List of publications

Scientific publications with participation of Novel Software Systems employees are listed below.


  1. Dementyeva EV, Medvedev SP, Kovalenko VR, Vyatkin YV, Kretov EI, Slotvitsky MM, Shtokalo DN, Pokushalov EA, Zakian SM. Applying Patient-Specific Induced Pluripotent Stem Cells to Create a Model of Hypertrophic Cardiomyopathy // Biochemistry (Mosc). 2019 Mar; 84(3):291-298. doi:10.1134/S0006297919030118
  2. Sherstyuk VV, Davletshina GI, Vyatkin YV, Shtokalo DN, Vlasov VV, Zakian SM. A New MicroRNA Cluster Involved in the Reprogramming to a Pluripotent State // Acta Naturae. 2019 Apr-Jun;11(2):92-97. doi: 10.32607/20758251-2019-11-2-92-97
  3. Sharipova DV, Kovalenko VR, Bairamova EM, Vartanova VA, Grigor'eva EV, Vyatkin YV, Khabarova EA, Rzaev DA, Zakian SM, Medvedev SP. Generation of two iPSC lines, (ICGi015-A and ICGi015-B), by reprogramming peripheral blood mononuclear cells from a patient with Parkinson's disease. // Stem Cell Res. 2019 Dec;41:101652. doi: 10.1016/j.scr.2019.101652


  1. Anisimenko M.S., Paul G.A., Kozyakov A.E., Gutkina N.I., Berdyugina D.A., Garanin A.Y., Butorina A.V., Gornostaeva E.V., Khafizov K.F., Vyatkin Y.V., Shtokalo D.N., Kovalenko S.P. The spectrum of BRCA1 gene mutations in early onset breast cancer patients from Russia // Siberian journal of oncology. 2018;17(4):53-58. (in Russian).
  2. Sherstyuk V.V., Medvedev S.P., Ri M.T., Vyatkin Y.V., Saik O.V., Shtokalo D.N., Zakian S.M. The search for microRNAs potentially involved in the self-renewal maintaining of laboratory rat pluripotent stem cells // Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2018;22(2):179-186. DOI 10.18699/VJ18.345 (in Russian)
  3. St. Laurent G, Toma I, Seilheimer B, Tackett M, Zhou J, Ri M, Shtokalo D, Vyatkin Y, Jepson T, Cesnulevicius K, McCaffrey T. THU0021 Differential effects of tr14 versus diclofenac on cox/lox pathways revealed by RNASeq // Annals of the Rheumatic Diseases 2018;77:238-239


  1. St Laurent G, Vyatkin Y, Kapranov P. Dark matter RNA illuminates the puzzle of genome-wide association studies. BMC Med. 2014 Jun 12;12(1):97. doi: 10.1186/1741-7015-12-97.
  2. Chernyi, V. S., Tarasova, P. V., Kozlov, V. V., Saik, O. V., Kushlinskii, N. E., & Gulyaeva, L. F. (2017). Search of MicroRNAs Regulating the Receptor Status of Breast Cancer In Silico and Experimental Confirmation of Their Expression in Tumors. Bulletin of experimental biology and medicine, 163(5), 655-659. DOI: 10.1007/s10517-017-3872-1
  3. Kel, A., Gössling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O., Wingender, E. (2003). MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic acids research. 31. 3576-3579. 10.1093/nar/gkg585.
  4. Andrey Palyanov, Sergey Khayrulin, Stephen D. Larson, and Alexander Dibert. Towards a virtual C. elegans: a framework for simulation and visualization of the neuromuscular system in a 3D physical environment // In Silico Biology. 2011-2012; 11(3-4):137-47. doi: 10.3233/ISB-2012-0445
  5. V.Sherstyuk, S.Medvedev, E.Elisaphenko, E.Vaskova, M.Ri, Y.Vyatkin, O.Saik, D.Shtokalo, E.Pokushalov, S.Zakian. Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells // Scientific reports. 2017 Jun 5;7(1):2787. doi: 10.1038/s41598-017-02632-0.
  6. G.St Laurent III, B. Seilheimer, M. Tackett, J. Zhou, D. Shtokalo, Y. Vyatkin, P. Kapranov, I. Toma, T. Mccaffrey. Deep sequencing transcriptome analysis of the effect of traumeel versus diclofenac therapeutic action in wound healing // Annals of the Rheumatic Diseases. V.76. P.202. June 2017. DOI: 10.1136/annrheumdis-2017-eular.4964
  7. St. Laurent G III, Seilheimer B, Tackett M, Zhou J, Shtokalo D, Vyatkin Y, Ri M, Toma I, Jones D and McCaffrey TA. Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14. // Front. Mol. Biosci. 4:57. 2017. doi: 10.3389/fmolb.2017.00057.
  8. G. St. Laurent, Y. Vyatkin, D. Antonets, M. Ri, Y. Qi, O. Saik, D. Shtokalo, M. J.L. de Hoon, H. Kawaji, M. Itoh, T. Lassmann, E. Arner, A.R.R. Forrest, The FANTOM consortium, E. Nicolas, T.A. McCaffrey, P. Carninci, Y. Hayashizaki, C. Wahlestedt, and P. Kapranov. Functional annotation of the vlinc class of non-coding RNAs using systems biology approach // Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw162.
  9. St Laurent G, Tackett MR, Nechkin S, Shtokalo D, Antonets D, Savva YA, Maloney R, Kapranov P, Lawrence CE, Reenan RA. Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila // Nature Structural and Molecular Biology. 2013 Sep 29. doi: 10.1038/nsmb.2675
  10. Georges St Laurent, Dmitry Shtokalo, Biao Dong, Michael R Tackett, Xiaoxuan Fan, Sandra Lazorthes, Estelle Nicolas, Nianli Sang, Timothy J Triche, Timothy A McCaffrey, Weidong Xiao and Philipp Kapranov. VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer // Genome Biology. 2013 July 22, 14:R73. doi:10.1186/gb-2013-14-7-r73
  11. St Laurent G 3rd, Shtokalo D, Heydarian M, Palyanov A, Babiy D, Zhou J, Kumar A, Urcuqui-Inchima S. Insights from the HuR-interacting transcriptome: ncRNAs, ubiquitin pathways, and patterns of secondary structure dependent RNA interactions // Molecular Genetics and Genomics. 2012 Dec; 287(11-12):867-79. doi: 10.1007/s00438-012-0722-8.
  12. Georges St Laurent, Dmitry Shtokalo, Michael R Tackett, Zhaoqing Yang, Tatyana Eremina, Claes Wahlestedt, Silvio Urcuqui-Inchima, Bernd Seilheimer, Timothy A McCaffrey and Philipp Kapranov. Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells // BMC Genomics. 2012 Sep 24;13:504. doi: 10.1186/1471-2164-13-504.
  13. St Laurent G, Shtokalo D, Tackett MR, Yang Z, Vyatkin Y, Milos PM, Seilheimer B, McCaffrey TA, Kapranov P. On the importance of small changes in RNA expression // Methods. 2013 Apr 4. pii: S1046-2023(13)00096-0. doi: 10.1016/j.ymeth.2013.03.027.
  14. Shtokalo D. On limiting transition to delayed equation in the model of synthesis of substance with reversibility and sinks // Siberian Journal of Industrial Math. 12:2 (2009), p.143-156 (in Russian).
  15. Shtokalo D. On limiting transition in the model of multistage multiphase synthesis of substance // Siberian Journal of Industrial Math. 15:4 (2012), p. 135–146 (in Russian).
  16. Nechkin S., Shtokalo D., Palyanov A., Sheremushkin E. Development of integrated environment for miRNA search and analysis // Intelligent software. PSI-2011, p. 176-179 (in Russian).
  17. Palyanov A., Sheremushkin E., Shtokalo D., Nechkin S., Heydarian M., G.St.Laurent. Structural analysis of RNA sequences interacted with HuR protein // Software products and systems, 2010, No.3 (in Russian).
  18. Nechkin S., Palyanov A., Cheremushkin E., Shtokalo D., Albert P., St.Laurent G. The integrated environment for miRNA search and analysis // Software products and systems, 2008, No.4, p.151-153 (in Russian).
  19. Fadeev S., Likhoshvai V., Shtokalo D. Study of a model of linear biomolecular synthesis with reversible processes. J. Appl. Indust. Math., 2007, v.1(2), p.178-189.
  20. Waleev T, Shtokalo D, Konovalova T, Voss N, Cheremushkin E, Stegmaier P, Kel-Margoulis O, Wingender E, Kel A. Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm // Nucleic Acids Research. 2006 Jul 1;34(Web Server issue):W541-5.
  21. Osmonov R., Shtokalo D. Transformation of cycles based on non-singular matrices // Problems of intellectualization and quality of informatics systems, “Construction and optimization of programs”. Novosibirsk, 2006, p.162-176 (in Russian).