A Stochastic Model of Epigenetic Dynamics in Somatic Cell Reprogramming (Q42216168)

18 October 2017

A stochastic model of epigenetic dynamics in somatic cell reprogramming (English)

1 reference

18 October 2017

A Stochastic Model of Epigenetic Dynamics in Somatic Cell Reprogramming (English)

1 reference

Crossref

DOI

10.3389/FPHYS.2012.00216

https://api.crossref.org/works/10.3389/FPHYS.2012.00216

5 January 2025

main subject

mathematical modelling

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:22754535

5 January 2025

epigenetic landscape

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:22754535

5 January 2025

3

Edda Klipp

0 references

author name string

Max Flöttmann

series ordinal

1

1 reference

18 October 2017

Till Scharp

series ordinal

2

1 reference

18 October 2017

language of work or name

English

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=22754535

5 January 2025

publication date

27 June 2012

1 reference

full work available at URL

18 October 2017

https://www.frontiersin.org/articles/10.3389/fphys.2012.00216/pdf

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:22754535

https://europepmc.org/articles/PMC3384084

5 January 2025

file format

HyperText Markup Language

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:22754535

https://europepmc.org/articles/PMC3384084?pdf=render

5 January 2025

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:22754535

5 January 2025

published in

Frontiers in Physiology

1 reference

18 October 2017

3

1 reference

18 October 2017

216

1 reference

Systematic search for recipes to generate induced pluripotent stem cells

18 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

DNA Demethylation Dynamics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Stem cells and reprogramming: breaking the epigenetic barrier?

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

A deterministic map of Waddington's epigenetic landscape for cell fate specification

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Epigenetics of induced pluripotency, the seven-headed dragon

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

A model for genetic and epigenetic regulatory networks identifies rare pathways for transcription factor induced pluripotency

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

CpG islands influence chromatin structure via the CpG-binding protein Cfp1.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Dynamic changes in the human methylome during differentiation

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Direct conversion of fibroblasts to functional neurons by defined factors

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Direct cell reprogramming is a stochastic process amenable to acceleration

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Human DNA methylomes at base resolution show widespread epigenomic differences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

A small-molecule inhibitor of tgf-Beta signaling replaces sox2 in reprogramming by inducing nanog

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Suppression of induced pluripotent stem cell generation by the p53-p21 pathway

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Linking the p53 tumour suppressor pathway to somatic cell reprogramming

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Generation of induced pluripotent stem cells using recombinant proteins

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Stem cell decision making and critical-like exploratory networks.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Linking DNA methylation and histone modification: patterns and paradigms

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

A computational model for understanding stem cell, trophectoderm and endoderm lineage determination

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Generation of mouse induced pluripotent stem cells without viral vectors

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Retroviral vector silencing during iPS cell induction: an epigenetic beacon that signals distinct pluripotent states

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Stochasticity and the molecular mechanisms of induced pluripotency

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Dissecting direct reprogramming through integrative genomic analysis

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Induction of pluripotent stem cells from adult human fibroblasts by defined factors

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

A gene regulatory network in mouse embryonic stem cells

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Characterization of human embryonic stem cell lines by the International Stem Cell Initiative

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Theoretical analysis of epigenetic cell memory by nucleosome modification.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Bifurcation dynamics in lineage-commitment in bipotent progenitor cells

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

How is pluripotency determined and maintained?

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Transcriptional dynamics of the embryonic stem cell switch

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Dissecting self-renewal in stem cells with RNA interference

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Core transcriptional regulatory circuitry in human embryonic stem cells

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Genetic regulation of stem cell origins in the mouse embryo.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Potential autoregulation of transcription factor PU.1 by an upstream regulatory element

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

A proposal for using the ensemble approach to understand genetic regulatory networks

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Demethylating agent, 5-azacytidine, reverses differentiation of embryonic stem cells

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Nuclear compartmentalization and gene activity

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Retrovirus vector silencing is de novo methylase independent and marked by a repressive histone code

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

DNA methyltransferase Dnmt1 associates with histone deacetylase activity

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

A GATA box in the GATA-1 gene hematopoietic enhancer is a critical element in the network of GATA factors and sites that regulate this gene

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Direct interaction of hematopoietic transcription factors PU.1 and GATA-1: functional antagonism in erythroid cells

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Targeted mutation of the DNA methyltransferase gene results in embryonic lethality

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

A Cyclic AMP Analog, 8-Br-cAMP, Enhances the Induction of Pluripotency in Human Fibroblast Cells

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Mathematical modelling of stem cell differentiation: the PU.1-GATA-1 interaction

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Modeling stochasticity and robustness in gene regulatory networks

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Understanding stem cell differentiation through self-organization theory

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Towards an understanding of lineage specification in hematopoietic stem cells: a mathematical model for the interaction of transcription factors GATA-1 and PU.1.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

The role of DNA methylation in setting up chromatin structure during development

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Cross-regulation of C/EBP alpha and PPAR gamma controls the transcriptional pathway of adipogenesis and insulin sensitivity.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384084

Why are cellular switches Boolean? General conditions for multistable genetic circuits

17 August 2018

1 reference

12 December 2020

Decrease in DNA methylase activity during preimplantation development in the mouse

1 reference

12 December 2020

Histone deacetylase inhibitor Trichostatin A induces global and gene-specific DNA demethylation in human cancer cell lines

1 reference

12 December 2020

Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells

1 reference

12 December 2020

Identifiers

DOI

10.3389/FPHYS.2012.00216

1 reference

18 October 2017

1 reference

18 October 2017

1 reference