Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mulberry2020 - Two-layered, self-organizing multicellular structure where all cells are of the same genotype

ABSTRACT: This model generates a two-layered, multicellular structure from a simple cell-cell signaling model. The cell signaling model is described by a system of ordinary differential equations, and is coupled with a cellular potts model. The model is in the MorpheusML format (https://morpheus.gitlab.io). The model will initialize with a random configuration of cells (which are all of the same type) which will then self-organize to form a two-layered structure. This file was used to produce Figure 10 in Mulberry and Keshet, 2020.

SUBMITTER: Nicola Mulberry

PROVIDER: MODEL2009210001 | biostudies-other |

SECONDARY ACCESSION(S): 10.1088/1478-3975/abb2dc

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Mulberry2020 - Two-layered, self-organizing multicellular structure where all cells are one of the two genotypes

Project description: Not available

| MODEL2009210003 | biostudies-other

Mulberry2020 - Two-layered, self-organizing multicellular structure where all cells are of the same genotype

Project description:This model generates a two-layered, multicellular structure from a simple cell-cell signaling model. The cell signaling model is described by a system of ordinary differential equations, and is coupled with a cellular potts model. The model is in the MorpheusML format (https://morpheus.gitlab.io). The model will initialize with a random configuration of cells (which are all of the same type) which will then self-organize to form a two-layered structure. This file was used to produce Figure 10 in Mulberry and Keshet, 2020.

2021-10-14 | MODEL2009210001 | BioModels

Mulberry2020 - Three-layered, self-organizing multicellular structure where all cells randomly belong to one of the two genotypes

Project description: Not available

| MODEL2009210002 | biostudies-other

Programming self-organizing multicellular structures with synthetic cell-cell signaling.

Project description: Not available

| S-EPMC6492944 | biostudies-literature

Mulberry2020 - Two-layered, self-organizing multicellular structure where all cells are one of the two genotypes

Project description:This model generates a two-layered, multicellular structure from a simple cell-cell signaling model. The cell signaling model is described by a system of ordinary differential equations, and is coupled with a cellular potts model. The model is in the MorpheusML format (https://morpheus.gitlab.io). The model will initialize with a random configuration of cells (which can be one of two types) which will then self-organize to form a two-layered structure. This file was used to produce Figure 2 in Mulberry and Keshet, 2020.

2021-10-14 | MODEL2009210003 | BioModels

Neocortical temporal patterning by a two-layered regulatory structure

Project description:In the developing neocortex, a diverse array of neurons with defined types and abundances are systematically generated by a limited population of radial glial progenitors (RGPs) as they undergo successive fate changes. How this temporal patterning is regulated at the molecular level remains largely unknown. Here we present an in-depth single-cell multi-omics assay for deep characterization of regulatory programs, along with an analytical framework that integrates joint dynamics in single-cell transcription and chromatin structure to interrogate the regulation of temporal identities and fate progression of RGPs. We found that RGP temporal patterning is governed by a two-layered regulatory structure consisting of global regulators acting upon a cascade of transcription factor (TF) hubs. This cascade proceeds not by confining cascaded TF expression to specific temporal windows, but through synergistic transcriptional and epigenetic dynamics that temporally modulate TF regulatory activity. Furthermore, global regulators exhibit a progressively increasing expression pattern, and our computational modeling analysis found that the gradient of this pattern specifies the duration of each cascading stage and, subsequently, the abundance of specific progeny output. Together, this two-layered regulatory structure offers a mechanistic control of temporal patterning and emphasizes the importance of global regulators in managing temporal programs.

2025-05-23 | GSE204701 | GEO

Missing genotype imputation in non-model species using self-organizing maps.

Project description: Not available

| S-EPMC11887599 | biostudies-literature

Mulberry2020 - Three-layered, self-organizing multicellular structure where all cells randomly belong to one of the two genotypes

Project description:This model generates a three-layered, multicellular structure from a simple cell-cell signaling model. The cell signaling model is described by a system of ordinary differential equations, and is coupled with a cellular potts model. The model is in the MorpheusML format (https://morpheus.gitlab.io). The model will initialize with a random configuration of cells (which can be one of two types) which will then self-organize to form a three-layered structure. This file was used to produce Figure 7 in Mulberry and Keshet, 2020.

2021-10-14 | MODEL2009210002 | BioModels

The same primary structure of the prion protein yields two distinct self-propagating states.

Project description: Not available

| S-EPMC2414308 | biostudies-literature

A 3D self-organizing multicellular epidermis model of barrier formation and hydration with realistic cell morphology based on EPISIM.

Project description: Not available

| S-EPMC5338006 | biostudies-literature