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Exact Bayesian lineage tree-based inference identifies Nanog negative autoregulation in mouse embryonic stem cells

https://doi.org/10.1101/053231
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/stem.1384openalex-snapshot
Concise Review: Pursuing Self-Renewal and Pluripotency with the Stem Cell Factor Nanog
inferredcites →https://doi.org/10.1007/s00285-015-0876-1openalex-snapshot
A geometric analysis of fast-slow models for stochastic gene expression
inferredcites →https://doi.org/10.1016/j.cell.2005.08.020openalex-snapshot
Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2008.01.015openalex-snapshot
Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming
inferredcites →https://doi.org/10.1016/j.cell.2008.09.050openalex-snapshot
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
inferredcites →https://doi.org/10.1016/j.cels.2015.08.001openalex-snapshot
Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise
inferredcites →https://doi.org/10.1016/j.molcel.2014.06.029openalex-snapshot
Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.stem.2008.07.027openalex-snapshot
Dynamic Equilibrium and Heterogeneity of Mouse Pluripotent Stem Cells with Distinct Functional and Epigenetic States
inferredcites →https://doi.org/10.1016/j.stem.2008.10.007openalex-snapshot
Heterogeneity of Embryonic and Adult Stem Cells
inferredcites →https://doi.org/10.1016/j.stem.2013.04.025openalex-snapshot
Biallelic Expression of Nanog Protein in Mouse Embryonic Stem Cells
inferredcites →https://doi.org/10.1021/j100540a008openalex-snapshot
Exact stochastic simulation of coupled chemical reactions
inferredcites →https://doi.org/10.1038/emboj.2012.321openalex-snapshot
OCT4/SOX2‐independent Nanog autorepression modulates heterogeneous Nanog gene expression in mouse ES cells
inferredcites →https://doi.org/10.1038/nature06403openalex-snapshot
Nanog safeguards pluripotency and mediates germline development
inferredcites →https://doi.org/10.1038/nature07760openalex-snapshot
Continuous single-cell imaging of blood generation from haemogenic endothelium
inferredcites →https://doi.org/10.1038/nature10098openalex-snapshot
Global quantification of mammalian gene expression control
inferredcites →https://doi.org/10.1038/nature11848openalex-snapshot
Correction: Corrigendum: Global quantification of mammalian gene expression control
inferredcites →https://doi.org/10.1038/ncb2603openalex-snapshot
Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity
inferredcites →https://doi.org/10.1038/ncb3237openalex-snapshot
Network plasticity of pluripotency transcription factors in embryonic stem cells
inferredcites →https://doi.org/10.1038/ng.281openalex-snapshot
Regulatory activity revealed by dynamic correlations in gene expression noise
inferredcites →https://doi.org/10.1038/nmeth.2601openalex-snapshot
Allele-specific detection of single mRNA molecules in situ
inferredcites →https://doi.org/10.1038/nprot.2011.432openalex-snapshot
Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy
inferredcites →https://doi.org/10.1038/nrmicro2056openalex-snapshot
Using movies to analyse gene circuit dynamics in single cells
inferredcites →https://doi.org/10.1038/srep07125openalex-snapshot
Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells
inferredcites →https://doi.org/10.1038/srep13339openalex-snapshot
Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation
inferredcites →https://doi.org/10.1039/c1mb05398aopenalex-snapshot
Dissecting ensemble networks in EScell populations reveals micro-heterogeneity underlying pluripotency
inferredcites →https://doi.org/10.1049/ip-f-2.1993.0015openalex-snapshot
Novel approach to nonlinear/non-Gaussian Bayesian state estimation
inferredcites →https://doi.org/10.1063/1.2145882openalex-snapshot
The finite state projection algorithm for the solution of the chemical master equation
inferredcites →https://doi.org/10.1063/1.2159468openalex-snapshot
Efficient step size selection for the tau-leaping simulation method
inferredcites →https://doi.org/10.1063/1.2745299openalex-snapshot
Adaptive explicit-implicit tau-leaping method with automatic tau selection
inferredcites →https://doi.org/10.1080/01621459.1999.10474153openalex-snapshot
Filtering via Simulation: Auxiliary Particle Filters
inferredcites →https://doi.org/10.1093/bioinformatics/btm397openalex-snapshot
An error model for protein quantification
inferredcites →https://doi.org/10.1093/bioinformatics/btn051openalex-snapshot
LibSBML: an API Library for SBML
inferredcites →https://doi.org/10.1093/dnares/dsn030openalex-snapshot
Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells
inferredcites →https://doi.org/10.1103/physreve.72.051907openalex-snapshot
Self-regulating gene: An exact solution
inferredcites →https://doi.org/10.1109/cdc.2011.6161329openalex-snapshot
Recursive Bayesian estimation of stochastic rate constants from heterogeneous cell populations
inferredcites →https://doi.org/10.1126/science.1070919openalex-snapshot
Stochastic Gene Expression in a Single Cell
inferredcites →https://doi.org/10.1126/science.1171461openalex-snapshot
Hematopoietic Cytokines Can Instruct Lineage Choice
inferredcites →https://doi.org/10.1126/science.1198817openalex-snapshot
Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics
inferredcites →https://doi.org/10.1146/annurev.cellbio.042308.113408openalex-snapshot
Quantitative Time-Lapse Fluorescence Microscopy in Single Cells
inferredcites →https://doi.org/10.1146/annurev.physchem.58.032806.104637openalex-snapshot
Stochastic Simulation of Chemical Kinetics
inferredcites →https://doi.org/10.1166/jcsmd.2015.1074openalex-snapshot
A case study on the use of scale separation-based analytical propagators for parameter inference in models of stochastic gene regulation
inferredcites →https://doi.org/10.1186/1471-2105-15-1openalex-snapshot
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily
inferredcites →https://doi.org/10.1186/1471-2164-14-s3-s5openalex-snapshot
A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations
inferredcites →https://doi.org/10.1201/b11812openalex-snapshot
Stochastic Modelling for Systems Biology
inferredcites →https://doi.org/10.1242/dev.102624openalex-snapshot
Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage
inferredcites →https://doi.org/10.1242/dev.108910openalex-snapshot
Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency
inferredcites →https://doi.org/10.1242/dev.116343openalex-snapshot
Computational modelling of embryonic stem-cell fate control
inferredcites →https://doi.org/10.1242/jcs.118349openalex-snapshot
Probing cellular processes by long-term live imaging – historic problems and current solutions
inferredcites →https://doi.org/10.1371/journal.pbio.0040309openalex-snapshot
Stochastic mRNA Synthesis in Mammalian Cells
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.pcbi.0020123openalex-snapshot
Transcriptional Dynamics of the Embryonic Stem Cell Switch
inferredcites →https://doi.org/10.1371/journal.pone.0003478openalex-snapshot
A Computational Model for Understanding Stem Cell, Trophectoderm and Endoderm Lineage Determination
inferredcites →https://doi.org/10.1371/journal.pone.0011238openalex-snapshot
Nanog Variability and Pluripotency Regulation of Embryonic Stem Cells - Insights from a Mathematical Model Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0059928openalex-snapshot
Generation and Characterization of a Novel Mouse Embryonic Stem Cell Line with a Dynamic Reporter of Nanog Expression
inferredcites →https://doi.org/10.2307/2291091openalex-snapshot
Bayes Factors
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