Agent-based modeling of morphogenetic systems: advantages and challenges.

Embryonic Stem Cell Lines Derived from Human Blastocysts

Thomson, J. A., Itskovitz‐Eldor, J., Shapiro, S. S., Waknitz, M. A., Swiergiel, J. J., Marshall, V. S., & Jones, J. M. (1998) · Science · doi:10.1126/science.282.5391.1145 · Cited by 15,947 · see citing works

The chemical basis of morphogenesis

Turing, A. M. (1952) · Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences · doi:10.1098/rstb.1952.0012 · Cited by 11,733 · see citing works

Establishment in culture of pluripotential cells from mouse embryos

Evans, M. J., & Kaufman, M. H. (1981) · Nature · doi:10.1038/292154a0 · Cited by 8,623 · see citing works

Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells.

Martin, G. R. (1981) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.78.12.7634 · Cited by 5,756 · see citing works

Identification of stem cells in small intestine and colon by marker gene Lgr5

Barker, N., van Es, J. H., Kuipers, J., Kujala, P., van den Born, M., Cozijnsen, M., Haegebarth, A., Korving, J., Begthel, H., Peters, P. J., et al. (2007) · Nature · doi:10.1038/nature06196 · Cited by 5,687 · see citing works

Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells

Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.020 · Cited by 4,505 · see citing works

Remodelling the extracellular matrix in development and disease

Bonnans, C., Chou, J., & Werb, Z. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3904 · Cited by 4,367 · see citing works

The Extracellular Matrix: Not Just Pretty Fibrils

Hynes, R. O. (2009) · Science · doi:10.1126/science.1176009 · Cited by 3,527 · see citing works

Formation of Pluripotent Stem Cells in the Mammalian Embryo Depends on the POU Transcription Factor Oct4

Nichols, J., Zevnik, B., Anastassiadis, K., Niwa, H., Klewe-Nebenius, D., Chambers, I., Schöler, H. R., & Smith, A. G. (1998) · Cell · doi:10.1016/s0092-8674(00)81769-9 · Cited by 3,394 · see citing works

The Homeoprotein Nanog Is Required for Maintenance of Pluripotency in Mouse Epiblast and ES Cells

Mitsui, K., Tokuzawa, Y., Itoh, H., Segawa, K., Murakami, M., Takahashi, K., Maruyama, M., Maeda, M., & Yamanaka, S. (2003) · Cell · doi:10.1016/s0092-8674(03)00393-3 · Cited by 3,192 · see citing works

A theory of biological pattern formation

Gierer, A., & Meinhardt, H. (1972) · Kybernetik · doi:10.1007/bf00289234 · Cited by 3,158 · see citing works

Positional information and the spatial pattern of cellular differentiation

Wolpert, L. (1969) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(69)80016-0 · Cited by 3,091 · see citing works

Multipotent cell lineages in early mouse development depend on SOX2 functionPreprint

Avilion, A. A., Nicolis, S. K., Pevny, L., Pérez, L., Vivian, N., & Lovell-Badge, R. H. (2003) · Genes & Development · doi:10.1101/gad.224503 · Cited by 2,372 · see citing works

Extracellular matrix: A dynamic microenvironment for stem cell niche

Gattazzo, F., Urciuolo, A., & Bonaldo, P. (2014) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.01.010 · Cited by 1,304 · see citing works

On Growth and Form

N., E., & Thompson, D. W. (1945) · The Journal of Philosophy · doi:10.2307/2019330 · Cited by 1,119 · see citing works

Principles of Development

Wolpert, L., Tickle, C. A., Arias, A. M., Lawrence, P. A., & Locke, J. C. W. (2019) · Oxford University Press eBooks · doi:10.1093/hesc/9780198800569.001.0001 · Cited by 991 · see citing works

A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells

Niwa, H., Ogawa, K., Shimosato, D., & Adachi, K. (2009) · Nature · doi:10.1038/nature08113 · Cited by 872 · see citing works

Dissipative structure: An explanation and an ecological example

Segel, L. A., & Jackson, J. L. (1972) · Journal of Theoretical Biology · doi:10.1016/0022-5193(72)90090-2 · Cited by 720 · see citing works

Positional Information in Chick Limb Morphogenesis

Summerbell, D., Lewis, J., & Wolpert, L. (1973) · Nature · doi:10.1038/244492a0 · Cited by 712 · see citing works

Probing the Limits to Positional Information

Gregor, T., Tank, D. W., Wieschaus, E. F., & Bialek, W. (2007) · Cell · doi:10.1016/j.cell.2007.05.025 · Cited by 681 · see citing works

Simple chemical reaction systems with limit cycle behaviour

Schnakenberg, J. (1979) · Journal of Theoretical Biology · doi:10.1016/0022-5193(79)90042-0 · Cited by 675 · see citing works

Chapter 6 Positional Information and Pattern Formation

Wolpert, L. (1971) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/s0070-2153(08)60641-9 · Cited by 670 · see citing works

Role of the Reelin Signaling Pathway in Central Nervous System Development

Rice, D. S., & Curran, T. (2001) · Annual Review of Neuroscience · doi:10.1146/annurev.neuro.24.1.1005 · Cited by 667 · see citing works

Positional Information and Pattern Formation

Wolpert, L. (2016) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2015.11.008 · Cited by 653 · see citing works

Patterns of neuronal migration in the embryonic cortex

Kriegstein, A. R., & Noctor, S. C. (2004) · Trends in Neurosciences · doi:10.1016/j.tins.2004.05.001 · Cited by 648 · see citing works

Artificial Adaptive Agents in Economic Theory

Holland, J. H., & Miller, J. H. (1991) · American Economic Review · Cited by 587 · see citing works

Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells

Wang, Z., Oron, E., Nelson, B., Razis, S., & Ivanova, N. B. (2012) · Cell stem cell · doi:10.1016/j.stem.2012.02.016 · Cited by 545 · see citing works

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

Thomson, M. W., Liu, S. J., Zou, L.-N., Smith, Z., Meissner, A., & Ramanathan, S. (2011) · Cell · doi:10.1016/j.cell.2011.05.017 · Cited by 533 · see citing works

Reelin Is a Secreted Glycoprotein Recognized by the CR-50 Monoclonal Antibody

D’Arcangelo, G., Nakajima, K., Miyata, T., Ogawa, M., Mikoshiba, K., & Curran, T. (1997) · The Journal of Neuroscience · doi:10.1523/jneurosci.17-01-00023.1997 · Cited by 515 · see citing works

Radiation Effects on Breast Cancer Risk: A Pooled Analysis of Eight Cohorts

Preston, D. L., Mattsson, A. F., Holmberg, E. C., Shore, R. E., Hildreth, N. G., & Boice, J. D. (2002) · Radiation Research · doi:10.1667/0033-7587(2002)158[0220:reobcr]2.0.co;2 · Cited by 512 · see citing works

Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients

Raspopovic, J., Marcon, L., Russo, L., & Sharpe, J. A. (2014) · Science · doi:10.1126/science.1252960 · Cited by 497 · see citing works

The interpretation of morphogen gradients

Ashe, H. L., & Briscoe, J. (2006) · Development · doi:10.1242/dev.02238 · Cited by 481 · see citing works

Applications of a theory of biological pattern formation based on lateral inhibition

Meinhardt, H., & Gierer, A. (1974) · Journal of Cell Science · doi:10.1242/jcs.15.2.321 · Cited by 469 · see citing works

Morphogens, their identification and regulation

Tabata, T., & Takei, Y. (2004) · Development · doi:10.1242/dev.01043 · Cited by 447 · see citing works

Positional information and reaction-diffusion: two big ideas in developmental biology combine

Green, J. B. A., & Sharpe, J. A. (2015) · Development · doi:10.1242/dev.114991 · Cited by 430 · see citing works

Biologically active synthetic peptides as probes of embryonic development: a competitive peptide inhibitor of fibronectin function inhibits gastrulation in amphibian embryos and neural crest cell migration in avian embryos.

Boucaut, J., Darribère, T., Poole, T. J., Aoyama, H., Yamada, K. M., & Thiery, J. P. (1984) · The Journal of Cell Biology · doi:10.1083/jcb.99.5.1822 · Cited by 422 · see citing works

Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo

Levin, M. G. (2014) · Molecular Biology of the Cell · doi:10.1091/mbc.e13-12-0708 · Cited by 397 · see citing works

Principles of Development

Gh, S. (2016) · Genetics & Genomic Sciences · doi:10.24966/ggs-2485/100001 · Cited by 389 · see citing works

Enteric nervous system development: migration, differentiation, and disease

Lake, J. I., & Heuckeroth, R. O. (2013) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00452.2012 · Cited by 383 · see citing works

Differential Diffusivity of Nodal and Lefty Underlies a Reaction-Diffusion Patterning System

Müller, P., Rogers, K. W., Jordan, B. M., Lee, J. S., Robson, D. N., Ramanathan, S., & Schier, A. F. (2012) · Science · doi:10.1126/science.1221920 · Cited by 377 · see citing works

Hox Genes Regulate Digit Patterning by Controlling the Wavelength of a Turing-Type Mechanism

Sheth, R., Marcon, L., Bastida, M. F., Junco, M., Quintana, L., Dahn, R. D., Kmita, M., Sharpe, J. A., & Ros, M. A. (2012) · Science · doi:10.1126/science.1226804 · Cited by 349 · see citing works

Fidelity in planar cell polarity signalling

Ma, D., Yang, C.-H., McNeill, H., Simon, M. A., & Axelrod, J. D. (2003) · Nature · doi:10.1038/nature01366 · Cited by 332 · see citing works

A short G1 phase is an intrinsic determinant of naïve embryonic stem cell pluripotency

Coronado, D., Godet, M., Bourillot, P.-Y., Tapponnier, Y., Bernat, A., Petit, M., Afanassieff, M., Markossian, S., Malashicheva, A., Iacone, R., et al. (2012) · Stem Cell Research · doi:10.1016/j.scr.2012.10.004 · Cited by 273 · see citing works

Agent-based simulation of notch-mediated tip cell selection in angiogenic sprout initialisation

Bentley, K., Gerhardt, H., & Bates, P. A. (2007) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2007.09.015 · Cited by 251 · see citing works

Enteric nervous system development: A crest cell’s journey from neural tube to colon

Nagy, N., & Goldstein, A. M. (2017) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2017.01.006 · Cited by 245 · see citing works

Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling

Merks, R. M. H., Brodsky, S. V., Goligorksy, M. S., Newman, S. A., & Glazier, J. A. (2005) · Developmental Biology · doi:10.1016/j.ydbio.2005.10.003 · Cited by 238 · see citing works

A mechanism for inside-out lamination in the neocortex

Cooper, J. A. (2008) · Trends in Neurosciences · doi:10.1016/j.tins.2007.12.003 · Cited by 236 · see citing works

Patterns of cell and fiber distribution in the neocortex of the reeler mutant mouse

Caviness, V. S. (1976) · The Journal of Comparative Neurology · doi:10.1002/cne.901700404 · Cited by 221 · see citing works

Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth

Merks, R. M. H., Perryn, E. D., Shirinifard, A., & Glazier, J. A. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000163 · Cited by 205 · see citing works

Regulation of Cell Proliferation by a Morphogen Gradient

Rogulja, D., & Irvine, K. D. (2005) · Cell · doi:10.1016/j.cell.2005.08.030 · Cited by 203 · see citing works

C ompu C ell , a multi-model framework for simulation of morphogenesis

Izaguirre, J. A., Chaturvedi, R., Huang, C., et al. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth050 · Cited by 201 · see citing works

Quantification of Crypt and Stem Cell Evolution in the Normal and Neoplastic Human Colon

Baker, A., Cereser, B., Melton, S., Fletcher, A. G., Rodriguez‐Justo, M., Tadrous, P. J., Humphries, A., Elia, G., McDonald, S. A. C., Wright, N. A., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.07.019 · Cited by 195 · see citing works

Mechanisms of endothelial cell migration

Michaelis, U. R. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1678-0 · Cited by 191 · see citing works

Cell proliferation drives neural crest cell invasion of the intestine

Simpson, M. J., Zhang, D. C., Mariani, M., et al. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.10.017 · Cited by 190 · see citing works

High performance cellular level agent-based simulation with FLAME for the GPU

Richmond, P., Walker, D., Coakley, S., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp073 · Cited by 181 · see citing works

Neuronal migration

de Rouvroit, C. L., & Goffinet, A. M. (2001) · Mechanisms of Development · doi:10.1016/s0925-4773(01)00396-3 · Cited by 176 · see citing works

Cell interactions and planar polarity in the abdominal epidermis of Drosophila

Lawrence, P. A., Casal, J., & Struhl, G. (2004) · Development · doi:10.1242/dev.01351 · Cited by 174 · see citing works

A review of mathematical models for the formation of vascular networks

Scianna, M., Bell, C., & Preziosi, L. (2013) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2013.04.037 · Cited by 167 · see citing works

A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt

Buske, P., Galle, J., Barker, N., Aust, G., Clevers, H. C., & Loeffler, M. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001045 · Cited by 166 · see citing works

Cell division and death in the mouse blastocyst before implantation

Handyside, A. H., & Hunter, S. (1986) · Development Genes and Evolution · doi:10.1007/bf00375893 · Cited by 164 · see citing works

Ectodermal-mesodermal interactions in the growth of limb buds in the chick embryo: Constancy and temporal limits of the ectodermal induction

Rubin, L., & Saunders, J. W. (1972) · Developmental Biology · doi:10.1016/0012-1606(72)90129-7 · Cited by 160 · see citing works

Gene Networks Capable of Pattern Formation: From Induction to Reaction–Diffusion

Salazar‐Ciudad, I., García‐Fernàndez, J., & Solé, R. V. (2000) · Journal of Theoretical Biology · doi:10.1006/jtbi.2000.2092 · Cited by 156 · see citing works

Reelin Is a Serine Protease of the Extracellular Matrix

Quattrocchi, C. C., Wannenes, F., Persico, A. M., Ciafré, S. A., D'Arcangelo, G., Farace, M. G., & Keller, F. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m106996200 · Cited by 154 · see citing works

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

Marcon, L., Diego, X., Sharpe, J. A., & Müller, P. (2016) · eLife · doi:10.7554/elife.14022 · Cited by 147 · see citing works

Multi-species simple exclusion processes

Simpson, M. J., Landman, K. A., & Hughes, B. D. (2008) · Physica A Statistical Mechanics and its Applications · doi:10.1016/j.physa.2008.10.038 · Cited by 146 · see citing works

On multiscale approaches to three-dimensional modelling of morphogenesis

Chaturvedi, R., Huang, C., Kaźmierczak, B., et al. (2005) · Journal of The Royal Society Interface · doi:10.1098/rsif.2005.0033 · Cited by 135 · see citing works

Impaired Neuronal Positioning and Dendritogenesis in the Neocortex after Cell-Autonomous Dab1 Suppression

Olson, E. C., Kim, S., & Walsh, C. A. (2006) · Journal of Neuroscience · doi:10.1523/jneurosci.3000-05.2006 · Cited by 125 · see citing works

Differentiation inhibiting activity () and mouse development

Smith, A. G., Nichols, J., Robertson, M., & Rathjen, P. D. (1992) · Developmental Biology · doi:10.1016/0012-1606(92)90174-f · Cited by 123 · see citing works

A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation

Hester, S. D., Belmonte, J. M., Gens, J. S., Clendenon, S. G., & Glazier, J. A. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002155 · Cited by 123 · see citing works

Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting

Qutub, A. A., & Popel, A. S. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-13 · Cited by 123 · see citing works

A Computational Model Predicting Disruption of Blood Vessel Development

Kleinstreuer, N., Dix, D. J., Rountree, M. R., Baker, N., Sipes, N. S., Reif, D. M., Spencer, R. M., & Knudsen, T. B. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002996 · Cited by 122 · see citing works

Biomechanical coupling facilitates spinal neural tube closure in mouse embryos

Galea, G. L., Cho, Y.-J., Galea, G., Molè, M. A., Rolo, A., Savery, D., MOULDING, D. A., Culshaw, L. H., Nikolopoulou, E., Greene, N. D. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1700934114 · Cited by 113 · see citing works

A First Course in Systems Biology

Voit, E. O. (2017) · Garland Science eBooks · doi:10.4324/9780203702260 · Cited by 110 · see citing works

Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms

Emmons‐Bell, M., Durant, F., Hammelman, J., Bessonov, N. M., Volpert, V. A., Morokuma, J., Pinet, K., Adams, D. S., Pietak, A. M., Lobo, D., et al. (2015) · International Journal of Molecular Sciences · doi:10.3390/ijms161126065 · Cited by 109 · see citing works

Cryptic Patterning of Avian Skin Confers a Developmental Facility for Loss of Neck Feathering

Mou, C., Frédérique Pitel, A., Gourichon, D., Vignoles, F., Tzika, A. C., Tato, P., Yu, L., Burt, D. W., Bed’Hom, B., Tixier‐Boichard, M., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001028 · Cited by 103 · see citing works

Bioelectric gene and reaction networks: computational modelling of genetic, biochemical and bioelectrical dynamics in pattern regulation

Pietak, A. M., & Levin, M. G. (2017) · Journal of The Royal Society Interface · doi:10.1098/rsif.2017.0425 · Cited by 96 · see citing works

Mixed-mode pattern in Doublefoot mutant mouse limb—Turing reaction–diffusion model on a growing domain during limb development

Miura, T., Shiota, K., Morriss‐Kay, G. M., et al. (2005) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2005.10.016 · Cited by 93 · see citing works

From Classical Models of Morphogenesis to Agent-Based Models of Pattern Formation

Bonabeau, E. W. (1997) · Artificial Life · doi:10.1162/artl.1997.3.191 · Cited by 90 · see citing works

Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model

Voß-Böhme, A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042852 · Cited by 88 · see citing works

Sculpturing digit shape by cell death

Montero, J. A., & Hurlé, J. M. (2009) · APOPTOSIS · doi:10.1007/s10495-009-0444-5 · Cited by 87 · see citing works

Dynamic mechanisms of blood vessel growth

Merks, R. M. H., & Glazier, J. A. (2005) · Nonlinearity · doi:10.1088/0951-7715/19/1/000 · Cited by 87 · see citing works

Mammary Stem Cells and Mammopoiesis

Visvader, J. E., & Lindeman, G. J. (2006) · Cancer Research · doi:10.1158/0008-5472.can-06-2254 · Cited by 87 · see citing works

Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework

Tkačik, G., Dubuis, J., Petkova, M. D., et al. (2014) · Genetics · doi:10.1534/genetics.114.171850 · Cited by 85 · see citing works

A First Course in Systems Biology

Voit, E. O. (2012) · Garland Science eBooks · doi:10.1201/9780429258510 · Cited by 83 · see citing works

Enteric neural crest-derived cells promote their migration by modifying their microenvironment through tenascin-C production

Akbareian, S. E., Nagy, N., Steiger, C. E., Mably, J. D., Miller, S., Hotta, R., Molnár, D., & Goldstein, A. M. (2013) · Developmental Biology · doi:10.1016/j.ydbio.2013.08.006 · Cited by 80 · see citing works

Modeling Gastrulation in the Chick Embryo: Formation of the Primitive Streak

Vasiev, B. N., Balter, A. I., Chaplain, M. A. J., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010571 · Cited by 77 · see citing works

Four-dimensional realistic modeling of pancreatic organogenesis

Setty, Y., Cohen, I. R., Dor, Y., & Harel, D. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808725105 · Cited by 77 · see citing works

Simulating Properties of In Vitro Epithelial Cell Morphogenesis

Grant, M. R., Mostov, K. E., Tlsty, T. D., et al. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020129 · Cited by 73 · see citing works

High-throughput fingerprinting of human pluripotent stem cell fate responses and lineage bias

Nazareth, E. J. P., Östblom, J., Lücker, P. B., Shukla, S., Alvarez, M., Oh, S. K. W., Yin, T., & Zandstra, P. W. (2013) · Nature Methods · doi:10.1038/nmeth.2684 · Cited by 70 · see citing works

Module-based multiscale simulation of angiogenesis in skeletal muscle

Liu, G., Qutub, A. A., Vempati, P., Gabhann, F. M., & Popel, A. S. (2011) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-8-6 · Cited by 68 · see citing works

3D hybrid modelling of vascular network formation

Perfahl, H., Hughes, B. D., Alarcón, T., et al. (2016) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2016.11.013 · Cited by 66 · see citing works

Combining Turing and 3D vertex models reproduces autonomous multicellular morphogenesis with undulation, tubulation, and branching

Okuda, S., Miura, T., Inoue, Y., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-20678-6 · Cited by 66 · see citing works

Fibronectin matrix composition and organization can regulate cell migration during amphibian development

Darribère, T., & Schwarzbauer, J. E. (2000) · Mechanisms of Development · doi:10.1016/s0925-4773(00)00245-8 · Cited by 65 · see citing works

Four simple rules that are sufficient to generate the mammalian blastocyst

Nissen, S. B., Perera, M., Gonzalez, J. M., et al. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2000737 · Cited by 63 · see citing works

Mechanism of fibronectin-mediated cell migration: Dependence or independence of cell migration susceptibility on RGDS-directed receptor (integrin)

Straus, A. H., Carter, W. G., Wayner, E. A., et al. (1989) · Experimental Cell Research · doi:10.1016/0014-4827(89)90423-0 · Cited by 60 · see citing works

A Computational Study of the Development of Epithelial Acini: I. Sufficient Conditions for the Formation of a Hollow Structure

Rejniak, K. A., & Anderson, A. R. A. (2008) · Bulletin of Mathematical Biology · doi:10.1007/s11538-007-9274-1 · Cited by 60 · see citing works

Neural crest regionalisation for enteric nervous system formation: Implications for Hirschsprung's disease and stem cell therapy

Zhang, D., Brinas, I., Binder, B. J., et al. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2009.12.014 · Cited by 59 · see citing works

From Classical Models of Morphogenesis to Agent-Based Models of Pattern Formation

Bonabeau, E. W. (1997) · Artificial Life · doi:10.1162/artl.1997.3.3.191 · Cited by 57 · see citing works

Kidney branching morphogenesis under the control of a ligand–receptor-based Turing mechanism

Menshykau, D., & Iber, D. (2013) · Physical Biology · doi:10.1088/1478-3975/10/4/046003 · Cited by 56 · see citing works

An interplay between extracellular signalling and the dynamics of the exit from pluripotency drives cell fate decisions in mouse ES cells

Turner, D. A., Trott, J., Hayward, P. C., Rué, P., & Arias, A. M. (2014) · Biology Open · doi:10.1242/bio.20148409 · Cited by 55 · see citing works

Investigating the Turing conditions for diffusion-driven instability in the presence of a binding immobile substrate

Korvasová, K., Gaffney, E. A., Maini, P. K., et al. (2014) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.11.024 · Cited by 54 · see citing works

Irradiation of Juvenile, but not Adult, Mammary Gland Increases Stem Cell Self-Renewal and Estrogen Receptor Negative Tumors

Tang, J., Fernandez‐Garcia, I., Vijayakumar, S., Martinez‐Ruiz, H., Illa-Bochaca, I., Nguyen, D. H. A., Mao, J., Costes, S. V., & Barcellos‐Hoff, M. H. (2013) · Stem Cells · doi:10.1002/stem.1533 · Cited by 53 · see citing works

Early Embryonic Vascular Patterning by Matrix-Mediated Paracrine Signalling: A Mathematical Model Study

Köhn‐Luque, A., de Back, W., Starruß, J., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024175 · Cited by 52 · see citing works

Derivation and Maintenance of Embryonic Stem Cell Cultures

Robertson, E. J. (2003) · Humana Press eBooks · doi:10.1385/0-89603-441-0:173 · Cited by 51 · see citing works

Exclusion processes on a growing domain

Binder, B. J., & Landman, K. A. (2009) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2009.04.025 · Cited by 48 · see citing works

Dynamics of angiogenesis during murine retinal development: a coupled in vivo and in silico study

Watson, M. G., McDougall, S. R., Chaplain, M. A. J., et al. (2012) · Journal of The Royal Society Interface · doi:10.1098/rsif.2012.0067 · Cited by 47 · see citing works

Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis

Lambert, B. C., MacLean, A. L., Fletcher, A. G., Combes, A. N., Little, M. H., & Byrne, H. M. (2018) · Journal of Mathematical Biology · doi:10.1007/s00285-018-1208-z · Cited by 46 · see citing works

Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling

Tang, J., Enderling, H., Becker-Weimann, S., Pham, C. J., Polyzos, A. A., Chen, C.-Y., & Costes, S. V. (2011) · Integrative Biology · doi:10.1039/c0ib00092b · Cited by 44 · see citing works

A calibrated agent-based computer model of stochastic cell dynamics in normal human colon crypts useful for in silico experiments

Bravo, R., & Axelrod, D. E. (2013) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-10-66 · Cited by 44 · see citing works

A Mechanochemical Model for Embryonic Pattern Formation: Coupling Tissue Mechanics and Morphogen Expression

Mercker, M., Hartmann, D., & Marciniak-Czochra, A. K. (2013) · PLoS ONE · doi:10.1371/journal.pone.0082617 · Cited by 44 · see citing works

Branching patterns emerge in a mathematical model of the dynamics of lung development

Guo, Y., Chen, T., Zeng, X., et al. (2013) · The Journal of Physiology · doi:10.1113/jphysiol.2013.261099 · Cited by 43 · see citing works

The Dynamics of Turing Patterns for Morphogen-Regulated Growing Domains with Cellular Response Delays

Lee, S. S., Gaffney, E. A., & Baker, R. E. (2011) · Bulletin of Mathematical Biology · doi:10.1007/s11538-011-9634-8 · Cited by 42 · see citing works

A Formal Methods Approach to Pattern Recognition and Synthesis in Reaction Diffusion Networks

Bartocci, E., Göl, E. A., Haghighi, I., & Belta, C. A. (2016) · IEEE Transactions on Control of Network Systems · doi:10.1109/tcns.2016.2609138 · Cited by 41 · see citing works

Simple rules for a “simple” nervous system? Molecular and biomathematical approaches to enteric nervous system formation and malformation

Newgreen, D. F., Dufour, S., Howard, M. J., et al. (2013) · Developmental Biology · doi:10.1016/j.ydbio.2013.06.029 · Cited by 40 · see citing works

Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks

Walpole, J., Chappell, J. C., Cluceru, J. G., et al. (2015) · Integrative Biology · doi:10.1039/c5ib00024f · Cited by 39 · see citing works

Dynamic modeling of branching morphogenesis of ureteric bud in early kidney development

Hirashima, T., Iwasa, Y., & Morishita, Y. (2009) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2009.03.017 · Cited by 38 · see citing works

On the evolution of morphogenetic models: mechano‐chemical interactions and an integrated view of cell differentiation, growth, pattern formation and morphogenesis

Urdy, S. (2012) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/j.1469-185x.2012.00221.x · Cited by 38 · see citing works

Cell lineage tracing in the developing enteric nervous system: superstars revealed by experiment and simulation

Cheeseman, B. L., Zhang, D., Binder, B. J., Newgreen, D. F., & Landman, K. A. (2014) · Journal of The Royal Society Interface · doi:10.1098/rsif.2013.0815 · Cited by 38 · see citing works

Dynamic intercellular transport modulates the spatial patterning of differentiation during early neural commitment

Glen, C. M., McDevitt, T. C., & Kemp, M. L. (2018) · Nature Communications · doi:10.1038/s41467-018-06693-1 · Cited by 38 · see citing works

Periodic pattern formation in reaction-diffusion systems: An introduction for numerical simulation

Miura, T., & Maini, P. K. (2004) · Anatomical Science International · doi:10.1111/j.1447-073x.2004.00079.x · Cited by 37 · see citing works

Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour

Wynn, M. L., Kulesa, P. M., & Schnell, S. D. (2012) · Journal of The Royal Society Interface · doi:10.1098/rsif.2011.0726 · Cited by 37 · see citing works

Computational modeling and simulation of genital tubercle development

Leung, M. C. K., Hutson, M. S., Seifert, A. W., Spencer, R. M., & Knudsen, T. B. (2016) · Reproductive Toxicology · doi:10.1016/j.reprotox.2016.05.005 · Cited by 37 · see citing works

Mechano-logical model of C. elegans germ line suggests feedback on the cell cycle

Atwell, K., Qin, Z., Gavaghan, D. J., et al. (2015) · Development · doi:10.1242/dev.126359 · Cited by 34 · see citing works

Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior

Robertson, S. H., Smith, C. K., Langhans, A. L., et al. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-46 · Cited by 33 · see citing works

Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling

White, D. E., Kinney, M. A., McDevitt, T. C., & Kemp, M. L. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002952 · Cited by 32 · see citing works

Simple mechanical cues could explain adipose tissue morphology

Peurichard, D., Delebecque, F., Lorsignol, A., Barreau, C., Rouquette, J., Descombes, X., Casteilla, L., & Degond, P. (2017) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2017.06.030 · Cited by 32 · see citing works

Agent‐based computational model of retinal angiogenesis simulates microvascular network morphology as a function of pericyte coverage

Walpole, J., Gabhann, F. M., Peirce, S. M., et al. (2017) · Microcirculation · doi:10.1111/micc.12393 · Cited by 32 · see citing works

A computational approach to resolve cell level contributions to early glandular epithelial cancer progression

Kim, S. H. J., Debnath, J., Mostov, K. E., Park, S., & Hunt, C. A. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-122 · Cited by 31 · see citing works

A multiscale computational framework to understand vascular adaptation

Garbey, M., Rahman, M. H., & Berceli, S. A. (2015) · Journal of Computational Science · doi:10.1016/j.jocs.2015.02.002 · Cited by 29 · see citing works

Pattern formation in a (2 + 1)-species activator-inhibitor-immobilizer system

Pearson, J. E. (1992) · Physica A Statistical Mechanics and its Applications · doi:10.1016/0378-4371(92)90264-q · Cited by 28 · see citing works

Computational models of airway branching morphogenesis

Varner, V. D., & Nelson, C. M. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.06.003 · Cited by 28 · see citing works

Adaptive agent abstractions to speed up spatial agent-based simulations

Shirazi, A. S., Davison, T., von Mammen, S., et al. (2013) · Simulation Modelling Practice and Theory · doi:10.1016/j.simpat.2013.09.001 · Cited by 26 · see citing works

Cell traction in collective cell migration and morphogenesis: The chase and run mechanism

Szabó, A., & Mayor, R. (2015) · Cell Adhesion & Migration · doi:10.1080/19336918.2015.1019997 · Cited by 25 · see citing works

Derivation and Maintenance of Embryonic Stem Cell Cultures

Robertson, E. J. (2003) · Humana Press eBooks · doi:10.1385/0-89603-150-0:223 · Cited by 23 · see citing works

Emergent Models of Supple Dynamics in Life and Mind

Bedau, M. A. (1997) · Brain and Cognition · doi:10.1006/brcg.1997.0904 · Cited by 22 · see citing works

Towards Anatomic Scale Agent-Based Modeling with a Massively Parallel Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT_HPC)

Cockrell, R. C., Christley, S., Chang, E. B., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0122192 · Cited by 21 · see citing works

A model of stem cell population dynamics: in silico analysis and in vivo validation

Setty, Y., Dalfó, D., Korta, D. Z., Hubbard, E. J. A., & Kugler, H. (2011) · Development · doi:10.1242/dev.067512 · Cited by 21 · see citing works

Multiscale modeling of cell mechanics and tissue organization

Beyer, T., & Meyer‐Hermann, M. (2009) · IEEE Engineering in Medicine and Biology Magazine · doi:10.1109/memb.2009.931790 · Cited by 21 · see citing works

A cellular automata model of bone formation

Scoy, G. K. V., George, E. L., Asantewaa, F. O., Kerns, L. X., Saunders, M. M., & Prieto-Langarica, A. (2017) · Mathematical Biosciences · doi:10.1016/j.mbs.2017.02.001 · Cited by 21 · see citing works

Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information

Hillenbrand, P., Gerland, U., & Tkačik, G. (2016) · PLoS ONE · doi:10.1371/journal.pone.0163628 · Cited by 20 · see citing works

"The Potency of the First Two Cleavage Cells in Echinoderm Development. Experimental Production of Partial and Double Formations" (1891-1892), by Hans Driesch

Kearl, M. (2012) · Cited by 19 · see citing works

How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex

Setty, Y., Chen, C., Secrier, M., Skoblov, N., Kalamatianos, D., & Emmott, S. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-154 · Cited by 18 · see citing works

An In Silico Agent-Based Model Demonstrates Reelin Function in Directing Lamination of Neurons during Cortical Development

Caffrey, J. R., Hughes, B. D., Britto, J. M., & Landman, K. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0110415 · Cited by 18 · see citing works

Synergistic activity of polarised osteoblasts inside condensations cause their differentiation

Kaul, H., Hall, B. K., Newby, C., & Ventikos, Y. (2015) · Scientific Reports · doi:10.1038/srep11838 · Cited by 18 · see citing works

Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories

White, D. E., Sylvester, J. B., Levario, T. J., et al. (2015) · Integrative Biology · doi:10.1039/c5ib00072f · Cited by 17 · see citing works

The molecular circuitry underlying pluripotency in embryonic stem cells

Warmflash, A., Arduini, B. L., & Brivanlou, A. H. (2012) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1182 · Cited by 16 · see citing works

An agent-based model of anoikis in the colon crypt displays novel emergent behaviour consistent with biological observations

Ingham-Dempster, T., Walker, D., & Corfe, B. M. (2017) · Royal Society Open Science · doi:10.1098/rsos.160858 · Cited by 16 · see citing works

Laminin-1 promotes enteric nervous system development in mouse embryo

Nakazawa, N., Miyahara, K., Okawada, M., et al. (2013) · Pediatric Surgery International · doi:10.1007/s00383-013-3388-3 · Cited by 15 · see citing works

Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics

Herberg, M., Glauche, I., Zerjatke, T., Winzi, M., Buchholz, F., & Roeder, I. (2016) · Journal of The Royal Society Interface · doi:10.1098/rsif.2016.0167 · Cited by 15 · see citing works

Image‐based quantification and mathematical modeling of spatial heterogeneity in ESC colonies

Herberg, M., Zerjatke, T., de Back, W., et al. (2015) · Cytometry Part A · doi:10.1002/cyto.a.22598 · Cited by 14 · see citing works

Spatial and temporal dynamics of cell generations within an invasion wave: A link to cell lineage tracing

Cheeseman, B. L., Newgreen, D. F., & Landman, K. A. (2014) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.08.016 · Cited by 13 · see citing works

An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis

Wang, Z., Ramsey, B. J., Wang, D., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0166551 · Cited by 13 · see citing works

Pattern synthesis in a 3D agent-based model of stem cell differentiation

Briers, D., Haghighi, I. M., White, D., et al. (2016) · Proceedings of the IEEE Conference on Decision & Control, including the Symposium on Adaptive Processes · doi:10.1109/cdc.2016.7798907 · Cited by 10 · see citing works

A minimally sufficient model for rib proximal-distal patterning based on genetic analysis and agent-based simulations

Fogel, J. L., Lakeland, D. L., Mah, I. K., & Mariani, F. V. (2017) · eLife · doi:10.7554/elife.29144 · Cited by 10 · see citing works

Hybrid approach for parameter estimation in agent-based modelsPreprint

Gallaher, J. A., Hawkins-Daarud, A. J., Massey, S. C., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/175661 · Cited by 9 · see citing works

Stochastic clonal expansion of “superstars” enhances the reserve capacity of enteric nervous system precursor cells

Zhang, D., Osborne, J. M., Abu-Bonsrah, K. D., Cheeseman, B. L., Landman, K. A., Jurkowicz, B., & Newgreen, D. F. (2018) · Developmental Biology · doi:10.1016/j.ydbio.2018.01.020 · Cited by 6 · see citing works

Large Scale Tissue Morphogenesis Simulation on Heterogenous Systems Based on a Flexible Biomechanical Cell Model

Jeannin‐Girardon, A., Ballet, P., & Rodin, V. (2015) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2015.2418994 · Cited by 4 · see citing works

Tissue Biology: In Search of a New Paradigm

Adler, M., Chavan, A. R., & Medzhitov, R. (2023) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-113830 · Cited by 40 · see citing works

Thoroughly Calibrated Modular Agent-Based Model of the Human Cardiovascular and Renal Systems for Blood Pressure Regulation in Health and Disease

Kutumova, E., Kiselev, I., Sharipov, R., Lifshits, G., & Kolpakov, F. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.746300 · Cited by 16 · see citing works

Optimal grasping based on non-dimensionalized performance indices

Kim, B., Oh, S., Yi, B.-J., et al. (2002) · doi:10.1109/iros.2001.976291 · Cited by 60 · see citing works

Human Grasping Simulation

León, B., Morales, A., & Sancho-Bru, J. L. (2013) · Cognitive systems monographs · doi:10.1007/978-3-319-01833-1_7

Contact Point Identification by Active Sensing in Enveloping Grasp.

FUNAHASHI, Y., & Tate, M. (1995) · TRANSACTIONS OF THE JAPAN SOCIETY OF MECHANICAL ENGINEERS Series C · doi:10.1299/kikaic.61.3607

3619 Planning of Grasp/Non-Grasp Constraining of Objects by a Multifingered Robot Hand

Kotaro, O. D. A., Makita, S., & Maeda, Y. (2008) · The proceedings of the JSME annual meeting · doi:10.1299/jsmemecjo.2008.5.0_195

Non-dimensionalized performance indices based optimal grasping for multi-fingered hands

Kim, B., Yi, B.-J., Oh, S., et al. (2003) · Mechatronics · doi:10.1016/s0957-4158(03)00039-4 · Cited by 40 · see citing works