Mathematical Models of Organoid Cultures

ya||a: GPU-Powered Spheroid Models for Mesenchyme and Epithelium

(2019) Philipp Germann et al.   Cell Systems

Organoids as a new model for improving regenerative medicine and cancer personalized therapy in renal diseases

(2019) Ludovica Grassi et al.   Cell Death & Disease

Cancer modeling meets human organoid technology

(2019) David Tuveson et al.   SCIENCE

Tumor Evolution and Drug Response in Patient-Derived Organoid Models of Bladder Cancer

(2018) Suk Hyung Lee et al.   CELL

Linking stem cell function and growth pattern of intestinal organoids

(2018) Torsten Thalheim et al.   DEVELOPMENTAL BIOLOGY

Towards personalized computational oncology: from spatial models of tumour spheroids, to organoids, to tissues

(2018) Aleksandra Karolak et al.   Journal of the Royal Society Interface

Patient-derived organoids model treatment response of metastatic gastrointestinal cancers

(2018) Georgios Vlachogiannis et al.   SCIENCE

Patient-derived tumor organoids for prediction of cancer treatment response

(2018) Peter W. Nagle et al.   SEMINARS IN CANCER BIOLOGY

Morphological alterations of cultured human colorectal matched tumour and healthy organoids

(2018) Seyed Mohammad Hossein Kashfi et al.   Oncotarget

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

(2018) Satoru Okuda et al.   Scientific Reports

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems

(2018) Ahmadreza Ghaffarizadeh et al.   PLoS Computational Biology

Translational potential of human brain organoids

(2018) Alfred X. Sun et al.   Annals of Clinical and Translational Neurology

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling

(2018) Gaelle Letort et al.   BIOINFORMATICS

Millifluidic culture improves human midbrain organoid vitality and differentiation

(2018) Emanuel Berger et al.   LAB ON A CHIP

Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

(2018) Leonardo Beccari et al.   NATURE

Strain-triggered mechanical feedback in self-organizing optic-cup morphogenesis

(2018) S. Okuda et al.   Science Advances

Intestinal Organoids

(2017) Thomas E. Wallach et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Human primary liver cancer–derived organoid cultures for disease modeling and drug screening

(2017) Laura Broutier et al.   NATURE MEDICINE

BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance

(2017) Alexandra A Duarte et al.   NATURE METHODS

Modeling Physiological Events in 2D vs. 3D Cell Culture

(2017) Kayla Duval et al.   PHYSIOLOGY

On the adhesion-cohesion balance and oxygen consumption characteristics of liver organoids

(2017) Giorgio Mattei et al.   PLoS One

Derivation of Human Midbrain-Specific Organoids from Neuroepithelial Stem Cells

(2017) Anna S. Monzel et al.   Stem Cell Reports

A Three-Dimensional Organoid Culture System Derived from Human Glioblastomas Recapitulates the Hypoxic Gradients and Cancer Stem Cell Heterogeneity of Tumors Found In Vivo

(2016) Christopher G. Hubert et al.   CANCER RESEARCH

Engineering Stem Cell Organoids

(2016) Xiaolei Yin et al.   Cell Stem Cell

Emergence of dorsal-ventral polarity in ESC-derived retinal tissue

(2016) Yuiko Hasegawa et al.   DEVELOPMENT

A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization

(2016) Fred Etoc et al.   DEVELOPMENTAL CELL

Analytic Models of Oxygen and Nutrient Diffusion, Metabolism Dynamics, and Architecture Optimization in Three-Dimensional Tissue Constructs with Applications and Insights in Cerebral Organoids

(2016) Richard J. McMurtrey   TISSUE ENGINEERING PART C-METHODS

Paneth Cell-Rich Regions Separated by a Cluster of Lgr5+ Cells Initiate Crypt Fission in the Intestinal Stem Cell Niche

(2016) Alistair J. Langlands et al.   PLOS BIOLOGY

Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model

(2015) Miquel Marin-Riera et al.   BIOINFORMATICS

Modeling cell apoptosis for simulating three-dimensional multicellular morphogenesis based on a reversible network reconnection framework

(2015) Satoru Okuda et al.   Biomechanics and Modeling in Mechanobiology

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

Organoid Models of Human and Mouse Ductal Pancreatic Cancer

(2015) Sylvia F. Boj et al.   CELL

An individual based computational model of intestinal crypt fission and its application to predicting unrestrictive growth of the intestinal epithelium

(2015) Carmen Pin et al.   Integrative Biology

Organoid Cultures Derived from Patients with Advanced Prostate Cancer

(2014) Dong Gao et al.   CELL

Symmetry breaking, germ layer specification and axial organisation in aggregates of mouse embryonic stem cells

(2014) S. C. van den Brink et al.   DEVELOPMENT

A method to recapitulate early embryonic spatial patterning in human embryonic stem cells

(2014) Aryeh Warmflash et al.   NATURE METHODS

Three-dimensional organotypic culture: experimental models of mammalian biology and disease

(2014) Eliah R. Shamir et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Organogenesis in a dish: Modeling development and disease using organoid technologies

(2014) M. A. Lancaster et al.   SCIENCE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Chaste: An Open Source C++ Library for Computational Physiology and Biology

(2013) Gary R. Mirams et al.   PLoS Computational Biology

Acute and Fractionated Irradiation Differentially Modulate Glioma Stem Cell Division Kinetics

(2012) X. Gao et al.   CANCER RESEARCH

Self-formation of layered neural structures in three-dimensional culture of ES cells

(2012) Mototsugu Eiraku et al.   CURRENT OPINION IN NEUROBIOLOGY

In vitro recapitulation of neural development using embryonic stem cells: From neurogenesis to histogenesis

(2012) Keiko Muguruma et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

On the biomechanics of stem cell niche formation in the gut - modelling growing organoids

(2012) Peter Buske et al.   FEBS Journal

Multispecies model of cell lineages and feedback control in solid tumors

(2012) H. Youssefpour et al.   JOURNAL OF THEORETICAL BIOLOGY

Modeling human cortical development in vitro using induced pluripotent stem cells

(2012) J. Mariani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath

(2012) Sara-Jane Dunn et al.   PLoS Computational Biology

Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

Subregional Specification of Embryonic Stem Cell-Derived Ventral Telencephalic Tissues by Timed and Combinatory Treatment with Extrinsic Signals

(2011) T. Danjo et al.   JOURNAL OF NEUROSCIENCE

Self-organizing optic-cup morphogenesis in three-dimensional culture

(2011) Mototsugu Eiraku et al.   NATURE

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 cell-based simulation software for multi-cellular systems

(2010) Stefan Hoehme et al.   BIOINFORMATICS

Ontogeny-recapitulating generation and tissue integration of ES cell–derived Purkinje cells

(2010) Keiko Muguruma et al.   NATURE NEUROSCIENCE

Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation

(2010) S. Kondo et al.   SCIENCE

Chaste: A test-driven approach to software development for biological modelling

(2009) Joe Pitt-Francis et al.   COMPUTER PHYSICS COMMUNICATIONS

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

Are animal models predictive for humans?

(2009) Niall Shanks et al.   Philosophy Ethics and Humanities in Medicine

Self-Organized Formation of Polarized Cortical Tissues from ESCs and Its Active Manipulation by Extrinsic Signals

(2008) Mototsugu Eiraku et al.   Cell Stem Cell

Thoughts on limitations of animal models

(2008) Thomas Hartung   PARKINSONISM & RELATED DISORDERS