Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements.

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Cell Systems

• Publication date

  2016-11-23

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/j.cels.2016.10.015PMID 27883889PMCID PMC5142829
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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

  2015cited by this paper
• Network plasticity of pluripotency transcription factors in embryonic stem cells

  2015cited by this paper
• Cell lineage analysis in human brain using endogenous retroelements.

  2015cited by this paper
• Dynamic Pluripotent Stem Cell States and Their Applications.

  2015cited by this paper
• Spatially resolved, highly multiplexed RNA profiling in single cells

  2015cited by this paper
• Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells

  2015cited by this paper
• A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis

  2015cited by this paper
• De novo generation of HSCs from somatic and pluripotent stem cell sources.

  2015cited by this paper
• Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands

  2015cited by this paper
• Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise.

  2015cited by this paper
• Genome sequencing of normal cells reveals developmental lineages and mutational processes

  2014cited by this paper
• Inferring epigenetic dynamics from kin correlations

  2014cited by this paper
• Spatially resolved transcriptomics and beyond

  2014cited by this paper
• Controlling low rates of cell differentiation through noise and ultrahigh feedback

  2014cited by this paper
• Deconstructing transcriptional heterogeneity in pluripotent stem cells

  2014influential reference
• Mathematical modeling of PDGF-driven glioblastoma reveals optimized radiation dosing schedules.

  2014cited by this paper
• TBX3 Directs Cell-Fate Decision toward Mesendoderm

  2014cited by this paper
• Fold change of nuclear NF-κB determines TNF-induced transcription in single cells.

  2014cited by this paper
• Single-cell in situ RNA profiling by sequential hybridization

  2014cited by this paper
• Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

  2014influential reference
• Memory and Modularity in Cell-Fate Decision Making

  2013cited by this paper
• Dedifferentiation of committed epithelial cells into stem cells in vivo

  2013cited by this paper
• Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination

  2013cited by this paper
• Generation of engraftable hematopoietic stem cells from induced pluripotent stem cells by way of teratoma formation.

  2013cited by this paper
• TBX3 Directs Cell-Fate Decision toward Mesendoderm

  2013cited by this paper
• Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

  2013cited by this paper
• PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells.

  2013cited by this paper
• Roles for Tbx3 in regulation of two-cell state and telomere elongation in mouse ES cells

  2013cited by this paper
• Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

  2013cited by this paper
• ES cell potency fluctuates with endogenous retrovirus activity

  2012cited by this paper
• Human Dedifferentiated Adipocytes Show Similar Properties to Bone Marrow‐Derived Mesenchymal Stem Cells

  2012cited by this paper
• Control of ground-state pluripotency by allelic regulation of Nanog

  2012cited by this paper
• p53 Dynamics Control Cell Fate

  2012cited by this paper
• Activation-Induced B Cell Fates Are Selected by Intracellular Stochastic Competition

  2012cited by this paper
• Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

  2012cited by this paper
• Single cell systems biology by super-resolution imaging and combinatorial labeling

  2012cited by this paper
• Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase.

  2012cited by this paper
• Pancreatic β cell dedifferentiation as a mechanism of diabetic β cell failure.

  2012cited by this paper
• Esrrb Is a Pivotal Target of the Gsk3/Tcf3 Axis Regulating Embryonic Stem Cell Self-Renewal

  2012cited by this paper
• Cell-Surface Proteomics Identifies Lineage-Specific Markers of Embryo-Derived Stem Cells

  2012cited by this paper
• Esrrb Is a Direct Nanog Target Gene that Can Substitute for Nanog Function in Pluripotent Cells

  2012cited by this paper
• Tumour evolution inferred by single-cell sequencing

  2011cited by this paper
• Strategies for homeostatic stem cell self-renewal in adult tissues.

  2011cited by this paper
• Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

  2011cited by this paper
• Complete kinetochore tracking reveals error-prone homologous chromosome biorientation in mammalian oocytes.

  2011cited by this paper
• Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells.

  2011cited by this paper
• Universal patterns of stem cell fate in cycling adult tissues

  2011cited by this paper
• Functional Heterogeneity of Embryonic Stem Cells Revealed through Translational Amplification of an Early Endodermal Transcript

  2010cited by this paper
• Zscan4 regulates telomere elongation and genomic stability in ES cells

  2010influential reference
• Mediator and Cohesin Connect Gene Expression and Chromatin Architecture

  2010cited by this paper
• Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors.

  2010cited by this paper
• Intestinal Stem Cell Replacement Follows a Pattern of Neutral Drift

  2010cited by this paper
• Dynamic single-cell imaging of direct reprogramming reveals an early specifying event

  2010cited by this paper
• Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells.

  2010cited by this paper
• FGF signal-dependent segregation of primitive endoderm and epiblast in the mouse blastocyst

  2010cited by this paper
• Dual Functions of T-Box 3 (Tbx3) in the Control of Self-renewal and Extraembryonic Endoderm Differentiation in Mouse Embryonic Stem Cells*

  2010cited by this paper
• Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb

  2009cited by this paper
• Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells

  2009cited by this paper
• Epithelial-mesenchymal transitions in development and disease.

  2009cited by this paper
• Direct cell reprogramming is a stochastic process amenable to acceleration

  2009cited by this paper
• A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells

  2009cited by this paper
• Identification and characterization of subpopulations in undifferentiated ES cell culture

  2008cited by this paper
• Imaging individual mRNA molecules using multiple singly labeled probes

  2008cited by this paper
• Supplementary Information for “ Stochastic mRNA Synthesis in Mammalian Cells ”

  2008cited by this paper
• Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states.

  2008cited by this paper
• A single type of progenitor cell maintains normal epidermis

  2007cited by this paper
• Stochastic patterning in the mouse pre-implantation embryo

  2007cited by this paper
• Nanog safeguards pluripotency and mediates germline development

  2007cited by this paper
• A Heterogeneous Expression Pattern for Nanog in Embryonic Stem Cells

  2007cited by this paper
• Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells.

  2007influential reference
• Dissecting self-renewal in stem cells with RNA interference

  2006cited by this paper
• Linking stochastic dynamics to population distribution: an analytical framework of gene expression.

  2006cited by this paper
• Stochastic mRNA Synthesis in Mammalian Cells

  2006cited by this paper
• 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 Embryo1

  2004cited by this paper
• Stochastic Gene Expression in a Single Cell

  2002cited by this paper
• Regulation of noise in the expression of a single gene

  2002cited by this paper
• Transdifferentiation and metaplasia--switching cell types.

  2001cited by this paper
• Visualization of single RNA transcripts in situ.

  1998cited by this paper
• Obesity associated with a mutation in a genetic regulator of adipocyte differentiation.

  1998cited by this paper
• Markovian Modeling of Gene-Product Synthesis

  1995cited by this paper
• Disparate differentiation in mouse hemopoietic colonies derived from paired progenitors.

  1984cited by this paper
• Analysis of differentiation of mouse hemopoietic stem cells in culture by sequential replating of paired progenitors.

  1984cited by this paper
• Single-cell origin of mouse hemopoietic colonies expressing multiple lineages in variable combinations.

  1983cited by this paper
• Organisers and genes.

  1943cited by this paper
• Opus: University of Bath Online Publication Store Zscan4 Is Regulated by Pi3-kinase and Dna-damaging Agents and Directly Interacts with the Transcriptional Repressors Lsd1 and Ctbp2 in Mouse Embryonic Stem Cells

  year unknowncited by this paper
• Stochastic Gene Expression in a Single Cell

  year unknowncited by this paper
• Edinburgh Research Explorer Estrogen-related receptor beta interacts with Oct4 to positively regulate Nanog gene expression

  year unknowncited by this paper

• Dissecting reversible and irreversible single cell state transitions from gene regulatory networks.

  2026cites this paper
• Shugoshin 2A stabilizes heterochromatin complexes to suppress the 2-cell-like state in embryonic stem cells.

  2026cites this paper
• An Efficient Solution to Hidden Markov Models on Trees With Coupled Branches

  2025cites this paper
• CellNavi predicts genes directing cellular transitions by learning a gene graph-enhanced cell state manifold

  2025cites this paper
• Combinatorial BMP4 and activin direct the choice between alternate routes to endoderm in a stem cell model of human gastrulation.

  2025cites this paper
• USP17L promotes the 2-cell-like program through deubiquitination of H2AK119ub1 and ZSCAN4

  2025cites this paper
• Nat10 maintains the homeostasis of pluripotent and 2-cell-like states in mouse embryonic stem cells through mRNA cytidine acetylation

  2025cites this paper
• A systems view of cellular heterogeneity: Unlocking the "wheel of fate".

  2025cites this paper
• GEMLI: Gene Expression Memory-Based Lineage Inference from Single-Cell RNA-Sequencing Datasets.

  2025cites this paper
• Spatial multi-omics reveals cell-type-specific nuclear compartments

  2025cites this paper
• Inference of lineage hierarchies, growth and drug response mechanisms in cancer cell populations – without tracking

  2025cites this paper
• Identification of an embryonic differentiation stage marked by Sox1 and FoxA2 co-expression using combined cell tracking and high dimensional protein imaging

  2024cites this paper
• An efficient solution to Hidden Markov Models on trees with coupled branches

  2024cites this paper
• The lives of cells, recorded

  2024cites this paper
• Entrainment and multi-stability of the p53 oscillator in human cells.

  2024cites this paper
• Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution

  2024cites this paper
• BANMF-S: a blockwise accelerated non-negative matrix factorization framework with structural network constraints for single cell imputation

  2024cites this paper
• Dissecting reversible and irreversible single cell state transitions from gene regulatory networks

  2024cites this paper
• Deciphering cellular heterogeneity in Spodoptera frugiperda midgut cell line through single cell RNA sequencing.

  2024cites this paper
• Lineage motifs as developmental modules for control of cell type proportions.

  2024cites this paper
• Reconstructing cell histories in space with image-readable base editor recording

  2024influential citation
• Transcription factor fluctuations underlie cell-to-cell variability in a signaling pathway response.

  2023cites this paper
• A review on gene regulatory network reconstruction algorithms based on single cell RNA sequencing

  2023cites this paper
• Identifying critical regulatory interactions in cell fate decision and transition by systematic perturbation analysis.

  2023cites this paper
• Phenotypic noise and plasticity in cancer evolution.

  2023cites this paper
• Constructing maps between distinct cell fates and parametric conditions by systematic perturbations

  2023cites this paper
• Introduction to bioimaging‐based spatial multi‐omic novel methods

  2023cites this paper
• Lineage motifs: developmental modules for control of cell type proportions

  2023cites this paper
• Reconstructing cell lineage trees with genomic barcoding: approaches and applications.

  2023cites this paper
• Optogenetic manipulation identifies the roles of ERK and AKT dynamics in controlling mouse embryonic stem cell exit from pluripotency.

  2023cites this paper
• Multiplex Protein Imaging through PACIFIC: Photoactive Immunofluorescence with Iterative Cleavage

  2023cites this paper
• Dynamics of Epithelial–Mesenchymal Plasticity: What Have Single-Cell Investigations Elucidated So Far?

  2023cites this paper
• Probing transient memory of cellular states using single-cell lineages

  2023cites this paper
• Defining ancestry, heritability and plasticity of cellular phenotypes in somatic evolution

  2023influential citation
• Cost-efficient boundary-free surface patterning achieves high effective-throughput of time-lapse microscopy experiments

  2022cites this paper
• Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding.

  2022cites this paper
• Barcode-free prediction of cell lineages from scRNA-seq datasets

  2022cites this paper
• Control of cell state transitions

  2022cites this paper
• Comparison of cell state models derived from single-cell RNA sequencing data: graph versus multi-dimensional space

  2022cites this paper
• scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across single cell samples

  2022cites this paper
• Statistical Mechanical theory for spatio-temporal evolution of Intra-tumor heterogeneity in cancers: Analysis of Multiregion sequencing data

  2022cites this paper
• FRAME-tags: genetically encoded fluorescent markers for multiplexed barcoding and time-resolved tracking of live cells

  2021cites this paper
• Phylodynamics for cell biologists

  2021cites this paper
• Quantitative measurements of early alphaviral replication dynamics in single cells reveals the basis for superinfection exclusion.

  2021cites this paper
• Learning dynamics by computational integration of single cell genomic and lineage information

  2021cites this paper
• Cell Tracking for Organoids: Lessons From Developmental Biology

  2021cites this paper
• Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations.

  2021cites this paper
• Heritable changes in division speed accompany the diversification of single T cell fate

  2021cites this paper
• Decoding the dynamics of multilayered stochastic antiviral IFN-I responses.

  2021cites this paper
• Gene Expression at a Single Molecule Level: Implications for MDS and AML.

  2021cites this paper
• Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors.

  2020influential citation
• Lineages of embryonic stem cells show non-Markovian state transitions

  2020cites this paper
• Advancing Stem Cell Research through Multimodal Single-Cell Analysis.

  2020cites this paper
• Early alphavirus replication dynamics in single cells reveal a passive basis for superinfection exclusion

  2020cites this paper
• CAN-20-0354-ET 3157..3169

  2020cites this paper
• Global architecture of the nucleus in single cells by DNA seqFISH+ and multiplexed immunofluorescence

  2020cites this paper
• Advanced technological tools to study multidrug resistance in cancer.

  2020cites this paper
• Integrated spatial genomics reveals global architecture of single nuclei

  2020cites this paper
• Single Molecule Imaging of Transcription Dynamics in Somatic Stem Cells

  2020cites this paper
• State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Development of Acute Myeloid Leukemia

  2020cites this paper
• Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data

  2019cites this paper
• Exploring single cells in space and time during tissue development, homeostasis and regeneration

  2019cites this paper
• From observing to predicting single-cell structure and function with high-throughput/high-content microscopy

  2019cites this paper
• Memory and relatedness of transcriptional activity in mammalian cell lineages

  2019cites this paper
• Cell states, fates and reprogramming : insights from neural networks, graphical and computational approaches

  2019cites this paper
• M-TRACK: a platform for live cell multiplex imaging reveals cell phenotypic transition dynamics inherently missing in snapshot data

  2019cites this paper
• Caliban: Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning

  2019cites this paper
• TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data

  2019influential citation
• Mathematical modeling with single-cell sequencing data

  2019cites this paper
• Morphological State Transition Dynamics in EGF-Induced Epithelial to Mesenchymal Transition

  2019cites this paper
• Inheritance of Cell-Cycle Duration in the Presence of Periodic Forcing

  2018cites this paper
• Leveraging and coping with uncertainty in the response of individual cells to therapy.

  2018cites this paper
• Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviors

  2018cites this paper
• Lineage EM algorithm for inferring latent states from cellular lineage trees

  2018cites this paper
• Mouse and human HSPC immobilization in liquid culture by CD43- or CD44-antibody coating.

  2018cites this paper
• Gene-specific transcriptional memory in mammalian cell lineages

  2018cites this paper
• Molecular evolution of biological sequences

  2018cites this paper
• Network inference from perturbation time course data

  2018cites this paper
• EM based algorithm to infer both phenotypic state and cell division properties from lineage information

  2018cites this paper
• Maps of variability in cell lineage trees

  2018cites this paper
• Deciphering Latent Growth-States from Cellular Lineage Trees

  2018cites this paper
• Deciphering Latent Growth-States from a Lineage Tree

  2018cites this paper
• A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment

  2018cites this paper
• Transition state characteristics during cell differentiation

  2018cites this paper
• Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm

  2018cites this paper
• The stretch to stray on time: Resonant length of random walks in a transient.

  2018cites this paper
• Single-Cell Transcriptomics Meets Lineage Tracing.

  2018cites this paper
• Parameter inference for stochastic single-cell dynamics from lineage tree data

  2017cites this paper
• Stem Cell Differentiation as a Non-Markov Stochastic Process

  2017cites this paper
• State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Leukemia Development

  2017cites this paper
• Illuminating stem cell transcription factor dynamics: long-term single-cell imaging of fluorescent protein fusions.

  2017cites this paper
• Rare-event sampling of epigenetic landscapes and phenotype transitions

  2017cites this paper
• Computational Methods for Modeling and Mapping Cellular Decision Networks

  2017influential citation
• Stem cell differentiation is a stochastic process with memory

  2017cites this paper
• Transcriptome dynamics describe and predict state transition from health to leukemia

  2017cites this paper
• STATISTICAL INFERENCE IN CELL LINEAGE TREES

  2017cites this paper
• Integrated Experimental and Theoretical Studies of Stem Cells

  2017cites this paper
• Cell Lineage Trees Bear Fruit.

  2016influential citation
• Synthetic recording and in situ readout of lineage information in single cells

  2016cites this paper