In silico evolution of gene cooption in pattern-forming gene networks

The Scientific World Journal

Volumn 2012, Issue , 2012, Pages

  Spirov, Alexander V ^a   Sabirov, Marat A ^b   Holloway, David M ^c  

^a STONY BROOK UNIVERSITY   (United States)

^b SECHENOV INSTITUTE OF EVOLUTIONARY PHYSIOLOGY AND BIOCHEMISTRY   (Russian Federation)

^c BRITISH COLUMBIA INSTITUTE OF TECHNOLOGY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; CHROMOSOME ANALYSIS; COMPUTER MODEL; DEVELOPMENTAL STAGE; DROSOPHILA; EVOLUTION; GENE EXPRESSION; GENE PRODUCT; GENE REGULATORY NETWORK; GENOME; INHIBITION KINETICS; NONHUMAN; OSCILLATION; QUANTITATIVE ANALYSIS; TRANSCRIPTION REGULATION; TRANSPOSON; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR EVOLUTION; MORPHOGENESIS; PRENATAL DEVELOPMENT;

HEXAPODA;

ALGORITHMS; ANIMALS; BODY PATTERNING; COMPUTER SIMULATION; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; MODELS, GENETIC; MORPHOGENESIS;

MLCS; MLOWN;

EID: 84872804090     PISSN: 1537744X     EISSN: 1537744X     Source Type: Journal    
DOI: 10.1100/2012/560101     Document Type: Article

References (104)

1. Sanetra M., Begemann G., Becker M. B., Meyer A., Conservation and co-option in developmental programmes: the importance of homology relationships. Frontiers in Zoology 2005 2, article 15 2-s2.0-27744554850 10.1186/1742-9994-2- 15 (Pubitemid 41618414)
2. Duboule D., Wilkins A. S., The evolution of 'bricolage'. Trends in Genetics 1998 14 2 54 59 2-s2.0-0032006747 10.1016/S0168-9525(97)01358-9 (Pubitemid 28122730)
3. True J. R., Carroll S. B., Gene co-option in physiological and morphological evolution. Annual Review of Cell and Developmental Biology 2002 18 53 80 2-s2.0-0036439421 10.1146/annurev.cellbio.18.020402.140619 (Pubitemid 35387345)
4. Carroll S. B., Grenier J. K., Weatherbee S. D., From DNA of Diversity: Molecular Genetics and the Evolution of Animal Design 2001 Malden, Mass, USA Blackwell
5. Carroll S. B., Evolution at two levels: on genes and form. PLoS Biology 2005 3 7, article e245 2-s2.0-28844475697
6. Makalowski W., Maraia J. R., SINEs as a genomic scrap yard. The Impact of Short Interspersed Elements (SINEs) on the Host Genome 1995 Austin, Tex, USA R.G. Landes Company Chapter 5
7. Siegal M. L., Bergman A., Waddington's canalization revisited: developmental stability and evolution. Proceedings of the National Academy of Sciences of the United States of America 2002 99 16 10528 10532 2-s2.0-0036678862 10.1073/pnas.102303999
8. Wilkins A. S., The Evolution of Developmental Pathways 2002 Sunderland, Mass, USA Sinauer Associates
9. Davidson E. H., Genomic Regulatory Systems: Development and Evolution 2001 San Diego, Calif, USA Academic Press
10. Arthur W., The concept of developmental reprogramming and the quest for an inclusive theory of evolutionary mechanisms. Evolution and Development 2000 2 1 49 57 2-s2.0-0033933382 10.1046/j.1525-142X.2000.00028.x (Pubitemid 30437821)
11. Abouheif E., Developmental genetics and homology: a hierarchical approach. Trends in Ecology and Evolution 1997 12 10 405 408 2-s2.0-0031418099 10.1016/S0169-5347(97)01125-7 (Pubitemid 28093524)
12. Abouheif E., Akam M., Dickinson W. J., Holland P. W. H., Meyer A., Patel N. H., Raff R. A., Roth V. L., Wray G. A., Homology and developmental genes. Trends Genet 1997 13 432 433
13. Lynch M., Force A., The probability of duplicate gene preservation by subfunctionalization. Genetics 2000 154 1 459 473 2-s2.0-0033972072 (Pubitemid 30045935)
14. Poustelnikova E., Pisarev A., Blagov M., Samsonova M., Reinitz J., A database for management of gene expression data in situ. Bioinformatics 2004 20 14 2212 2221 2-s2.0-3142591896 10.1093/bioinformatics/bth222 (Pubitemid 39341609)
15. Gompel N., Prud'homme B., Wittkopp P. J., Kassner V. A., Carroll S. B., Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 2005 433 7025 481 487 2-s2.0-13444304173 10.1038/nature03235 (Pubitemid 40204298)
16. Dayal S., Kiyama T., Villinski J. T., Zhang N., Liang S., Klein W. H., Creation of cis-regulatory elements during sea urchin evolution by co-option and optimization of a repetitive sequence adjacent to the spec2a gene. Developmental Biology 2004 273 2 436 453 2-s2.0-4344636789 10.1016/j.ydbio.2004. 06.011 (Pubitemid 39140914)
17. Holland L. Z., Short S., Gene duplication, co-option and recruitment during the origin of the vertebrate brain from the invertebrate chordate brain. Brain, Behavior and Evolution 2008 72 2 91 105 2-s2.0-53549099690 10.1159/000151470
18. Kawasaki K., Suzuki T., Weiss K. M., Genetic basis for the evolution of vertebrate mineralized tissue. Proceedings of the National Academy of Sciences of the United States of America 2004 101 31 11356 11361 2-s2.0-3843056697 10.1073/pnas.0404279101 (Pubitemid 39038351)
19. Wang W., Grimmer J. F., Van De Water T. R., Lufkin T., Hmx2 and Hmx3 homeobox genes direct development of the murine inner ear and hypothalamus and can be functionally replaced by Drosophila Hmx. Developmental Cell 2004 7 3 439 453 2-s2.0-4544244485 10.1016/j.devcel.2004.06.016 (Pubitemid 39232978)
20. Peterson K. J., Davidson E. H., Regulatory evolution and the origin of the bilaterians. Proceedings of the National Academy of Sciences of the United States of America 2000 97 9 4430 4433 2-s2.0-0034712752 10.1073/pnas.97.9.4430 (Pubitemid 30238572)
21. Levine M., Tjian R., Transcription regulation and animal diversity. Nature 2003 424 6945 147 151 2-s2.0-0037819447 10.1038/nature01763 (Pubitemid 36858677)
22. Carroll S. B., Endless forms: the evolution of gene regulation and morphological diversity. Cell 2000 101 6 577 580 2-s2.0-0034625265
23. Raff R. A., Evo-devo: the evolution of a new discipline. Nature Reviews 2000 1 1 74 79 2-s2.0-0034305497
24. Raff R. A., The Shape of Life: Genes, Development and the Evolution of Animal Form 1996 Chicago, Ill, USA Chicago University Press
25. Davidson E. H., Genomic Regulatory Systems. Development and Evolution 2001 San Diego, Calif, USA Academic Press
26. Arthur W., The emerging conceptual framework of evolutionary developmental biology. Nature 2002 415 6873 757 764 2-s2.0-0037074974 (Pubitemid 34150491)
27. Arthur W., The concept of developmental reprogramming and the quest for an inclusive theory of evolutionary mechanisms. Evolution and Development 2000 2 1 49 57 2-s2.0-0033933382 10.1046/j.1525-142X.2000.00028.x (Pubitemid 30437821)
28. Arthur W., Developmental drive: an important determinant of the direction of phenotypic evolution. Evolution and Development 2001 3 4 271 278 2-s2.0-0034926657 10.1046/j.1525-142X.2001.003004271.x (Pubitemid 32665254)
29. Waddington C. H., Canalization of development and the inheritance of acquired characters. Nature 1942 150 3811 563 565 2-s2.0-51149203927
30. Waddington C. H., Genetic assimilation of an acquired character. Evolution 1953 7 118 126
31. Waddington C. H., Genetic assimilation of the bithorax phenotype. Evolution 1956 10 1 13
32. McLaren A., Too late for the midwife toad: stress, variability and Hsp90. Trends in Genetics 1999 15 5 169 171 2-s2.0-0032936661 10.1016/S0168-9525(99) 01732-1 (Pubitemid 29217063)
33. Manu, Surkova S., Spirov A. V., Gursky V. V., Janssens H., Kim A. R., Radulescu O., Vanario-Alonso C. E., Sharp D. H., Samsonova M., Reinitz J., Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biology 2009 7 3, article e1000049 2-s2.0-79958078913
34. Manu, Surkova S., Spirov A. V., Gursky V. V., Janssens H., Kim A. R., Radulescu O., Vanario-Alonso C. E., Sharp D. H., Samsonova M., Reinitz J., Canalization of gene expression and domain shifts in the drosophila blastoderm by dynamical attractors. PLoS Computational Biology 2009 5 3 2-s2.0-63549100975 10.1371/journal.pcbi.1000303
35. Arthur W., Jowett T., Panchen A., Segments, limbs, homology, and co-option. Evolution and Development 1999 1 2 74 76 2-s2.0-0033188409 (Pubitemid 129692233)
36. Chipman A. D., Parallel evolution of segmentation by co-option of ancestral gene regulatory networks. BioEssays 2010 32 1 60 70 2-s2.0-74949090490 10.1002/bies.200900130
37. Patel N. H., Ball E. E., Goodman C. S., Changing role of even-skipped during the evolution of insect pattern formation. Nature 1992 357 6376 339 342 2-s2.0-0026703415 10.1038/357339a0
38. Patel N. H., Developmental evolution: insights from studies of insect segmentation. Science 1994 266 5185 581 590 2-s2.0-0028163938 (Pubitemid 24363513)
39. Jaeger J., Surkova S., Blagov M., Janssens H., Kosman D., Kozlov K. H., Manu, Myasnikova E., Vanario-Alonso C. E., Samsonova M., Sharp D. H., Reinitz J., Dynamic control of positional information in the early Drosophila embryo. Nature 2004 430 6997 368 371 2-s2.0-3142734333 10.1038/nature02678 (Pubitemid 38937746)
40. Clyde D. E., Corado M. S. G., Wu X., Paré A., Papatsenko D., Small S., A self-organizing system of repressor gradients establishes segmental oomplexity in Drosophila. Nature 2003 426 6968 849 853 2-s2.0-0347987855 10.1038/nature02189 (Pubitemid 38056871)
41. Jaeger J., The gap gene network. Cellular and Molecular Life Sciences 2011 68 2 243 274 2-s2.0-78651369529 10.1007/s00018-010-0536-y
42. Chipman A. D., Arthur W., Akam M., A double segment periodicity underlies segment generation in centipede development. Current Biology 2004 14 14 1250 1255 2-s2.0-3342934159 10.1016/j.cub.2004.07.026 (Pubitemid 38991811)
43. Chipman A. D., Akam M., The segmentation cascade in the centipede Strigamia maritima: involvement of the Notch pathway and pair-rule gene homologues. Developmental Biology 2008 319 1 160 169 2-s2.0-44749086994 10.1016/j.ydbio.2008.02.038
44. Goodwin B. C., Kauffman S. A., Spatial harmonics and pattern specification in early Drosophila development. Part I. Bifurcation sequences and gene expression. Journal of Theoretical Biology 1990 144 3 303 319 2-s2.0-0025375470 (Pubitemid 20189614)
45. Reinitz J., Sharp D. H., Mechanism of eve stripe formation. Mechanisms of Development 1995 49 1-2 133 158 2-s2.0-0028897360 10.1016/0925-4773(94)00310-J
46. Hunding A., Kauffman S. A., Goodwin B. C., Drosophila segmentation: supercomputer simulation of prepattern hierarchy. Journal of Theoretical Biology 1990 145 3 369 384 2-s2.0-0025158060 (Pubitemid 20255219)
47. Burstein Z., A network model of developmental gene hierarchy. Journal of Theoretical Biology 1995 174 1 1 11 2-s2.0-0029003231 10.1006/jtbi.1995.0075
48. Sánchez L., Thieffry D., A logical analysis of the Drosophila gap-gene system. Journal of Theoretical Biology 2001 211 2 115 141 2-s2.0-0035928464 10.1006/jtbi.2001.2335 (Pubitemid 32664864)
49. Spirov A. V., Bowler T., Reinitz J., HOX Pro: a specialized database for clusters and networks of homeobox genes. Nucleic Acids Research 2000 28 1 337 340 2-s2.0-0033957595 (Pubitemid 30047800)
50. Spirov A. V., Borovsky M., Spirova O. A., HOX Pro DB: the functional genomics of hox ensembles. Nucleic Acids Research 2002 30 1 351 353 2-s2.0-0036086414 (Pubitemid 34679583)
51. Li W. X., Functions and mechanisms of receptor tyrosine kinase Torso signaling: lessons from Drosophila embryonic terminal development. Developmental Dynamics 2005 232 3 656 672 2-s2.0-14644388169 10.1002/dvdy.20295 (Pubitemid 40315286)
52. Kim Y., Paroush Z., Nairz K., Hafen E., Jiménez G., Shvartsman S. Y., Substrate-dependent control of MAPK phosphorylation in vivo. Molecular Systems Biology 2011 7, article 467 2-s2.0-79551577046 10.1038/msb.2010.121
53. De Jong K. A., Evolutionary Computation: A Unified Approach 2006 Cambridge, Mass, USA MIT Press
54. Wagner A., Does evolutionary plasticity evolve? Evolution 1996 50 3 1008 1023 2-s2.0-0029661331
55. Salazar-Ciudad I., Garcia-Fernández J., Solé R. V., Gene networks capable of pattern formation: from induction to reaction-diffusion. Journal of Theoretical Biology 2000 205 4 587 603 2-s2.0-18344398543 10.1006/jtbi.2000.2092 (Pubitemid 30627572)
56. Bergman A., Siegal M. L., Evolutionary capacitance as a general feature of complex gene networks. Nature 2003 424 6948 549 552 2-s2.0-0042154192 10.1038/nature01765 (Pubitemid 36975775)
57. Solé R. V., Fernández P., Kauffman S. A., Adaptive walks in a gene network model of morphogenesis: insights into the Cambrian explosion. International Journal of Developmental Biology 2003 47 7-8 685 693 2-s2.0-1642553332 (Pubitemid 38112092)
58. Azevedo R. B. R., Lohaus R., Srinivasan S., Dang K. K., Burch C. L., Sexual reproduction selects for robustness and negative epistasis in artificial gene networks. Nature 2006 440 7080 87 90 2-s2.0-33644745138 10.1038/nature04488 (Pubitemid 43336272)
59. Huerta-Sanchez E., Durrett R., Wagner's canalization model. Theoretical Population Biology 2007 71 2 121 130 2-s2.0-33846562969 10.1016/j.tpb.2006.10. 006 (Pubitemid 46186468)
60. Ciliberti S., Martin O. C., Wagner A., Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Computational Biology 2007 3 2, article e15 2-s2.0-33847268619 10.1371/journal.pcbi.0030015
61. Ciliberti S., Martin O. C., Wagner A., Innovation and robustness in complex regulatory gene networks. Proceedings of the National Academy of Sciences of the United States of America 2007 104 34 13591 13596 2-s2.0-35348892535 10.1073/pnas.0705396104 (Pubitemid 350003365)
62. MacCarthy T., Bergman A., Coevolution of robustness, epistasis, and recombination favors asexual reproduction. Proceedings of the National Academy of Sciences of the United States of America 2007 104 31 12801 12806 2-s2.0-34547890683 10.1073/pnas.0705455104 (Pubitemid 47255235)
63. Martin O. C., Wagner A., Multifunctionality and robustness trade-offs in model genetic circuits. Biophysical Journal 2008 94 8 2927 2937 2-s2.0-43149098529 10.1529/biophysj.107.114348
64. Masel J., Genetic assimilation can occur in the absence of selection for the assimilating phenotype, suggesting a role for the canalization heuristic. Journal of Evolutionary Biology 2004 17 5 1106 1110 2-s2.0-4444375614 10.1111/j.1420-9101.2004.00739.x (Pubitemid 39175177)
65. Siegal M. L., Promislow D. E. L., Bergman A., Functional and evolutionary inference in gene networks: does topology matter? Genetica 2007 129 1 83 103 2-s2.0-33845637127 10.1007/s10709-006-0035-0 (Pubitemid 44949618)
66. MacCarthy T., Bergman A., The limits of subfunctionalization. BMC Evolutionary Biology 2007 7 1, article 213 2-s2.0-38649142412 10.1186/1471-2148-7-213 (Pubitemid 351169907)
67. Espinosa-Soto C., Wagner A., Specialization can drive the evolution of modularity. PLoS Computational Biology 2010 6 3 2-s2.0-77950854888 10.1371/journal.pcbi.1000719
68. Kimbrell T., Holt R. D., Canalization breakdown and evolution in a source-sink system. American Naturalist 2007 169 3 370 382 2-s2.0-33847345150 10.1086/511314 (Pubitemid 46340043)
69. Draghi J., Wagner G. P., The evolutionary dynamics of evolvability in a gene network model. Journal of Evolutionary Biology 2009 22 3 599 611 2-s2.0-60649098397 10.1111/j.1420-9101.2008.01663.x
70. Spirov A., Holloway D., Evolution in silico of genes with multiple regulatory modules on the example of the Drosophila segmentation gene hunchback. Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology May 2012 San Diego, Calif, USA 244 251
71. Knabe J. F., Wegner K., Nehaniv C. L., Schilstra M. J., Fenyo D., Genetic algorithms and their application to in silico evolution of genetic regulatory networks. Computational Biology 2010 Humana Press 297 321
72. Spirov A. V., Holloway D. M., Design of a dynamic model of genes with multiple autonomous regulatory modules by evolutionary computations. proceedings of the 10th International Conference on Computational Science 2010 (ICCS '10) June 2010 1005 1014 2-s2.0-78650287484 10.1016/j.procs.2010.04.111
73. François P., Hakim V., Siggia E. D., Deriving structure from evolution: metazoan segmentation. Molecular Systems Biology 2007 3, article 154 2-s2.0-37349116795 10.1038/msb4100192 (Pubitemid 350292255)
74. Gursky V. V., Panok L., Myasnikova E. M., Manu, Samsonova M. G., Reinitz J., Samsonov A. M., Mechanisms of gap gene expression canalization in the Drosophila blastoderm. BMC Systems Biology 2011 5 1, article 118 2-s2.0-79960671456 10.1186/1752-0509-5-118
75. Spirov A. V., Holloway D. M., Retroviral genetic algorithms: implementation with tags and validation against benchmark functions. 2011 Proceedings of the International Conference on Evolutionary Computation Theory and Applications (ECTA-FCTA) (IJCCI '11) 2011 233 238
76. Spirov A. V., Holloway D. M., Roeva O., New approaches to designing genes by evolution in the computer. Real-World Applications of Genetic Algorithms 2012 InTech Press 235 260
77. Spirov A. V., Self-assemblage of gene networks in evolution via recruiting of new netters. Lecture Notes in Computer Science 1996 1141 91 100 (Pubitemid 126128297)
78. Spirov A. V., Samsonova M. G., Strategy of co-evolution of transposons and host genome: application to evolutionary computations. Proceedings of the Third Nordic Workshop on Genetic Algorithms and their Applications 1997 Helsinki University 71 82
79. Spirov A. V., Kadyrov A. S., Transposon element technique applied to GA-based John Muir's trail test. High-Performance Computing and Networking 1998 925 928 (Pubitemid 128067788)
80. Spirov A. V., Kazansky A. B., Jumping genes-mutators can raise efficacy of evolutionary search. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO '02) 2002 San Francisco, Calif, USA Morgan Kaufmann Publishers 561 568
81. Spirov A. V., Kazansky A. B., The usage of artificial transposons for the protection of already found building blocks: the tests with royal road functions. Proceedings of the 6th World Multiconference on Systemics, Cybernetics and Informatics (SCI '02) 2002 Orlando, Fla, USA International Institute of Informatics and Systemics 75 80
82. Spirov A. V., Kazansky A. B., Zamdborg L., Forced evolution in silico by artificial transposons and their genetic operators: the John Muir Ant problem. http://arxiv.org/abs/0910.5542
83. Holloway D. M., Kazansky A. B., Spirov A. V., Complexification of gene networks by co-evolution of genomes and genomic parasites. Proceedings of the 4th International Conference on Evolutionary Computation Theory and Applications (ECTA '12) October 2012 Barcelona, Spain
84. Lozovskaya E. R., Hartl D. L., Petrov D. A., Genomic regulation of transposable elements in Drosophila. Current Opinion in Genetics and Development 1995 5 6 768 773 2-s2.0-0029559808 10.1016/0959-437X(95)80009-T (Pubitemid 26003879)
85. Wallace M. R., Andersen L. B., Saulino A. M., Gregory P. E., Glover T. W., Collins F. S., A de novo Alu insertion results in neurofibromatosis type 1. Nature 1991 353 6347 864 866 2-s2.0-0025951042 10.1038/353864a0 (Pubitemid 21912644)
86. Girard L., Freeling M., Regulatory changes as a consequence of transposon insertion. Developmental Genetics 1999 25 4 291 296 2-s2.0-0032760813
87. King C. C., Modular transposition and the dynamical structure of eukaryote regulatory evolution. Genetica 1992 86 1-3 127 142 2-s2.0-0027015575 10.1007/BF00133716
88. Haseltine E. L., Arnold F. H., Synthetic gene circuits: design with directed evolution. Annual Review of Biophysics and Biomolecular Structure 2007 36 1 19 10.1146/annurev.biophys.36.040306.132600 (Pubitemid 46998107)
89. Yokobayashi Y., Weiss R., Arnold F. H., Directed evolution of a genetic circuit. Proceedings of the National Academy of Sciences of the United States of America 2002 99 26 16587 16591 2-s2.0-0037168510 10.1073/pnas.252535999 (Pubitemid 36034016)
90. Houchmandzadeh B., Wieschaus E., Leibler S., Establishment of developmental precision and proportions in the early Drosophila embryo. Nature 2002 415 6873 798 802 2-s2.0-0037075022 (Pubitemid 34150502)
91. Holloway D. M., Reinitz J., Spirov A., Vanario-Alonso C. E., Sharp borders from fuzzy gradients. Trends in Genetics 2002 18 8 385 387 2-s2.0-0036683142 10.1016/S0168-9525(02)02724-5 (Pubitemid 34874530)
92. Spirov A. V., Holloway D. M., Making the body plan: precision in the genetic hierarchy of Drosophila embryo segmentation. In Silico Biology 2003 3 1-2 89 100 2-s2.0-0042536457 (Pubitemid 37028350)
93. Houchmandzadeh B., Wieschaus E., Leibler S., Precise domain specification in the developing Drosophila embryo. Physical Review E 2005 72 6 2-s2.0-33244480304 10.1103/PhysRevE.72.061920 061920 (Pubitemid 43272943)
94. Holloway D. M., Harrison L. G., Kosman D., Vanario-Alonso C. E., Spirov A. V., Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products. Developmental Dynamics 2006 235 11 2949 2960 2-s2.0-33750995578 10.1002/dvdy.20940 (Pubitemid 44749683)
95. Gregor T., Tank D. W., Wieschaus E. F., Bialek W., Probing the Limits to Positional Information. Cell 2007 130 1 153 164 2-s2.0-34447099234 10.1016/j.cell.2007.05.025 (Pubitemid 47031318)
96. Wagner A., Distributed robustness versus redundancy as causes of mutational robustness. BioEssays 2005 27 2 176 188 2-s2.0-14344263352 10.1002/bies.20170 (Pubitemid 40292389)
97. Kraut R., Levine M., Spatial regulation of the gap giant during Drosophila development. Development 1991 111 2 601 609 2-s2.0-0025981572 (Pubitemid 21920441)
98. Mjolsness E., Sharp D. H., Reinitz J., A connectionist model of development. Journal of Theoretical Biology 1991 152 4 429 453 2-s2.0-0025991216
99. Surkova S., Kosman D., Kozlov K., Manu, Myasnikova E., Samsonova A. A., Spirov A., Vanario-Alonso C. E., Samsonova M., Reinitz J., Characterization of the Drosophila segment determination morphome. Developmental Biology 2008 313 2 844 862 2-s2.0-38049032428 10.1016/j.ydbio.2007.10.037
100. Poustelnikova E., Pisarev A., Blagov M., Samsonova M., Reinitz J., A database for management of gene expression data in situ. Bioinformatics 2004 20 2212 2221 (Pubitemid 39341609)
101. Press W. H., Flannery B. P., Teukolsky S. A., Vetterling W. T., Numerical Recipes 1988 Cambridge, UK Cambridge University Press
102. Hardway H., Mukhopadhyay B., Burke T., Hitchman T. J., Forman R., Modeling the precision and robustness of Hunchback border during Drosophila embryonic development. Journal of Theoretical Biology 2008 254 2 390 399 2-s2.0-50149087694 10.1016/j.jtbi.2008.05.021
103. Perkins T. J., Jaeger J., Reinitz J., Glass L., Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Computational Biology 2006 2 5 417 428 2-s2.0-33646901020 10.1371/journal.pcbi.0020051 (Pubitemid 43794335)
104. Muratov C. B., Shvartsman S. Y., An asymptotic study of the inductive pattern formation mechanism in Drosophila egg development. Physica D 2003 186 1-2 93 108 2-s2.0-0242579380 10.1016/S0167-2789(03)00182-9