness
P. Kraikivski. Mind and Matter (2017), Volume 15, Number 2, pp. 185-195(11)
Bharadwaj A., D.P. Singh, A. Ritz, A. N. Tegge, C.L. Poirel, P. Kraikivski, N. Adames, K. Luther, S.D. Kale, J. Peccoud, J.J. Tyson, T.M. Murali. Bioinformatics (2017), Volume 33, Issue 19, Pages 3134–3136, https://doi.org/10.1093/bioinformatics/btx382
Engineered tug-of-war between kinesin and dynein controls direction of microtubule transport in vivo
Rezaul K., D. Gupta, I. Semenova, K. Ikeda, P. Kraikivski, Ji Yu, A. Cowan, I. Zaliapin, and V. Rodionov. Traffic (2016) 17(5): 475–486.
Kraikivski P., K.C. Chen, T. Laomettachit, T.M. Murali, and J. J. Tyson. Nature Partner Journal, Systems Biology and Applications 1:15016 (2015), doi:10.1038/npjsba.2015.16.
Semenova I, Ikeda K, Resaul K, Kraikivski P, Aguiar M, Gygi S, Zaliapin I, Cowan A, and Rodionov V. Molecular Biology of the Cell. 25(20):3119-32 (2014). PubMed PMID: 25143402; PubMed Central PMCID: PMC4196864
P. KraikivskiBiophysical Journal, Volume 104, Issue 10, 2121-2122, 21 May 2013
A. J. Lomakin*, P. Kraikivski*, I.Semenova, K. Ikeda, I. Zaliapin, J. S. Tirnauer, A. Akhmanova, and V. Rodionov. (* these athors contributed equally to this work). Molecular Biology of the Cell. vol. 22 no. 21 4029-4037 (2011)
I. L. Novak, F. Gao, P. Kraikivski, and B. M. Slepchenko. J. Chem. Phys. 134 pp. 154104 (2011).
P. Kraikivski and B. M. Slepchenko. Biophys. J. 99(3), pp. 708-715 (2010).
A. J. Lomakin, I. Semenova, I. Zaliapin, P. Kraikivski, E. Nadezhdina, B. M. Slepchenko, A. Akhmanova, and V. Rodionov. Developmental Cell 17, pp. 323–333 (2009).
I. L. Novak, P. Kraikivski, and B. M. Slepchenko. Biophys. J. 97(3), pp. 758-767 (2009).
P. Kraikivski, B. M. Slepchenko, and I. L. Novak. Phys. Rev. Lett. 101, pp. 128102(4) (2008).
J. Kierfeld, K. Frentzel, P. Kraikivski, and R. Lipowsky. Eur. Phys. J. Special Topics 157, pp. 123-133 (2008).
J. Kierfeld, P. Kraikivski, and R. Lipowsky. Biophys. Rev. Lett. 1, pp. 363-374 (2006).
J. Kierfeld, P. Gutjahr, T. Kühne, P. Kraikivski, and R. Lipowsky. J. Comput. Theor. Nanosci. 3, pp. 898-911 (2006).
P. Kraikivski, B. Pouligny, R. Dimova. Rev. Sci. Instrum. 77, pp. 113703(10) (2006).
P. Kraikivski, R. Lipowsky and J. Kierfeld. Phys. Rev. Lett. 96, pp. 258103(4) (2006).
P. Kraikivski, R. Lipowsky and J. Kierfeld. Europhys. Lett. 71 (1), pp. 138-144 (2005).
P. Kraikivski, R. Lipowsky and J. Kierfeld. Eur. Phys. J. E 16, pp. 319-340 (2005).
P. Kraikivski, R. Lipowsky and J. Kierfeld. Europhys. Lett. 66, pp. 763-769 (2004).
Book contributions
Case Studies in Systems Biology
P. Kraikivski (Ed) (Springer, 2021). doi: 10.1007/978-3-030-67742-8
J. Kierfeld, P. Kraikivski, T. Kühne, and R. Lipowsky. in Traffic and Granular Flow `05, edited by A. Schadschneider, T. Pöschel, R. Kühne, M. Schreckenberg, D.E. Wolf, pages 239-249 (Springer, Berlin, 2007).
Published conference proceedings
Kraikivski P. and B. M.Slepchenko. 2010. Kinetic Analysis of Actin Dendritic Nucleation from a Physicist's Standpoint. Biophys. J. 98(3) pp. 556A.
Kraikivski P., Novak I., Slepchenko B.M. 2007. A model of protruding lamellipodia: stability of the shape and filopodial extensions. Biophys. J. pp. 482A.
Kraikivski P., Lipowsky R., Kierfeld J. 2007. Active filament ordering in motility assays for motor proteins. Biophys. J. pp. 483A.
Novak I. L., Kraikivski P., Slepchenko B. M. 2007. Effects of crowding on intracellular diffusion. Biophys. J. pp. 564A.
Kraikivski P., Kierfeld J., Lipowsky R. 2005. Simulation of collective filament dynamics in motility assays for motor proteins. Biophys. J. 88(1) pp. 502A.
Thesis
PhD thesis: Non-equilibrium Dynamics of Adsorbed Polymers and Filaments. P. Kraikivski, Ph.D.-Thesis, Max-Planck Institute for Colloids and Interfaces - Universität Potsdam, Germany (2005).
PhD thesis: P. Kraikivski, Ph.D.-Thesis, Institute for Analytical Instrumentation Russian Academy of Science, Russia