Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements (Q46063788)

http://europepmc.org/abstract/PMC/5142829

19 December 2017

title

Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements (English)

1 reference

http://europepmc.org/abstract/PMC/5142829

19 December 2017

author

Yaron Antebi

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

author name string

Sahand Hormoz

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Zakary S Singer

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

James M Linton

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Boris I Shraiman

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Michael B Elowitz

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

publication date

1 November 2016

1 reference

http://europepmc.org/abstract/PMC/5142829

19 December 2017

published in

Cell Systems

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

volume

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

page(s)

419-433.e8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

Dynamic Pluripotent Stem Cell States and Their Applications

6 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Inferring epigenetic dynamics from kin correlations

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

De novo generation of HSCs from somatic and pluripotent stem cell sources

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Cell lineage analysis in human brain using endogenous retroelements.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Deconstructing transcriptional heterogeneity in pluripotent stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Dynamic heterogeneity and DNA methylation in embryonic stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Controlling low rates of cell differentiation through noise and ultrahigh feedback

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Single-cell in situ RNA profiling by sequential hybridization

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Fold change of nuclear NF-κB determines TNF-induced transcription in single cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Mathematical modeling of PDGF-driven glioblastoma reveals optimized radiation dosing schedules

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

TBX3 Directs Cell-Fate Decision toward Mesendoderm

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Memory and modularity in cell-fate decision making

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Dedifferentiation of committed epithelial cells into stem cells in vivo

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Generation of engraftable hematopoietic stem cells from induced pluripotent stem cells by way of teratoma formation.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Lineage structure of the human antibody repertoire in response to influenza vaccination

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Genome-wide detection of single-nucleotide and copy-number variations of a single human cell

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Esrrb is a pivotal target of the Gsk3/Tcf3 axis regulating embryonic stem cell self-renewal

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Esrrb is a direct Nanog target gene that can substitute for Nanog function in pluripotent cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Pancreatic β cell dedifferentiation as a mechanism of diabetic β cell failure

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

p53 dynamics control cell fate

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Single-cell systems biology by super-resolution imaging and combinatorial labeling

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Cell-surface proteomics identifies lineage-specific markers of embryo-derived stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Human dedifferentiated adipocytes show similar properties to bone marrow-derived mesenchymal stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Universal patterns of stem cell fate in cycling adult tissues

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Strategies for homeostatic stem cell self-renewal in adult tissues

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Mammalian genes are transcribed with widely different bursting kinetics

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Tumour evolution inferred by single-cell sequencing

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Dual functions of T-box 3 (Tbx3) in the control of self-renewal and extraembryonic endoderm differentiation in mouse embryonic stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Mediator and cohesin connect gene expression and chromatin architecture

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Functional heterogeneity of embryonic stem cells revealed through translational amplification of an early endodermal transcript.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Dynamic single-cell imaging of direct reprogramming reveals an early specifying event

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Zscan4 regulates telomere elongation and genomic stability in ES cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

FGF signal-dependent segregation of primitive endoderm and epiblast in the mouse blastocyst

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Epithelial-mesenchymal transitions in development and disease

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Direct cell reprogramming is a stochastic process amenable to acceleration

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

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

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Imaging individual mRNA molecules using multiple singly labeled probes

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Identification and characterization of subpopulations in undifferentiated ES cell culture

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Nanog safeguards pluripotency and mediates germline development

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

A heterogeneous expression pattern for Nanog in embryonic stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Stochastic mRNA synthesis in mammalian cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Dissecting self-renewal in stem cells with RNA interference

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Stochastic gene expression in a single cell

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Regulation of noise in the expression of a single gene

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Transdifferentiation and metaplasia--switching cell types

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Obesity associated with a mutation in a genetic regulator of adipocyte differentiation

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Visualization of single RNA transcripts in situ

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Disparate differentiation in mouse hemopoietic colonies derived from paired progenitors

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Single-cell origin of mouse hemopoietic colonies expressing multiple lineages in variable combinations

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Network plasticity of pluripotency transcription factors in embryonic stem cells.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Spatially resolved transcriptomics and beyond.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Genome sequencing of normal cells reveals developmental lineages and mutational processes

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Activation-induced B cell fates are selected by intracellular stochastic competition.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Intestinal stem cell replacement follows a pattern of neutral drift

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

A single type of progenitor cell maintains normal epidermis.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Embryonic stem cells expressing both platelet endothelial cell adhesion molecule-1 and stage-specific embryonic antigen-1 differentiate predominantly into epiblast cells in a chimeric embryo.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5142829

Stochastic patterning in the mouse pre-implantation embryo

15 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27883889

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Analysis of differentiation of mouse hemopoietic stem cells in culture by sequential replating of paired progenitors

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27883889

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Linking stochastic dynamics to population distribution: an analytical framework of gene expression

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27883889

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.CELS.2016.10.015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27883889%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

PubMed publication ID

27883889

1 reference