Paul Bourgine and Nadine Peyriéas -This study has been presented under various forms at the conferences "The developmental biology of the sea urchin" XXI and XXIIStochastic physics in biology, This chapter) and at the Gordon Research Conference, 2012. ,
Precision and reproducibility of macroscopic developmental patterns. arXiv preprint arXiv:1309, Bibliography, vol.6273, 2013. ,
The ring of algebraic functions on persistence bar codes, Homology, Homotopy and Applications, vol.18, issue.1, 2012. ,
DOI : 10.4310/HHA.2016.v18.n1.a21
Exploring the effects of mechanical feedback on epithelial topology, Development, vol.137, issue.3, pp.499-506, 2010. ,
DOI : 10.1242/dev.041731
Ontogenesis and Morphological Diversification, American Zoologist, vol.20, issue.4, pp.653-667, 1980. ,
DOI : 10.1093/icb/20.4.653
Size and shape in ontogeny and phylogeny, Paleobiology, vol.175, issue.03, pp.296-317, 1979. ,
DOI : 10.2307/2407703
Statistical mechanics of complex networks, Reviews of Modern Physics, vol.74, issue.1, p.47, 2002. ,
DOI : 10.1103/RevModPhys.74.47
Exchangeability and related topics, 1985. ,
ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS, Proceedings of the National Academy of Sciences, vol.51, issue.5, p.786, 1964. ,
DOI : 10.1073/pnas.51.5.786
Methods of information geometry, American Mathematical Soc, vol.191, 2007. ,
Animal?vegetal axis patterning mechanisms in the early sea urchin embryo, Developmental biology, vol.218, issue.1, pp.1-12, 2000. ,
A model of epigenetic evolution based on theory of open quantum systems, Systems and Synthetic Biology, vol.5, issue.3, pp.161-173, 2013. ,
DOI : 10.1007/s11693-013-9109-3
al. The simplicity of metazoan cell lineages, Nature, issue.7022, pp.433152-156, 2005. ,
Randomness and determinism in the interplay between the continuum and the discrete, Mathematical Structures in Computer Science, vol.17, issue.02, pp.289-305, 2007. ,
DOI : 10.1017/S0960129507006007
Mathematics and the natural sciences: the physical singularity of life, 2011. ,
DOI : 10.1142/p774
Automated cell lineage tracing in Caenorhabditis elegans, Proceedings of the National Academy of Sciences, vol.103, issue.8, pp.2707-2712, 2006. ,
DOI : 10.1073/pnas.0511111103
Quantum-like interference effect in gene expression: glucose-lactose destructive interference, Systems and Synthetic Biology, vol.3, issue.3, pp.59-68, 2011. ,
DOI : 10.1007/s11693-011-9081-8
Forces Driving Epithelial Spreading in Zebrafish Gastrulation, Science, vol.338, issue.6104, pp.338257-260, 2012. ,
DOI : 10.1126/science.1224143
Geometry of quantum states: an introduction to quantum entanglement, 2006. ,
DOI : 10.1017/CBO9780511535048
Proof of the ergodic theorem, Proceedings of the National Academy of Sciences, vol.17, issue.12, pp.656-660, 1931. ,
Mécanique quantique: une introduction philosophique. Editions Flammarion, 1996. ,
DOI : 10.14375/NP.9782081214866
La mécanique quantique comme théorie des probabilités généralisées, Prévision et Probabilité dans les Sciences . Éditions Frontières, 1998. ,
Théorie quantique et sciences humaines, CNRS, 2009. ,
DOI : 10.4000/books.editionscnrs.7885
Stress-Induced Mutagenesis in Bacteria, Science, vol.300, issue.5624, pp.3001404-1409, 2003. ,
DOI : 10.1126/science.1082240
Multicellular Rosette Formation Links Planar??Cell??Polarity to Tissue Morphogenesis, Developmental Cell, vol.11, issue.4, pp.459-470, 2006. ,
DOI : 10.1016/j.devcel.2006.09.007
Four sided domains in hierarchical space dividing patterns. Physical review letters, p.54503, 2005. ,
Hierarchical crack pattern as formed by successive domain divisions., Physical Review E, vol.71, issue.4, p.46214, 2005. ,
DOI : 10.1103/PhysRevE.71.046214
Mechanical Control of Morphogenesis by Fat/Dachsous/Four-Jointed Planar Cell Polarity Pathway, Science, vol.336, issue.6082, pp.336724-727, 2012. ,
DOI : 10.1126/science.1221071
ZFIN: enhancements and updates to the zebrafish model organism database, Nucleic Acids Research, vol.39, issue.Database, pp.822-829, 2011. ,
DOI : 10.1093/nar/gkq1077
From Developmental Constraint to Evolvability: How Concepts Figure in Explanation and Disciplinary Identity, Conceptual Change in Biology, pp.305-325, 2015. ,
DOI : 10.1007/978-94-017-9412-1_14
In the beginning??? Animal fertilization and sea urchin development, Developmental Biology, vol.300, issue.1, pp.15-26, 2006. ,
DOI : 10.1016/j.ydbio.2006.07.014
Products and convolutions of gaussian distributions, Medical School, vol.3, 2003. ,
Randomness and multilevel interactions in biology, Theory in Biosciences, vol.31, issue.7, pp.139-158, 2013. ,
DOI : 10.1007/s12064-013-0179-2
Computing a glimpse of randomness, Experimental Mathematics, vol.11, issue.3, pp.361-370, 2002. ,
Classical, quantum and biological randomness as relative incomputability ,
DOI : 10.1007/s11047-015-9533-2
URL : https://hal.archives-ouvertes.fr/hal-01380600/file/CaludeLongoRandom.pdf
Opinion: Epistasis: too often neglected in complex trait studies?, Nature Reviews Genetics, vol.138, issue.8, pp.618-625, 2004. ,
DOI : 10.1089/10665270260518272
Topology and data. Bulletin of the, pp.255-308, 2009. ,
Topological pattern recognition for point cloud data, Acta Numerica, vol.1, issue.5, pp.289-368 ,
DOI : 10.1051/0004-6361/201116485
The Theory of Multidimensional Persistence, Discrete & Computational Geometry, vol.33, issue.2, pp.71-93, 2009. ,
DOI : 10.1007/s00454-009-9176-0
Statistical Inference., Biometrics, vol.49, issue.1, 1990. ,
DOI : 10.2307/2532634
A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis ,
URL : https://hal.archives-ouvertes.fr/hal-01054811
Transcriptome-wide noise controls lineage choice in mammalian progenitor cells, Nature, issue.7194, pp.453544-547, 2008. ,
erratum: The zebrafish Nodal signal Squint functions as a morphogen, Nature, vol.411, issue.6846, pp.411607-610, 2001. ,
DOI : 10.1038/35087633
Probability theory: independence, interchangeability , martingales, 2003. ,
Vines and vineyards by updating persistence in linear time, Proceedings of the twenty-second annual symposium on Computational geometry , SCG '06, pp.119-126, 2006. ,
DOI : 10.1145/1137856.1137877
Gonzalo Travieso, and Paulino Ribeiro Villas Boas. Characterization of complex networks: A survey of measurements, Advances in Physics, vol.56, issue.1, pp.167-242, 2007. ,
On the origins of species by means of natural selection, 1859. ,
DOI : 10.5962/bhl.title.24329
Specification of cell fate in the sea urchin embryo: summary and some proposed mechanisms, Development, vol.125, issue.17, pp.3269-90, 1998. ,
Lineage-specific gene expression and the regulative capacities of the sea urchin embryo: a proposed mechanism, Development, vol.105, issue.3, pp.421-445, 1989. ,
Gene activity in early development, 2012. ,
Cesar Arenas-Mena, et al. A genomic regulatory network for development, Science, issue.5560, pp.2951669-1678, 2002. ,
Mapping phenotypes: canalization, plasticity and developmental stability, Trends in Ecology & Evolution, vol.16, issue.10, pp.555-561, 2001. ,
DOI : 10.1016/S0169-5347(01)02266-2
Computational Modeling and Simulation of Animal Early Embryogenesis with the MecaGen Platform, Computational Systems Biology, pp.359-405 ,
DOI : 10.1016/B978-0-12-405926-9.00016-2
Mecagen: A cell-based computational model of embryogenesis coupling mechanical behavior and gene regulation. submitted, 2015. ,
Two-photon laser scanning fluorescence microscopy, Science, vol.248, issue.4951, pp.73-76, 1990. ,
DOI : 10.1126/science.2321027
Finite exchangeable sequences. The Annals of Probability, pp.745-764, 1980. ,
Accurate measurements of dynamics and reproducibility in small genetic networks, Molecular systems biology, vol.9, issue.1, p.2013 ,
The echinoid mitotic gradient: effect of cell size on the micromere cleavage cycle. Molecular reproduction and development, pp.10-11868, 2011. ,
Role of Pleiotropy in the Evolution of a Cryptic Developmental Variation in Caenorhabditis elegans, PLoS Biology, vol.125, issue.1, p.1001230, 2012. ,
DOI : 10.1371/journal.pbio.1001230.s012
URL : https://hal.archives-ouvertes.fr/hal-00665102
Computational topology: an introduction, 2010. ,
DOI : 10.1090/mbk/069
The medusa of spatial sorting: topological construction. arXiv preprint arXiv:1207, 2012. ,
Can quantum-mechanical description of physical reality be considered complete? Physical review, p.47777, 1935. ,
Stochastic gene expression in a single cell, Science, vol.297, issue.5584, pp.1183-1186, 2002. ,
A century of sea urchin development, American zoologist, vol.37, issue.3, pp.250-259, 1997. ,
Epithelial organisation revealed by a network of cellular contacts, Nature communications, vol.2, p.526, 2011. ,
Cyclin: A protein specified by maternal mRNA in sea urchin eggs that is destroyed at each cleavage division, Cell, vol.33, issue.2, pp.389-396, 1983. ,
DOI : 10.1016/0092-8674(83)90420-8
Phenotypic variation and resilience in sea urchin morphogenesis ,
Zebrafish organizer development and germ-layer formation require nodal-related signals, Nature, issue.6698, pp.395181-185, 1998. ,
The Plasma Membrane Flattens Out to Fuel Cell-Surface Growth during Drosophila Cellularization, Developmental Cell, vol.27, issue.6, pp.648-655, 2013. ,
DOI : 10.1016/j.devcel.2013.11.006
Clarifying tetrapod embryogenesis, a physicist's point of view, The European Physical Journal Applied Physics, vol.45, issue.3, p.30101, 2009. ,
DOI : 10.1051/epjap/2009033
Clarifying tetrapod embryogenesis by a dorso-ventral analysis of the tissue flows during early stages of chicken development, Biosystems, vol.109, issue.3, pp.460-474, 2012. ,
DOI : 10.1016/j.biosystems.2012.04.003
Biological physics of the developing embryo, 2005. ,
DOI : 10.1017/CBO9780511755576
The ergodic hierarchy ,
Stanford encyclopedia of philosophy, Proceedings of the first ACM/IEEE-CS joint conference on Digital libraries , JCDL '01, 2014. ,
DOI : 10.1145/379437.379789
Effective symbolic dynamics, random points, statistical behavior, complexity and entropy, Information and Computation, vol.208, issue.1, pp.23-41, 2010. ,
DOI : 10.1016/j.ic.2009.05.001
URL : https://hal.archives-ouvertes.fr/inria-00517382
Developmental motifs reveal complex structure in cell lineages, Complexity, vol.11, issue.4, pp.48-57, 2011. ,
DOI : 10.1002/cplx.20341
The emergence of geometric order in proliferating metazoan epithelia, Nature, vol.442, issue.7106, pp.1038-1041, 2006. ,
Cell topology, geometry, and morphogenesis in proliferating epithelia, Current topics in developmental biology, vol.89, pp.87-114, 2009. ,
Control of the mitotic cleavage plane by local epithelial topology, Cell, vol.144, issue.3, pp.427-438, 2011. ,
Developmental Biology, 2000. ,
Philosophical theories of probability, Routledge, 2000. ,
Versuch die Metamorphose der Pflanzen zu erklären, 1790. ,
Wonderful Life: The Burgess Shale and the Nature of History, 1989. ,
Ontogeny and phylogeny, 1977. ,
Simulation of biological cell sorting using a two-dimensional extended potts model. Physical review letters, p.2013, 1992. ,
Topological graph theory, 2001. ,
Mechanics of Epithelial Tissue Homeostasis and Morphogenesis, Science, vol.340, issue.6137, pp.1185-1189, 2013. ,
DOI : 10.1126/science.1235249
The identification of genes with unique and essential functions in the development of the zebrafish, danio rerio, Development, vol.123, issue.1, pp.1-36, 1996. ,
De l'intuition aux applications, Probabilités & statistiques Diderot éditeur, collection Arts et Sciences, 1996. ,
Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation, Nature, vol.120, issue.7496, pp.392-396, 2014. ,
DOI : 10.1038/nature13070
Randomness in biology, Mathematical Structures in Computer Science, vol.52, issue.03, p.240308, 2014. ,
DOI : 10.1371/journal.pgen.1000049
URL : https://hal.archives-ouvertes.fr/hal-01194088
Forces in Tissue Morphogenesis and Patterning, Cell, vol.153, issue.5, pp.948-962, 2013. ,
DOI : 10.1016/j.cell.2013.05.008
Deep tissue two-photon microscopy, Nature Methods, vol.63, issue.12, pp.932-940, 2005. ,
DOI : 10.1038/nmeth818
URL : http://hdl.handle.net/11858/00-001M-0000-0019-9B52-A
Separating intrinsic from extrinsic fluctuations in dynamic biological systems, Proceedings of the National Academy of Sciences, vol.108, issue.29, pp.12167-12172, 2011. ,
DOI : 10.1073/pnas.1018832108
An exercise in rational taxonomy, Journal of Theoretical Biology, vol.147, issue.1, pp.43-57, 1990. ,
DOI : 10.1016/S0022-5193(05)80251-6
Ether-induced segmentation disturbances in drosophila melanogaster. Roux's archives of developmental biology, pp.511-521, 1987. ,
Rational taxonomy and the natural system, Acta Biotheoretica, vol.25, issue.suppl, pp.289-304, 1993. ,
DOI : 10.1007/BF00709367
Isolation and genetic characterization of celllineage mutants of the nematode caenorhabditis elegans, Genetics, vol.96, issue.2, pp.435-454, 1980. ,
Non-genetic heterogeneity of cells in development: more than just noise, Development, vol.136, issue.23, pp.3853-3862, 2009. ,
DOI : 10.1242/dev.035139
The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology?, BioEssays, vol.24, issue.2, pp.149-157, 2012. ,
DOI : 10.1002/bies.201100031
Random partitioning of molecules at cell division, Proceedings of the National Academy of Sciences, pp.15004-15009, 2011. ,
DOI : 10.1073/pnas.1013171108
Evolution. the modern synthesis. Evolution. The Modern Synthesis, 1942. ,
Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis, Nature Communications, vol.2, p.248, 2011. ,
DOI : 10.1038/nprot.2007.324
Comparative study of non-invasive force and stress inference methods in tissue, The European Physical Journal E, vol.150, issue.4, pp.1-13, 2013. ,
DOI : 10.1140/epje/i2013-13045-8
Bayesian inference of force dynamics during morphogenesis, Journal of Theoretical Biology, vol.313, pp.201-211, 2012. ,
DOI : 10.1016/j.jtbi.2012.08.017
The Changing Concept of Epigenetics, Annals of the New York Academy of Sciences, vol.401, issue.Suppl. 1, pp.82-96, 2002. ,
DOI : 10.1111/j.1749-6632.2002.tb04913.x
Genetic regulatory mechanisms in the synthesis of proteins, Journal of Molecular Biology, vol.3, issue.3, pp.318-356, 1961. ,
DOI : 10.1016/S0022-2836(61)80072-7
Cavefish as a model system in evolutionary developmental biology, Developmental biology, vol.231, issue.1, pp.1-12, 2001. ,
Information theory and the central limit theorem, World Scientific, vol.8, 2004. ,
DOI : 10.1142/p341
Gene expression divergence recapitulates the developmental hourglass model, Nature, issue.7325, pp.468811-814, 2010. ,
Critique of judgment, 1790. ,
The origins of order: Self-organization and selection in evolution, 1993. ,
Heritable stochastic switching revealed by single-cell genealogy, PLoS biology, vol.5, issue.9, p.239, 2007. ,
Here is the evidence, now what is the hypothesis? the complementary roles of inductive and hypothesis-driven science in the post-genomic era, Bioessays, vol.26, issue.1, pp.99-105, 2004. ,
An introduction to genetic statistics, 1957. ,
Two-dimensional viscous froth model for foam dynamics, Physical Review E, vol.70, issue.4, p.41411, 2004. ,
DOI : 10.1103/PhysRevE.70.041411
Branching Processes in Biology, Interdisciplinary Applied Mathematics, vol.19, 2002. ,
Evolution and development of shape: integrating quantitative approaches, Nature Reviews Genetics, vol.11, issue.9, pp.623-635, 2010. ,
Grundbegriffe der Wahrscheilichkeitsrechnung, 1933. ,
Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation, Science, vol.329, issue.5999, pp.1616-1620, 2010. ,
DOI : 10.1126/science.1179047
3D early embryogenesis image filtering by nonlinear partial differential equations, Medical Image Analysis, vol.14, issue.4, pp.510-526, 2010. ,
DOI : 10.1016/j.media.2010.03.003
L'origine des individus. Fayard, 2008. ,
Ni Dieu ni gène, pour une autre théorie de l'hérédité. Seuil, 2000. ,
Kinetics of gene derepression by ERK signaling, Proceedings of the National Academy of Sciences, pp.10330-10335, 2013. ,
DOI : 10.1073/pnas.1303635110
Log-normal Distributions across the Sciences: Keys and Clues, BioScience, vol.51, issue.5, pp.341-352, 2001. ,
DOI : 10.1641/0006-3568(2001)051[0341:LNDATS]2.0.CO;2
Description intégrative des cinématiques de la structure embryonnaire: morphogenèse précoce du poisson zébré, 2010. ,
jeu de l'imitation" aléas, déterminisme et programmes dans le test de turing, Intellectica, vol.35, issue.2, pp.131-161, 2002. ,
Mathematical infinity "in prospettiva" and spaces of possibilities, Visible, a Semiotics Journal, vol.9, 2011. ,
From physics to biology by extending criticality and symmetry breakings, Progress in biophysics and molecular biology, p.106, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01192902
Perspectives on Organisms: Biological Time, Symmetries and Singularities, 2013. ,
DOI : 10.1007/978-3-642-35938-5
URL : https://hal.archives-ouvertes.fr/hal-01349797
No entailing laws, but enablement in the evolution of the biosphere, Proceedings of the fourteenth international conference on Genetic and evolutionary computation conference companion, GECCO Companion '12, pp.1379-1392, 2012. ,
DOI : 10.1145/2330784.2330946
Stochasticity and Cell Fate, Science, vol.320, issue.5872, pp.65-68, 2008. ,
DOI : 10.1126/science.1147888
Mutations of bacteria from virus sensitivity to virus resistance, Genetics, vol.28, issue.6, p.491, 1943. ,
The Origins of Genome Complexity, Science, vol.302, issue.5649, pp.1401-1404, 2003. ,
DOI : 10.1126/science.1089370
Tra ordine e caos: metodi e linguaggi tra fisica, matematica e filosofia, Aracne, 2011. ,
The definition of random sequences, Information and Control, vol.9, issue.6, pp.602-619, 1966. ,
DOI : 10.1016/S0019-9958(66)80018-9
Animal species and evolution. Animal species and their evolution, 1963. ,
DOI : 10.4159/harvard.9780674865327
Evolutionary crossroads in developmental biology: sea urchins, Development, vol.138, issue.13, pp.2639-2648, 2011. ,
Handbook of biological statistics, 2009. ,
A protease-resistant protein is a structural component of the scrapie prion, Cell, vol.35, issue.1, pp.57-62, 1983. ,
Dynamic Analyses of Drosophila Gastrulation Provide Insights into Collective Cell Migration, Science, vol.322, issue.5907 ,
DOI : 10.1126/science.1167094
Introduction of cloned dna into sea urchin egg cytoplasm: replication and persistence during embryogenesis, Developmental biology, vol.108, issue.2, pp.420-430, 1985. ,
Imaging in systems biology, Cell, vol.130, issue.5, pp.784-795, 2007. ,
Versuche über Pflanzenhybriden, 1866. ,
DOI : 10.1007/978-3-663-19714-0
hasard évolutionnaire" de toute mutation génétique, ou la vision consensuelle de la synthèse moderne. Bulletin d'Histoire et d'épistémologie des sciences de la vie, pp.79-108, 2011. ,
Histoire de la biologie moléculaire ,
Heterochronic genes and the nature of developmental time, Current Biology, vol.17, issue.11, pp.425-434, 2007. ,
Applications of Persistent Homology to Time Varying Systems, 2013. ,
Mathematical biology i: An introduction, 2002. ,
Interactions between zebrafish pigment cells responsible for the generation of Turing patterns, Proceedings of the National Academy of Sciences, pp.8429-8434, 2009. ,
DOI : 10.1073/pnas.0808622106
Random graphs with arbitrary degree distributions and their applications, Physical Review E, vol.64, issue.2, p.26118, 2001. ,
Sided and symmetrized bregman centroids. Information Theory, IEEE Transactions on, vol.55, issue.6, pp.2882-2904, 2009. ,
DOI : 10.1109/tit.2009.2018176
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.172.2671
ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON, Proceedings of the National Academy of Sciences, vol.43, issue.7, p.553, 1957. ,
DOI : 10.1073/pnas.43.7.553
Mutations affecting segment number and polarity in Drosophila, Nature, vol.52, issue.5785, pp.795-801, 1980. ,
DOI : 10.1038/287795a0
Epigenetic Dynamics of Imprinted X Inactivation During Early Mouse Development, Science, vol.303, issue.5658, pp.644-649, 2004. ,
DOI : 10.1126/science.1092727
Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy, Science, vol.329, issue.5994, pp.329967-971, 2010. ,
DOI : 10.1126/science.1189428
URL : https://hal.archives-ouvertes.fr/hal-00519834
Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulations, Journal of Computational Physics, vol.79, issue.1, pp.12-49, 1988. ,
DOI : 10.1016/0021-9991(88)90002-2
Three-Dimensional Epithelial Morphogenesis in the Developing Drosophila Egg, Developmental Cell, vol.24, issue.4, pp.400-410, 2013. ,
DOI : 10.1016/j.devcel.2013.01.017
Advances in whole-embryo imaging: a quantitative transition is underway, Nature Reviews Molecular Cell Biology, vol.459, issue.5, pp.327-339, 2014. ,
DOI : 10.1038/nrm3786
URL : https://hal.archives-ouvertes.fr/hal-00998245
Modeling and inferring cleavage patterns in proliferating epithelia, PLoS computational biology, vol.5, issue.6, p.1000412, 2009. ,
Summing up the noise in gene networks, Nature, vol.427, issue.6973, pp.415-418, 2004. ,
DOI : 10.1038/nature02257
Identification of common and unique modifiers of zebrafish midline bifurcation and cyclopia, Developmental Biology, vol.326, issue.1, pp.201-211, 2009. ,
DOI : 10.1016/j.ydbio.2008.11.008
Environmental and genetic modifiers of squint penetrance during zebrafish embryogenesis, Developmental Biology, vol.308, issue.2, pp.368-378, 2007. ,
DOI : 10.1016/j.ydbio.2007.05.026
Predictive computation of genomic logic processing functions in embryonic development, Proceedings of the National Academy of Sciences, pp.16434-16442, 2012. ,
Methods in clonal analysis and applications, Reproduction Nutrition Development, vol.45, issue.3, pp.321-339, 2005. ,
DOI : 10.1051/rnd:2005024
URL : https://hal.archives-ouvertes.fr/hal-00900564
Holoprosencephaly: signaling interactions between the brain and the face, the environment and the genes, and the phenotypic variability in animal models and humans, Wiley Interdisciplinary Reviews: Developmental Biology, vol.143, issue.suppl, pp.17-32, 2015. ,
DOI : 10.1002/wdev.161
Epistasis?the essential role of gene interactions in the structure and evolution of genetic systems, Nature Reviews Genetics, vol.9, issue.11, pp.855-867, 2008. ,
Topological characteristics of random triangulated surfaces. Random Structures & Algorithms, pp.247-288, 2006. ,
Le débat entre cuvier et geoffroy saint-hilaire sur l'unité de plan et de composition. Revue d'histoire des sciences et de leurs applications, pp.343-363, 1950. ,
Science and Method, 2013. ,
Sur le problème des trois corps et les équations de la dynamique, Acta mathematica, vol.13, issue.1, pp.3-270, 1890. ,
Life at low Reynolds number, American Journal of Physics, 1977. ,
Information and the Accuracy Attainable in the Estimation of Statistical Parameters, Bulletin of the Calcutta Mathematical Society, vol.37, issue.3, pp.81-91, 1945. ,
DOI : 10.1007/978-1-4612-0919-5_16
Variability in gene expression underlies incomplete penetrance, Nature, vol.460, issue.7283, pp.913-918, 2010. ,
DOI : 10.1038/nature08781
Timescales of genetic and epigenetic inheritance, Cell, vol.128, issue.4, pp.655-668, 2007. ,
Homeo box genes of the Antennapedia and Bithorax Complexes of Drosophila, Cell, vol.43, issue.1, pp.71-80, 1985. ,
DOI : 10.1016/0092-8674(85)90013-3
Towards 3D in silico modeling of the sea urchin embryonic development, Journal of Chemical Biology, vol.6, issue.10, pp.17-28 ,
DOI : 10.1007/s12154-013-0101-x
URL : https://hal.archives-ouvertes.fr/hal-01054767
René Doursat, and Nadine Peyriéras. Predicting sea urchin's normal development from a small cohort of digital embryos, 2015. ,
Über die variabilität in der manifestierung eines erblichen merkmales (abdomen abnormalis) bei drosophila funebris f, Journal für Psychologie und Neurologie, vol.31, pp.323-325, 1925. ,
A quantum-theoretic approach to genetic problems. The bulletin of mathematical biophysics, pp.227-255, 1960. ,
Über die Entwicklungsmechanik der Organismen, 1890. ,
A Modeling Study on How Cell Division Affects Properties of Epithelial Tissues Under Isotropic Growth, PLoS ONE, vol.106, issue.7, p.11750, 2010. ,
DOI : 10.1371/journal.pone.0011750.t002
Topological Progression in Proliferating Epithelia Is Driven by a Unique Variation in Polygon Distribution, PLoS ONE, vol.139, issue.11, p.79227, 2013. ,
DOI : 10.1371/journal.pone.0079227.s004
Correlating cell behavior with tissue topology in embryonic epithelia, PloS one, vol.6, issue.4, p.18081, 2011. ,
Lineage correlations of single cell division time as a probe of cell-cycle dynamics, Nature, vol.105, issue.7544, pp.519468-471, 2015. ,
DOI : 10.1038/nature14318
Subjective surfaces: A method for completing missing boundaries, Proceedings of the National Academy of Sciences, pp.6258-6263, 2000. ,
DOI : 10.1073/pnas.110135797
??-catenin translocation into nuclei demarcates the dorsalizing centers in frog and fish embryos, Mechanisms of Development, vol.57, issue.2, pp.191-198, 1996. ,
DOI : 10.1016/0925-4773(96)00546-1
What is life, 1944. ,
The Sources of Kolmogorov???s Grundbegriffe, Statistical Science, vol.21, issue.1, pp.70-98, 2006. ,
DOI : 10.1214/088342305000000467
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks, Bioinformatics, vol.18, issue.2, pp.261-274, 2002. ,
DOI : 10.1093/bioinformatics/18.2.261
Developmental constraints and evolution: a perspective from the mountain lake conference on development and evolution, Quarterly Review of Biology, pp.265-287, 1985. ,
The persistent cosmic web and its filamentary structure - I. Theory and implementation, Monthly Notices of the Royal Astronomical Society, vol.414, issue.1, pp.350-383, 2011. ,
DOI : 10.1111/j.1365-2966.2011.18394.x
One hundred years of pleiotropy: a retrospective, Genetics, vol.186, issue.3, pp.767-773, 2010. ,
Post-embryonic cell lineages of the nematode, caenorhabditis elegans, Developmental biology, vol.56, issue.1, pp.110-156, 1977. ,
Intrinsic and extrinsic contributions to stochasticity in gene expression, Proceedings of the National Academy of Sciences, pp.12795-12800, 2002. ,
Über den einfluss des genotypus auf das phänotypen auftreten eines einzelnes gens, Journal für Psychologie und Neurologie, vol.31, pp.305-310, 1925. ,
Multi-Cellular Rosettes in the Mouse Visceral Endoderm Facilitate the Ordered Migration of Anterior Visceral Endoderm Cells, PLoS Biology, vol.226, issue.2, p.1001256, 2012. ,
DOI : 10.1371/journal.pbio.1001256.s009
Deep and fast live imaging with two-photon scanned light-sheet microscopy, Nature methods, vol.8, issue.9, pp.757-760, 2011. ,
The chemical basis of morphogenesis, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol.237, issue.641, pp.37-72, 1952. ,
La reconstruction phénoménologique par simulation : vers une épaisseur du simulat, Formes, systèmes et milieux techniques, pp.107-123 ,
Random triangulated surfaces with arbitrary degree distribution reveal embryonic epithelial organization, Algebraic Topology -Methods, p.2014 ,
Vers une modélisation multi-échelle de la variabilité biologique?, Modéliser & Simuler. Epistémologie et pratique de la modélisation et de la simulation Editions matériologiques, pp.643-664, 2014. ,
Biological diversity and quantum formalism: Entanglement of genotype-phenotype relations, preparation, 2015. ,
Topological analysis of epithelia uncovers high-order structures in spatial distribution of cells, 2015. ,
A probabilistic modeling of the cell lineage highlights interindividual variability in paracentrotus lividus early development, The Developmental Biology of the Sea Urchin XXII, 2014. ,
Über Entwicklungsgeschichte der Thiere Beobachtung und Reflexion, pp.1828-1837, 1828. ,
DOI : 10.5962/bhl.title.112232
URL : http://dspace.library.uu.nl:8080/handle/1874/268325
The strategy of the genes, Allen and Unwin, 1957. ,
Differential positioning of adherens junctions is associated with initiation of epithelial folding, Nature, vol.15, issue.7394, pp.484390-393, 2012. ,
DOI : 10.1038/nature10938
The origin of species: a structuralist approach, Journal of Social and Biological Systems, vol.5, issue.1, pp.15-47, 1982. ,
DOI : 10.1016/S0140-1750(82)91390-2
Interplay of Cell Shape and Division Orientation Promotes Robust Morphogenesis of Developing Epithelia, Cell, vol.159, issue.2, pp.415-427, 2014. ,
DOI : 10.1016/j.cell.2014.09.007
Specified Neural Progenitors Sort to Form Sharp Domains after Noisy Shh Signaling, Cell, vol.153, issue.3, pp.550-561, 2013. ,
DOI : 10.1016/j.cell.2013.03.023
Planar polarity and tissue morphogenesis, Cell, vol.129, issue.6, pp.1051-1063, 2007. ,
Cells Segmentation From 3-D Confocal Images of Early Zebrafish Embryogenesis, IEEE Transactions on Image Processing, vol.19, issue.3, pp.770-781, 2010. ,
DOI : 10.1109/TIP.2009.2033629
URL : https://hal.archives-ouvertes.fr/hal-00444516
Computing persistent homology ,