1. Aleksandra A. Chertkova, Joshua S. Schiffman, Sergey V. Nuzhdin, Konstantin N. Kozlov, Maria G. Samsonova and Vitaly V. Gursky
    In silico evolution of the Drosophila gap gene regulatory sequence under elevated mutational pressure
    (2017) BMC Evolutionary 17(Suppl 1):4 DOI: 10.1186/s12862-016-0866-y
  2. Kozlov K.N., Samsonov A.M., Samsonova M.G.
    A software for parameter optimization with Differential Evolution Entirely Parallel method
    // PeerJ Computer Science. 2016. August. Vol. 2. P. e74.
  3. Rukolaine S.A. Generalized linear Boltzmann equation, describing nonclassical particle transport, and related asymptotic solutions for small mean free paths // Physica A. 2016. Vol. 450. Pp. 205–216.
  4. S. Yu. Surkova, E. V. Golubkova, L. A. Mamon, M. G. Samsonova (2016). Morphogenetic networks which determine the spatial expression of zygotic genes in early Drosophila embryo. Russian Journal of Developmental Biology 47(4):181-189
  5. Lavrik I.N., Samsonova M.G. Systems biology of signaling pathways (2016) . Biofizika. 2016; 61(1): 93-101
  6. Demidov G.M., Samsonova M.G., Gursky V.V. A Stochastic Model for the Formation of Enhancer Molecular Configurations Biofizika. 2016; 61(1): 40-9. Russian
  7. Rukolainea S.A, Chistiakova O.I. Probing the D1 approximation to the linear Boltzmann equation in 3D (2015) Int. J. Heat and Mass Transfer, 95, 7-14
  8. Kozlov K.N, Gursky V.V., Kulakovskiy I.V., Dymova A., Samsonova M.G. Analysis of Functional Importance of Binding Sites in the Drosophila Gap Gene Network Model (2015) BMC Genomics, 16, Suppl 13: s7
  9. Kozlov K.N., Samsonov A.M, Samsonova M.G. Method of entirely parallel differential evolution for model adaptation in systems biology. Biofizika. 2015 Nov-Dec;60(6):1219-20. Russian.
  10. Pisarev A.S, Rukolaine S.A., Samsonov A.M, Samsonova M.G. Numerical analysis of particle trajectories in living cells under uncertainty conditions, Biofizika. 2015 Sep-Oct;60(5):981-9. Russian.
  11. М.А.Дук, А.М.Самсонов, М.Г.Самсонова (2015). Динамика контуров с упреждением с разным вторым регулятором - миРНК или транскрипционным фактором - говорит о различии их роли в клетке. Биофизика, 2015, том 60, вып. 2, c. 213–224
  12. С.А. Андреев, М. Г. Самсонова, В. В. Гурский (2015) Моделирование сети генов gap в дрозофиле в условиях изменчивости морфогена Bicoid Биофизика, 60, 2, 225 - 233
  13. Konstantin Kozlov, Dmitry Chebotarov, Mehedi Hassan, Petr Triska, Martin Triska, Pavel Flegontov, Tatiana V Tatarinova (2015).Differential Evolution Approach to Detect Recent Admixture. BMC Genomics, 2015, 16, p.S9 http://dx.doi.org/10.1101/01544
  14. Ivanisenko N.V., Mishchenko E.L., Akberdin I.R., Demenkov P.S., Likhoshvai V.A., Kozlov K.N., Todorov D.I., Gursky V.V., Samsonova M.G., Samsonov A.M., Clausznitzer D., Kaderali L., Kolchanov N.A., Ivanisenko V.A.(2014). A new stochastic model for subgenomic hepatitis C virus replication considers drug resistant mutants. PLoS One. 2014 Mar 18;9(3):e91502.
  15. Konstantin Kozlov, Vitaly Gursky, Ivan Kulakovskiy, Maria Samsonova (2014). Sequence-Based Model of Gap Gene Regulatory Network. BMC Genomics, 15(Suppl 12):S6 doi:10.1186/1471-2164-15-S12-S6 Published: 19 December 2014 http://dx.doi.org/10.1101/015776
  16. Igor Gula, Alexander M. Samsonov (2014). Gap gene expression model based on the Jeffreys type equation. Bioinformatics, 2014, Mar. 1;31(5):714-9.
  17. Maria A. Duk, Maria G. Samsonova and Alexander M. Samsonov (2014). Dynamics of miRNA-driven feed-forward loop depends upon miRNA action mechanisms. BMC Genomics, 2014, 15(Suppl 12):S9 doi:10.1186/1471-2164-15-S12-S9
  18. Kozlov K.N., Baumann P., Waldmann J., Samsonova M.G. (2013) TeraPro, a system for processing large biomedical images. 2013, Pattern Recognition and Image Analysis 23 (4), pp. 488-497
  19. Kozlov K., Ivanisenko N., Ivanisenko V., Kolchanov N., Samsonova M., Samsonov A.M. (2013) Enhanced differential evolution entirely parallel method for biomedical applications. 2013, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 7979 LNCS, pp. 409-416
  20. Surkova S, Myasnikova E, Kozlov KN, Pisarev A, Reinitz J, Samsonova M. (2013) Quantitative imaging of gene expression in Drosophila embryos. Cold Spring Harb Protoc. 2013 Jun 1;2013(6):488-97. doi: 10.1101/pdb.top075101.
  21. Surkova S, Myasnikova E, Kozlov KN, Pisarev A, Reinitz J, Samsonova M. (2013) Preparation of Drosophila embryos for quantitative imaging of gene expression. Cold Spring Harb Protoc. 2013 Jun 1;2013(6):533-6. doi: 10.1101/pdb.prot075093.
  22. Н.В. Иваниcенко, Е.Л. Мищенко, И.P. Акбеpдин, П.C. Деменков, В.А. Лиxошвай, К.Н. Козлов, Д.И. Тодоpов, М.Г. Cамcонова, А.М. Cамcонов, Н.А. Колчанов, В.А. Иваниcенко (2013) Репликация субгеномного репликона вируса гепатита Ц в присутствии ингибиторов NS3-протеазы: стохастическая модель. Биофизика, 2013, том 58, вып. 5, c. 758–774
  23. Surkova S, Golubkova E, Manu, Panok L, Mamon L, Reinitz J, Samsonova M. (2013) Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila KrГјppel and knirps mutants (2013). Dev Biol. 376: 99-112. DOI information: 10.1016/j.ydbio.2013.01.008
  24. Janssens H, Crombach A, Richard Wotton K, Cicin-Sain D, Surkova S, Lu Lim C, Samsonova M, Akam M, Jaeger J. (2013) Lack of tailless leads to an increase in expression variability in Drosophila embryos. Dev Biol. 2013 Jan 18. doi:pii: S0012-1606(13)00015-8. 10.1016/j.ydbio.2013.01.010
  25. A.Pisarev, M.Samsonova (2013) A method for solution of the multi-objective inverse problems under uncertainty. Biofizika(Rus), 58,2:221-232
  26. Kozlov K, Surkova S, Myasnikova E, Reinitz J, Samsonova M. Modeling of gap gene expression in Drosophila Kruppel mutants. PLoS Comput Biol. 2012 Aug;8(8):e1002635.
  27. Gursky VV, Surkova SY, Samsonova MG. Mechanisms of developmental robustness. Biosystems. 2012 Sep;109(3):329-35.
  28. Konstantin Kozlov, Alexander Samsonov (2011). DEEP - Differential Evolution Entirely Parallel Method for Gene Regulatory Networks, Journal of Supercomputing, Volume 57, pp.172-178.
  29. Vitaly V Gursky, Lena Panok, Ekaterina M. Myasnikova, Manu, Maria G. Samsonova, John Reinitz, and Alexander M Samsonov. Mechanisms of gap gene expression canalization in the Drosophila blastoderm. BMC Systems Biology, 5:118, 2011. doi:10.1186/1752-0509-5-118. [pdf]
  30. Myasnikova E., Surkova S., Stein G., Pisarev A., Samsonova M. (2011). A regression system for estimation of errors introduced by confocal imaging into gene expression data in situ. BMC Bioinformatics 12: 320, doi:10.1186/1471-2105-12-320.
  31. S. Yu. Surkova, V. V. Gurskiy, J. Reinitz and M. G. Samsonova (2011). Study of stability mechanisms of embryonic development in fruit fly Drosophila. Russian Journal of Developmental Biology, 42 (1): 1-15. DOI: 10.1134/S1062360411010115
  32. Svetlana Surkova, Ekaterina Myasnikova, Konstantin N. Kozlov, Andrei Pisarev, John Reinitz and Maria Samsonova (2011). Quantitative imaging of gene expression in Drosophila embryos. In Imaging in Developmental Biology: A Laboratory Manual (ed. J. Sharpe and RO. Wong). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 683-697
  33. Surkova S.Yu., Myasnikova E.M. Reinitz J., Samsonova M.G. (2010). Acquisition and processing of quantitative data on the basis of confocal images of gene expression patterns in situ. //Introduction to information biology and bioinformatics: in 5 v. /Eds N.A. Kolchanov et al./ Novosibirsk:NSU, Vol. 3, pp. 130-156 (Russian).
  34. Kozlov K.N., Samsonova M.G. (2010). Applied packages for image analysis in bioinformatics. //Introduction into the information biology and bioinformatics: in 5 v. /Eds N.A. Kolchanov et al./ Novosibirsk:NSU, Vol. 5, pp.151-162 (Russian).
  35. Konstantin Kozlov, Alexander Samsonov (2010). DEEP - Differential Evolution Entirely Parallel Method for Gene Regulatory Networks, Journal of Supercomputing, DOI:10.1007/s11227-010-0390-6.
  36. M.G.Samsonova, S.J.Surkova, K.N.Kozlov, A.S.Pisarev (2009) Bioinformatics - what for? Works of SPb polytechnical university, 511, "Scientific directions at physicomechanical faculty SPbGPU", 169-191
  37. Konstantin N. Kozlov, Ekaterina Myasnikova, Anastasia A. Samsonova, Svetlana Surkova, John Reinitz and Maria Samsonova (2009) GCPReg package for registration of the segmentation gene expression data in Drosophila. Fly 3, 2,151-156.
  38. Матвеева А.Д., Ионидес Дж., Самсонова М.Г., Райниц Дж.Моделирование механизмов регуляции экспрессии гена even-skipped у дрозофилы.Вестник ВОГиС, 2009, 13, 1, 194-200
  39. Manu, S. Surkova, A. V. Spirov, V. Gursky, H. Janssens, Ah-Ram Kim, O. Radulescu, C. E. Vanario-Alonso, D. H. Sharp, M. Samsonova and John Reinitz (2009). Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors. PLoS Comp. Biology (2009) 5, 3, e1000303.
  40. Manu, S. Surkova, A. V. Spirov, V. Gursky, H. Janssens, Ah-Ram Kim, O. Radulescu, C. E. Vanario-Alonso, D. H. Sharp, M. Samsonova and John Reinitz (2009). Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biology (2009) 7, 3, e1000049.
  41. E. Myasnikova, S. Surkova, L. Panok, M. Samsonova and J. Reinitz (2009). Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila. Bioinformatics, 25: 346 - 352.
  42. V. V. Gursky, K. N. Kozlov, A. M. Samsonov, J. Reinitz (2008). Model with asymptotically robust dynamics for gap genes network in Drosophila. Biofizika. 53(2): 235-249 (Russian).
  43. Andrei Pisarev, Ekaterina Poustelnikova, Maria Samsonova, John Reinitz (2009). FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nucl. Acids Res., 37: D560 - D566.
  44. Svetlana Surkova, Ekaterina Myasnikova, Hilde Janssens, Konstantin N. Kozlov, Anastasia A. Samsonova, John Reinitz and Maria Samsonova (2008). Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images. FLY, 2(2): 58-66.
  45. S. Yu. Surkova, E. M. Myasnikova, K. N. Kozlov, A. A. Samsonova, J. Reinitz and M. G. Samsonova (2008). Methods for acquisition of quantitative data from the confocal images of gene expression in situ. Tsitologiia, 50(4): 352-69 (Russian). Review PMID: 18664119.
  46. Surkova, S.Ju., Myasnikova, E.M., Reinitz, J., Samsonova, M. (2008). Dynamic filtration of the variability of expression patterns of zygotic segmentation genes Drosophila. Biofizika. 53(3):475-81 (Russian). PMID: 18634321.
  47. Svetlana Surkova, David Kosman, Konstantin Kozlov, Manu, Ekaterina Myasnikova, Anastasia A. Samsonova, Alexander Spirov, Carlos E. Vanario-Alonso, Maria Samsonova and John Reinitz (2008). Characterization of the Drosophila segment determination morphome. Developmental Biology, 313(2): 844-862. PMID: 18067886.
  48. Yu Feng Wu, Ekaterina Myasnikova, John Reinitz (2007). Master equation simulation analysis of immunostained Bicoid morphogen gradient. BMC Systems Biology 2007, 1: 52. PMID: 18021413.
  49. V. V. Gursky, K. N. Kozlov, A. M. Samsonov, and J. Reinitz (2006). Cell divisions as a mechanism for selection in stable steady states of multi-stationary gene circuits. Physica D, 218: 70-76.
  50. M. G. Samsonova, V. V. Gursky, K. N. Kozlov and A. M. Samsonov (2006). System approach to the development of organisms. Science-Technical Bulletin of St. Petersburg State Polytechnical University, V. 2, 222-234 (Russian).
  51. M. Samsonova, A. Pisarev, K. Kozlov, E. Poustelnikova, and A. Tkachenko (2006). An information management system for collaboration within distributed working environment. LNBI 4075, volume 40, U. Leser, F. Naumann, and B. Eckman, eds, Berlin Heidelberg, Springer-Verlag, 204-215.
  52. H. Janssens, S. Hou, J. Jaeger, A.R. Kim, E. Myasnikova, D. Sharp and J. Reinitz (2006). Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even-skipped gene. Nature Genetics, 38(10): 1159-1165. PMID: 16980977.
  53. C. O. S. Sorzano, M. Blagov, P. Thevenaz, E. Myasnikova, M. Samsonova and M. Unser (2006). Algorithm for Spline-Based Elastic Registration in Application to Confocal Images of Gene Expression. Pattern Recognition and Image Analysis, 16(1): 93-96.
  54. M. G. Samsonova, A. M. Samsonov, V. V. Gursky and C. E. Vanario-Alonso (2005). A survey of gene circuit approach applied to modelling of segment determination in fruit fly. In: Multiple aspects of DNA and RNA: from Biophysics to Bioinformatics, Session LXXXII (Eds. D. Chatenay, S. Cocco, R. Monasson, D. Thieffry and J. Dalibard). Elsevier, Inc. 2005, pp. 305-323.
  55. E. Myasnikova, A. Samsonova, S. Surkova, M. Samsonova, J. Reinitz (2005). Determination of the developmental age of a Drosophila embryo from confocal images of its segmentation gene expression patterns. In: Bioinformatics of Genome Regulation and Structure II. (Eds. N.Kolchanov and R. Hofestaedt) Springer Science+Business Media, Inc. 2005, pp. 467-478.
  56. A. Pisarev, M. Blagov, E. Poustelnikova, E. Myasnikova, M. Samsonova (2005). A system for on-line processing and analysis of images of gene expression patterns. Pattern Recognition and Image Analysis: Advances in Mathematical Theory and Applications, 15(2): 432-435.
  57. H. Janssens, D. Kosman, C-E Vanario-Alonso, J. Jaeger, M. Samsonova and J. Reinitz (2005). A high-throughput method for quantifying gene expression data from early Drosophila embryo. Development, Genes and Evolution, 225(7): 374-381. PMID: 15834586.
  58. A. Pisarev, E. Poustelnikova, K. Kozlov, E. Myasnikova, M. Samsonova and J. Reinitz (2005). ImageServer, a Tool for On-line Processing and Analysis of Biological Images. In: Yearbook Bioinformatics 2004, R. HofestпїЅdt (ed.), pp. 15-24. Magdeburg: IMBio, Informationsmanagement in der Biotechnologie e.V., 2005.
  59. Ekaterina Myasnikova, Maria Samsonova, David Kosman and John Reinitz (2005). Removal of background signal from in situ data on the expression of segmentation genes in Drosophila. Development, Genes and Evolution, 215(6): 320-326. PMID: 15711806.
  60. Vitaly V. Gursky, Johannes Jaeger, Konstantin N. Kozlov, John Reinitz, and Alexander M. Samsonov (2004). Pattern formation and nuclear divisions are uncoupled in Drosophila segmentation: Comparison of spatially discrete and continuous models. Physica D, 197: 286-302.
  61. Johannes Jaeger, Svetlana Surkova, Maxim Blagov, Hilde Janssens, David Kosman, Konstantin N. Kozlov, Manu, Ekaterina Myasnikova, Carlos E. Vanario-Alonso, Maria Samsonova, David H. Sharp, and John Reinitz (2004). Dynamic control of positional information in the early Drosophila embryo. Nature, 430: 368-371. PMID: 15254541.
  62. Johannes Jaeger, Maxim Blagov, David Kosman, Konstantin N. Kozlov, Manu, Ekaterina Myasnikova, Svetlana Surkova, Carlos E. Vanario-Alonso, Maria Samsonova, David H. Sharp, and John Reinitz (2004). Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics, 167: 1721-1737. PMID: 15342511.
  63. Ekaterina Poustelnikova, Andrei Pisarev, Maxim Blagov, Maria Samsonova, and John Reinitz (2004). A database for management of gene expression data in situ. Bioinformatics, 20: 2212-2221. PMID: 15059825.
  64. M. Samsonova, A. Pisarev and M. Blagov (2003). Processing of natural language queries to a relational database. Bioinformatics, 19, Suppl. 1, i241-i249. PMID: 12855465.
  65. Kozlov K.N., Samsonov A.M. New Data Processing Technique Based on the Optimal Control Theory. Techn. Physics, vol. 48, пїЅ11, pp. 6 - 14, 2003.
  66. A.Pisarev, E.Poustelnikova, M.Samsonova, P.Baumann. Mooshka: a system for management of multidimensional gene expression data in situ (2003). Information Systems, 28(4): 269-285.
  67. Kozlov, K.N.; Petuhov, L.V., Samsonov, A.M., Samsonova, M.G. (2002) Steepest descent method of the 1st order applied to find the phenomenological parameters of the gene circuits model. SPbSTU Transactions, `Applied Mathematics`, 485: 73-83.
  68. E. Myasnikova, A. Samsonova, M. Samsonova and J. Reinitz. Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns (2002). Bioinformatics, 18, S87-S95. PMID: 12169535.
  69. Igor Aizenberg, Ekaterina Myasnikova, Maria Samsonova, and John Reinitz. Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method. (2002). Mathematical Biosciences, 176: 145-159. PMID: 11867088.
  70. K. Kozlov, E. Myasnikova, A.Pisarev, M. Samsonova and J. Reinitz (2002) A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ. (2002) In Silico Biology, 2: 125-141. PMID: 12066837.
  71. Aizenberg I., Myasnikova E., Samsonova M. and Reinitz J. (2001) Application of the Neural Networks Based on Multi-Valued Neurons to Classification of the Images of Gene Expression Patterns. Computational Intelligence: Theory and Applications, Lecture Notes in Computer Sciences (B.Reusch - Ed.), Vol. 2206, Springer, pp. 291-303.
  72. V. V. Gursky, J. Reinitz, A. M. Samsonov. How gap genes make their domains: An analytical study based on data driven approximations, Chaos 11(1) (2001) 132-141.
  73. Ekaterina Myasnikova, Anatassia Samsonova, Maria Samsonova, and John Reinitz. Spatial registration of in situ gene expression data. Molekularnaya Biologia (Rus.) (2001), 35 (6): 1110 - 1115. PMID: 11771137.
  74. Ekaterina Myasnikova, Anastassia Samsonova, Konstantin Kozlov, Maria Samsonova, and John Reinitz. Registration of the expression patterns of Drosophila segmentation genes by two independent methods (2001). Bioinformatics, 17: 3-12. PMID: 11222257.
  75. Konstantin Kozlov, Ekaterina Myasnikova, Maria Samsonova, John Reinitz, and David Kosman (2000). Method for spatial registration of the expression patterns of Drosophila segmentation genes using wavelets. Computational Technologies, 5: 112-119.
  76. M.G.Samsonova, V.N.Serov NetWork: an interactive interface to the tools for the analysis of genetic network structure and dynamics (1999). Proceedings of Pacific Symposium on Biocomputing, 4: 102-111.
  77. V.N.Serov, O.V.Kirillova, M.G.Samsonova NetWork: a tool for visualization of genetic network structure and dynamics (1999). In "Visual Representations and Interpretations", pp.156-160, R.Paton & I.Neilson eds., Springer Verlag.
  78. Myasnikova, E.M., Kosman, D., Reinitz, J., Samsonova, M.G. Spatio-temporal registration of the expression patterns of Drosophila segmentation genes (1999). Proceedings of the 7th Int. Conference on Intelligent Systems for Molecular Biology, pp 195-201, T.Lengauer, R. Schneider, P.Bork, D.Brutlag, J.Glasgow, H.-W.Mewes and R.Zimmer eds., AAAI press. PMID: 10786302.
  79. V.N.Serov, A.V.Spirov, M.G.Samsonova Graphical interface to the genetic network database GeNet (1998) Bioinformatics, 14(6): 546-547. PMID: 9694997.
  80. M.G.Samsonova, K.G.Savostyanova, V.N.Serov, S.Yu.Surkova, A.V.Spirov GeNet: a database of genetic networks CSTB Bulletin (Spr. 1998) http://dbm.ulb.ac.be/~denis/cstbspring98/CSTB-Spring98-Samsonova.html.
  81. A.V.Spirov, M.G.Samsonova GeNet database as a tool for analysis of regulatory genetic networks (1998) Information Processing in Cells and Tissues, M.Holcombe and R.Paton (Eds) Plennum Press, 285-294.
  82. V.N.Serov, E.G.Savostyanova, S.Yu.Surkova, O.V.Kirillova, A.V.Spirov, J.Reinitz, M.G.Samsonova A database of genetic networks controlling embryogenesis. CSTB Bulletin, Spring 1998. http://www.mar.dfo-mpo.gc.ca/science/mesd/he/science/cstb/papers/serov/.