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Tipping-point analysis uncovers critical transition signals from gene expression profiles

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1 of the 83 references listed on this page is in the Retraction Watch database as retracted (export 2026-10-28): 10.1186/s13045-020-00857-7 (notice 2023-08-15).

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Detecting and Anticipating Climate Tipping Points
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Peroxisome proliferator‐activated receptor‐β/δ inhibits human neuroblastoma cell tumorigenesis by inducing p53‐ and SOX2‐mediated cell differentiation
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Computing Communities in Large Networks Using Random Walks
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Development of the lung
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Genetic susceptibility to neuroblastoma: current knowledge and future directions
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Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
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Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase
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Comprehensive Integration of Single-Cell Data
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Single-Cell Analysis Identifies Distinct Stages of Human Endothelial-to-Hematopoietic Transition
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Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation
inferredcites →https://doi.org/10.1016/j.cels.2019.09.008openalex-snapshot
Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
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Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
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Ligands for the peroxisome proliferator-activated receptor-γ have inhibitory effects on growth of human neuroblastoma cells in vitro
inferredcites →https://doi.org/10.1016/j.ydbio.2020.06.007openalex-snapshot
Ets1 functions partially redundantly with Etv2 to promote embryonic vasculogenesis and angiogenesis in zebrafish
inferredcites →https://doi.org/10.1038/nature08227openalex-snapshot
Early-warning signals for critical transitions
inferredcites →https://doi.org/10.1038/nature13173openalex-snapshot
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
inferredcites →https://doi.org/10.1038/nbt.2859openalex-snapshot
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
inferredcites →https://doi.org/10.1038/ncomms12088openalex-snapshot
Notch-independent RBPJ controls angiogenesis in the adult heart
inferredcites →https://doi.org/10.1038/ncomms15599openalex-snapshot
Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome
inferredcites →https://doi.org/10.1038/nmeth.3583openalex-snapshot
Comparing the performance of biomedical clustering methods
inferredcites →https://doi.org/10.1038/nmeth.4402openalex-snapshot
Reversed graph embedding resolves complex single-cell trajectories
inferredcites →https://doi.org/10.1038/nrg.2016.98openalex-snapshot
Transition states and cell fate decisions in epigenetic landscapes
inferredcites →https://doi.org/10.1038/s41423-020-00554-yopenalex-snapshot
Transcription tipping points for T follicular helper cell and T-helper 1 cell fate commitment
inferredcites →https://doi.org/10.1038/s41467-017-00667-5openalex-snapshot
A CRISPR screen identifies genes controlling Etv2 threshold expression in murine hemangiogenic fate commitment
inferredcites →https://doi.org/10.1038/s41467-018-03024-2openalex-snapshot
Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma
inferredcites →https://doi.org/10.1038/s41467-018-03214-yopenalex-snapshot
Reconstruction of complex single-cell trajectories using CellRouter
inferredcites →https://doi.org/10.1038/s41467-018-03424-4openalex-snapshot
A comprehensive evaluation of module detection methods for gene expression data
inferredcites →https://doi.org/10.1038/s41467-018-07770-1openalex-snapshot
Single cell RNA analysis identifies cellular heterogeneity and adaptive responses of the lung at birth
inferredcites →https://doi.org/10.1038/s41467-019-09684-yopenalex-snapshot
Early warning signals of recovery in complex systems
inferredcites →https://doi.org/10.1038/s41467-020-15956-9openalex-snapshot
Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line
inferredcites →https://doi.org/10.1038/s41540-019-0095-2openalex-snapshot
Identification of an early cell fate regulator by detecting dynamics in transcriptional heterogeneity and co-regulation during astrocyte differentiation
inferredcites →https://doi.org/10.1038/s41556-017-0013-zopenalex-snapshot
Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation
inferredcites →https://doi.org/10.1038/s41576-021-00341-zopenalex-snapshot
Statistical mechanics meets single-cell biology
inferredcites →https://doi.org/10.1038/s41586-019-0933-9openalex-snapshot
A single-cell molecular map of mouse gastrulation and early organogenesis
inferredcites →https://doi.org/10.1038/s41586-020-2712-zopenalex-snapshot
Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis
inferredcites →https://doi.org/10.1038/s41598-019-45839-zopenalex-snapshot
The ENCODE Blacklist: Identification of Problematic Regions of the Genome
inferredcites →https://doi.org/10.1038/srep00342openalex-snapshot
Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers
inferredcites →https://doi.org/10.1038/srep17501openalex-snapshot
Identifying early-warning signals of critical transitions with strong noise by dynamical network markers
inferredcites →https://doi.org/10.1056/nejmoa1001527openalex-snapshot
Outcome after Reduced Chemotherapy for Intermediate-Risk Neuroblastoma
inferredcites →https://doi.org/10.1063/1.5025235openalex-snapshot
Lévy noise induced transition and enhanced stability in a gene regulatory network
inferredcites →https://doi.org/10.1073/pnas.0704044104openalex-snapshot
Canonical Wnt signaling is a positive regulator of mammalian cardiac progenitors
inferredcites →https://doi.org/10.1073/pnas.0804455105openalex-snapshot
High Myc pathway activity and low stage of neuronal differentiation associate with poor outcome in neuroblastoma
inferredcites →https://doi.org/10.1073/pnas.1222404110openalex-snapshot
MYC inhibition induces metabolic changes leading to accumulation of lipid droplets in tumor cells
inferredcites →https://doi.org/10.1073/pnas.1408993111openalex-snapshot
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
inferredcites →https://doi.org/10.1073/pnas.1432147100openalex-snapshot
GATA-1-dependent transcriptional repression of GATA-2 via disruption of positive autoregulation and domain-wide chromatin remodeling
inferredcites →https://doi.org/10.1073/pnas.1621412114openalex-snapshot
Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells
inferredcites →https://doi.org/10.1073/pnas.1913773116openalex-snapshot
Anticipating critical transitions in epithelial–hybrid-mesenchymal cell-fate determination
inferredcites →https://doi.org/10.1074/jbc.273.44.29032openalex-snapshot
Transcriptional Regulation of the Stem Cell Leukemia Gene by PU.1 and Elf-1
inferredcites →https://doi.org/10.1074/jbc.m115.662197openalex-snapshot
Feedback Mechanisms Regulate Ets Variant 2 (Etv2) Gene Expression and Hematoendothelial Lineages
inferredcites →https://doi.org/10.1074/jbc.m605870200openalex-snapshot
Tumor-specific and Proliferation-specific Gene Expression Typifies Murine Transgenic B Cell Lymphomagenesis
inferredcites →https://doi.org/10.1089/ten.teb.2014.0662openalex-snapshot
Signaling Pathways and Gene Regulatory Networks in Cardiomyocyte Differentiation
inferredcites →https://doi.org/10.1093/bioinformatics/btt703openalex-snapshot
Causal analysis approaches in Ingenuity Pathway Analysis
inferredcites →https://doi.org/10.1093/cvr/cvx133openalex-snapshot
Etv2 as an essential regulator of mesodermal lineage development
inferredcites →https://doi.org/10.1093/nar/gkz204openalex-snapshot
Cell lineage and communication network inference via optimization for single-cell transcriptomics
inferredcites →https://doi.org/10.1093/nsr/nwy162openalex-snapshot
Detection for disease tipping points by landscape dynamic network biomarkers
inferredcites →https://doi.org/10.1101/gad.11.6.774openalex-snapshot
Multilineage gene expression precedes commitment in the hemopoietic system.
inferredcites →https://doi.org/10.1101/gad.13.3.295openalex-snapshot
Roles of ephrinB ligands and EphB receptors in cardiovascular development: demarcation of arterial/venous domains, vascular morphogenesis, and sprouting angiogenesis
inferredcites →https://doi.org/10.1103/physreve.92.062805openalex-snapshot
Critical tipping point distinguishing two types of transitions in modular network structures
inferredcites →https://doi.org/10.1126/science.1225244openalex-snapshot
Anticipating Critical Transitions
inferredcites →https://doi.org/10.1126/science.aat6768openalex-snapshot
A mechanistic classification of clinical phenotypes in neuroblastoma
inferredcites →https://doi.org/10.1128/mcb.00927-09openalex-snapshot
Hepatocyte Nuclear Factor 4α Coordinates a Transcription Factor Network Regulating Hepatic Fatty Acid Metabolism
inferredcites →https://doi.org/10.1155/2016/3038164openalex-snapshot
PPAR Gamma in Neuroblastoma: The Translational Perspectives of Hypoglycemic Drugs
inferredcites →https://doi.org/10.1161/atvbaha.120.314488openalex-snapshot
ETV2 (Ets Variant Transcription Factor 2)- Rhoj Cascade Regulates Endothelial Progenitor Cell Migration During Embryogenesis
inferredcites →https://doi.org/10.1164/rccm.201103-0545ocopenalex-snapshot
Critical Role of the Axonal Guidance Cue EphrinB2 in Lung Growth, Angiogenesis, and Repair
inferredcites →https://doi.org/10.1182/blood-2016-05-716480openalex-snapshot
A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation
inferredcites →https://doi.org/10.1186/s12859-015-0510-7openalex-snapshot
Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia
inferredcites →https://doi.org/10.1186/s12870-018-1589-6openalex-snapshot
Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis
inferredcites →https://doi.org/10.1186/s13045-020-00857-7openalex-snapshot
RETRACTED ARTICLE: HNF4A-AS1/hnRNPU/CTCF axis as a therapeutic target for aerobic glycolysis and neuroblastoma progression
inferredcites →https://doi.org/10.1186/s13059-015-0694-1openalex-snapshot
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction
inferredcites →https://doi.org/10.1242/dev.173740openalex-snapshot
Transition state dynamics during a stochastic fate choice
inferredcites →https://doi.org/10.1242/dev.173807openalex-snapshot
Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord
inferredcites →https://doi.org/10.1242/dev.182097openalex-snapshot
Single cell transcriptome dynamics from pluripotency to FLK1+ mesoderm
inferredcites →https://doi.org/10.1371/journal.pbio.1000149openalex-snapshot
Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells
inferredcites →https://doi.org/10.1371/journal.pbio.1002585openalex-snapshot
Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process
inferredcites →https://doi.org/10.1371/journal.pbio.2000640openalex-snapshot
Cell Fate Decision as High-Dimensional Critical State Transition
inferredcites →https://doi.org/10.1371/journal.pcbi.1005633openalex-snapshot
Quantifying critical states of complex diseases using single-sample dynamic network biomarkers
inferredcites →https://doi.org/10.1371/journal.pone.0041010openalex-snapshot
Methods for Detecting Early Warnings of Critical Transitions in Time Series Illustrated Using Simulated Ecological Data
inferredcites →https://doi.org/10.15252/embr.201439939openalex-snapshot
Induction of hematopoietic and endothelial cell program orchestrated by ETS transcription factor ER71/ETV2
inferredcites →https://doi.org/10.1587/nolta.9.166openalex-snapshot
On the covariance matrix of the stationary distribution of a noisy dynamical system
inferredcites →https://doi.org/10.2202/1544-6115.1175openalex-snapshot
A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
inferredcites →https://doi.org/10.3390/ijms19071869openalex-snapshot
PPARs and Energy Metabolism Adaptation during Neurogenesis and Neuronal Maturation
inferredcites →https://doi.org/10.3905/jpm.2004.110openalex-snapshot
Honey, I Shrunk the Sample Covariance Matrix

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1186/s13005-024-00457-7openalex-snapshot
Early recurrence as a pivotal event in nasopharyngeal carcinoma: identifying predictors and key molecular signals for survivors
inferred← citeshttps://doi.org/10.7551/mitpress/14126.003.0011openalex-snapshot
The Developmental Basis for Evolvability
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