Agent-based modeling of morphogenetic systems: Advantages and challenges
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[1] D. Gavaghan,et al. Mechano-logical model of C. elegans germ line suggests feedback on the cell cycle , 2015, Development.
[2] Santiago Schnell,et al. Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour , 2012, Journal of The Royal Society Interface.
[3] Vincent Rodin,et al. Large Scale Tissue Morphogenesis Simulation on Heterogenous Systems Based on a Flexible Biomechanical Cell Model , 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[4] Alexander G. Fletcher,et al. Quantification of Crypt and Stem Cell Evolution in the Normal and Neoplastic Human Colon , 2014, Cell reports.
[5] Gary An,et al. Towards Anatomic Scale Agent-Based Modeling with a Massively Parallel Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT_HPC) , 2015, PloS one.
[6] Hitoshi Niwa,et al. A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells , 2009, Nature.
[7] Gašper Tkačik,et al. Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information , 2016, PloS one.
[8] J. Schwarzbauer,et al. Fibronectin matrix composition and organization can regulate cell migration during amphibian development , 2000, Mechanisms of Development.
[9] L Preziosi,et al. A review of mathematical models for the formation of vascular networks. , 2013, Journal of theoretical biology.
[10] R. Solé,et al. Gene networks capable of pattern formation: from induction to reaction-diffusion. , 2000, Journal of theoretical biology.
[11] D'arcy W. Thompson,et al. On Growth and Form , 1917, Nature.
[12] P. Bonaldo,et al. Extracellular matrix: A dynamic microenvironment for stem cell niche , 2014, Biochimica et biophysica acta.
[13] Matthew J. Simpson,et al. Multi-species simple exclusion processes , 2009 .
[14] Bevan L. Cheeseman,et al. Cell lineage tracing in the developing enteric nervous system: superstars revealed by experiment and simulation , 2014, Journal of The Royal Society Interface.
[15] Kerry A Landman,et al. Neural crest regionalisation for enteric nervous system formation: implications for Hirschsprung's disease and stem cell therapy. , 2010, Developmental biology.
[16] Michael Levin,et al. Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo , 2014, Molecular biology of the cell.
[17] Lewis Wolpert,et al. Chapter 6 Positional Information and Pattern Formation , 1971 .
[18] Philip K Maini,et al. Periodic pattern formation in reaction—diffusion systems: An introduction for numerical simulation , 2004, Anatomical science international.
[19] Mitsuru Nenoi,et al. Regulation of , 2004 .
[20] Chad M Glen,et al. Dynamic intercellular transport modulates the spatial patterning of differentiation during early neural commitment , 2018, Nature Communications.
[21] A. Anderson,et al. A Computational Study of the Development of Epithelial Acini: I. Sufficient Conditions for the Formation of a Hollow Structure , 2008, Bulletin of mathematical biology.
[22] Jamie Schwendinger-Schreck,et al. A First Course in Systems Biology , 2012, The Yale Journal of Biology and Medicine.
[23] Timothy Davison,et al. Adaptive agent abstractions to speed up spatial agent-based simulations , 2014, Simul. Model. Pract. Theory.
[24] Roeland M. H. Merks,et al. Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling. , 2006, Developmental biology.
[25] James Sharpe,et al. High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals , 2016, eLife.
[26] Dragana Rogulja,et al. Regulation of Cell Proliferation by a Morphogen Gradient , 2005, Cell.
[27] J. L. Jackson,et al. Dissipative structure: an explanation and an ecological example. , 1972, Journal of theoretical biology.
[28] Roeland M. H. Merks,et al. Dynamic mechanisms of blood vessel growth , 2006, Nonlinearity.
[29] Shayn M Peirce,et al. Agent‐based computational model of retinal angiogenesis simulates microvascular network morphology as a function of pericyte coverage , 2017, Microcirculation.
[30] E. Robertson,et al. Derivation and maintenance of embryonic stem cell cultures. , 1997, Methods in molecular biology.
[31] Arnold R Kriegstein,et al. Patterns of neuronal migration in the embryonic cortex , 2004, Trends in Neurosciences.
[32] James Briscoe,et al. The interpretation of morphogen gradients , 2006, Development.
[33] Kerry A Landman,et al. Exclusion processes on a growing domain. , 2009, Journal of theoretical biology.
[34] M. Bedau. Emergent Models of Supple Dynamics in Life and Mind , 1997, Brain and Cognition.
[35] Calin Belta,et al. A Formal Methods Approach to Pattern Recognition and Synthesis in Reaction Diffusion Networks , 2018, IEEE Transactions on Control of Network Systems.
[36] Matt Thomson,et al. Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers , 2011, Cell.
[37] Jason A. Papin,et al. Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior , 2007, BMC Systems Biology.
[38] Manabu Okawada,et al. Laminin-1 promotes enteric nervous system development in mouse embryo , 2013, Pediatric Surgery International.
[39] Jeffrey D. Axelrod,et al. Fidelity in planar cell polarity signalling , 2003, Nature.
[40] T. Beyer,et al. Multiscale modeling of cell mechanics and tissue organization , 2009, IEEE Engineering in Medicine and Biology Magazine.
[41] Roeland M. H. Merks,et al. Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth , 2005, PLoS Comput. Biol..
[42] Seonhee Kim,et al. Impaired Neuronal Positioning and Dendritogenesis in the Neocortex after Cell-Autonomous Dab1 Suppression , 2006, The Journal of Neuroscience.
[43] Aleksander S Popel,et al. Module-based multiscale simulation of angiogenesis in skeletal muscle , 2011, Theoretical Biology and Medical Modelling.
[44] V S Caviness,et al. Patterns of cell and fiber distribution in the neocortex of the reeler mutant mouse , 1976, The Journal of comparative neurology.
[45] T J Poole,et al. 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 , 1984, The Journal of cell biology.
[46] Megan Kearl. "The Potency of the First Two Cleavage Cells in Echinoderm Development. Experimental Production of Partial and Double Formations" (1891-1892), by Hans Driesch , 2012 .
[47] Hillel Kugler,et al. Development and Stem Cells Research Article , 2022 .
[48] Anna Marciniak-Czochra,et al. A Mechanochemical Model for Embryonic Pattern Formation: Coupling Tissue Mechanics and Morphogen Expression , 2013, PloS one.
[49] Holger Gerhardt,et al. Agent-based simulation of notch-mediated tip cell selection in angiogenic sprout initialisation. , 2008, Journal of theoretical biology.
[50] Lewis Wolpert,et al. Principles of Development , 1997 .
[51] Kevin J. Painter,et al. Cryptic Patterning of Avian Skin Confers a Developmental Facility for Loss of Neck Feathering , 2011, PLoS biology.
[52] L. Wolpert. Positional information and the spatial pattern of cellular differentiation. , 1969, Journal of theoretical biology.
[53] Jonathan A. Cooper. A mechanism for inside-out lamination in the neocortex , 2008, Trends in Neurosciences.
[54] S. Urdy,et al. On the evolution of morphogenetic models: mechano‐chemical interactions and an integrated view of cell differentiation, growth, pattern formation and morphogenesis , 2012, Biological reviews of the Cambridge Philosophical Society.
[55] Sylvain V Costes,et al. Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling. , 2011, Integrative biology : quantitative biosciences from nano to macro.
[56] Z. Werb,et al. Remodelling the extracellular matrix in development and disease , 2014, Nature Reviews Molecular Cell Biology.
[57] Kwai Wong,et al. An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis , 2016, PloS one.
[58] Flavio Keller,et al. Reelin Is a Serine Protease of the Extracellular Matrix* , 2002, The Journal of Biological Chemistry.
[59] J. Thomson,et al. Embryonic stem cell lines derived from human blastocysts. , 1998, Science.
[60] Richard O. Hynes,et al. The Extracellular Matrix: Not Just Pretty Fibrils , 2009, Science.
[61] Jane M. Oppenheimer. The Potency of the First Two Cleavage Cells in Echinoderm Development . Experimental Production of Partial and Double Formations " ( 1891-1892 ) , by Hans Driesch , 2017 .
[62] David Harel,et al. Four-dimensional realistic modeling of pancreatic organogenesis , 2008, Proceedings of the National Academy of Sciences.
[63] P. Degond,et al. Simple mechanical cues could explain adipose tissue morphology. , 2017, Journal of theoretical biology.
[64] Yoshihiro Morishita,et al. Dynamic modeling of branching morphogenesis of ureteric bud in early kidney development. , 2009, Journal of theoretical biology.
[65] Melissa L Kemp,et al. Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories. , 2015, Integrative biology : quantitative biosciences from nano to macro.
[66] H. Schöler,et al. Formation of Pluripotent Stem Cells in the Mammalian Embryo Depends on the POU Transcription Factor Oct4 , 1998, Cell.
[67] Matthew J Simpson,et al. Cell proliferation drives neural crest cell invasion of the intestine. , 2007, Developmental biology.
[68] Ingo Roeder,et al. Image‐based quantification and mathematical modeling of spatial heterogeneity in ESC colonies , 2015, Cytometry. Part A : the journal of the International Society for Analytical Cytology.
[69] Thomas B Knudsen,et al. Computational modeling and simulation of genital tubercle development. , 2016, Reproductive toxicology.
[70] David Dix,et al. A Computational Model Predicting Disruption of Blood Vessel Development , 2013, PLoS Comput. Biol..
[71] Dagmar Iber,et al. Kidney branching morphogenesis under the control of a ligand–receptor-based Turing mechanism , 2013, Physical biology.
[72] P K Maini,et al. Investigating the Turing conditions for diffusion-driven instability in the presence of a binding immobile substrate. , 2015, Journal of theoretical biology.
[73] Peter W. Zandstra,et al. High-throughput fingerprinting of human pluripotent stem cell factor responsiveness and lineage induction bias , 2013, Nature Methods.
[74] J. Montero,et al. Sculpturing digit shape by cell death , 2010, Apoptosis.
[75] J. Visvader,et al. Mammary stem cells and mammopoiesis. , 2006, Cancer research.
[76] J. W. Saunders,et al. Ectodermal-mesodermal interactions in the growth of limb buds in the chick embryo: constancy and temporal limits of the ectodermal induction. , 1972, Developmental biology.
[77] H. Meinhardt,et al. A theory of biological pattern formation , 1972, Kybernetik.
[78] Stephen Emmott,et al. How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex , 2011, BMC Systems Biology.
[79] Daniela M. Romano,et al. High performance cellular level agent-based simulation with FLAME for the GPU , 2010, Briefings Bioinform..
[80] Calin Belta,et al. Pattern synthesis in a 3D agent-based model of stem cell differentiation , 2016, 2016 IEEE 55th Conference on Decision and Control (CDC).
[81] Eric Bonabeau,et al. From Classical Models of Morphogenesis to Agent-Based Models of Pattern Formation , 1997, Artificial Life.
[82] Aleksander S. Popel,et al. Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting , 2009, BMC Systems Biology.
[83] R. Lovell-Badge,et al. Multipotent cell lineages in early mouse development depend on SOX2 function. , 2003, Genes & development.
[84] Erik Holmberg,et al. Radiation Effects on Breast Cancer Risk: A Pooled Analysis of Eight Cohorts , 2002, Radiation research.
[85] Andreas Deutsch,et al. Early Embryonic Vascular Patterning by Matrix-Mediated Paracrine Signalling: A Mathematical Model Study , 2011, PloS one.
[86] András Szabó,et al. Cell traction in collective cell migration and morphogenesis: The chase and run mechanism , 2015, Cell adhesion & migration.
[87] Philip K Maini,et al. 3D hybrid modelling of vascular network formation. , 2016, Journal of theoretical biology.
[88] J. Nichols,et al. Differentiation inhibiting activity (DIA/LIF) and mouse development. , 1992, Developmental biology.
[89] A. Goldstein,et al. Enteric nervous system development: A crest cell's journey from neural tube to colon. , 2017, Seminars in cell & developmental biology.
[90] D'arcy W. Thompson. On growth and form i , 1943 .
[91] A. Voss-Böhme. Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model , 2012, PloS one.
[92] James A. Glazier,et al. Modeling Gastrulation in the Chick Embryo: Formation of the Primitive Streak , 2010, PloS one.
[93] Kerry A Landman,et al. Spatial and temporal dynamics of cell generations within an invasion wave: a link to cell lineage tracing. , 2014, Journal of theoretical biology.
[94] H. Meinhardt,et al. Applications of a theory of biological pattern formation based on lateral inhibition. , 1974, Journal of cell science.
[95] Helen M Byrne,et al. Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis , 2017, Journal of Mathematical Biology.
[96] W. Carter,et al. Mechanism of fibronectin-mediated cell migration: dependence or independence of cell migration susceptibility on RGDS-directed receptor (integrin). , 1989, Experimental cell research.
[97] J. Holland,et al. Artificial Adaptive Agents in Economic Theory , 1991 .
[98] A. Goffinet,et al. Neuronal migration , 2001, Mechanisms of Development.
[99] D. SUMMERBELL,et al. Positional Information in Chick Limb Morphogenesis , 1973, Nature.
[100] Marc Garbey,et al. A multiscale computational framework to understand vascular adaptation , 2015, J. Comput. Sci..
[101] James Sharpe,et al. Rushikesh Sheth of a Turing-Type Mechanism Genes Regulate Digit Patterning by Controlling the Wavelength Hox , 2012 .
[102] James A. Glazier,et al. A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation , 2011, PLoS Comput. Biol..
[103] Marnie M Saunders,et al. A cellular automata model of bone formation. , 2017, Mathematical biosciences.
[104] Peter A Lawrence,et al. Cell interactions and planar polarity in the abdominal epidermis of Drosophila , 2004, Development.
[105] Bernard M. Corfe,et al. An agent-based model of anoikis in the colon crypt displays novel emergent behaviour consistent with biological observations , 2017, Royal Society Open Science.
[106] Barry D. Hughes,et al. An In Silico Agent-Based Model Demonstrates Reelin Function in Directing Lamination of Neurons during Cortical Development , 2014, PloS one.
[107] J. Sharpe,et al. Positional information and reaction-diffusion: two big ideas in developmental biology combine , 2015, Development.
[108] S A Newman,et al. On multiscale approaches to three-dimensional modelling of morphogenesis , 2005, Journal of The Royal Society Interface.
[109] R. Heuckeroth,et al. Enteric nervous system development: migration, differentiation, and disease , 2013, American journal of physiology. Gastrointestinal and liver physiology.
[110] Marielle Afanassieff,et al. A short G1 phase is an intrinsic determinant of naïve embryonic stem cell pluripotency. , 2013, Stem cell research.
[111] M. Murakami,et al. The Homeoprotein Nanog Is Required for Maintenance of Pluripotency in Mouse Epiblast and ES Cells , 2003, Cell.
[112] G. Martin,et al. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[113] Yiannis Ventikos,et al. Synergistic activity of polarised osteoblasts inside condensations cause their differentiation , 2015, Scientific Reports.
[114] Alexander R. A. Anderson,et al. Hybrid approach for parameter estimation in agent-based models , 2017, bioRxiv.
[115] Tetsuya Tabata,et al. Morphogens, their identification and regulation , 2004, Development.
[116] Kim Sneppen,et al. Four simple rules that are sufficient to generate the mammalian blastocyst , 2017, PLoS biology.
[117] J Walpole,et al. Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks. , 2015, Integrative biology : quantitative biosciences from nano to macro.
[118] Hans Clevers,et al. A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt , 2011, PLoS Comput. Biol..
[119] M. Kaufman,et al. Establishment in culture of pluripotential cells from mouse embryos , 1981, Nature.
[120] M A J Chaplain,et al. Dynamics of angiogenesis during murine retinal development: a coupled in vivo and in silico study , 2012, Journal of The Royal Society Interface.
[121] Philip K Maini,et al. Mixed-mode pattern in Doublefoot mutant mouse limb--Turing reaction-diffusion model on a growing domain during limb development. , 2006, Journal of theoretical biology.
[122] Megan F. Cole,et al. Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells , 2005, Cell.
[123] S. Seirin Lee,et al. The Dynamics of Turing Patterns for Morphogen-Regulated Growing Domains with Cellular Response Delays , 2011, Bulletin of mathematical biology.
[124] Kerry A Landman,et al. Stochastic clonal expansion of "superstars" enhances the reserve capacity of enteric nervous system precursor cells. , 2018, Developmental biology.
[125] U. R. Michaelis,et al. Mechanisms of endothelial cell migration , 2014, Cellular and Molecular Life Sciences.
[126] A. M. Turing,et al. The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.
[127] C. Anthony Hunt,et al. Simulating Properties of In Vitro Epithelial Cell Morphogenesis , 2006, PLoS Comput. Biol..
[128] H. Clevers,et al. Identification of stem cells in small intestine and colon by marker gene Lgr5 , 2007, Nature.
[129] Sunwoo Park,et al. A computational approach to resolve cell level contributions to early glandular epithelial cancer progression , 2009, BMC Systems Biology.
[130] Julien O. Dubuis,et al. Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework , 2014, Genetics.
[131] Sylvain V Costes,et al. Irradiation of Juvenile, but not Adult, Mammary Gland Increases Stem Cell Self‐Renewal and Estrogen Receptor Negative Tumors , 2014, Stem cells.
[132] Xingjuan Zeng,et al. Branching patterns emerge in a mathematical model of the dynamics of lung development , 2014, The Journal of physiology.
[133] Fallon Durant,et al. Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms , 2015, International journal of molecular sciences.
[134] Taiji Adachi,et al. Combining Turing and 3D vertex models reproduces autonomous multicellular morphogenesis with undulation, tubulation, and branching , 2018, Scientific Reports.
[135] Brigitte L. Arduini,et al. The molecular circuitry underlying pluripotency in embryonic stem cells , 2012, Wiley interdisciplinary reviews. Systems biology and medicine.
[136] K. Mikoshiba,et al. Reelin Is a Secreted Glycoprotein Recognized by the CR-50 Monoclonal Antibody , 1997, The Journal of Neuroscience.
[137] David Molnar,et al. Enteric neural crest-derived cells promote their migration by modifying their microenvironment through tenascin-C production. , 2013, Developmental biology.
[138] J Raspopovic,et al. Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients , 2014, Science.
[139] T. Curran,et al. Role of the reelin signaling pathway in central nervous system development. , 2001, Annual review of neuroscience.
[140] Ana Rolo,et al. Biomechanical coupling facilitates spinal neural tube closure in mouse embryos , 2017, Proceedings of the National Academy of Sciences.
[141] D. Axelrod,et al. A calibrated agent-based computer model of stochastic cell dynamics in normal human colon crypts useful for in silico experiments , 2013, Theoretical Biology and Medical Modelling.
[142] Todd C. McDevitt,et al. Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling , 2013, PLoS Comput. Biol..
[143] Michael Levin,et al. Bioelectric gene and reaction networks: computational modelling of genetic, biochemical and bioelectrical dynamics in pattern regulation , 2017, Journal of The Royal Society Interface.
[144] Drew N. Robson,et al. Supplementary Materials for Differential Diffusivity of Nodal and Lefty Underlies a Reaction-Diffusion Patterning System , 2012 .
[145] Jesús A. Izaguirre,et al. COMPUCELL, a multi-model framework for simulation of morphogenesis , 2004, Bioinform..
[146] Kerry A Landman,et al. Simple rules for a "simple" nervous system? Molecular and biomathematical approaches to enteric nervous system formation and malformation. , 2013, Developmental biology.
[147] In Kyoung Mah,et al. A minimally sufficient model for rib proximal-distal patterning based on genetic analysis and agent-based simulations , 2017, bioRxiv.
[148] A. Handyside,et al. Cell division and death in the mouse blastocyst before implantation , 1986, Roux's archives of developmental biology.
[149] J. Schnakenberg,et al. Simple chemical reaction systems with limit cycle behaviour. , 1979, Journal of theoretical biology.
[150] Ingo Roeder,et al. Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics , 2016, Journal of The Royal Society Interface.
[151] Victor D. Varner,et al. Computational models of airway branching morphogenesis. , 2017, Seminars in cell & developmental biology.
[152] E. Robertson,et al. Derivation and maintenance of embryonic stem cell cultures. , 1990, Methods in molecular biology.
[153] Natalia B. Ivanova,et al. Distinct lineage specification roles for NANOG, OCT4, and SOX2 in human embryonic stem cells. , 2012, Cell stem cell.
[154] W. Bialek,et al. Probing the Limits to Positional Information , 2007, Cell.
[155] A. M. Arias,et al. An interplay between extracellular signalling and the dynamics of the exit from pluripotency drives cell fate decisions in mouse ES cells , 2014, Biology Open.
[156] John E. Pearson,et al. Pattern formation in a (2 + 1)-species activator-inhibitor-immobilizer system , 1992 .