Agent-based modeling of morphogenetic systems: Advantages and challenges
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Agent-based modeling of morphogenetic systems: Advantages and challenges
Authors
Keywords
Morphogenesis, Cell differentiation, Agent-based modeling, Morphogens, Cell cycle and cell division, Pluripotency, Apoptosis, Pattern formation
Journal
PLoS Computational Biology
Volume 15, Issue 3, Pages e1006577
Publisher
Public Library of Science (PLoS)
Online
2019-03-29
DOI
10.1371/journal.pcbi.1006577
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Combining Turing and 3D vertex models reproduces autonomous multicellular morphogenesis with undulation, tubulation, and branching
- (2018) Satoru Okuda et al. Scientific Reports
- Dynamic intercellular transport modulates the spatial patterning of differentiation during early neural commitment
- (2018) Chad M. Glen et al. Nature Communications
- Bioelectric gene and reaction networks: computational modelling of genetic, biochemical and bioelectrical dynamics in pattern regulation
- (2017) Alexis Pietak et al. Journal of the Royal Society Interface
- Simple mechanical cues could explain adipose tissue morphology
- (2017) D. Peurichard et al. JOURNAL OF THEORETICAL BIOLOGY
- 3D hybrid modelling of vascular network formation
- (2017) Holger Perfahl et al. JOURNAL OF THEORETICAL BIOLOGY
- A cellular automata model of bone formation
- (2017) Gabrielle K. Van Scoy et al. MATHEMATICAL BIOSCIENCES
- Agent-based computational model of retinal angiogenesis simulates microvascular network morphology as a function of pericyte coverage
- (2017) Joseph Walpole et al. MICROCIRCULATION
- Computational models of airway branching morphogenesis
- (2017) Victor D. Varner et al. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
- Enteric nervous system development: A crest cell’s journey from neural tube to colon
- (2017) Nandor Nagy et al. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
- Four simple rules that are sufficient to generate the mammalian blastocyst
- (2017) Silas Boye Nissen et al. PLOS BIOLOGY
- A minimally sufficient model for rib proximal-distal patterning based on genetic analysis and agent-based simulations
- (2017) Jennifer L Fogel et al. eLife
- An agent-based model of anoikis in the colon crypt displays novel emergent behaviour consistent with biological observations
- (2017) Tim Ingham-Dempster et al. Royal Society Open Science
- Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics
- (2016) Maria Herberg et al. Journal of the Royal Society Interface
- Computational modeling and simulation of genital tubercle development
- (2016) Maxwell C.K. Leung et al. REPRODUCTIVE TOXICOLOGY
- High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals
- (2016) Luciano Marcon et al. eLife
- Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information
- (2016) Patrick Hillenbrand et al. PLoS One
- An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis
- (2016) Zi Wang et al. PLoS One
- Image-based quantification and mathematical modeling of spatial heterogeneity in ESC colonies
- (2015) Maria Herberg et al. CYTOMETRY PART A
- Positional information and reaction-diffusion: two big ideas in developmental biology combine
- (2015) J. B. A. Green et al. DEVELOPMENT
- Mechano-logical model ofC. elegansgerm line suggests feedback on the cell cycle
- (2015) Kathryn Atwell et al. DEVELOPMENT
- Large Scale Tissue Morphogenesis Simulation on Heterogenous Systems Based on a Flexible Biomechanical Cell Model
- (2015) Anne Jeannin-Girardon et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories
- (2015) Douglas E. White et al. Integrative Biology
- Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks
- (2015) J. Walpole et al. Integrative Biology
- Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms
- (2015) Maya Emmons-Bell et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Investigating the Turing conditions for diffusion-driven instability in the presence of a binding immobile substrate
- (2015) K. Korvasová et al. JOURNAL OF THEORETICAL BIOLOGY
- Cell traction in collective cell migration and morphogenesis: The chase and run mechanism
- (2015) András Szabó et al. Cell Adhesion & Migration
- Synergistic activity of polarised osteoblasts inside condensations cause their differentiation
- (2015) Himanshu Kaul et al. Scientific Reports
- A multiscale computational framework to understand vascular adaptation
- (2015) M. Garbey et al. Journal of Computational Science
- Towards Anatomic Scale Agent-Based Modeling with a Massively Parallel Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT_HPC)
- (2015) Robert Chase Cockrell et al. PLoS One
- Extracellular matrix: A dynamic microenvironment for stem cell niche
- (2014) Francesca Gattazzo et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- Mechanisms of endothelial cell migration
- (2014) U. Ruth Michaelis CELLULAR AND MOLECULAR LIFE SCIENCES
- Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework
- (2014) G. Tka ik et al. GENETICS
- Cell lineage tracing in the developing enteric nervous system: superstars revealed by experiment and simulation
- (2014) B. L. Cheeseman et al. Journal of the Royal Society Interface
- Spatial and temporal dynamics of cell generations within an invasion wave: A link to cell lineage tracing
- (2014) Bevan L. Cheeseman et al. JOURNAL OF THEORETICAL BIOLOGY
- Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo
- (2014) Michael Levin MOLECULAR BIOLOGY OF THE CELL
- Remodelling the extracellular matrix in development and disease
- (2014) Caroline Bonnans et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- An In Silico Agent-Based Model Demonstrates Reelin Function in Directing Lamination of Neurons during Cortical Development
- (2014) James R. Caffrey et al. PLoS One
- Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients
- (2014) J. Raspopovic et al. SCIENCE
- Quantification of Crypt and Stem Cell Evolution in the Normal and Neoplastic Human Colon
- (2014) Ann-Marie Baker et al. Cell Reports
- An interplay between extracellular signalling and the dynamics of the exit from pluripotency drives cell fate decisions in mouse ES cells
- (2014) D. A. Turner et al. Biology Open
- Enteric nervous system development: migration, differentiation, and disease
- (2013) Jonathan I. Lake et al. AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY
- Simple rules for a “simple” nervous system? Molecular and biomathematical approaches to enteric nervous system formation and malformation
- (2013) Donald F. Newgreen et al. DEVELOPMENTAL BIOLOGY
- Enteric neural crest-derived cells promote their migration by modifying their microenvironment through tenascin-C production
- (2013) Sophia E. Akbareian et al. DEVELOPMENTAL BIOLOGY
- Branching patterns emerge in a mathematical model of the dynamics of lung development
- (2013) Yina Guo et al. JOURNAL OF PHYSIOLOGY-LONDON
- A review of mathematical models for the formation of vascular networks
- (2013) M. Scianna et al. JOURNAL OF THEORETICAL BIOLOGY
- High-throughput fingerprinting of human pluripotent stem cell fate responses and lineage bias
- (2013) Emanuel J P Nazareth et al. NATURE METHODS
- Laminin-1 promotes enteric nervous system development in mouse embryo
- (2013) Nana Nakazawa et al. PEDIATRIC SURGERY INTERNATIONAL
- Kidney branching morphogenesis under the control of a ligand–receptor-based Turing mechanism
- (2013) Denis Menshykau et al. PHYSICAL BIOLOGY
- A Mechanochemical Model for Embryonic Pattern Formation: Coupling Tissue Mechanics and Morphogen Expression
- (2013) Moritz Mercker et al. PLoS One
- Adaptive agent abstractions to speed up spatial agent-based simulations
- (2013) Abbas Sarraf Shirazi et al. SIMULATION MODELLING PRACTICE AND THEORY
- Irradiation of Juvenile, but not Adult, Mammary Gland Increases Stem Cell Self-Renewal and Estrogen Receptor Negative Tumors
- (2013) Jonathan Tang et al. STEM CELLS
- A Computational Model Predicting Disruption of Blood Vessel Development
- (2013) Nicole Kleinstreuer et al. PLoS Computational Biology
- Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling
- (2013) Douglas E. White et al. PLoS Computational Biology
- On the evolution of morphogenetic models: mechano-chemical interactions and an integrated view of cell differentiation, growth, pattern formation and morphogenesis
- (2012) Séverine Urdy BIOLOGICAL REVIEWS
- Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells
- (2012) Zheng Wang et al. Cell Stem Cell
- Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour
- (2012) M. L. Wynn et al. Journal of the Royal Society Interface
- Dynamics of angiogenesis during murine retinal development: a coupled in vivo and in silico study
- (2012) M. G. Watson et al. Journal of the Royal Society Interface
- Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model
- (2012) Anja Voss-Böhme PLoS One
- Differential Diffusivity of Nodal and Lefty Underlies a Reaction-Diffusion Patterning System
- (2012) P. Muller et al. SCIENCE
- Hox Genes Regulate Digit Patterning by Controlling the Wavelength of a Turing-Type Mechanism
- (2012) R. Sheth et al. SCIENCE
- A short G1 phase is an intrinsic determinant of naïve embryonic stem cell pluripotency
- (2012) Diana Coronado et al. Stem Cell Research
- The molecular circuitry underlying pluripotency in embryonic stem cells
- (2012) Aryeh Warmflash et al. Wiley Interdisciplinary Reviews-Systems Biology and Medicine
- How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex
- (2011) Yaki Setty et al. BMC Systems Biology
- The Dynamics of Turing Patterns for Morphogen-Regulated Growing Domains with Cellular Response Delays
- (2011) S. Seirin Lee et al. BULLETIN OF MATHEMATICAL BIOLOGY
- Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers
- (2011) Matt Thomson et al. CELL
- A model of stem cell population dynamics: in silico analysis and in vivo validation
- (2011) Y. Setty et al. DEVELOPMENT
- Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling
- (2011) Jonathan Tang et al. Integrative Biology
- Early Embryonic Vascular Patterning by Matrix-Mediated Paracrine Signalling: A Mathematical Model Study
- (2011) Alvaro Köhn-Luque et al. PLoS One
- Module-based multiscale simulation of angiogenesis in skeletal muscle
- (2011) Gang Liu et al. Theoretical Biology and Medical Modelling
- Cryptic Patterning of Avian Skin Confers a Developmental Facility for Loss of Neck Feathering
- (2011) Chunyan Mou et al. PLOS BIOLOGY
- A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt
- (2011) Peter Buske et al. PLoS Computational Biology
- A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation
- (2011) Susan D. Hester et al. PLoS Computational Biology
- A computational approach to resolve cell level contributions to early glandular epithelial cancer progression
- (2010) Sean HJ Kim et al. BMC Systems Biology
- High performance cellular level agent-based simulation with FLAME for the GPU
- (2010) P. Richmond et al. BRIEFINGS IN BIOINFORMATICS
- Neural crest regionalisation for enteric nervous system formation: Implications for Hirschsprung's disease and stem cell therapy
- (2010) Dongcheng Zhang et al. DEVELOPMENTAL BIOLOGY
- Modeling Gastrulation in the Chick Embryo: Formation of the Primitive Streak
- (2010) Bakhtier Vasiev et al. PLoS One
- Sculpturing digit shape by cell death
- (2009) Juan A. Montero et al. APOPTOSIS
- Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting
- (2009) Amina A Qutub et al. BMC Systems Biology
- Multiscale modeling of cell mechanics and tissue organization
- (2009) T. Beyer et al. IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE
- Dynamic modeling of branching morphogenesis of ureteric bud in early kidney development
- (2009) Tsuyoshi Hirashima et al. JOURNAL OF THEORETICAL BIOLOGY
- Exclusion processes on a growing domain
- (2009) Benjamin J. Binder et al. JOURNAL OF THEORETICAL BIOLOGY
- A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells
- (2009) Hitoshi Niwa et al. NATURE
- The Extracellular Matrix: Not Just Pretty Fibrils
- (2009) R. O. Hynes SCIENCE
- A Computational Study of the Development of Epithelial Acini: I. Sufficient Conditions for the Formation of a Hollow Structure
- (2008) Katarzyna A. Rejniak et al. BULLETIN OF MATHEMATICAL BIOLOGY
- Multi-species simple exclusion processes
- (2008) Matthew J. Simpson et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Four-dimensional realistic modeling of pancreatic organogenesis
- (2008) Y. Setty et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A mechanism for inside-out lamination in the neocortex
- (2008) Jonathan A. Cooper TRENDS IN NEUROSCIENCES
- Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth
- (2008) Roeland M. H. Merks et al. PLoS Computational Biology
- Agent-based simulation of notch-mediated tip cell selection in angiogenic sprout initialisation
- (2007) Katie Bentley et al. JOURNAL OF THEORETICAL BIOLOGY
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation