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  • 1
    Publication Date: 2012-04-14
    Description: Computational approaches are breaking new ground in understanding how embryos form. Here, we discuss recent studies that couple precise measurements in the embryo with appropriately matched modeling and computational methods to investigate classic embryonic patterning strategies. We include signaling gradients, activator-inhibitor systems, and coupled oscillators, as well as emerging paradigms such as tissue deformation. Parallel progress in theory and experiment will play an increasingly central role in deciphering developmental patterning.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morelli, Luis G -- Uriu, Koichiro -- Ares, Saul -- Oates, Andrew C -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):187-91. doi: 10.1126/science.1215478.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499940" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Body Patterning ; Computational Biology ; *Computer Simulation ; Drosophila/embryology ; Embryo, Nonmammalian/cytology/metabolism ; Embryonic Development ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; *Models, Biological ; Signal Transduction ; Zebrafish/embryology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-07-12
    Description: During embryonic development, temporal and spatial cues are coordinated to generate a segmented body axis. In sequentially segmenting animals, the rhythm of segmentation is reported to be controlled by the time scale of genetic oscillations that periodically trigger new segment formation. However, we present real-time measurements of genetic oscillations in zebrafish embryos showing that their time scale is not sufficient to explain the temporal period of segmentation. A second time scale, the rate of tissue shortening, contributes to the period of segmentation through a Doppler effect. This contribution is modulated by a gradual change in the oscillation profile across the tissue. We conclude that the rhythm of segmentation is an emergent property controlled by the time scale of genetic oscillations, the change of oscillation profile, and tissue shortening.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Soroldoni, Daniele -- Jorg, David J -- Morelli, Luis G -- Richmond, David L -- Schindelin, Johannes -- Julicher, Frank -- Oates, Andrew C -- 098025/Wellcome Trust/United Kingdom -- MC_UP_1202/3/Medical Research Council/United Kingdom -- WT098025MA/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2014 Jul 11;345(6193):222-5. doi: 10.1126/science.1253089.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany. Medical Research Council (MRC)-National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK. Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK. ; Max Planck Institute for the Physics of Complex Systems, Nothnitzer Strasse 38, 01187 Dresden, Germany. ; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany. Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Fisica de Buenos Aires, Consejo Nacional de Investigaciones Cientificas y Tecnicas, Pabellon 1, Ciudad Universitaria, 1428 Buenos Aires, Argentina. ; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany. ; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany. Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, 271 Animal Sciences, 1675 Observatory Drive, Madison, WI 53706, USA. ; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany. Medical Research Council (MRC)-National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK. Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK. aoates@nimr.mrc.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25013078" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Body Patterning/*genetics ; *Doppler Effect ; Embryo, Nonmammalian/physiology ; *Periodicity ; Zebrafish/embryology/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    The European physical journal 43 (2005), S. 243-250 
    ISSN: 1434-6036
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract. We analyze the phenomenon of frequency clustering in a system of coupled phase oscillators. The oscillators, which in the absence of coupling have uniformly distributed natural frequencies, are coupled through a small-world network, built according to the Watts-Strogatz model. We study the time evolution and determine variations in the transient times depending on the disorder of the network and on the coupling strength. We investigate the effects of fluctuations in the average frequencies, and discuss the definition of the threshold for synchronization. We characterize the structure of clusters and the distribution of cluster sizes in the synchronization transition, and define suitable order parameters to describe the aggregation of the oscillators as the network disorder and the coupling strength change. The non-monotonic behavior observed in some order parameters is related to fluctuations in the mean frequencies.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    The European physical journal 38 (2004), S. 495-500 
    ISSN: 1434-6036
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract. We study a model of associative memory based on a neural network with small-world structure. The efficacy of the network to retrieve one of the stored patterns exhibits a phase transition at a finite value of the disorder. The more ordered networks are unable to recover the patterns, and are always attracted to non-symmetric mixture states. Besides, for a range of the number of stored patterns, the efficacy has a maximum at an intermediate value of the disorder. We also give a statistical characterization of the spurious attractors for all values of the disorder of the network.
    Type of Medium: Electronic Resource
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  • 5
    Publication Date: 2005-01-01
    Print ISSN: 1434-6028
    Electronic ISSN: 1434-6036
    Topics: Physics
    Published by Springer
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  • 6
    Publication Date: 2004-04-01
    Print ISSN: 1434-6028
    Electronic ISSN: 1434-6036
    Topics: Physics
    Published by Springer
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