Публикации

Rozhmina, T., Samsonova, A., Kanapin, A., & Samsonova, M. (2022). An account of Fusarium wilt resistance in flax Linum usitatissimum: The disease severity data. Data in brief, 41, 107869. https://doi.org/10.1016/j.dib.2022.107869
Samsonova A, Kanapin A, Bankin M, Logachev A, Gretsova M, Rozhmina T, Samsonova M. A Genomic Blueprint of Flax Fungal Parasite Fusarium oxysporum f. sp. lini. Int J Mol Sci. 2021 Mar 6;22(5):2665. doi: 10.3390/ijms22052665. PMID: 33800857; PMCID: PMC7961770.
Pavlinova P, Samsonova MG, Gursky VV. Dynamical Modeling of the Core Gene Network Controlling Transition to Flowering in Pisum sativum. Front Genet. 2021 Mar 11;12:614711. doi: 10.3389/fgene.2021.614711. PMID: 33777095; PMCID: PMC7990781.
Surkova S, Görne J, Nuzhdin S, Samsonova M. Interplay between sex determination cascade and major signaling pathways during Drosophila eye development: Perspectives for future research. Dev Biol. 2021 Mar 18;476:41-52. doi: 10.1016/j.ydbio.2021.03.005. Epub ahead of print. PMID: 33745943.
Duk, M., Kanapin, A., Rozhmina, T., Bankin, M., Surkova, S., Samsonova, A., & Samsonova, M. (2021). The Genetic Landscape of Fiber Flax. Frontiers in plant science, 12, 764612. https://doi.org/10.3389/fpls.2021.76461
Tang, S., Shahriari, M., Xiang, J., Pasternak, T., Igolkina, A., Aminizade, S., Zhi, H., Gao, Y., Roodbarkelari, F., Sui, Y., Jia, G., Wu, C., Zhang, L., Zhao, L., Li, X., Meshcheryakov, G., Samsonova, M., Diao, X., Palme, K., & Teale, W. (2021). The role of AUX1 during lateral root development in the domestication of the model C4 grass Setaria italica. Journal of experimental botany, erab556. Advance online publication. https://doi.org/10.1093/jxb/erab556
Duk, M. A., Gursky, V. V., Samsonova, M. G., & Surkova, S. Y. (2021). Application of Domain- and Genotype-Specific Models to Infer Post-Transcriptional Regulation of Segmentation Gene Expression in Drosophila. Life (Basel, Switzerland), 11(11), 1232. https://doi.org/10.3390/life11111232
Kanapin, A., Bankin, M., Rozhmina, T., Samsonova, A., & Samsonova, M. (2021). Genomic Regions Associated with Fusarium Wilt Resistance in Flax. International journal of molecular sciences, 22(22), 12383. https://doi.org/10.3390/ijms222212383
Rozhmina, T., Bankin, M., Samsonova, A., Kanapin, A., & Samsonova, M. (2021). A comprehensive dataset of flax (Linum uitatissimum L.) phenotypes. Data in brief, 37, 107224. https://doi.org/10.1016/j.dib.2021.107224
Pavlov, S., Gursky, V. V., Samsonova, M., Kanapin, A., & Samsonova, A. (2021). Stochastic Effects in Retrotransposon Dynamics Revealed by Modeling under Competition for Cellular Resources. Life (Basel, Switzerland), 11(11), 1209. https://doi.org/10.3390/life11111209
Salihov, S.; Maltsov, D.; Samsonova, M.; Kozlov, K. Solution of Mixed-Integer Optimization Problems in Bioinformatics with Differential Evolution Method. Mathematics 2021, 9, 3329. https:// doi.org/10.3390/math9243329
Ageev, A.; Lee, C.-R.; Ting, C.-T.; Schafleitner, R.; Bishop-von Wettberg, E.; Nuzhdin, S.V.; Samsonova, M.; Kozlov, K. Modeling of Flowering Time in Vigna radiata with Approximate Bayesian Computation. Agronomy 2021, 11, 2317. https://doi.org/10.3390/ agronomy11112317
Sokolkova, A., Burlyaeva, M., Valiannikova, T., Vishnyakova, M., Schafleitner, R., Lee, C. R., Ting, C. T., Nair, R. M., Nuzhdin, S., Samsonova, M., & von Wettberg, E. (2020). Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan). BMC plant biology, 20(Suppl 1), 363.
Sokolkova, A., Bulyntsev, S. V., Chang, P. L., Carrasquilla-Garcia, N., Igolkina, A. A., Noujdina, N. V., von Wettberg, E., Vishnyakova, M. A., Cook, D. R., Nuzhdin, S. V., and Samsonova, M. G. (2020). Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection. International journal of molecular sciences, 21(11), E3952.
Kozlov, K., Sokolkova, A., Lee, C. R., Ting, C. T., Schafleitner, R., Bishop-von Wettberg, E., Nuzhdin, S., & Samsonova, M. (2020). Dynamical climatic model for time to flowering in Vigna radiata. BMC plant biology, 20(Suppl 1), 202.
Kanapin, A., Samsonova, A., Rozhmina, T., Bankin, M., Logachev, A., & Samsonova, M. (2020). The Genome Sequence of Five Highly Pathogenic Isolates of Fusarium oxysporum f. sp. lini. Molecular plant-microbe interactions : MPMI, 33(9), 1112–1115.
Igolkina, A. A., Meshcheryakov, G., Gretsova, M. V., Nuzhdin, S. V., and Samsonova, M. G. (2020). Multi-trait multi-locus SEM model discriminates SNPs of different effects. BMC genomics, 21(Suppl 8), 490.
Konstantin Kozlov, Anupam Singh, Jens Berger, Eric Bishop-von Wettberg, Abdullah Kahraman, Abdulkadir Aydogan, Douglas Cook, Sergey Nuzhdin and Maria Samsonova) Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors BMC Plant Biol. 2019 Mar 19;19(Suppl 2):94.
Burlyaeva M.O., Vishnyakova M.A., Gurkina M.V., Kozlov K.N., Lee C.R., Ting C.T., Schafleitne R., Nuzhdin S.V., Samsonova M.G., von Wettberg E. Collections of Mungbean [Vigna radiata) (L.) R. Wilczek] and urdbean [V. mungo (L.) Hepper] in Vavilov Institute (VIR): traits diversity and trends in the breeding process over the last 100 years. Genet Resour Crop Evol (2019) 66: 767.
Shin MG, Bulyntsev SV, Chang PL, Korbu LB, Carrasquila-Garcia N, Vishnyakova MA, Samsonova MG, Cook DR, Nuzhdin SV. Multi-trait analysis of domestication genes in Cicer arietinum – Cicer reticulatum hybrids with a multidimensional approach: Modeling wide crosses for crop improvement. Plant science 285 (2019) 122-131.
Surkova S, Sokolkova A, Kozlov K, Nuzhdin SV, Samsonova M.Quantitative analysis reveals genotype- and domain- specific differences between mRNA and protein expression of segmentation genes in Drosophila. Dev Biol. 2019 Jan 7. pii: S0012-1606(18)30129-5.
Kozlov K, Singh A, Berger J, Bishop-von Wettberg E, Kahraman A, Aydogan A, Cook D, Nuzhdin S, Samsonova M. Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors. BMC Plant Biol. 2019 Mar 19;19(Suppl 2):94. doi: 10.1186/s12870-019-1685-2.
Igolkina A.A., Armoskus C., Newman J.R.B., Evgrafov O.V., McIntyre L.M., Nuzhdin S.V., Samsonova M.G. Analysis of Gene Expression Variance in Schizophrenia Using Structural Equation Modeling. FRONTIERS IN MOLECULAR NEUROSCIENCE Volume: 11 Article Number: 192 Published: JUN 11 2018
Petukhov V, Guo J, Baryawno N, Severe N, Scadden DT, Samsonova MG, Kharchenko PV. dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. GENOME BIOLOGY Volume: 19 Article Number: 78 Published: JUN 19 2018
Plekhanova E, Nuzhdin SV, Utkin LV, Samsonova MG. Prediction of deleterious mutations in coding regions of mammals with transfer learning (2018) Evol Appl. 2018 May 9;12(1):18-28.https://doi.org/10.1111/eva.12607
Maxim S Kovalev, Anna A Igolkina, Maria G Samsonova, Sergey V Nuzhdin, A pipeline for classifying deleterious coding mutations in agricultural plants Front. Plant Sci. Front Plant Sci. 2018 Nov 28;9:1734
Vitaly V. Gursky, Konstantin N. Kozlov, Sergey V. Nuzhdin, Maria G. Samsonova Dynamical Modeling of the Core Gene Network Controlling Flowering Suggests Cumulative Activation from the FLOWERING LOCUS T Gene Homologs in Chickpea Front Genet. 2018 Nov 20;9:547
Surkova S, Golubkova E, Mamon L, Samsonova M. Dynamic maternal gradients and morphogenetic networks in Drosophila early embryo. Biosystems. 2018 Nov;173:207-213
Gursky VV, Kozlov KN, Kulakovskiy IV, Zubair A, Marjoram P, Lawrie DS, Nuzhdin SV, Samsonova MG. Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network. (2017) PLoS One, 12(9):e0184657
Plekhanova, E., M. A. Vishnyakova, S. Bulyntsev, P. L. Chang, N. Carrasquilla-Garcia, K. Negash, E. von Wettberg, N. Noujdina, D. R. Cook, M. G. Samsonova and S. V. Nuzhdin. Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits (2017). Scientific Reports 7 (1), 1-12. doi:10.1038/s41598-017-05087-5.
Kozlov K, Kosheverova V, Kamentseva R, Kharchenko M, Sokolkova A, Kornilova E, Samsonova M. Quantitative analysis of heterogeneous population of endocytic vesicles. J Bioinform Comput Biol. 2017 Apr;15(2):1750008.
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
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.
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.
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
Lavrik I.N., Samsonova M.G. Systems biology of signaling pathways (2016) . Biofizika. 2016; 61(1): 93-101
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
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
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
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.
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.
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
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.
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
Igor Gula, Alexander M. Samsonov (2014). Gap gene expression model based on the Jeffreys type equation. Bioinformatics, 2014, Mar. 1;31(5):714-9.
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
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
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
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.
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.
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
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
A.Pisarev, M.Samsonova (2013) A method for solution of the multi-objective inverse problems under uncertainty. Biofizika(Rus), 58,2:221-232
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.
Gursky VV, Surkova SY, Samsonova MG. Mechanisms of developmental robustness. Biosystems. 2012 Sep;109(3):329-35.
Konstantin Kozlov, Alexander Samsonov (2011). DEEP — Differential Evolution Entirely Parallel Method for Gene Regulatory Networks, Journal of Supercomputing, Volume 57, pp.172-178.
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]
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.
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
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
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).
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).
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.
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
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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