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@article{Martin:2021,
title = {Arp2/3-Dependent Mechanical Control of Morphogenetic Robustness in an Inherently Challenging Environment},
author = {Martin, Emmanuel and Theis, Sophie and Gay, Guillaume and Monier, Bruno and Rouvière, Christian and Suzanne, Magali},
date = {2021-02-02},
journaltitle = {Developmental Cell},
issn = {1534-5807},
url = {https://www.sciencedirect.com/science/article/pii/S1534580721000368?via%3Dihub.},
doi = {10.1016/j.devcel.2021.01.005}
}
@article{Eritano:2020,
author = {Eritano, Anthony S. and Bromley, Claire L. and {Bolea Albero}, Antonio and Sch{\"{u}}tz, Lucas and Wen, Fu-Lai and Shibata, Tatsuo and Takeda, Michiko and Sami, Mustafa M. and Lemke, Steffen and Wang, Yu-Chiun},
doi = {10.2139/ssrn.3378007},
file = {:home/admin-suz/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Eritano et al. - 2020 - Tissue-Scale Mechanical Coupling Reduces Morphogenetic Noise to Ensure Precision During Epithelial Folding.pdf:pdf},
journal = {Developmental cell},
pages = {1--17},
title = {{Tissue-Scale Mechanical Coupling Reduces Morphogenetic Noise to Ensure Precision During Epithelial Folding}},
volume = {53},
year = {2020}
}
@article{Cooper:2020,
author = {Cooper, Fergus and Baker, Ruth and Bernabeu, Miguel and Bordas, Rafel and Bowler, Louise and Bueno-Orovio, Alfonso and Byrne, Helen and Carapella, Valentina and Cardone-Noott, Louie and Cooper, Jonathan and Dutta, Sara and Evans, Benjamin and Fletcher, Alexander and Grogan, James and Guo, Wenxian and Harvey, Daniel and Hendrix, Maurice and Kay, David and Kursawe, Jochen and Maini, Philip and McMillan, Beth and Mirams, Gary and Osborne, James and Pathmanathan, Pras and Pitt-Francis, Joe and Robinson, Martin and Rodriguez, Blanca and Spiteri, Raymond and Gavaghan, David},
doi = {10.21105/joss.01848},
issn = {2475-9066},
journal = {Journal of Open Source Software},
mendeley-groups = {Modeling},
month = {mar},
number = {47},
pages = {1848},
publisher = {The Open Journal},
title = {{Chaste: Cancer, Heart and Soft Tissue Environment}},
url = {https://joss.theoj.org/papers/10.21105/joss.01848},
volume = {5},
year = {2020}
}
@ARTICLE{Virtanen:2020,
author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and
Haberland, Matt and Reddy, Tyler and Cournapeau, David and
Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
Bright, Jonathan and {van der Walt}, St{\'e}fan J. and
Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and
Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and
Kern, Robert and Larson, Eric and Carey, C J and
Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and
{VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and
Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and
Harris, Charles R. and Archibald, Anne M. and
Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and
{van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
title = {{{SciPy} 1.0: Fundamental Algorithms for Scientific
Computing in Python}},
journal = {Nature Methods},
year = {2020},
volume = {17},
pages = {261--272},
adsurl = {https://rdcu.be/b08Wh},
doi = {10.1038/s41592-019-0686-2}
}
@ARTICLE{Harris:2020,
author = {Harris, Charles R. and Millman, K. Jarrod and
van der Walt, Stéfan J and Gommers, Ralf and
Virtanen, Pauli and Cournapeau, David and
Wieser, Eric and Taylor, Julian and Berg, Sebastian and
Smith, Nathaniel J. and Kern, Robert and Picus, Matti and
Hoyer, Stephan and van Kerkwijk, Marten H. and
Brett, Matthew and Haldane, Allan and
Fernández del Río, Jaime and Wiebe, Mark and
Peterson, Pearu and Gérard-Marchant, Pierre and
Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and
Abbasi, Hameer and Gohlke, Christoph and
Oliphant, Travis E.},
title = {Array programming with {NumPy}},
journal = {Nature},
year = {2020},
volume = {585},
pages = {357–362},
doi = {10.1038/s41586-020-2649-2}
}
@article{Gracia:2019,
author = {Gracia, M{\'{e}}lanie and Theis, Sophie and Proag, Amsha and Gay, Guillaume and Benassayag, Corinne and Suzanne, Magali},
doi = {10.1038/s41467-019-10720-0},
issn = {2041-1723},
journal = {Nature Communications},
keywords = {Epithelial,Mesoderm,Myosin,mesenchymal transition},
month = {dec},
number = {1},
pages = {2951},
publisher = {Nature Publishing Group},
title = {{Mechanical impact of epithelial−mesenchymal transition on epithelial morphogenesis in Drosophila}},
url = {http://www.nature.com/articles/s41467-019-10720-0},
volume = {10},
year = {2019}
}
@article{Finegan:2019,
author = {{Tara M Finegan} and {Nathan Hervieux} and {Alexander Nestor-Bergmann} and {Alexander G. Fletcher} and {Guy B. Blanchard} and Sanson, B{\'{e}}n{\'{e}}dicte and Finegan, Tara M. and Hervieux, Nathan and Nestor-Bergmann, Alexander and Fletcher, Alexander G. and Blanchard, Guy B. and Sanson, B{\'{e}}n{\'{e}}dicte},
doi = {10.1101/704932},
editor = {Tapon, Nicolas},
issn = {1545-7885},
journal = {PLOS Biology},
month = {dec},
number = {12},
pages = {e3000522},
title = {{The tricellular vertex-specific adhesion molecule Sidekick facilitates polarised cell intercalation during Drosophila axis extension}},
url = {https://dx.plos.org/10.1371/journal.pbio.3000522 http://dx.doi.org/10.1101/704932},
volume = {17},
year = {2019}
}
@article{Sui:2018,
author = {Sui, Liyuan and Alt, Silvanus and Weigert, Martin and Dye, Natalie and Eaton, Suzanne and Jug, Florian and Myers, Eugene W. and J{\"{u}}licher, Frank and Salbreux, Guillaume and Dahmann, Christian},
doi = {10.1038/s41467-018-06497-3},
issn = {2041-1723},
journal = {Nature Communications},
keywords = {Actin,Computational models,Drosophila,Morphogenesis},
month = {dec},
number = {1},
pages = {4620},
publisher = {Nature Publishing Group},
title = {{Differential lateral and basal tension drive folding of Drosophila wing discs through two distinct mechanisms}},
url = {http://dx.doi.org/10.1038/s41467-018-06497-3 http://www.nature.com/articles/s41467-018-06497-3},
volume = {9},
year = {2018}
}
@article{Heer:2017,
author = {Heer, Natalie C and Miller, Pearson W. and Chanet, Soline and Stoop, Norbert and Dunkel, J{\"{o}}rn and Martin, Adam C},
doi = {10.1242/dev.146761},
isbn = {0000000260039},
issn = {0950-1991},
journal = {Development},
keywords = {Epithelia,Fold,Gradient,Myosin,Twist},
month = {may},
number = {10},
pages = {1876--1886},
pmid = {28432215},
publisher = {Oxford University Press for The Company of Biologists Limited},
title = {{Actomyosin-based tissue folding requires a multicellular myosin gradient}},
url = {http://dev.biologists.org/lookup/doi/10.1242/dev.146761},
volume = {144},
year = {2017}
}
@article{Alt:2017,
author = {Alt, Silvanus and Ganguly, Poulami and Salbreux, Guillaume},
doi = {10.1098/rstb.2015.0520},
issn = {1471-2970},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
keywords = {epithelial mechanics,morphogenesis,simulations,tissue mechanics,vertex models},
month = {may},
number = {1720},
pages = {20150520},
pmid = {28348254},
publisher = {The Royal Society},
title = {{Vertex models: from cell mechanics to tissue morphogenesis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/28348254 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5379026},
volume = {372},
year = {2017}
}
@article{Bi:2015,
author = {Bi, Dapeng and Lopez, J. H. and Schwarz, J. M. and Manning, M. Lisa},
doi = {10.1038/nphys3471},
issn = {1745-2473},
journal = {Nature Physics},
keywords = {Biological physics,Cellular motility,Computational biophysics,Glasses,Phase transitions and critical phenomena},
month = {dec},
number = {12},
pages = {1074--1079},
publisher = {Nature Publishing Group},
title = {{A density-independent rigidity transition in biological tissues}},
url = {http://www.nature.com/articles/nphys3471},
volume = {11},
year = {2015}
}
@article{Monier:2015,
author = {Monier, Bruno and Gettings, Melanie and Gay, Guillaume and Mangeat, Thomas and Schott, Sonia and Guarner, Ana and Suzanne, Magali},
doi = {10.1038/nature14152},
issn = {0028-0836},
journal = {Nature},
keywords = {Apoptosis,Morphogenesis,Myosin},
month = {feb},
number = {7538},
pages = {245--248},
publisher = {Nature Publishing Group},
title = {{Apico-basal forces exerted by apoptotic cells drive epithelium folding}},
url = {http://www.nature.com/articles/nature14152},
volume = {518},
year = {2015}
}
@article{Okuda:2015,
author = {Okuda, Satoru and Inoue, Yasuhiro and Eiraku, Mototsugu and Adachi, Taiji and Sasai, Yoshiki},
doi = {10.1007/s10237-015-0724-7},
issn = {1617-7959},
journal = {Biomechanics and Modeling in Mechanobiology},
mendeley-groups = {Modeling},
month = {aug},
number = {4},
pages = {805--816},
title = {{Modeling cell apoptosis for simulating three-dimensional multicellular morphogenesis based on a reversible network reconnection framework}},
url = {http://link.springer.com/10.1007/s10237-015-0724-7},
volume = {15},
year = {2015}
}
@article{Okuda:2012,
author = {Okuda, Satoru and Inoue, Yasuhiro and Eiraku, Mototsugu and Sasai, Yoshiki and Adachi, Taiji},
doi = {10.1007/s10237-012-0430-7},
issn = {1617-7959},
journal = {Biomechanics and Modeling in Mechanobiology},
mendeley-groups = {Modeling},
month = {aug},
number = {4},
pages = {627--644},
publisher = {Springer-Verlag},
title = {{Reversible network reconnection model for simulating large deformation in dynamic tissue morphogenesis}},
url = {http://link.springer.com/10.1007/s10237-012-0430-7},
volume = {12},
year = {2012}
}
@article{Salbreux:2012,
author = {Salbreux, Guillaume and Barthel, Linda K. and Raymond, Pamela A. and Lubensky, David K.},
doi = {10.1371/journal.pcbi.1002618},
issn = {1553-7358},
journal = {PLoS Computational Biology},
month = {aug},
number = {8},
pages = {e1002618},
publisher = {Public Library of Science},
title = {{Coupling Mechanical Deformations and Planar Cell Polarity to Create Regular Patterns in the Zebrafish Retina}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1002618},
volume = {8},
year = {2012}
}
@article{Aegerter:2012,
author = {Aegerter-Wilmsen, Tinri and Heimlicher, Maria B. and Smith, Alister C. and de Reuille, Pierre Barbier and Smith, Richard S. and Aegerter, Christof M. and Konrad, Basler},
doi = {10.1242/dev.082800},
file = {:home/admin-suz/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Aegerter-Wilmsen et al. - 2012 - Integrating force-sensing and signaling pathways in a model for the regulation of wing imaginal disc si.pdf:pdf},
journal = {Development},
title = {{Integrating force-sensing and signaling pathways in a model for the regulation of wing imaginal disc size}},
url = {http://dev.biologists.org/content/develop/139/17/3221.full.pdf?with-ds=yes},
year = {2012}
}
@article{Staple:2010,
title = {{Cell Flow Reorients the Axis of Planar Polarity in the Wing Epithelium of Drosophila}},
author = {Aigouy, Benoît and Farhadifar, Reza and Staple, Douglas B. and Sagner, Andreas and Röper, Jens-Christian and Jülicher, Frank and Eaton, Suzanne},
date = {2010-09-03},
journal = {Cell},
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pages = {773--786},
issn = {0092-8674},
doi = {10.1016/j.cell.2010.07.042},
url = {https://www.sciencedirect.com/science/article/pii/S0092867410008901},
publisher = {Cell Press},
}
@article{Sherrard:2010,
author = {Sherrard, Kristin and Robin, Fran{\c{c}}ois and Lemaire, Patrick and Munro, Edwin},
doi = {10.1016/J.CUB.2010.06.075},
issn = {0960-9822},
journal = {Current Biology},
month = {sep},
number = {17},
pages = {1499--1510},
publisher = {Cell Press},
title = {{Sequential Activation of Apical and Basolateral Contractility Drives Ascidian Endoderm Invagination}},
url = {https://www.sciencedirect.com/science/article/pii/S0960982210008730?via%3Dihub},
volume = {20},
year = {2010}
}
@inproceedings{mckinney:2010,
author = {McKinney, Wes},
booktitle = {{P}roceedings of the 9th {P}ython in {S}cience {C}onference},
doi = {10.25080/Majora-92bf1922-00a},
editor = {van der Walt, St{\'{e}}fan and Millman, Jarrod},
pages = {56--61},
title = {{{D}ata {S}tructures for {S}tatistical {C}omputing in {P}ython}},
year = {2010}
}
@article{Farhadifar:2007,
author = {Farhadifar, Reza and R{\"{o}}per, Jens-Christian and Aigouy, Benoit and Eaton, Suzanne and J{\"{u}}licher, Frank},
doi = {10.1016/J.CUB.2007.11.049},
issn = {0960-9822},
journal = {Current Biology},
month = {dec},
number = {24},
pages = {2095--2104},
publisher = {Cell Press},
title = {{The Influence of Cell Mechanics, Cell-Cell Interactions, and Proliferation on Epithelial Packing}},
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year = {2007}
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@ARTICLE{Hunter:2007,
author={Hunter, John D.},
journal={Computing in Science Engineering},
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year={2007},
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number={3},
pages={90-95},
doi={10.1109/MCSE.2007.55}}
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publisher = {J Biomech},
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@article{Honda:1983,
title = "Geometrical Models for Cells in Tissues",
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author = "Hisao Honda",
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@article{Honda:1978,
title = "Description of cellular patterns by Dirichlet domains: The two-dimensional case",
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number = "3",
pages = "523 - 543",
year = "1978",
issn = "0022-5193",
doi = {10.1016/0022-5193(78)90315-6},
url = "http://www.sciencedirect.com/science/article/pii/0022519378903156",
author = "Hisao Honda",
}