Self-Assemblage of Gene Nets in Evolution via Recruiting of New Netters. - Alexander V. Spirov (PPSN, 1996)

Transposon Element Technique Applied to GA-Based John Muir's Trail Test. - Alexander V. Spirov; A. S. Kadyrov (HPCN Europe, 1998)

Graphical interface to the genetic network database GeNet. - Vassili N. Serov; Alexander V. Spirov; Maria Samsonova (Bioinform., 1998)

Experimental Determination of Drosophila Embryonic Coordinates by Genetic Algorithms, the Simplex method, and Their Hybrid. - Alexander V. Spirov; Dmitry L. Timakin; John Reinitz; David Kosman (EvoWorkshops, 2000)

HOX Pro: a specialized database for clusters and networks of homeobox genes. - Alexander V. Spirov; Timothy Bowler; John Reinitz (Nucleic Acids Res., 2000)

Using of Evolutionary Computations in Image Processing for Quantitative Atlas of Drosophila Genes Expression. - Alexander V. Spirov; Dmitry L. Timakin; John Reinitz; David Kosman (EvoWorkshops, 2001)

Jumping Genes-mutators Can Rise Efficacy Of Evolutionary Search. - Alexander V. Spirov; Alexander B. Kazansky (GECCO, 2002)

HOX Pro DB: the functional genomics of hox ensembles. - Alexander V. Spirov; Mikhail Borovsky; Olesya A. Spirova (Nucleic Acids Res., 2002)

Reconstruction of the Dynamics of Drosophila Genes Expression from Sets of Images Sharing a Common Pattern. - Alexander V. Spirov; Alexander B. Kazansky; Dmitry L. Timakin; John Reinitz (Real Time Imaging, 2002)

Evolutionary Techniques for Image Processing a Large Dataset of Early Drosophila Gene Expression. - Alexander V. Spirov; David M. Holloway (EURASIP J. Adv. Signal Process., 2003)

Making the body plan: Precision in the genetic hierarchy of Drosophila embryo segmentation. - Alexander V. Spirov; David M. Holloway (Silico Biol., 2003)

Singular Spectrum Analysis of Gene Expression Profiles of Early Drosophila embryo: Exponential-in-Distance Patterns. - Theodore Alexandrov; Nina Golyandina; Alexander V. Spirov (J. Electr. Comput. Eng., 2008)

Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo. - Francisco J. P. Lopes; Fernando M. C. Vieira; David M. Holloway; Paulo Mascarello Bisch; Alexander V. Spirov (PLoS Comput. Biol., 2008)

Forced Evolution in Silico by Artificial Transposons and their Genetic Operators: The John Muir Ant Problem - Alexander V. Spirov; Alexander B. Kazansky; Leonid Zamdborg; Juan Julián Merelo Guervós; Vladimir F. Levchenko (CoRR, 2009)

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors. - Manu; Svetlana Surkova; Alexander V. Spirov; Vitaly V. Gursky; Hilde Janssens; Ah-Ram Kim; Ovidiu Radulescu; Carlos E. Vanario-Alonso; David H. Sharp; Maria Samsonova; John Reinitz (PLoS Comput. Biol., 2009)

Design of a dynamic model of genes with multiple autonomous regulatory modules by evolutionary computations. - Alexander V. Spirov; David M. Holloway (ICCS, 2010)

Retroviral Genetic Algorithms - Implementation with Tags and Validation Against Benchmark Functions. - Alexander V. Spirov; David M. Holloway (IJCCI (ECTA-FCTA), 2011)

Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation. - David M. Holloway; Francisco J. P. Lopes; Luciano da Fontoura Costa; Bruno Augusto Nassif Travençolo; Nina Golyandina; Konstantin Usevich; Alexander V. Spirov (PLoS Comput. Biol., 2011)

Evolution in silico of genes with multiple regulatory modules on the example of the Drosophila segmentation gene hunchback. - Alexander V. Spirov; David M. Holloway (CIBCB, 2012)

Measuring Gene Expression Noise in Early Drosophila Embryos: The Highly Dynamic Compartmentalized Micro-environment of the Blastoderm Is One of the Main Sources of Noise. - Alexander V. Spirov; Nina Golyandina; David M. Holloway; Theodore Alexandrov; Ekaterina N. Spirova; Francisco J. P. Lopes (EvoBIO, 2012)

Complexification of Gene Networks by Co-evolution of Genomes and Genomic Parasites. - David M. Holloway; Alexander B. Kazansky; Alexander V. Spirov (IJCCI, 2012)

Measuring Gene Expression Noise in Early Drosophila Embryos: Nucleus-to-nucleus Variability. - Nina Golyandina; David M. Holloway; Francisco J. P. Lopes; Alexander V. Spirov; Ekaterina N. Spirova; Konstantin Usevich (ICCS, 2012)

Modeling the Evolution of Gene Regulatory Networks for Spatial Patterning in Embryo Development. - Alexander V. Spirov; David M. Holloway (ICCS, 2013)

Experimental Determination of Intrinsic Drosophila Embryo Coordinates by Evolutionary Computation. - Alexander V. Spirov; Carlos E. Vanario-Alonso; Ekaterina N. Spirova; David M. Holloway (PRIB, 2013)

In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression. - Elizaveta A. Zagrijchuk; Marat A. Sabirov; David M. Holloway; Alexander V. Spirov (J. Bioinform. Comput. Biol., 2014)

Evolutionary Design of Gene Networks: Forced Evolution by Genomic Parasites. - Alexander V. Spirov; Elizaveta A. Zagriychuk; David M. Holloway (Parallel Process. Lett., 2014)

Forced evolution in silico by artificial transposons and their genetic operators: The ant navigation problem. - Leonid Zamdborg; David M. Holloway; Juan Julián Merelo Guervós; Vladimir F. Levchenko; Alexander V. Spirov (Inf. Sci., 2015)

Sequential construction of a model for modular gene expression control, applied to spatial patterning of the Drosophila gene hunchback. - Alexander V. Spirov; Ekaterina M. Myasnikova; David M. Holloway (J. Bioinform. Comput. Biol., 2016)

Robustness of expression pattern formation due to dynamic equilibrium in gap gene system of an early Drosophila embryo. - Ekaterina M. Myasnikova; Alexander V. Spirov (Biosyst., 2018)

Modularity in biological evolution and evolutionary computation. - Anton V. Eremeev; Alexander V. Spirov (CoRR, 2018)

Relative sensitivity analysis of the predictive properties of sloppy models. - Ekaterina M. Myasnikova; Alexander V. Spirov (J. Bioinform. Comput. Biol., 2018)

Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data. - Theodore Alexandrov; Nina Golyandina; David M. Holloway; Alexander Shlemov; Alexander V. Spirov (J. Comput. Biol., 2018)

Evaluation of runtime bounds for SELEX procedure with high selection pressure. - Anton V. Eremeev; Alexander V. Spirov (GECCO (Companion), 2019)

Techniques from evolutionary computation to implement as experimental approaches in synthetic biology: tests in silico. - Alexander V. Spirov; Ekaterina M. Myasnikova (GECCO (Companion), 2019)

Linguistic modelling of gene regulation: Translation from the language of experiments to the language of modelling. - Alexander V. Spirov; Ekaterina M. Myasnikova (ICT Express, 2019)

Noise model estimation with application to gene expression. - Polina Zhornikova; Nina Golyandina; Alexander V. Spirov (J. Bioinform. Comput. Biol., 2019)

Quantitative Analysis of the Dynamics of Maternal Gradients in the Early Drosophila Embryo. - Ekaterina M. Myasnikova; Victoria Yu. Samuta; Alexander V. Spirov (ISBRA, 2020)

Gene regulatory networks in Drosophila early embryonic development as a model for the study of the temporal identity of neuroblasts. - Ekaterina M. Myasnikova; Alexander V. Spirov (Biosyst., 2020)

Modeling SELEX for regulatory regions using Royal Road and Royal Staircase fitness functions. - Anton V. Eremeev; Alexander V. Spirov (Biosyst., 2021)

Quantitative Analysis of the Dynamics of Maternal Gradients in the Early Drosophila Embryo. - Ekaterina M. Myasnikova; Marat A. Sabirov; Alexander V. Spirov (J. Comput. Biol., 2021)

Problem of Domain/Building Block Preservation in the Evolution of Biological Macromolecules and Evolutionary Computation. - Alexander V. Spirov; Ekaterina M. Myasnikova (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Evolution of the RNA world: From signals to codes. - Alexander V. Spirov (Biosyst., 2023)

Body plan evolvability: The role of variability in gene regulatory networks. - Alexander V. Spirov; Ekaterina M. Myasnikova; David M. Holloway (J. Bioinform. Comput. Biol., 2024)