Fly Publications
Noise and Precision
Holloway D.M. (2018). Experimental and modeling approaches for understanding the effect of gene expression noise in biological development. Frontiers in Physics 6: 36.
www.frontiersin.org/articles/10.3389/fphy.2018.00036
Holloway D.M. and Spirov A.V. (2017). Transcriptional bursting in Drosophila development: stochastic dynamics of eve stripe 2 expression. PLOS ONE 12(4): e0176228.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0176228
Holloway D.M. and Spirov A.V. (2017). Stochastic dynamics of gene expression in developing fly embryos. IEEE Xplore, iss. 20-23 June 2017. doi: 10.1109/ICNF.2017.7985933.
ieeexplore.ieee.org/document/7985933/
Holloway D.M. and Spirov A.V. (2015). Mid-embryo patterning and precision in Drosophila segmentation: Krüppel dual regulation of hunchback. PLOS ONE 10(3): e0118450.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118450
Holloway, D.M., Lopes, F.J.P., da Fontoura Costa, L., Travençolo, B.A.N., Golyandina, N., Usevich, K., and Spirov, A.V. (2011). Gene expression noise in spatial patterning: hunchback promoter structure affects noise amplitude and distribution in Drosophila segmentation. PLoS Computational Biology 7(2): e1001069.
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001069
Holloway, D.M. and Spirov, A.V. (2011). Gene expression noise in embryonic spatial patterning: reliable formation of the head-to-tail axis in the fruit fly. IEEE Xplore , iss. 12-16 June 2011, pp. 495-498. doi: 10.1109/ICNF.2011.5994379. http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5994379&isnumber=5994268
Lopes, F.J.P., Vieira, F.M.C., Holloway, D.M., Bisch, P.M., Spirov, A.V. (2008). Spatial bistability generates hunchback expression sharpness in the Drosophila embryo. PLoS Computational Biology 4: e1000184.
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000184
Holloway, D.M., Harrison, L.G., Kosman, D., Vanario-Alonso, C.E., and Spirov, A.V. (2006). Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products. Developmental Dynamics 235: 2949-2960.
Spirov, A.V., and Holloway, D.M. (2003). Making the body plan: precision in the genetic hierarchy of Drosophila embryo segmentation. In Silico Biology 3: 89-100.
Holloway, D.M., Harrison, L.G., and Spirov, A.V. (2003). Noise in the segmentation gene network of Drosophila, with implications for mechanisms of body axis specification. Proceedings of SPIE 5110: 180-191.
Holloway, D.M., Reinitz, J., Spirov, A., and Vanario-Alonso, C.E. (2002). Sharp borders from fuzzy gradients. Trends in Genetics 18: 385-387.
Holloway, D.M., and Harrison, L.G. (1999). Suppression of positional errors in biological development. Mathematical Biosciences 156: 271-290.
www.frontiersin.org/articles/10.3389/fphy.2018.00036
Holloway D.M. and Spirov A.V. (2017). Transcriptional bursting in Drosophila development: stochastic dynamics of eve stripe 2 expression. PLOS ONE 12(4): e0176228.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0176228
Holloway D.M. and Spirov A.V. (2017). Stochastic dynamics of gene expression in developing fly embryos. IEEE Xplore, iss. 20-23 June 2017. doi: 10.1109/ICNF.2017.7985933.
ieeexplore.ieee.org/document/7985933/
Holloway D.M. and Spirov A.V. (2015). Mid-embryo patterning and precision in Drosophila segmentation: Krüppel dual regulation of hunchback. PLOS ONE 10(3): e0118450.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118450
Holloway, D.M., Lopes, F.J.P., da Fontoura Costa, L., Travençolo, B.A.N., Golyandina, N., Usevich, K., and Spirov, A.V. (2011). Gene expression noise in spatial patterning: hunchback promoter structure affects noise amplitude and distribution in Drosophila segmentation. PLoS Computational Biology 7(2): e1001069.
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001069
Holloway, D.M. and Spirov, A.V. (2011). Gene expression noise in embryonic spatial patterning: reliable formation of the head-to-tail axis in the fruit fly. IEEE Xplore , iss. 12-16 June 2011, pp. 495-498. doi: 10.1109/ICNF.2011.5994379. http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5994379&isnumber=5994268
Lopes, F.J.P., Vieira, F.M.C., Holloway, D.M., Bisch, P.M., Spirov, A.V. (2008). Spatial bistability generates hunchback expression sharpness in the Drosophila embryo. PLoS Computational Biology 4: e1000184.
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000184
Holloway, D.M., Harrison, L.G., Kosman, D., Vanario-Alonso, C.E., and Spirov, A.V. (2006). Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products. Developmental Dynamics 235: 2949-2960.
Spirov, A.V., and Holloway, D.M. (2003). Making the body plan: precision in the genetic hierarchy of Drosophila embryo segmentation. In Silico Biology 3: 89-100.
Holloway, D.M., Harrison, L.G., and Spirov, A.V. (2003). Noise in the segmentation gene network of Drosophila, with implications for mechanisms of body axis specification. Proceedings of SPIE 5110: 180-191.
Holloway, D.M., Reinitz, J., Spirov, A., and Vanario-Alonso, C.E. (2002). Sharp borders from fuzzy gradients. Trends in Genetics 18: 385-387.
Holloway, D.M., and Harrison, L.G. (1999). Suppression of positional errors in biological development. Mathematical Biosciences 156: 271-290.
Gene Networks
Spirov, A.V., Sabirov, M.A., and Holloway, D.M. (2018). Systems evolutionary biology of Waddington's canalization and genetic assimilation. In Evolutionary Physiology and Biochemistry - Advances and Perspectives, ed. V.F. Levchenko, pp. 167-185, InTech Press. Available at http://dx.doi.org/10.5772/intechopen.73662
Spirov A.V., Myasnikova E.M., and Holloway D.M. (2016). Sequential construction of a model for modular gene expression control, applied to spatial patterning of the Drosophila gene hunchback. Journal of Bioinformatics and Computational Biology 14, 1641005. http://dx.doi.org/10.1142/S0219720016410055
Zamdborg L., Holloway D.M., Merelo J.J., Levchenko V.F., and Spirov A.V. (2015). Forced evolution in silico by artificial transposons and their genetic operators: the ant navigation problem. Information Sciences 306, 88-110.
Spirov A., and Holloway D. (2015). Using EA to study the evolution of GRNs controlling biological development. In Evolutionary Algorithms in Gene Regulatory Network Research, eds. N. Noman, H. Iba, pp. 240-268. Wiley Interscience.
Spirov, A., Zagriychuck, E., Holloway, D. (2014). Evolutionary design of gene networks: forced evolution by genomic parasites. Parallel Processing Letters 24, 1440004.
Zagrijchuck, E.A., Sabirov, M.A., Holloway, D.M., and Spirov, A.V. (2014). In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression. Journal of Bioinformatics and Computational Biology 12, 1441009. http://dx.doi.org/10.1142/S0219720014410091
Spirov, A.V. and Holloway, D.M. (2013). Using evolutionary computations to understand the design and evolution of gene and cell regulatory networks. Methods 62, 39-55.
Spirov, A.V. and Holloway, D.M. (2013). Modeling the evolution of gene regulatory networks for spatial patterning in embryo development. Procedia Computer Science 18, 1362-1371.
http://www.sciencedirect.com/science/article/pii/S1877050913004468
Spirov, A., Sabirov, M, and Holloway, D.M. (2012). In silico evolution of gene co-option in pattern-forming gene networks. The Scientific World Journal, special issue on Computational Systems Biology, Article ID 560101, doi: 10.1100/2012/560101. http://www.tswj.com/2012/560101/
Spirov, A., Kazansky, A., and Holloway, D. (2012). Complexification of gene networks by co-evolution of genomes and genomic parasites. Proceedings of the 4th International Joint Conference on Computational Intelligence, Barcelona, Spain, pp. 238-244 DOI: 10.5220/0004170802380244
Spirov, A.V. and Holloway, D.M. (2012). Variable patterning in fruit fly embryos due to basins of attraction in underlying gene regulatory dynamics. Chaotic Modeling and Simulation (CMSIM) 4, 671-677. http://www.cmsim.eu/papers_pdf/october_2012_papers/13_CMSIM_2012_Spirov_Holloway_4_671-677.pdf
Also see proceedings article: pp. 601-606, http://www.cmsim.org/chaos2012proceedings.html
Spirov, A.V. and Holloway, D.M. (2012). Evolution in silico of genes with multiple regulatory modules, on the example of the Drosophila segmentation gene hunchback. IEEE Proceedings of Computational Intelligence in Bioinformatics and Computational Biology 2012, 244-251. BEST OVERALL PAPER AWARD.
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6217237&content+Publications&refinements%3D4284044025%26sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A6217201%29
Spirov, A.V. and Holloway, D.M. (2012). New approaches to designing genes by evolution in the computer. In Real-World Applications of Genetic Algorithms, ed. O. Roeva, pp. 235-260, InTech Press. Available at
http://www.intechopen.com/books/real-world-applications-of-genetic-algorithms/new-approaches-to-designing-genes-by-evolution-in-the-computer
Spirov, A.V., and Holloway, D.M. (2011). Retroviral genetic algorithms: implementation with tags and validation against benchmark functions. International Conference on Evolutionary Computation Theory and Applications, Proceedings.
Spirov, A.V, and Holloway, D.M. (2010). Design of a dynamic model of genes with multiple autonomous regulatory modules by evolutionary computations. Procedia Computer Science 1, 999-1008.
Spirov, A.V. and Holloway, D.M. (2009). The effects of gene recruitment on the evolvability and robustness of gene networks. In Advances in Computational Algorithms and Data Analysis, eds. S.I. Ao, B. Rieger, S-S. Chen, pp. 29-50, Springer, Lecture Notes in Electrical Engineering 14.
Spirov, A.V. and Holloway, D.M. (2007). Recruiting new genes in evolving genetic networks: simulation by the genetic algorithms technique. In Proceedings of the World Congress on Engineering and Computer Science, eds. S.I. Ao, C. Douglas, W.S. Grundfest, L. Schruben, X. Wu, pp. 16-22, Newswood Limited. <http://www.iaeng.org/publication/WCECS2007>
Spirov A.V., Myasnikova E.M., and Holloway D.M. (2016). Sequential construction of a model for modular gene expression control, applied to spatial patterning of the Drosophila gene hunchback. Journal of Bioinformatics and Computational Biology 14, 1641005. http://dx.doi.org/10.1142/S0219720016410055
Zamdborg L., Holloway D.M., Merelo J.J., Levchenko V.F., and Spirov A.V. (2015). Forced evolution in silico by artificial transposons and their genetic operators: the ant navigation problem. Information Sciences 306, 88-110.
Spirov A., and Holloway D. (2015). Using EA to study the evolution of GRNs controlling biological development. In Evolutionary Algorithms in Gene Regulatory Network Research, eds. N. Noman, H. Iba, pp. 240-268. Wiley Interscience.
Spirov, A., Zagriychuck, E., Holloway, D. (2014). Evolutionary design of gene networks: forced evolution by genomic parasites. Parallel Processing Letters 24, 1440004.
Zagrijchuck, E.A., Sabirov, M.A., Holloway, D.M., and Spirov, A.V. (2014). In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression. Journal of Bioinformatics and Computational Biology 12, 1441009. http://dx.doi.org/10.1142/S0219720014410091
Spirov, A.V. and Holloway, D.M. (2013). Using evolutionary computations to understand the design and evolution of gene and cell regulatory networks. Methods 62, 39-55.
Spirov, A.V. and Holloway, D.M. (2013). Modeling the evolution of gene regulatory networks for spatial patterning in embryo development. Procedia Computer Science 18, 1362-1371.
http://www.sciencedirect.com/science/article/pii/S1877050913004468
Spirov, A., Sabirov, M, and Holloway, D.M. (2012). In silico evolution of gene co-option in pattern-forming gene networks. The Scientific World Journal, special issue on Computational Systems Biology, Article ID 560101, doi: 10.1100/2012/560101. http://www.tswj.com/2012/560101/
Spirov, A., Kazansky, A., and Holloway, D. (2012). Complexification of gene networks by co-evolution of genomes and genomic parasites. Proceedings of the 4th International Joint Conference on Computational Intelligence, Barcelona, Spain, pp. 238-244 DOI: 10.5220/0004170802380244
Spirov, A.V. and Holloway, D.M. (2012). Variable patterning in fruit fly embryos due to basins of attraction in underlying gene regulatory dynamics. Chaotic Modeling and Simulation (CMSIM) 4, 671-677. http://www.cmsim.eu/papers_pdf/october_2012_papers/13_CMSIM_2012_Spirov_Holloway_4_671-677.pdf
Also see proceedings article: pp. 601-606, http://www.cmsim.org/chaos2012proceedings.html
Spirov, A.V. and Holloway, D.M. (2012). Evolution in silico of genes with multiple regulatory modules, on the example of the Drosophila segmentation gene hunchback. IEEE Proceedings of Computational Intelligence in Bioinformatics and Computational Biology 2012, 244-251. BEST OVERALL PAPER AWARD.
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6217237&content+Publications&refinements%3D4284044025%26sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A6217201%29
Spirov, A.V. and Holloway, D.M. (2012). New approaches to designing genes by evolution in the computer. In Real-World Applications of Genetic Algorithms, ed. O. Roeva, pp. 235-260, InTech Press. Available at
http://www.intechopen.com/books/real-world-applications-of-genetic-algorithms/new-approaches-to-designing-genes-by-evolution-in-the-computer
Spirov, A.V., and Holloway, D.M. (2011). Retroviral genetic algorithms: implementation with tags and validation against benchmark functions. International Conference on Evolutionary Computation Theory and Applications, Proceedings.
Spirov, A.V, and Holloway, D.M. (2010). Design of a dynamic model of genes with multiple autonomous regulatory modules by evolutionary computations. Procedia Computer Science 1, 999-1008.
Spirov, A.V. and Holloway, D.M. (2009). The effects of gene recruitment on the evolvability and robustness of gene networks. In Advances in Computational Algorithms and Data Analysis, eds. S.I. Ao, B. Rieger, S-S. Chen, pp. 29-50, Springer, Lecture Notes in Electrical Engineering 14.
Spirov, A.V. and Holloway, D.M. (2007). Recruiting new genes in evolving genetic networks: simulation by the genetic algorithms technique. In Proceedings of the World Congress on Engineering and Computer Science, eds. S.I. Ao, C. Douglas, W.S. Grundfest, L. Schruben, X. Wu, pp. 16-22, Newswood Limited. <http://www.iaeng.org/publication/WCECS2007>
Data Analysis
Shlemov, A., Alexandrov, T., Golyandina, N., Holloway, D., Baumgartner, S., Spirov, A.V. (2021). Quantification reveals early dynamics in Drosophila maternal gradients. PLoS ONE 16(8): e0244701. https://doi.org/10.1371/journal.pone.0244701
Alexandrov, T., Golyandina, N., Holloway, D., Shlemov, A., and Spirov, A. (2018). Two-exponential models of gene expression patterns for noisy experimental data. Journal of Computational Biology 25, ahead of print.
http://doi.org/10.1089/cmb.2017.0063
Shlemov, A., Golyandina, N., Holloway, D., and Spirov, A. (2015). Shaped 3D singular spectrum analysis for quantifying gene expression, with application to the early Zebrafish embryo. BioMed Research International 2015, article 986436.
http://dx.doi.org/10.1155/2015/986436
Shlemov, A., Golyandina, N., Holloway, D., and Spirov, A. (2015). Shaped singular spectrum analysis for quantifying gene expression, with application to the early Drosophila embryo. BioMed Research International 2015, article 689745.
http://dx.doi.org/10.1155/2015/689745
Spirov, A.V., Vanario-Alonso, C.E., Spirova, E.N., and Holloway, D.M. (2013). Experimental determination of intrinsic Drosophila embryo coordinates by evolutionary computation. Lecture Notes in Bioinformatics (LNBI) 7986, 126-137.
Golyandina, N.E, Holloway, D.M., Lopes, F.J.P., Spirov, A.V., Spirova, E.N., Usevich, K.D. (2012). Measuring gene expression noise in early Drosophila embryos: nucleus-to-nucleus variability. Procedia Computer Science 9, 373-382. http://www.sciencedirect.com/science/article/pii/S1877050912001615
Spirov, A.V., Golyandina, N.E., Holloway, D.M., Alexandrov, T., Spirova, E.N., Lopes, F.J.P. (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. In: M. Giacobini, L. Vanneschi, and W.S. Bush (Eds.), EvoBIO 2012, LNCS 7246, Springer-Verlag Berlin Heidelberg, 2012, pp. 177-188.
Spirov, A.V., and Holloway, D.M. (2003). Evolutionary techniques for image processing a large dataset of early Drosophila gene expression. EURASIP Journal on Applied Signal Processing 2003, no. 8: 824-833.
Alexandrov, T., Golyandina, N., Holloway, D., Shlemov, A., and Spirov, A. (2018). Two-exponential models of gene expression patterns for noisy experimental data. Journal of Computational Biology 25, ahead of print.
http://doi.org/10.1089/cmb.2017.0063
Shlemov, A., Golyandina, N., Holloway, D., and Spirov, A. (2015). Shaped 3D singular spectrum analysis for quantifying gene expression, with application to the early Zebrafish embryo. BioMed Research International 2015, article 986436.
http://dx.doi.org/10.1155/2015/986436
Shlemov, A., Golyandina, N., Holloway, D., and Spirov, A. (2015). Shaped singular spectrum analysis for quantifying gene expression, with application to the early Drosophila embryo. BioMed Research International 2015, article 689745.
http://dx.doi.org/10.1155/2015/689745
Spirov, A.V., Vanario-Alonso, C.E., Spirova, E.N., and Holloway, D.M. (2013). Experimental determination of intrinsic Drosophila embryo coordinates by evolutionary computation. Lecture Notes in Bioinformatics (LNBI) 7986, 126-137.
Golyandina, N.E, Holloway, D.M., Lopes, F.J.P., Spirov, A.V., Spirova, E.N., Usevich, K.D. (2012). Measuring gene expression noise in early Drosophila embryos: nucleus-to-nucleus variability. Procedia Computer Science 9, 373-382. http://www.sciencedirect.com/science/article/pii/S1877050912001615
Spirov, A.V., Golyandina, N.E., Holloway, D.M., Alexandrov, T., Spirova, E.N., Lopes, F.J.P. (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. In: M. Giacobini, L. Vanneschi, and W.S. Bush (Eds.), EvoBIO 2012, LNCS 7246, Springer-Verlag Berlin Heidelberg, 2012, pp. 177-188.
Spirov, A.V., and Holloway, D.M. (2003). Evolutionary techniques for image processing a large dataset of early Drosophila gene expression. EURASIP Journal on Applied Signal Processing 2003, no. 8: 824-833.